nml Module (NeuroML Core classes)#
These NeuroML core classes are Python representations of the Component Types defined in the NeuroML standard . These can be used to build NeuroML models in Python, and these models can then be exported to the standard XML NeuroML representation. These core classes also contain some utility functions to make it easier for users to carry out common tasks.
Each NeuroML Component Type is represented here as a Python class.
Due to implementation limitations, whereas NeuroML Component Types use lower camel case naming, the Python classes here use upper camel case naming.
So, for example, the adExIaFCell Component Type in the NeuroML schema becomes the AdExIaFCell class here, and expTwoSynapse becomes the ExpTwoSynapse class.
The child and children elements that NeuroML Component Types can have are represented in the Python classes as variables.
The variable names, to distinguish them from class names, use snake case.
So for example, the cell NeuroML Component Type has a corresponding Cell Python class here.
The biophysicalProperties child Component Type in cell is represented as the biophysical_properties list variable in the Cell Python class.
The class signatures list all the child/children elements and text fields that the corresponding Component Type possesses.
To again use the Cell class as an example, the construction signature is this:
class neuroml.nml.nml.Cell(neuro_lex_id=None, id=None, metaid=None, notes=None, properties=None, annotation=None, morphology_attr=None, biophysical_properties_attr=None, morphology=None, biophysical_properties=None, extensiontype_=None, **kwargs_)
As can be seen here, it includes both the biophysical_properties and morphology child elements as variables.
Please see the examples in the NeuroML documentation to see usage examples of libNeuroML. Please also note that this module is also included in the top level of the neuroml package, so you can use these classes by importing neuroml:
from neuroml import AdExIaFCell
List of Component classes#
This documentation is auto-generated from the NeuroML schema. In case of issues, please refer to the schema documentation for clarifications. If the schema documentation does not resolve the issue, please contact us.
GeneratedsSuperSuper#
- class neuroml.nml.generatedssupersuper.GeneratedsSuperSuper#
Bases:
objectSuper class for GeneratedsSuper.
Any bits that must go into every libNeuroML class should go here.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
GdsCollector#
AdExIaFCell#
- class neuroml.nml.nml.AdExIaFCell(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, C: a Nml2Quantity_capacitance (required) = None, g_l: a Nml2Quantity_conductance (required) = None, EL: a Nml2Quantity_voltage (required) = None, reset: a Nml2Quantity_voltage (required) = None, VT: a Nml2Quantity_voltage (required) = None, thresh: a Nml2Quantity_voltage (required) = None, del_t: a Nml2Quantity_voltage (required) = None, tauw: a Nml2Quantity_time (required) = None, refract: a Nml2Quantity_time (required) = None, a: a Nml2Quantity_conductance (required) = None, b: a Nml2Quantity_current (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseCellMembPotCapAdExIaFCell – Model based on Brette R and Gerstner W ( 2005 ) Adaptive Exponential Integrate-and-Fire Model as an Effective Description of Neuronal Activity. J Neurophysiol 94:3637-3642
- Parameters:
gL (conductance) – Leak conductance
EL (voltage) – Leak reversal potential
VT (voltage) – Spike threshold
thresh (voltage) – Spike detection threshold
reset (voltage) – Reset potential
delT (voltage) – Slope factor
tauw (time) – Adaptation time constant
refract (time) – Refractory period
a (conductance) – Sub-threshold adaptation variable
b (current) – Spike-triggered adaptation variable
C (capacitance) – Total capacitance of the cell membrane
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
AlphaCondSynapse#
- class neuroml.nml.nml.AlphaCondSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, tau_syn: a float (required) = None, e_rev: a float (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BasePynnSynapseAlphaCondSynapse – Alpha synapse: rise time and decay time are both tau_syn. Conductance based synapse.
- Parameters:
e_rev (none) –
tau_syn (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
AlphaCurrSynapse#
- class neuroml.nml.nml.AlphaCurrSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, tau_syn: a float (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BasePynnSynapseAlphaCurrSynapse – Alpha synapse: rise time and decay time are both tau_syn. Current based synapse.
- Parameters:
tau_syn (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
AlphaCurrentSynapse#
- class neuroml.nml.nml.AlphaCurrentSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, tau: a Nml2Quantity_time (required) = None, ibase: a Nml2Quantity_current (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseCurrentBasedSynapseAlphaCurrentSynapse – Alpha current synapse: rise time and decay time are both tau.
- Parameters:
tau (time) – Time course for rise and decay
ibase (current) – Baseline current increase after receiving a spike
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
AlphaSynapse#
- class neuroml.nml.nml.AlphaSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, gbase: a Nml2Quantity_conductance (required) = None, erev: a Nml2Quantity_voltage (required) = None, tau: a Nml2Quantity_time (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseConductanceBasedSynapseAlphaSynapse – Ohmic synapse model where rise time and decay time are both tau. Max conductance reached during this time ( assuming zero conductance before ) is gbase * weight.
- Parameters:
tau (time) – Time course of rise/decay
gbase (conductance) – Baseline conductance, generally the maximum conductance following a single spike
erev (voltage) – Reversal potential of the synapse
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Annotation#
- class neuroml.nml.nml.Annotation(anytypeobjs_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdAnnotation – A structured annotation containing metadata, specifically RDF or property elements
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Base#
- class neuroml.nml.nml.Base(id: a NmlId (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdBase – Anything which can have a unique (within its parent) id of the form NmlId (spaceless combination of letters, numbers and underscore).
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
BaseCell#
- class neuroml.nml.nml.BaseCell(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneBaseCell – Base type of any cell ( e. g. point neuron like izhikevich2007Cell , or a morphologically detailed Cell with segment s ) which can be used in a population
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
BaseCellMembPotCap#
- class neuroml.nml.nml.BaseCellMembPotCap(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, C: a Nml2Quantity_capacitance (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseCellBaseCellMembPotCap – Any cell with a membrane potential v with voltage units and a membrane capacitance C. Also defines exposed value iSyn for current due to external synapses and iMemb for total transmembrane current ( usually channel currents plus iSyn )
- Parameters:
C (capacitance) – Total capacitance of the cell membrane
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
BaseConductanceBasedSynapse#
- class neuroml.nml.nml.BaseConductanceBasedSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, gbase: a Nml2Quantity_conductance (required) = None, erev: a Nml2Quantity_voltage (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseVoltageDepSynapseBaseConductanceBasedSynapse – Synapse model which exposes a conductance g in addition to producing a current. Not necessarily ohmic!! cno_0000027
- Parameters:
gbase (conductance) – Baseline conductance, generally the maximum conductance following a single spike
erev (voltage) – Reversal potential of the synapse
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
BaseConductanceBasedSynapseTwo#
- class neuroml.nml.nml.BaseConductanceBasedSynapseTwo(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, gbase1: a Nml2Quantity_conductance (required) = None, gbase2: a Nml2Quantity_conductance (required) = None, erev: a Nml2Quantity_voltage (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseVoltageDepSynapseBaseConductanceBasedSynapseTwo – Synapse model suited for a sum of two expTwoSynapses which exposes a conductance g in addition to producing a current. Not necessarily ohmic!! cno_0000027
- Parameters:
gbase1 (conductance) – Baseline conductance 1
gbase2 (conductance) – Baseline conductance 2
erev (voltage) – Reversal potential of the synapse
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
BaseConnection#
- class neuroml.nml.nml.BaseConnection(id: a NmlId (required) = None, neuro_lex_id: a NeuroLexId (optional) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseNonNegativeIntegerIdBaseConnection – Base of all synaptic connections (chemical/electrical/analog, etc.) inside projections
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
BaseConnectionNewFormat#
- class neuroml.nml.nml.BaseConnectionNewFormat(id: a NmlId (required) = None, neuro_lex_id: a NeuroLexId (optional) = None, pre_cell: a string (required) = None, pre_segment: a NonNegativeInteger (optional) = '0', pre_fraction_along: a ZeroToOne (optional) = '0.5', post_cell: a string (required) = None, post_segment: a NonNegativeInteger (optional) = '0', post_fraction_along: a ZeroToOne (optional) = '0.5', extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseConnectionBaseConnectionNewFormat – Base of all synaptic connections with preCell, postSegment, etc. See BaseConnectionOldFormat
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
BaseConnectionOldFormat#
- class neuroml.nml.nml.BaseConnectionOldFormat(id: a NmlId (required) = None, neuro_lex_id: a NeuroLexId (optional) = None, pre_cell_id: a Nml2PopulationReferencePath (required) = None, pre_segment_id: a NonNegativeInteger (optional) = '0', pre_fraction_along: a ZeroToOne (optional) = '0.5', post_cell_id: a Nml2PopulationReferencePath (required) = None, post_segment_id: a NonNegativeInteger (optional) = '0', post_fraction_along: a ZeroToOne (optional) = '0.5', extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseConnectionBaseConnectionOldFormat – Base of all synaptic connections with preCellId, postSegmentId, etc. Note: this is not the best name for these attributes, since Id is superfluous, hence BaseConnectionNewFormat
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
- validate_Nml2PopulationReferencePath(value)#
- validate_Nml2PopulationReferencePath_patterns_ = [['^((\\.\\./)?([a-zA-Z_][a-zA-Z0-9_]*)((\\[[0-9]+\\])|(/[0-9]+)+((/[a-zA-Z_][a-zA-Z0-9_]*)?)/?))$']]#
BaseCurrentBasedSynapse#
- class neuroml.nml.nml.BaseCurrentBasedSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseSynapseBaseCurrentBasedSynapse – Synapse model which produces a synaptic current.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
BaseNonNegativeIntegerId#
- class neuroml.nml.nml.BaseNonNegativeIntegerId(id: a NmlId (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdBaseNonNegativeIntegerId – Anything which can have a unique (within its parent) id, which must be an integer zero or greater.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
BaseProjection#
- class neuroml.nml.nml.BaseProjection(id: a NmlId (required) = None, presynaptic_population: a NmlId (required) = None, postsynaptic_population: a NmlId (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseBaseProjection – Base for projection (set of synaptic connections) between two populations
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
BasePynnSynapse#
- class neuroml.nml.nml.BasePynnSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, tau_syn: a float (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseSynapseBasePynnSynapse – Base type for all PyNN synapses. Note, the current I produced is dimensionless, but it requires a membrane potential v with dimension voltage
- Parameters:
tau_syn (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
BaseSynapse#
- class neuroml.nml.nml.BaseSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneBaseSynapse – Base type for all synapses, i. e. ComponentTypes which produce a current ( dimension current ) and change Dynamics in response to an incoming event. cno_0000009
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
BaseVoltageDepSynapse#
- class neuroml.nml.nml.BaseVoltageDepSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseSynapseBaseVoltageDepSynapse – Base type for synapses with a dependence on membrane potential
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
BaseWithoutId#
- class neuroml.nml.nml.BaseWithoutId(extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
GeneratedsSuperBaseWithoutId – Base element without ID specified yet, e.g. for an element with a particular requirement on its id which does not comply with NmlId (e.g. Segment needs nonNegativeInteger).
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
BiophysicalProperties#
- class neuroml.nml.nml.BiophysicalProperties(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, membrane_properties: a MembraneProperties (required) = None, intracellular_properties: a IntracellularProperties (optional) = None, extracellular_properties: a ExtracellularProperties (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneBiophysicalProperties – The biophysical properties of the cell , including the membraneProperties and the intracellularProperties
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
BiophysicalProperties2CaPools#
- class neuroml.nml.nml.BiophysicalProperties2CaPools(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, membrane_properties2_ca_pools: a MembraneProperties2CaPools (required) = None, intracellular_properties2_ca_pools: a IntracellularProperties2CaPools (optional) = None, extracellular_properties: a ExtracellularProperties (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneBiophysicalProperties2CaPools – The biophysical properties of the cell , including the membraneProperties2CaPools and the intracellularProperties2CaPools for a cell with two Ca pools
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
BlockMechanism#
- class neuroml.nml.nml.BlockMechanism(type: a BlockTypes (required) = None, species: a NmlId (required) = None, block_concentration: a Nml2Quantity_concentration (required) = None, scaling_conc: a Nml2Quantity_concentration (required) = None, scaling_volt: a Nml2Quantity_voltage (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutId- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
BlockingPlasticSynapse#
- class neuroml.nml.nml.BlockingPlasticSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, gbase: a Nml2Quantity_conductance (required) = None, erev: a Nml2Quantity_voltage (required) = None, tau_decay: a Nml2Quantity_time (required) = None, tau_rise: a Nml2Quantity_time (required) = None, plasticity_mechanism: a PlasticityMechanism (optional) = None, block_mechanism: a BlockMechanism (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
ExpTwoSynapseBlockingPlasticSynapse – Biexponential synapse that allows for optional block and plasticity mechanisms, which can be expressed as child elements.
- Parameters:
tauRise (time) –
tauDecay (time) –
gbase (conductance) – Baseline conductance, generally the maximum conductance following a single spike
erev (voltage) – Reversal potential of the synapse
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Case#
- class neuroml.nml.nml.Case(condition: a string (optional) = None, value: a string (required) = None, gds_collector_=None, **kwargs_)#
Bases:
GeneratedsSuper- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Cell#
- class neuroml.nml.nml.Cell(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, morphology_attr: a NmlId (optional) = None, biophysical_properties_attr: a NmlId (optional) = None, morphology: a Morphology (optional) = None, biophysical_properties: a BiophysicalProperties (optional) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseCellCell – Cell with segment s specified in a morphology element along with details on its biophysicalProperties . NOTE: this can only be correctly simulated using jLEMS when there is a single segment in the cell, and v of this cell represents the membrane potential in that isopotential segment.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- add_channel_density(nml_cell_doc, cd_id, ion_channel, cond_density, erev='0.0 mV', group_id='all', ion='non_specific', ion_chan_def_file='')#
Add channel density.
- Parameters:
nml_cell_doc (NeuroMLDocument) – cell NeuroML document to which channel density is to be added
cd_id (str) – id for channel density
ion_channel (str) – name of ion channel
cond_density (str) – value of conductance density with units
erev (str) – value of reversal potential with units
group_id (str) – segment groups to add to
ion (str) – name of ion
ion_chan_def_file (str) – path to NeuroML2 file defining the ion channel, if empty, it assumes the channel is defined in the same file
- Returns:
added channel density
- Return type:
- add_channel_density_v(channel_density_type, nml_cell_doc, ion_chan_def_file='', **kwargs)#
Generic function to add channel density components to a Cell.
- Parameters:
channel_density_type (str) – type of channel density to add. See https://docs.neuroml.org/Userdocs/Schemas/Cells.html for the complete list.
nml_cell_doc (NeuroMLDocument) – cell NeuroML document to which channel density is to be added
ion_chan_def_file (str) – path to NeuroML2 file defining the ion channel, if empty, it assumes the channel is defined in the same file
kwargs (Any) – named arguments for required channel density type
- Returns:
added channel density
- add_intracellular_property(property_name, **kwargs)#
Generic function to add an intracellular property to the cell.
For a full list of membrane properties, see: https://docs.neuroml.org/Userdocs/Schemas/Cells.html?#intracellularproperties
- Parameters:
property_name (str) – name of intracellular property to add
kwargs (Any) – named arguments for intracellular property to be added
- Returns:
added property
- add_membrane_property(property_name, **kwargs)#
Generic function to add a membrane property to the cell.
For a full list of membrane properties, see: https://docs.neuroml.org/Userdocs/Schemas/Cells.html?#membraneproperties
Please also see specific functions in this module, which are designed to be easier to use than this generic function.
- Parameters:
property_name (str) – name of membrane to add
kwargs (Any) – named arguments for membrane property to be added
- Returns:
added property
- add_segment(prox, dist, seg_id=None, name=None, parent=None, fraction_along=1.0, group_id=None, use_convention=True, seg_type=None, reorder_segment_groups=True, optimise_segment_groups=True)#
Add a segment to the cell, to the provided segment group, creating it if required.
- Parameters:
prox (list with 4 float entries: [x, y, z, diameter]) – proximal segment information
dist (list with 4 float entries: [x, y, z, diameter]) – dist segment information
seg_id (str) – explicit ID to set for segment When not provided, the function will automatically add an ID based on the number of segments already included in the cell. It is best to either always set an explicit ID or let the function set it automatically, but not to mix the two. A ValueError is raised if a segment with the provided ID already exists
name (str) – name of segment If a name is given, it is used. If no name is given, but a segment group is provided, the segment is named: “Seg<number>_<group name>” where <number> is the number of the segment in the segment group. (to be read as “segment <number> in <group>”; the group name should indicate the type here) If no name is given, and no segment group is provided, the segment is simply named: “Seg<segment id>”.
parent (Segment) – parent segment object
fraction_along (float) – where the new segment is connected to the parent (0: distal point, 1: proximal point)
group_id (str) –
id of segment group to add the segment to If a segment group with this id does not exist, a new segment group will be created.
The suggested convention is: axon_, soma_, dend_ for axonal, somatic, and dendritic segment groups respectively.
Note that a newly created segment group will not be marked as an unbranched segment group. If you wish to add a segment to an unbranched segment group, please create one using add_unbranched_segment_group and then add segments to it.
use_convention (bool) – whether the segment or its group should be added to the global segment groups. The seg_type notes what global group this segment or its segment group should also be added to.
reorder_segment_groups (bool) –
whether the groups should be reordered to put the default segment groups last after the segment has been added. This is required for a valid NeuroML file because segment groups included in the default groups should be declared before they are used in the default groups. When adding lots of segments, one may want to only reorder at the end of the process instead of after each segment is added.
This is only relevant if use_convention=True.
optimise_segment_groups (bool) – toggle whether segment groups should be optimised after operation
- Seg_type:
type of segment (“axon”, “dendrite”, “soma”) If use_convention is True, and a group_id is provided, the segment group will also be added to the default segment groups if it has not been previously added. If group_id is None, the segment will be added to the default groups instead.
If use_convention is False, this is unused.
- Returns:
the created segment
- Return type:
- Raises:
ValueError – if seg_id is provided and a segment with this ID already exists
- add_segment_group(group_id, neuro_lex_id=None, notes=None)#
Add a new general segment group.
The segments included in this group do not need to be contiguous. This segment group will not be automatically marked as a section using the required NeuroLex ID.
If a segment group with provided ID already exists, it will not be overwritten.
- Parameters:
group_id (str) – ID of segment group
neuro_lex_id (str) – NeuroLex ID to use for segment group
notes (str) – Notes text to add
- Returns:
new segment group
- Return type:
- add_unbranched_segment_group(group_id, notes=None)#
Add a new unbranched segment group.
This is similar to the add_segment_group method, but this segment group will be used to store contiguous segments, which form an unbranched section of a cell. It adds the NeuroLex ID for a neuronal branch to the segment group.
- Parameters:
group_id (str) – ID of segment group
notes (str) – notes to add
- Returns:
new segment group
- Return type:
- add_unbranched_segments(points, parent=None, fraction_along=1.0, group_id=None, use_convention=True, seg_type=None, reorder_segment_groups=True, optimise_segment_groups=True)#
Add an unbranched list of segments to the cell.
The list of points will include the first proximal point where this should be joined to the cell, followed by a list of distal points:
|-----|-----|-----|------|.....---| p1 d1 d2 d3 d4 d N-1
So, a list of N points will create a list of N-1 segments
The list of points will be of the form:
[[x1, y1, z1, d1], [x2, y2, z2, d2] ...]
Please ensure that the first point, p1, is correctly set to ensure that this segment list is correctly connected to the rest of the cell.
- Parameters:
points (list of [x, y, z, d] points) – 3D points to create the segments
parent (SegmentParent) – parent segment where first segment of list is to be attached
fraction_along (float) – where the new segment list is connected to the parent (0: distal point, 1: proximal point) Note that the second and following segments will all be added at the distal point of the previous segment
group_id (SegmentGroup) – segment group to add the segment to if a segment group does not already exist, it will be created
use_convention (bool) – whether helper segment groups should be created using the default convention See the documentation of the add_segment method for more information on the convention
seg_type (str) – type of segments (“axon”, “soma”, “dendrite”)
reorder_segment_groups (bool) –
whether the groups should be reordered to put the default segment groups last after the segment has been added. This is required for a valid NeuroML file because segment groups included in the default groups should be declared before they are used in the default groups. When adding lots of segments, one may want to only reorder at the end of the process instead of after each segment is added.
This is only relevant if use_convention=True.
optimise_segment_groups (bool) – toggle whether segment groups should be optimised after operation
- Returns:
the segment group containing this new list of segments
- Return type:
- biophysinfo()#
Get information on the biophysical properties of the cell. :returns: None
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- create_unbranched_segment_group_branches(root_segment_id: int, use_convention: bool = True, reorder_segment_groups=True, optimise_segment_groups=True)#
Organise the segments of the cell into new segment groups that each form a single contiguous unbranched cell branch.
Note that the first segment (root segment) of a branch must have a proximal point that connects it to the rest of the neuronal morphology. If, when constructing these branches, a root segment is found that does not include a proximal point, one will be added using the get_actual_proximal method.
No other changes will be made to any segments, or to any pre-existing segment groups.
- Parameters:
root_segment_id (int) – id of segment considered the root of the tree, generally the first soma segment
use_convention (bool) – toggle using NeuroML convention for segment groups
reorder_segment_groups (bool) –
whether the groups should be reordered to put the default segment groups last after the segment has been added. This is required for a valid NeuroML file because segment groups included in the default groups should be declared before they are used in the default groups. When adding lots of segments, one may want to only reorder at the end of the process instead of after each segment is added.
This is only relevant if use_convention=True.
optimise_segment_groups (bool) – toggle whether segment groups should be optimised after operation
- Returns:
modified cell with new section groups
- Return type:
neuroml.Cell
- get_actual_proximal(segment_id: str) Point3DWithDiam#
Get the proximal point of a segment.
If the proximal for the segment is set to None, calculate the proximal on the parent using fraction_along and return it.
- Parameters:
segment_id – ID of segment
- Returns:
proximal point
- get_all_distances_from_segment(seg_id=0)#
Get distances of all segments from the segment with id seg_id.
Useful to get distances of segments from the soma.
Uses networkx.single_source_dijkstra on the cell graph, without a target.
- Parameters:
seg_id (int) – id of segment to get distances from
- Returns:
pair of dictionaries for distance, path The return value is a tuple of two dictionaries keyed by target nodes. The first dictionary stores distance to each target node. The second stores the path to each target node.
- get_all_segments_in_group(segment_group: SegmentGroup, assume_all_means_all: bool = True) List[int]#
Get all the segments in a segment group of the cell.
- Parameters:
segment_group – segment group to get all segments of
assume_all_means_all – return all segments if the “all” segment group wasn’t explicitly defined
- Returns:
list of segment ids
- Return type:
list[int]
- Raises:
Exception – if no segment group is found in the cell.
- get_branching_points()#
Get segments where the cell morphology branches.
That is, the out-degree of the segment is > 1
- Returns:
list of segment ids
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- get_distance(dest, source=0)#
Get path length between between two segments on a cell.
Uses networkx.dijkstra_path_length to compute the shortest path between source and dest
- Parameters:
from (int) – id of segment to get distance from
to (int) – id of segment to get distance to
- Returns:
float
- get_extremeties()#
Get segments that are at the ends/tips of the neuronal morphology, with their distances from the soma.
- Returns:
dict of segment ids and their distances from cell root as values
- get_graph()#
Get a networkx DiGraph of the morphology of the cell with distances between the proximal point of a parent and the point where a child connects to it as the weights of the edges of the graph.
Please see https://networkx.org/documentation/stable/reference for information on networkx routines that can be used on this graph.
This method also stores the graph in the self.cell_graph attribute for future use.
- Returns:
networkx.Graph
- get_morphology_root()#
Return the root of the complete cell morphology.
This is usually the first segment of the soma, and there should only be one such segment.
- Returns:
id of the root segment
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- get_ordered_segments_in_groups(group_list: List, check_parentage: bool = False, include_cumulative_lengths: bool = False, include_path_lengths: bool = False, path_length_metric: str = 'Path Length from root') Any#
Get ordered list of segments in specified groups, with additional information.
Note that this method orders segments by id, so the assumption is that all segment with id N + m will be a descendent of segment with id N in the segment group.
- Parameters:
group_list (str or list(str)) – a group id or list of group ids to get segments from
check_parentage (bool) – verify parentage
include_cumulative_lengths (bool) – also include cummulative length of each segment from root
include_path_lengths (bool) – also include path lengths from segment group’s root segment to proximal and distal points of each segment
path_length_metric (str) – metric to use for path length (“Path Length from root” is currently the only supported option, and the default)
- Returns:
depending on provided arguments:
if no additional options are provided, returns a dictionary with segment group ids as keys, and lists of ordered segments in those segment groups as values (ord_segs)
if only include_path_lengths is set, returns a tuple: [ord_segs, path_lengths_to_proximal , path_lengths_to_distal]
if only include_cumulative_lengths is set, returns a tuple: [ord_segs, cumulative_lengths]
if both include_path_lengths and include_cumulative_lengths are set, returns a tuple: [ord_segs, cumulative_lengths, path_lengths_to_proximal , path_lengths_to_distal]
- Raises:
Exception if check_parentage is True and parentage cannot be verified
- get_segment(segment_id: int) Segment#
Get segment object by its id
- Parameters:
segment_id – ID of segment
- Returns:
segment
- Raises:
ValueError – if the segment is not found in the cell
- get_segment_adjacency_list()#
Get the adjacency list of all segments in the cell morphology. Returns a dict where each key is a parent segment, and the value is the list of its children segments.
Segment without children (leaf segments) are not included as parents in the adjacency list.
This method also stores the computed adjacency list in self.adjacency_list for future use by other methods.
self.adjacency_list is populated each time this method is run, to ensure that users can regenerate it after making modifications to the cell morphology. If the morphology has not changed, one only needs to populate it once and then re-use it as required.
- Returns:
dict with parent segment ids as keys and ids of their children as values
- Return type:
dict[int, list[int]]
- get_segment_group(sg_id: str) SegmentGroup#
Return the SegmentGroup object for the specified segment group id.
- Parameters:
sg_id (str) – id of segment group to find
- Returns:
SegmentGroup object of specified ID
- Raises:
ValueError – if segment group is not found in cell
- get_segment_group_info(group_id)#
Get information about a segment group
- Parameters:
group_id (int) – id of segment group
- Returns:
None
- get_segment_groups_by_substring(substring: str) dict#
Get a dictionary of segment group IDs and the segment groups matching the specified substring
- Parameters:
substring (str) – substring to match
- Returns:
dictionary with segment group ID as key, and segment group as value
- Raises:
ValueError – if no matching segment groups are found in cell
- get_segment_ids_vs_segments() Dict#
Get a dictionary of segment IDs and the segments in the cell.
- Returns:
dictionary with segment ID as key, and segment as value
- get_segment_length(segment_id: str) float#
Get the length of the segment.
- Parameters:
segment_id – ID of segment
- Returns:
length of segment
- get_segment_location_info(seg_id)#
Get location information about a particular segment.
- Parameters:
seg_id (int) – id of segment to get information for
- Returns:
a dictionary with various metrics about the segment
length of segment
distance from cell root
distance from nearest branching point
name of unbranched segment group segment belongs to (if any)
id of root segment of the unbranched segment group
distance from the segment group root segment
- get_segment_surface_area(segment_id: str) float#
Get the surface area of the segment.
- Parameters:
segment_id – ID of the segment
- Returns:
surface area of segment
- get_segment_volume(segment_id: str) float#
Get volume of segment
- Parameters:
segment_id – ID of the segment
- Returns:
volume of the segment
- get_segments_at_distance(distance, src_seg=0)#
Get all segments at distance from the provided src_seg.
For each segment, it returns the fraction along the segment that the provided distance is at. For example, if segment N is 500 units long, and the distance cut-off is at 200, the fraction along is: 200/500.
- Parameters:
src_seg (int) – id of segment to get distances from
distance (float) – distance to get segments at
- Returns:
dict with segment ids as keys, and fraction along at which the cut off is as values
- get_segments_by_substring(substring: str) dict#
Get a dictionary of segment IDs and the segment matching the specified substring
- Parameters:
substring (str) – substring to match
- Returns:
dictionary with segment ID as key, and segment as value
- Raises:
Exception – if no segments are found
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- morphinfo(segment_detail=False)#
Show info on morphology of the cell. By default, since cells can have large numbers of segments and segment groups, it only provides metrics on the total numbers. To see details, pass segment_detail=True.
See also: get_segment_group_info.
- Parameters:
segment_detail (bool) – toggle whether to show detailed information on segment groups and their segments
- Returns:
None
- optimise_segment_group(seg_group_id)#
Optimise segment group with id seg_group_id.
- Parameters:
seg_group_id (str) – id of segment group to optimise
- optimise_segment_groups()#
Optimise all segment groups in the cell.
This will:
deduplicate members and includes in segment groups
remove members that have already been included using a segment group
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- reorder_segment_groups()#
Move default segment groups to the end.
This is required so that the segment groups included in the default groups are defined before they are used.
- Returns:
None
- set_init_memb_potential(v, group_id='all')#
Set the initial membrane potential of the cell.
- Parameters:
v (str) – value to set for membrane potential with units
group_id (str) – id of segment group to modify
- set_resistivity(resistivity, group_id='all') None#
Set the resistivity of the cell
- Parameters:
group_id (str) – segment group to modify
- set_specific_capacitance(spec_cap, group_id='all')#
Set the specific capacitance for the cell.
- Parameters:
spec_cap (str) – value of specific capacitance with units
group_id (str) – segment group to modify
- set_spike_thresh(v, group_id='all')#
Set the spike threshold of the cell.
- Parameters:
v (str) – value to set for spike threshold with units
group_id (str) – id of segment group to modify
- setup_default_segment_groups(use_convention=True, default_groups=['all', 'soma_group'])#
Create default segment groups for the cell.
If use_convention is True, it also creates the provided default_groups SegmentGroups for convenience. By default, it creates the “all”, and “soma_group” groups since each cell must at least have a soma. Allowed values are: “all”, “soma_group”, “axon_group”, “dendrite_group”.
- Parameters:
use_convention (bool) – whether helper segment groups should be created using the default convention
default_groups (list of strings) – list of default segment groups to create
- Returns:
list of created segment groups (or empty list if none created)
- Return type:
list
- setup_nml_cell(use_convention=True, overwrite=False, default_groups=['all', 'soma_group'])#
Correctly initialise a NeuroML cell.
To be called after a new component has been created to initialise the cell with these properties:
Morphology: id=”morphology”
BiophysicalProperties: id=”biophys”:
MembraneProperties
IntracellularProperties
If use_convention is True, it also creates the provided default_groups SegmentGroups for convenience. By default, it creates the “all”, and “soma_group” groups since each cell must at least have a soma.
When dendritic and axonal segments are added, the add_segment function will create dendrite_group and axon_group groups as required.
Note that since this cell does not currently include a segment in its morphology, it is not a valid NeuroML construct. Use the add_segment and add_unbranched_segments functions to add segments and branches. They will also populate the default segment groups.
- Parameters:
id (str) – id of the cell
use_convention (bool) – whether helper segment groups should be created using the default convention
overwrite (bool) – overwrite existing components
default_groups (list of strings) – list of default segment groups to create
- Returns:
None
- Return type:
None
- summary(morph=True, biophys=True)#
Print cell summary.
Shows the number of segments and segment groups, and information on the biophysical properties of the cell. See the morphinfo and biophysinfo methods for more details.
- Parameters:
morph (bool) – toggle showing/hiding morphology information
biophys (bool) – toggle showing/hiding biophysology information
- Returns:
None
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Cell2CaPools#
- class neuroml.nml.nml.Cell2CaPools(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, morphology_attr: a NmlId (optional) = None, biophysical_properties_attr: a NmlId (optional) = None, morphology: a Morphology (optional) = None, biophysical_properties: a BiophysicalProperties (optional) = None, biophysical_properties2_ca_pools: a BiophysicalProperties2CaPools (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
CellCell2CaPools – Variant of cell with two independent Ca2+ pools. Cell with segment s specified in a morphology element along with details on its biophysicalProperties . NOTE: this can only be correctly simulated using jLEMS when there is a single segment in the cell, and v of this cell represents the membrane potential in that isopotential segment.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- add_channel_density(nml_cell_doc, cd_id, ion_channel, cond_density, erev='0.0 mV', group_id='all', ion='non_specific', ion_chan_def_file='')#
Add channel density.
- Parameters:
nml_cell_doc (NeuroMLDocument) – cell NeuroML document to which channel density is to be added
cd_id (str) – id for channel density
ion_channel (str) – name of ion channel
cond_density (str) – value of conductance density with units
erev (str) – value of reversal potential with units
group_id (str) – segment groups to add to
ion (str) – name of ion
ion_chan_def_file (str) – path to NeuroML2 file defining the ion channel, if empty, it assumes the channel is defined in the same file
- Returns:
added channel density
- Return type:
- add_channel_density_v(channel_density_type, nml_cell_doc, ion_chan_def_file='', **kwargs)#
Generic function to add channel density components to a Cell.
- Parameters:
channel_density_type (str) – type of channel density to add. See https://docs.neuroml.org/Userdocs/Schemas/Cells.html for the complete list.
nml_cell_doc (NeuroMLDocument) – cell NeuroML document to which channel density is to be added
ion_chan_def_file (str) – path to NeuroML2 file defining the ion channel, if empty, it assumes the channel is defined in the same file
kwargs (Any) – named arguments for required channel density type
- Returns:
added channel density
- add_intracellular_property(property_name, **kwargs)#
Generic function to add an intracellular property to the cell.
For a full list of membrane properties, see: https://docs.neuroml.org/Userdocs/Schemas/Cells.html?#intracellularproperties
- Parameters:
property_name (str) – name of intracellular property to add
kwargs (Any) – named arguments for intracellular property to be added
- Returns:
added property
- add_membrane_property(property_name, **kwargs)#
Generic function to add a membrane property to the cell.
For a full list of membrane properties, see: https://docs.neuroml.org/Userdocs/Schemas/Cells.html?#membraneproperties
Please also see specific functions in this module, which are designed to be easier to use than this generic function.
- Parameters:
property_name (str) – name of membrane to add
kwargs (Any) – named arguments for membrane property to be added
- Returns:
added property
- add_segment(prox, dist, seg_id=None, name=None, parent=None, fraction_along=1.0, group_id=None, use_convention=True, seg_type=None, reorder_segment_groups=True, optimise_segment_groups=True)#
Add a segment to the cell, to the provided segment group, creating it if required.
- Parameters:
prox (list with 4 float entries: [x, y, z, diameter]) – proximal segment information
dist (list with 4 float entries: [x, y, z, diameter]) – dist segment information
seg_id (str) – explicit ID to set for segment When not provided, the function will automatically add an ID based on the number of segments already included in the cell. It is best to either always set an explicit ID or let the function set it automatically, but not to mix the two. A ValueError is raised if a segment with the provided ID already exists
name (str) – name of segment If a name is given, it is used. If no name is given, but a segment group is provided, the segment is named: “Seg<number>_<group name>” where <number> is the number of the segment in the segment group. (to be read as “segment <number> in <group>”; the group name should indicate the type here) If no name is given, and no segment group is provided, the segment is simply named: “Seg<segment id>”.
parent (Segment) – parent segment object
fraction_along (float) – where the new segment is connected to the parent (0: distal point, 1: proximal point)
group_id (str) –
id of segment group to add the segment to If a segment group with this id does not exist, a new segment group will be created.
The suggested convention is: axon_, soma_, dend_ for axonal, somatic, and dendritic segment groups respectively.
Note that a newly created segment group will not be marked as an unbranched segment group. If you wish to add a segment to an unbranched segment group, please create one using add_unbranched_segment_group and then add segments to it.
use_convention (bool) – whether the segment or its group should be added to the global segment groups. The seg_type notes what global group this segment or its segment group should also be added to.
reorder_segment_groups (bool) –
whether the groups should be reordered to put the default segment groups last after the segment has been added. This is required for a valid NeuroML file because segment groups included in the default groups should be declared before they are used in the default groups. When adding lots of segments, one may want to only reorder at the end of the process instead of after each segment is added.
This is only relevant if use_convention=True.
optimise_segment_groups (bool) – toggle whether segment groups should be optimised after operation
- Seg_type:
type of segment (“axon”, “dendrite”, “soma”) If use_convention is True, and a group_id is provided, the segment group will also be added to the default segment groups if it has not been previously added. If group_id is None, the segment will be added to the default groups instead.
If use_convention is False, this is unused.
- Returns:
the created segment
- Return type:
- Raises:
ValueError – if seg_id is provided and a segment with this ID already exists
- add_segment_group(group_id, neuro_lex_id=None, notes=None)#
Add a new general segment group.
The segments included in this group do not need to be contiguous. This segment group will not be automatically marked as a section using the required NeuroLex ID.
If a segment group with provided ID already exists, it will not be overwritten.
- Parameters:
group_id (str) – ID of segment group
neuro_lex_id (str) – NeuroLex ID to use for segment group
notes (str) – Notes text to add
- Returns:
new segment group
- Return type:
- add_unbranched_segment_group(group_id, notes=None)#
Add a new unbranched segment group.
This is similar to the add_segment_group method, but this segment group will be used to store contiguous segments, which form an unbranched section of a cell. It adds the NeuroLex ID for a neuronal branch to the segment group.
- Parameters:
group_id (str) – ID of segment group
notes (str) – notes to add
- Returns:
new segment group
- Return type:
- add_unbranched_segments(points, parent=None, fraction_along=1.0, group_id=None, use_convention=True, seg_type=None, reorder_segment_groups=True, optimise_segment_groups=True)#
Add an unbranched list of segments to the cell.
The list of points will include the first proximal point where this should be joined to the cell, followed by a list of distal points:
|-----|-----|-----|------|.....---| p1 d1 d2 d3 d4 d N-1
So, a list of N points will create a list of N-1 segments
The list of points will be of the form:
[[x1, y1, z1, d1], [x2, y2, z2, d2] ...]
Please ensure that the first point, p1, is correctly set to ensure that this segment list is correctly connected to the rest of the cell.
- Parameters:
points (list of [x, y, z, d] points) – 3D points to create the segments
parent (SegmentParent) – parent segment where first segment of list is to be attached
fraction_along (float) – where the new segment list is connected to the parent (0: distal point, 1: proximal point) Note that the second and following segments will all be added at the distal point of the previous segment
group_id (SegmentGroup) – segment group to add the segment to if a segment group does not already exist, it will be created
use_convention (bool) – whether helper segment groups should be created using the default convention See the documentation of the add_segment method for more information on the convention
seg_type (str) – type of segments (“axon”, “soma”, “dendrite”)
reorder_segment_groups (bool) –
whether the groups should be reordered to put the default segment groups last after the segment has been added. This is required for a valid NeuroML file because segment groups included in the default groups should be declared before they are used in the default groups. When adding lots of segments, one may want to only reorder at the end of the process instead of after each segment is added.
This is only relevant if use_convention=True.
optimise_segment_groups (bool) – toggle whether segment groups should be optimised after operation
- Returns:
the segment group containing this new list of segments
- Return type:
- biophysinfo()#
Get information on the biophysical properties of the cell. :returns: None
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- create_unbranched_segment_group_branches(root_segment_id: int, use_convention: bool = True, reorder_segment_groups=True, optimise_segment_groups=True)#
Organise the segments of the cell into new segment groups that each form a single contiguous unbranched cell branch.
Note that the first segment (root segment) of a branch must have a proximal point that connects it to the rest of the neuronal morphology. If, when constructing these branches, a root segment is found that does not include a proximal point, one will be added using the get_actual_proximal method.
No other changes will be made to any segments, or to any pre-existing segment groups.
- Parameters:
root_segment_id (int) – id of segment considered the root of the tree, generally the first soma segment
use_convention (bool) – toggle using NeuroML convention for segment groups
reorder_segment_groups (bool) –
whether the groups should be reordered to put the default segment groups last after the segment has been added. This is required for a valid NeuroML file because segment groups included in the default groups should be declared before they are used in the default groups. When adding lots of segments, one may want to only reorder at the end of the process instead of after each segment is added.
This is only relevant if use_convention=True.
optimise_segment_groups (bool) – toggle whether segment groups should be optimised after operation
- Returns:
modified cell with new section groups
- Return type:
neuroml.Cell
- get_actual_proximal(segment_id: str) Point3DWithDiam#
Get the proximal point of a segment.
If the proximal for the segment is set to None, calculate the proximal on the parent using fraction_along and return it.
- Parameters:
segment_id – ID of segment
- Returns:
proximal point
- get_all_distances_from_segment(seg_id=0)#
Get distances of all segments from the segment with id seg_id.
Useful to get distances of segments from the soma.
Uses networkx.single_source_dijkstra on the cell graph, without a target.
- Parameters:
seg_id (int) – id of segment to get distances from
- Returns:
pair of dictionaries for distance, path The return value is a tuple of two dictionaries keyed by target nodes. The first dictionary stores distance to each target node. The second stores the path to each target node.
- get_all_segments_in_group(segment_group: SegmentGroup, assume_all_means_all: bool = True) List[int]#
Get all the segments in a segment group of the cell.
- Parameters:
segment_group – segment group to get all segments of
assume_all_means_all – return all segments if the “all” segment group wasn’t explicitly defined
- Returns:
list of segment ids
- Return type:
list[int]
- Raises:
Exception – if no segment group is found in the cell.
- get_branching_points()#
Get segments where the cell morphology branches.
That is, the out-degree of the segment is > 1
- Returns:
list of segment ids
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- get_distance(dest, source=0)#
Get path length between between two segments on a cell.
Uses networkx.dijkstra_path_length to compute the shortest path between source and dest
- Parameters:
from (int) – id of segment to get distance from
to (int) – id of segment to get distance to
- Returns:
float
- get_extremeties()#
Get segments that are at the ends/tips of the neuronal morphology, with their distances from the soma.
- Returns:
dict of segment ids and their distances from cell root as values
- get_graph()#
Get a networkx DiGraph of the morphology of the cell with distances between the proximal point of a parent and the point where a child connects to it as the weights of the edges of the graph.
Please see https://networkx.org/documentation/stable/reference for information on networkx routines that can be used on this graph.
This method also stores the graph in the self.cell_graph attribute for future use.
- Returns:
networkx.Graph
- get_morphology_root()#
Return the root of the complete cell morphology.
This is usually the first segment of the soma, and there should only be one such segment.
- Returns:
id of the root segment
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- get_ordered_segments_in_groups(group_list: List, check_parentage: bool = False, include_cumulative_lengths: bool = False, include_path_lengths: bool = False, path_length_metric: str = 'Path Length from root') Any#
Get ordered list of segments in specified groups, with additional information.
Note that this method orders segments by id, so the assumption is that all segment with id N + m will be a descendent of segment with id N in the segment group.
- Parameters:
group_list (str or list(str)) – a group id or list of group ids to get segments from
check_parentage (bool) – verify parentage
include_cumulative_lengths (bool) – also include cummulative length of each segment from root
include_path_lengths (bool) – also include path lengths from segment group’s root segment to proximal and distal points of each segment
path_length_metric (str) – metric to use for path length (“Path Length from root” is currently the only supported option, and the default)
- Returns:
depending on provided arguments:
if no additional options are provided, returns a dictionary with segment group ids as keys, and lists of ordered segments in those segment groups as values (ord_segs)
if only include_path_lengths is set, returns a tuple: [ord_segs, path_lengths_to_proximal , path_lengths_to_distal]
if only include_cumulative_lengths is set, returns a tuple: [ord_segs, cumulative_lengths]
if both include_path_lengths and include_cumulative_lengths are set, returns a tuple: [ord_segs, cumulative_lengths, path_lengths_to_proximal , path_lengths_to_distal]
- Raises:
Exception if check_parentage is True and parentage cannot be verified
- get_segment(segment_id: int) Segment#
Get segment object by its id
- Parameters:
segment_id – ID of segment
- Returns:
segment
- Raises:
ValueError – if the segment is not found in the cell
- get_segment_adjacency_list()#
Get the adjacency list of all segments in the cell morphology. Returns a dict where each key is a parent segment, and the value is the list of its children segments.
Segment without children (leaf segments) are not included as parents in the adjacency list.
This method also stores the computed adjacency list in self.adjacency_list for future use by other methods.
self.adjacency_list is populated each time this method is run, to ensure that users can regenerate it after making modifications to the cell morphology. If the morphology has not changed, one only needs to populate it once and then re-use it as required.
- Returns:
dict with parent segment ids as keys and ids of their children as values
- Return type:
dict[int, list[int]]
- get_segment_group(sg_id: str) SegmentGroup#
Return the SegmentGroup object for the specified segment group id.
- Parameters:
sg_id (str) – id of segment group to find
- Returns:
SegmentGroup object of specified ID
- Raises:
ValueError – if segment group is not found in cell
- get_segment_group_info(group_id)#
Get information about a segment group
- Parameters:
group_id (int) – id of segment group
- Returns:
None
- get_segment_groups_by_substring(substring: str) dict#
Get a dictionary of segment group IDs and the segment groups matching the specified substring
- Parameters:
substring (str) – substring to match
- Returns:
dictionary with segment group ID as key, and segment group as value
- Raises:
ValueError – if no matching segment groups are found in cell
- get_segment_ids_vs_segments() Dict#
Get a dictionary of segment IDs and the segments in the cell.
- Returns:
dictionary with segment ID as key, and segment as value
- get_segment_length(segment_id: str) float#
Get the length of the segment.
- Parameters:
segment_id – ID of segment
- Returns:
length of segment
- get_segment_location_info(seg_id)#
Get location information about a particular segment.
- Parameters:
seg_id (int) – id of segment to get information for
- Returns:
a dictionary with various metrics about the segment
length of segment
distance from cell root
distance from nearest branching point
name of unbranched segment group segment belongs to (if any)
id of root segment of the unbranched segment group
distance from the segment group root segment
- get_segment_surface_area(segment_id: str) float#
Get the surface area of the segment.
- Parameters:
segment_id – ID of the segment
- Returns:
surface area of segment
- get_segment_volume(segment_id: str) float#
Get volume of segment
- Parameters:
segment_id – ID of the segment
- Returns:
volume of the segment
- get_segments_at_distance(distance, src_seg=0)#
Get all segments at distance from the provided src_seg.
For each segment, it returns the fraction along the segment that the provided distance is at. For example, if segment N is 500 units long, and the distance cut-off is at 200, the fraction along is: 200/500.
- Parameters:
src_seg (int) – id of segment to get distances from
distance (float) – distance to get segments at
- Returns:
dict with segment ids as keys, and fraction along at which the cut off is as values
- get_segments_by_substring(substring: str) dict#
Get a dictionary of segment IDs and the segment matching the specified substring
- Parameters:
substring (str) – substring to match
- Returns:
dictionary with segment ID as key, and segment as value
- Raises:
Exception – if no segments are found
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- morphinfo(segment_detail=False)#
Show info on morphology of the cell. By default, since cells can have large numbers of segments and segment groups, it only provides metrics on the total numbers. To see details, pass segment_detail=True.
See also: get_segment_group_info.
- Parameters:
segment_detail (bool) – toggle whether to show detailed information on segment groups and their segments
- Returns:
None
- optimise_segment_group(seg_group_id)#
Optimise segment group with id seg_group_id.
- Parameters:
seg_group_id (str) – id of segment group to optimise
- optimise_segment_groups()#
Optimise all segment groups in the cell.
This will:
deduplicate members and includes in segment groups
remove members that have already been included using a segment group
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- reorder_segment_groups()#
Move default segment groups to the end.
This is required so that the segment groups included in the default groups are defined before they are used.
- Returns:
None
- set_init_memb_potential(v, group_id='all')#
Set the initial membrane potential of the cell.
- Parameters:
v (str) – value to set for membrane potential with units
group_id (str) – id of segment group to modify
- set_resistivity(resistivity, group_id='all') None#
Set the resistivity of the cell
- Parameters:
group_id (str) – segment group to modify
- set_specific_capacitance(spec_cap, group_id='all')#
Set the specific capacitance for the cell.
- Parameters:
spec_cap (str) – value of specific capacitance with units
group_id (str) – segment group to modify
- set_spike_thresh(v, group_id='all')#
Set the spike threshold of the cell.
- Parameters:
v (str) – value to set for spike threshold with units
group_id (str) – id of segment group to modify
- setup_default_segment_groups(use_convention=True, default_groups=['all', 'soma_group'])#
Create default segment groups for the cell.
If use_convention is True, it also creates the provided default_groups SegmentGroups for convenience. By default, it creates the “all”, and “soma_group” groups since each cell must at least have a soma. Allowed values are: “all”, “soma_group”, “axon_group”, “dendrite_group”.
- Parameters:
use_convention (bool) – whether helper segment groups should be created using the default convention
default_groups (list of strings) – list of default segment groups to create
- Returns:
list of created segment groups (or empty list if none created)
- Return type:
list
- setup_nml_cell(use_convention=True, overwrite=False, default_groups=['all', 'soma_group'])#
Correctly initialise a NeuroML cell.
To be called after a new component has been created to initialise the cell with these properties:
Morphology: id=”morphology”
BiophysicalProperties: id=”biophys”:
MembraneProperties
IntracellularProperties
If use_convention is True, it also creates the provided default_groups SegmentGroups for convenience. By default, it creates the “all”, and “soma_group” groups since each cell must at least have a soma.
When dendritic and axonal segments are added, the add_segment function will create dendrite_group and axon_group groups as required.
Note that since this cell does not currently include a segment in its morphology, it is not a valid NeuroML construct. Use the add_segment and add_unbranched_segments functions to add segments and branches. They will also populate the default segment groups.
- Parameters:
id (str) – id of the cell
use_convention (bool) – whether helper segment groups should be created using the default convention
overwrite (bool) – overwrite existing components
default_groups (list of strings) – list of default segment groups to create
- Returns:
None
- Return type:
None
- summary(morph=True, biophys=True)#
Print cell summary.
Shows the number of segments and segment groups, and information on the biophysical properties of the cell. See the morphinfo and biophysinfo methods for more details.
- Parameters:
morph (bool) – toggle showing/hiding morphology information
biophys (bool) – toggle showing/hiding biophysology information
- Returns:
None
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
CellSet#
- class neuroml.nml.nml.CellSet(id: a NmlId (required) = None, select: a string (required) = None, anytypeobjs_=None, gds_collector_=None, **kwargs_)#
Bases:
Base- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ChannelDensity#
- class neuroml.nml.nml.ChannelDensity(id: a NmlId (required) = None, ion_channel: a NmlId (required) = None, cond_density: a Nml2Quantity_conductanceDensity (optional) = None, erev: a Nml2Quantity_voltage (required) = None, segment_groups: a NmlId (optional) = 'all', segments: a NonNegativeInteger (optional) = None, ion: a NmlId (required) = None, variable_parameters: list of VariableParameter(s) (optional) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseChannelDensity – Specifies a time varying ohmic conductance density, gDensity, which is distributed on an area of the cell ( specified in membraneProperties ) with fixed reversal potential erev producing a current density iDensity
- Parameters:
erev (voltage) – The reversal potential of the current produced
condDensity (conductanceDensity) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ChannelDensityGHK#
- class neuroml.nml.nml.ChannelDensityGHK(id: a NmlId (required) = None, ion_channel: a NmlId (required) = None, permeability: a Nml2Quantity_permeability (required) = None, segment_groups: a NmlId (optional) = 'all', segments: a NonNegativeInteger (optional) = None, ion: a NmlId (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseChannelDensityGHK – Specifies a time varying conductance density, gDensity, which is distributed on an area of the cell, producing a current density iDensity and whose reversal potential is calculated from the Goldman Hodgkin Katz equation. Hard coded for Ca only! See OpenSourceBrain/ghk-nernst.
- Parameters:
permeability (permeability) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ChannelDensityGHK2#
- class neuroml.nml.nml.ChannelDensityGHK2(id: a NmlId (required) = None, ion_channel: a NmlId (required) = None, cond_density: a Nml2Quantity_conductanceDensity (optional) = None, segment_groups: a NmlId (optional) = 'all', segments: a NonNegativeInteger (optional) = None, ion: a NmlId (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseChannelDensityGHK2 – Time varying conductance density, gDensity, which is distributed on an area of the cell, producing a current density iDensity. Modified version of Jaffe et al. 1994 ( used also in Lawrence et al. 2006 ). See OpenSourceBrain/ghk-nernst.
- Parameters:
condDensity (conductanceDensity) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ChannelDensityNernst#
- class neuroml.nml.nml.ChannelDensityNernst(id: a NmlId (required) = None, ion_channel: a NmlId (required) = None, cond_density: a Nml2Quantity_conductanceDensity (optional) = None, segment_groups: a NmlId (optional) = 'all', segments: a NonNegativeInteger (optional) = None, ion: a NmlId (required) = None, variable_parameters: list of VariableParameter(s) (optional) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseChannelDensityNernst – Specifies a time varying conductance density, gDensity, which is distributed on an area of the cell, producing a current density iDensity and whose reversal potential is calculated from the Nernst equation. Hard coded for Ca only! See OpenSourceBrain/ghk-nernst.
- Parameters:
condDensity (conductanceDensity) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ChannelDensityNernstCa2#
- class neuroml.nml.nml.ChannelDensityNernstCa2(id: a NmlId (required) = None, ion_channel: a NmlId (required) = None, cond_density: a Nml2Quantity_conductanceDensity (optional) = None, segment_groups: a NmlId (optional) = 'all', segments: a NonNegativeInteger (optional) = None, ion: a NmlId (required) = None, variable_parameters: list of VariableParameter(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
ChannelDensityNernstChannelDensityNernstCa2 – This component is similar to the original component type channelDensityNernst but it is changed in order to have a reversal potential that depends on a second independent Ca++ pool ( ca2 ). See OpenSourceBrain/ghk-nernst.
- Parameters:
condDensity (conductanceDensity) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ChannelDensityNonUniform#
- class neuroml.nml.nml.ChannelDensityNonUniform(id: a NmlId (required) = None, ion_channel: a NmlId (required) = None, erev: a Nml2Quantity_voltage (required) = None, ion: a NmlId (required) = None, variable_parameters: list of VariableParameter(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseChannelDensityNonUniform – Specifies a time varying ohmic conductance density, which is distributed on a region of the cell. The conductance density of the channel is not uniform, but is set using the variableParameter . Note, there is no dynamical description of this in LEMS yet, as this type only makes sense for multicompartmental cells. A ComponentType for this needs to be present to enable export of NeuroML 2 multicompartmental cells via LEMS/jNeuroML to NEURON
- Parameters:
erev (voltage) – The reversal potential of the current produced
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ChannelDensityNonUniformGHK#
- class neuroml.nml.nml.ChannelDensityNonUniformGHK(id: a NmlId (required) = None, ion_channel: a NmlId (required) = None, ion: a NmlId (required) = None, variable_parameters: list of VariableParameter(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseChannelDensityNonUniformGHK – Specifies a time varying conductance density, which is distributed on a region of the cell, and whose current is calculated from the Goldman-Hodgkin-Katz equation. Hard coded for Ca only!. The conductance density of the channel is not uniform, but is set using the variableParameter . Note, there is no dynamical description of this in LEMS yet, as this type only makes sense for multicompartmental cells. A ComponentType for this needs to be present to enable export of NeuroML 2 multicompartmental cells via LEMS/jNeuroML to NEURON
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ChannelDensityNonUniformNernst#
- class neuroml.nml.nml.ChannelDensityNonUniformNernst(id: a NmlId (required) = None, ion_channel: a NmlId (required) = None, ion: a NmlId (required) = None, variable_parameters: list of VariableParameter(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseChannelDensityNonUniformNernst – Specifies a time varying conductance density, which is distributed on a region of the cell, and whose reversal potential is calculated from the Nernst equation. Hard coded for Ca only!. The conductance density of the channel is not uniform, but is set using the variableParameter . Note, there is no dynamical description of this in LEMS yet, as this type only makes sense for multicompartmental cells. A ComponentType for this needs to be present to enable export of NeuroML 2 multicompartmental cells via LEMS/jNeuroML to NEURON
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ChannelDensityVShift#
- class neuroml.nml.nml.ChannelDensityVShift(id: a NmlId (required) = None, ion_channel: a NmlId (required) = None, cond_density: a Nml2Quantity_conductanceDensity (optional) = None, erev: a Nml2Quantity_voltage (required) = None, segment_groups: a NmlId (optional) = 'all', segments: a NonNegativeInteger (optional) = None, ion: a NmlId (required) = None, variable_parameters: list of VariableParameter(s) (optional) = None, v_shift: a Nml2Quantity_voltage (required) = None, gds_collector_=None, **kwargs_)#
Bases:
ChannelDensityChannelDensityVShift – Same as channelDensity , but with a vShift parameter to change voltage activation of gates. The exact usage of vShift in expressions for rates is determined by the individual gates.
- Parameters:
vShift (voltage) –
erev (voltage) – The reversal potential of the current produced
condDensity (conductanceDensity) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ChannelPopulation#
- class neuroml.nml.nml.ChannelPopulation(id: a NmlId (required) = None, ion_channel: a NmlId (required) = None, number: a NonNegativeInteger (required) = None, erev: a Nml2Quantity_voltage (required) = None, segment_groups: a NmlId (optional) = 'all', segments: a NonNegativeInteger (optional) = None, ion: a NmlId (required) = None, variable_parameters: list of VariableParameter(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseChannelPopulation – Population of a number of ohmic ion channels. These each produce a conductance channelg across a reversal potential erev, giving a total current i. Note that active membrane currents are more frequently specified as a density over an area of the cell using channelDensity
- Parameters:
number (none) – The number of channels present. This will be multiplied by the time varying conductance of the individual ion channel ( which extends baseIonChannel ) to produce the total conductance
erev (voltage) – The reversal potential of the current produced
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ClosedState#
- class neuroml.nml.nml.ClosedState(id: a NmlId (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseClosedState – A KSState with relativeConductance of 0
- Parameters:
relativeConductance (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ComponentType#
- class neuroml.nml.nml.ComponentType(name: a string (required) = None, extends: a string (optional) = None, description: a string (optional) = None, Property: list of Property(s) (optional) = None, Parameter: list of Parameter(s) (optional) = None, DerivedParameter: list of DerivedParameter(s) (optional) = None, Constant: list of Constant(s) (optional) = None, Exposure: list of Exposure(s) (optional) = None, Requirement: list of Requirement(s) (optional) = None, InstanceRequirement: list of InstanceRequirement(s) (optional) = None, Dynamics: list of Dynamics(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
GeneratedsSuperComponentType – Contains an extension to NeuroML by creating custom LEMS ComponentType.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
CompoundInput#
- class neuroml.nml.nml.CompoundInput(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, pulse_generators: list of PulseGenerator(s) (optional) = None, sine_generators: list of SineGenerator(s) (optional) = None, ramp_generators: list of RampGenerator(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneCompoundInput – Generates a current which is the sum of all its child basePointCurrent element, e. g. can be a combination of pulseGenerator , sineGenerator elements producing a single i. Scaled by weight, if set
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
CompoundInputDL#
- class neuroml.nml.nml.CompoundInputDL(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, pulse_generator_dls: list of PulseGeneratorDL(s) (optional) = None, sine_generator_dls: list of SineGeneratorDL(s) (optional) = None, ramp_generator_dls: list of RampGeneratorDL(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneCompoundInputDL – Generates a current which is the sum of all its child basePointCurrentDL elements, e. g. can be a combination of pulseGeneratorDL , sineGeneratorDL elements producing a single i. Scaled by weight, if set
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ConcentrationModel_D#
- class neuroml.nml.nml.ConcentrationModel_D(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, ion: a NmlId (required) = None, resting_conc: a Nml2Quantity_concentration (required) = None, decay_constant: a Nml2Quantity_time (required) = None, shell_thickness: a Nml2Quantity_length (required) = None, type: a string (required) = 'decayingPoolConcentrationModel', gds_collector_=None, **kwargs_)#
Bases:
DecayingPoolConcentrationModel- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ConditionalDerivedVariable#
- class neuroml.nml.nml.ConditionalDerivedVariable(name: a string (required) = None, dimension: a string (required) = None, description: a string (optional) = None, exposure: a string (optional) = None, Case: list of Case(s) (required) = None, gds_collector_=None, **kwargs_)#
Bases:
NamedDimensionalVariableConditionalDerivedVariable – LEMS ComponentType for ConditionalDerivedVariable
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Connection#
- class neuroml.nml.nml.Connection(id: a NonNegativeInteger (required) = None, neuro_lex_id: a NeuroLexId (optional) = None, pre_cell_id: a Nml2PopulationReferencePath (required) = None, pre_segment_id: a NonNegativeInteger (optional) = '0', pre_fraction_along: a ZeroToOne (optional) = '0.5', post_cell_id: a Nml2PopulationReferencePath (required) = None, post_segment_id: a NonNegativeInteger (optional) = '0', post_fraction_along: a ZeroToOne (optional) = '0.5', gds_collector_=None, **kwargs_)#
Bases:
BaseConnectionOldFormatConnection – Event connection directly between named components, which gets processed via a new instance of a synapse component which is created on the target component. Normally contained inside a projection element.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- get_post_cell_id()#
Get the ID of the post-synaptic cell
- Returns:
ID of post-synaptic cell
- Return type:
str
- get_post_fraction_along()#
Get post-synaptic fraction along information
- get_post_info()#
Get post-synaptic information summary
- get_post_segment_id()#
Get the ID of the post-synpatic segment
- Returns:
ID of post-synaptic segment.
- Return type:
str
- get_pre_cell_id()#
Get the ID of the pre-synaptic cell
- Returns:
ID of pre-synaptic cell
- Return type:
str
- get_pre_fraction_along()#
Get pre-synaptic fraction along information
- get_pre_info()#
Get pre-synaptic information summary
- get_pre_segment_id()#
Get the ID of the pre-synpatic segment
- Returns:
ID of pre-synaptic segment.
- Return type:
str
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
- validate_Nml2PopulationReferencePath(value)#
- validate_Nml2PopulationReferencePath_patterns_ = [['^((\\.\\./)?([a-zA-Z_][a-zA-Z0-9_]*)((\\[[0-9]+\\])|(/[0-9]+)+((/[a-zA-Z_][a-zA-Z0-9_]*)?)/?))$']]#
ConnectionWD#
- class neuroml.nml.nml.ConnectionWD(id: a NonNegativeInteger (required) = None, neuro_lex_id: a NeuroLexId (optional) = None, pre_cell_id: a Nml2PopulationReferencePath (required) = None, pre_segment_id: a NonNegativeInteger (optional) = '0', pre_fraction_along: a ZeroToOne (optional) = '0.5', post_cell_id: a Nml2PopulationReferencePath (required) = None, post_segment_id: a NonNegativeInteger (optional) = '0', post_fraction_along: a ZeroToOne (optional) = '0.5', weight: a float (required) = None, delay: a Nml2Quantity_time (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseConnectionOldFormatConnectionWD – Event connection between named components, which gets processed via a new instance of a synapse component which is created on the target component, includes setting of weight and delay for the synaptic connection
- Parameters:
weight (none) –
delay (time) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- get_delay_in_ms()#
Get connection delay in milli seconds
- Returns:
connection delay in milli seconds
- Return type:
float
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- get_post_cell_id()#
Get the ID of the post-synaptic cell
- Returns:
ID of post-synaptic cell
- Return type:
str
- get_post_fraction_along()#
Get post-synaptic fraction along information
- get_post_info()#
Get post-synaptic information summary
- get_post_segment_id()#
Get the ID of the post-synpatic segment
- Returns:
ID of post-synaptic segment.
- Return type:
str
- get_pre_cell_id()#
Get the ID of the pre-synaptic cell
- Returns:
ID of pre-synaptic cell
- Return type:
str
- get_pre_fraction_along()#
Get pre-synaptic fraction along information
- get_pre_info()#
Get pre-synaptic information summary
- get_pre_segment_id()#
Get the ID of the pre-synpatic segment
- Returns:
ID of pre-synaptic segment.
- Return type:
str
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
- validate_Nml2PopulationReferencePath(value)#
- validate_Nml2PopulationReferencePath_patterns_ = [['^((\\.\\./)?([a-zA-Z_][a-zA-Z0-9_]*)((\\[[0-9]+\\])|(/[0-9]+)+((/[a-zA-Z_][a-zA-Z0-9_]*)?)/?))$']]#
Constant#
- class neuroml.nml.nml.Constant(name: a string (required) = None, dimension: a string (required) = None, value: a Nml2Quantity (required) = None, description: a string (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdConstant – LEMS ComponentType for Constant.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ContinuousConnection#
- class neuroml.nml.nml.ContinuousConnection(id: a NonNegativeInteger (required) = None, neuro_lex_id: a NeuroLexId (optional) = None, pre_cell: a string (required) = None, pre_segment: a NonNegativeInteger (optional) = '0', pre_fraction_along: a ZeroToOne (optional) = '0.5', post_cell: a string (required) = None, post_segment: a NonNegativeInteger (optional) = '0', post_fraction_along: a ZeroToOne (optional) = '0.5', pre_component: a NmlId (required) = None, post_component: a NmlId (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseConnectionNewFormatContinuousConnection – An instance of a connection in a continuousProjection between presynapticPopulation to another postsynapticPopulation through a preComponent at the start and postComponent at the end. Can be used for analog synapses.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- get_post_cell_id()#
Get the ID of the post-synaptic cell
- Returns:
ID of post-synaptic cell
- Return type:
str
- get_post_fraction_along()#
Get post-synaptic fraction along information
- get_post_info()#
Get post-synaptic information summary
- get_post_segment_id()#
Get the ID of the post-synpatic segment
- Returns:
ID of post-synaptic segment.
- Return type:
str
- get_pre_cell_id()#
Get the ID of the pre-synaptic cell
- Returns:
ID of pre-synaptic cell
- Return type:
str
- get_pre_fraction_along()#
Get pre-synaptic fraction along information
- get_pre_info()#
Get pre-synaptic information summary
- get_pre_segment_id()#
Get the ID of the pre-synpatic segment
- Returns:
ID of pre-synaptic segment.
- Return type:
str
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ContinuousConnectionInstance#
- class neuroml.nml.nml.ContinuousConnectionInstance(id: a NonNegativeInteger (required) = None, neuro_lex_id: a NeuroLexId (optional) = None, pre_cell: a string (required) = None, pre_segment: a NonNegativeInteger (optional) = '0', pre_fraction_along: a ZeroToOne (optional) = '0.5', post_cell: a string (required) = None, post_segment: a NonNegativeInteger (optional) = '0', post_fraction_along: a ZeroToOne (optional) = '0.5', pre_component: a NmlId (required) = None, post_component: a NmlId (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
ContinuousConnectionContinuousConnectionInstance – An instance of a connection in a continuousProjection between presynapticPopulation to another postsynapticPopulation through a preComponent at the start and postComponent at the end. Populations need to be of type populationList and contain instance and location elements. Can be used for analog synapses.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- get_post_cell_id()#
Get the ID of the post-synaptic cell
- Returns:
ID of post-synaptic cell
- Return type:
str
- get_post_fraction_along()#
Get post-synaptic fraction along information
- get_post_info()#
Get post-synaptic information summary
- get_post_segment_id()#
Get the ID of the post-synpatic segment
- Returns:
ID of post-synaptic segment.
- Return type:
str
- get_pre_cell_id()#
Get the ID of the pre-synaptic cell
- Returns:
ID of pre-synaptic cell
- Return type:
str
- get_pre_fraction_along()#
Get pre-synaptic fraction along information
- get_pre_info()#
Get pre-synaptic information summary
- get_pre_segment_id()#
Get the ID of the pre-synpatic segment
- Returns:
ID of pre-synaptic segment.
- Return type:
str
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ContinuousConnectionInstanceW#
- class neuroml.nml.nml.ContinuousConnectionInstanceW(id: a NonNegativeInteger (required) = None, neuro_lex_id: a NeuroLexId (optional) = None, pre_cell: a string (required) = None, pre_segment: a NonNegativeInteger (optional) = '0', pre_fraction_along: a ZeroToOne (optional) = '0.5', post_cell: a string (required) = None, post_segment: a NonNegativeInteger (optional) = '0', post_fraction_along: a ZeroToOne (optional) = '0.5', pre_component: a NmlId (required) = None, post_component: a NmlId (required) = None, weight: a float (required) = None, gds_collector_=None, **kwargs_)#
Bases:
ContinuousConnectionInstanceContinuousConnectionInstanceW – An instance of a connection in a continuousProjection between presynapticPopulation to another postsynapticPopulation through a preComponent at the start and postComponent at the end. Populations need to be of type populationList and contain instance and location elements. Can be used for analog synapses. Includes setting of weight for the connection
- Parameters:
weight (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- get_post_cell_id()#
Get the ID of the post-synaptic cell
- Returns:
ID of post-synaptic cell
- Return type:
str
- get_post_fraction_along()#
Get post-synaptic fraction along information
- get_post_info()#
Get post-synaptic information summary
- get_post_segment_id()#
Get the ID of the post-synpatic segment
- Returns:
ID of post-synaptic segment.
- Return type:
str
- get_pre_cell_id()#
Get the ID of the pre-synaptic cell
- Returns:
ID of pre-synaptic cell
- Return type:
str
- get_pre_fraction_along()#
Get pre-synaptic fraction along information
- get_pre_info()#
Get pre-synaptic information summary
- get_pre_segment_id()#
Get the ID of the pre-synpatic segment
- Returns:
ID of pre-synaptic segment.
- Return type:
str
- get_weight()#
Get weight.
If weight is not set, the default value of 1.0 is returned.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ContinuousProjection#
- class neuroml.nml.nml.ContinuousProjection(id: a NmlId (required) = None, presynaptic_population: a NmlId (required) = None, postsynaptic_population: a NmlId (required) = None, continuous_connections: list of ContinuousConnection(s) (optional) = None, continuous_connection_instances: list of ContinuousConnectionInstance(s) (optional) = None, continuous_connection_instance_ws: list of ContinuousConnectionInstanceW(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseProjectionContinuousProjection – A projection between presynapticPopulation and postsynapticPopulation through components preComponent at the start and postComponent at the end of a continuousConnection or continuousConnectionInstance . Can be used for analog synapses.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- exportHdf5(h5file, h5Group)#
Export to HDF5 file.
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
DecayingPoolConcentrationModel#
- class neuroml.nml.nml.DecayingPoolConcentrationModel(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, ion: a NmlId (required) = None, resting_conc: a Nml2Quantity_concentration (required) = None, decay_constant: a Nml2Quantity_time (required) = None, shell_thickness: a Nml2Quantity_length (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneDecayingPoolConcentrationModel – Model of an intracellular buffering mechanism for ion ( currently hard Coded to be calcium, due to requirement for iCa ) which has a baseline level restingConc and tends to this value with time course decayConstant. The ion is assumed to occupy a shell inside the membrane of thickness shellThickness.
- Parameters:
restingConc (concentration) –
decayConstant (time) –
shellThickness (length) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
DerivedParameter#
- class neuroml.nml.nml.DerivedParameter(name: a string (required) = None, dimension: a string (required) = None, description: a string (optional) = None, value: a string (required) = None, gds_collector_=None, **kwargs_)#
Bases:
NamedDimensionalTypeDerivedParameter – LEMS DerivedParamter element
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
DerivedVariable#
- class neuroml.nml.nml.DerivedVariable(name: a string (required) = None, dimension: a string (required) = None, description: a string (optional) = None, exposure: a string (optional) = None, value: a string (optional) = None, select: a string (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
NamedDimensionalVariableDerivedVariable – LEMS ComponentType for DerivedVariable
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
DistalDetails#
- class neuroml.nml.nml.DistalDetails(normalization_end: a double (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdDistalDetails – What to do at the distal point when creating an inhomogeneous parameter
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
DoubleSynapse#
- class neuroml.nml.nml.DoubleSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, synapse1: a NmlId (required) = None, synapse2: a NmlId (required) = None, synapse1_path: a string (required) = None, synapse2_path: a string (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseVoltageDepSynapseDoubleSynapse – Synapse consisting of two independent synaptic mechanisms ( e. g. AMPA-R and NMDA-R ), which can be easily colocated in connections
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Dynamics#
- class neuroml.nml.nml.Dynamics(StateVariable: list of StateVariable(s) (optional) = None, DerivedVariable: list of DerivedVariable(s) (optional) = None, ConditionalDerivedVariable: list of ConditionalDerivedVariable(s) (optional) = None, TimeDerivative: list of TimeDerivative(s) (optional) = None, OnStart: a OnStart (optional) = None, OnEvent: list of OnEvent(s) (optional) = None, OnCondition: list of OnCondition(s) (optional) = None, Regime: list of Regime(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
GeneratedsSuperDynamics – LEMS ComponentType for Dynamics
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
EIF_cond_alpha_isfa_ista#
- class neuroml.nml.nml.EIF_cond_alpha_isfa_ista(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, cm: a float (required) = None, i_offset: a float (required) = None, tau_syn_E: a float (required) = None, tau_syn_I: a float (required) = None, v_init: a float (required) = None, tau_m: a float (required) = None, tau_refrac: a float (required) = None, v_reset: a float (required) = None, v_rest: a float (required) = None, v_thresh: a float (required) = None, e_rev_E: a float (required) = None, e_rev_I: a float (required) = None, a: a float (required) = None, b: a float (required) = None, delta_T: a float (required) = None, tau_w: a float (required) = None, v_spike: a float (required) = None, gds_collector_=None, **kwargs_)#
Bases:
EIF_cond_exp_isfa_istaEIF_cond_alpha_isfa_ista – Adaptive exponential integrate and fire neuron according to Brette R and Gerstner W ( 2005 ) with alpha-function-shaped post-synaptic conductance
- Parameters:
v_spike (none) –
delta_T (none) –
tau_w (none) –
a (none) –
b (none) –
e_rev_E (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
e_rev_I (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
tau_refrac (none) –
v_thresh (none) –
tau_m (none) –
v_rest (none) –
v_reset (none) –
cm (none) –
i_offset (none) –
tau_syn_E (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
tau_syn_I (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
v_init (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
EIF_cond_exp_isfa_ista#
- class neuroml.nml.nml.EIF_cond_exp_isfa_ista(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, cm: a float (required) = None, i_offset: a float (required) = None, tau_syn_E: a float (required) = None, tau_syn_I: a float (required) = None, v_init: a float (required) = None, tau_m: a float (required) = None, tau_refrac: a float (required) = None, v_reset: a float (required) = None, v_rest: a float (required) = None, v_thresh: a float (required) = None, e_rev_E: a float (required) = None, e_rev_I: a float (required) = None, a: a float (required) = None, b: a float (required) = None, delta_T: a float (required) = None, tau_w: a float (required) = None, v_spike: a float (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
basePyNNIaFCondCellEIF_cond_exp_isfa_ista – Adaptive exponential integrate and fire neuron according to Brette R and Gerstner W ( 2005 ) with exponentially-decaying post-synaptic conductance
- Parameters:
v_spike (none) –
delta_T (none) –
tau_w (none) –
a (none) –
b (none) –
e_rev_E (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
e_rev_I (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
tau_refrac (none) –
v_thresh (none) –
tau_m (none) –
v_rest (none) –
v_reset (none) –
cm (none) –
i_offset (none) –
tau_syn_E (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
tau_syn_I (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
v_init (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ElectricalConnection#
- class neuroml.nml.nml.ElectricalConnection(id: a NonNegativeInteger (required) = None, neuro_lex_id: a NeuroLexId (optional) = None, pre_cell: a string (required) = None, pre_segment: a NonNegativeInteger (optional) = '0', pre_fraction_along: a ZeroToOne (optional) = '0.5', post_cell: a string (required) = None, post_segment: a NonNegativeInteger (optional) = '0', post_fraction_along: a ZeroToOne (optional) = '0.5', synapse: a NmlId (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseConnectionNewFormatElectricalConnection – To enable connections between populations through gap junctions.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- get_post_cell_id()#
Get the ID of the post-synaptic cell
- Returns:
ID of post-synaptic cell
- Return type:
str
- get_post_fraction_along()#
Get post-synaptic fraction along information
- get_post_info()#
Get post-synaptic information summary
- get_post_segment_id()#
Get the ID of the post-synpatic segment
- Returns:
ID of post-synaptic segment.
- Return type:
str
- get_pre_cell_id()#
Get the ID of the pre-synaptic cell
- Returns:
ID of pre-synaptic cell
- Return type:
str
- get_pre_fraction_along()#
Get pre-synaptic fraction along information
- get_pre_info()#
Get pre-synaptic information summary
- get_pre_segment_id()#
Get the ID of the pre-synpatic segment
- Returns:
ID of pre-synaptic segment.
- Return type:
str
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ElectricalConnectionInstance#
- class neuroml.nml.nml.ElectricalConnectionInstance(id: a NonNegativeInteger (required) = None, neuro_lex_id: a NeuroLexId (optional) = None, pre_cell: a string (required) = None, pre_segment: a NonNegativeInteger (optional) = '0', pre_fraction_along: a ZeroToOne (optional) = '0.5', post_cell: a string (required) = None, post_segment: a NonNegativeInteger (optional) = '0', post_fraction_along: a ZeroToOne (optional) = '0.5', synapse: a NmlId (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
ElectricalConnectionElectricalConnectionInstance – To enable connections between populations through gap junctions. Populations need to be of type populationList and contain instance and location elements.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- get_post_cell_id()#
Get the ID of the post-synaptic cell
- Returns:
ID of post-synaptic cell
- Return type:
str
- get_post_fraction_along()#
Get post-synaptic fraction along information
- get_post_info()#
Get post-synaptic information summary
- get_post_segment_id()#
Get the ID of the post-synpatic segment
- Returns:
ID of post-synaptic segment.
- Return type:
str
- get_pre_cell_id()#
Get the ID of the pre-synaptic cell
- Returns:
ID of pre-synaptic cell
- Return type:
str
- get_pre_fraction_along()#
Get pre-synaptic fraction along information
- get_pre_info()#
Get pre-synaptic information summary
- get_pre_segment_id()#
Get the ID of the pre-synpatic segment
- Returns:
ID of pre-synaptic segment.
- Return type:
str
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ElectricalConnectionInstanceW#
- class neuroml.nml.nml.ElectricalConnectionInstanceW(id: a NonNegativeInteger (required) = None, neuro_lex_id: a NeuroLexId (optional) = None, pre_cell: a string (required) = None, pre_segment: a NonNegativeInteger (optional) = '0', pre_fraction_along: a ZeroToOne (optional) = '0.5', post_cell: a string (required) = None, post_segment: a NonNegativeInteger (optional) = '0', post_fraction_along: a ZeroToOne (optional) = '0.5', synapse: a NmlId (required) = None, weight: a float (required) = None, gds_collector_=None, **kwargs_)#
Bases:
ElectricalConnectionInstanceElectricalConnectionInstanceW – To enable connections between populations through gap junctions. Populations need to be of type populationList and contain instance and location elements. Includes setting of weight for the connection
- Parameters:
weight (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- get_post_cell_id()#
Get the ID of the post-synaptic cell
- Returns:
ID of post-synaptic cell
- Return type:
str
- get_post_fraction_along()#
Get post-synaptic fraction along information
- get_post_info()#
Get post-synaptic information summary
- get_post_segment_id()#
Get the ID of the post-synpatic segment
- Returns:
ID of post-synaptic segment.
- Return type:
str
- get_pre_cell_id()#
Get the ID of the pre-synaptic cell
- Returns:
ID of pre-synaptic cell
- Return type:
str
- get_pre_fraction_along()#
Get pre-synaptic fraction along information
- get_pre_info()#
Get pre-synaptic information summary
- get_pre_segment_id()#
Get the ID of the pre-synpatic segment
- Returns:
ID of pre-synaptic segment.
- Return type:
str
- get_weight()#
Get the weight of the connection
If a weight is not set (or is set to None), returns the default value of 1.0.
- Returns:
weight of connection or 1.0 if not set
- Return type:
float
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ElectricalProjection#
- class neuroml.nml.nml.ElectricalProjection(id: a NmlId (required) = None, presynaptic_population: a NmlId (required) = None, postsynaptic_population: a NmlId (required) = None, electrical_connections: list of ElectricalConnection(s) (optional) = None, electrical_connection_instances: list of ElectricalConnectionInstance(s) (optional) = None, electrical_connection_instance_ws: list of ElectricalConnectionInstanceW(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseProjectionElectricalProjection – A projection between presynapticPopulation to another postsynapticPopulation through gap junctions.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- exportHdf5(h5file, h5Group)#
Export to HDF5 file.
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
EventOut#
- class neuroml.nml.nml.EventOut(port: a string (required) = None, gds_collector_=None, **kwargs_)#
Bases:
GeneratedsSuper- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ExpCondSynapse#
- class neuroml.nml.nml.ExpCondSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, tau_syn: a float (required) = None, e_rev: a float (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BasePynnSynapseExpCondSynapse – Conductance based synapse with instantaneous rise and single exponential decay ( with time constant tau_syn )
- Parameters:
e_rev (none) –
tau_syn (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ExpCurrSynapse#
- class neuroml.nml.nml.ExpCurrSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, tau_syn: a float (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BasePynnSynapseExpCurrSynapse – Current based synapse with instantaneous rise and single exponential decay ( with time constant tau_syn )
- Parameters:
tau_syn (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ExpOneSynapse#
- class neuroml.nml.nml.ExpOneSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, gbase: a Nml2Quantity_conductance (required) = None, erev: a Nml2Quantity_voltage (required) = None, tau_decay: a Nml2Quantity_time (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseConductanceBasedSynapseExpOneSynapse – Ohmic synapse model whose conductance rises instantaneously by ( gbase * weight ) on receiving an event, and which decays exponentially to zero with time course tauDecay
- Parameters:
tauDecay (time) – Time course of decay
gbase (conductance) – Baseline conductance, generally the maximum conductance following a single spike
erev (voltage) – Reversal potential of the synapse
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ExpThreeSynapse#
- class neuroml.nml.nml.ExpThreeSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, gbase1: a Nml2Quantity_conductance (required) = None, gbase2: a Nml2Quantity_conductance (required) = None, erev: a Nml2Quantity_voltage (required) = None, tau_decay1: a Nml2Quantity_time (required) = None, tau_decay2: a Nml2Quantity_time (required) = None, tau_rise: a Nml2Quantity_time (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseConductanceBasedSynapseTwoExpThreeSynapse – Ohmic synapse similar to expTwoSynapse but consisting of two components that can differ in decay times and max conductances but share the same rise time.
- Parameters:
tauRise (time) –
tauDecay1 (time) –
tauDecay2 (time) –
gbase1 (conductance) – Baseline conductance 1
gbase2 (conductance) – Baseline conductance 2
erev (voltage) – Reversal potential of the synapse
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ExpTwoSynapse#
- class neuroml.nml.nml.ExpTwoSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, gbase: a Nml2Quantity_conductance (required) = None, erev: a Nml2Quantity_voltage (required) = None, tau_decay: a Nml2Quantity_time (required) = None, tau_rise: a Nml2Quantity_time (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseConductanceBasedSynapseExpTwoSynapse – Ohmic synapse model whose conductance waveform on receiving an event has a rise time of tauRise and a decay time of tauDecay. Max conductance reached during this time ( assuming zero conductance before ) is gbase * weight.
- Parameters:
tauRise (time) –
tauDecay (time) –
gbase (conductance) – Baseline conductance, generally the maximum conductance following a single spike
erev (voltage) – Reversal potential of the synapse
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ExplicitInput#
- class neuroml.nml.nml.ExplicitInput(target: a Nml2PopulationReferencePath (required) = None, input: a NmlId (required) = None, destination: a NmlId (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdExplicitInput – An explicit input ( anything which extends basePointCurrent ) to a target cell in a population
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- get_fraction_along()#
Get fraction along.
Returns 0.5 is fraction_along was not set.
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- get_segment_id()#
Get the ID of the segment.
Returns 0 if segment_id was not set.
- get_target_cell_id()#
Get target cell ID
- get_target_population()#
Get target population.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
- validate_Nml2PopulationReferencePath(value)#
- validate_Nml2PopulationReferencePath_patterns_ = [['^((\\.\\./)?([a-zA-Z_][a-zA-Z0-9_]*)((\\[[0-9]+\\])|(/[0-9]+)+((/[a-zA-Z_][a-zA-Z0-9_]*)?)/?))$']]#
Exposure#
- class neuroml.nml.nml.Exposure(name: a string (required) = None, dimension: a string (required) = None, description: a string (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdExposure – LEMS Exposure (ComponentType property)
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ExtracellularProperties#
- class neuroml.nml.nml.ExtracellularProperties(id: a NmlId (required) = None, species: list of Species(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
Base- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ExtracellularPropertiesLocal#
- class neuroml.nml.nml.ExtracellularPropertiesLocal(id: a NmlId (required) = None, species: list of Species(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
Base- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
FitzHughNagumo1969Cell#
- class neuroml.nml.nml.FitzHughNagumo1969Cell(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, a: a Nml2Quantity_none (required) = None, b: a Nml2Quantity_none (required) = None, I: a Nml2Quantity_none (required) = None, phi: a Nml2Quantity_none (required) = None, V0: a Nml2Quantity_none (required) = None, W0: a Nml2Quantity_none (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseCellFitzHughNagumo1969Cell – The Fitzhugh Nagumo model is a two-dimensional simplification of the Hodgkin-Huxley model of spike generation in squid giant axons. This system was suggested by FitzHugh ( FitzHugh R. [1961]: Impulses and physiological states in theoretical models of nerve membrane. Biophysical J. 1:445-466 ), who called it “ Bonhoeffer-van der Pol model “, and the equivalent circuit by Nagumo et al. ( Nagumo J. , Arimoto S. , and Yoshizawa S. [1962] An active pulse transmission line simulating nerve axon. Proc IRE. 50:2061-2070. 1962 ). This version corresponds to the one described in FitzHugh R. [1969]: Mathematical models of excitation and propagation in nerve. Chapter 1 ( pp. 1-85 in H. P. Schwan, ed. Biological Engineering, McGraw-Hill Book Co. , N. Y. )
- Parameters:
a (none) –
b (none) –
I (none) – plays the role of an external injected current
phi (none) –
V0 (none) –
W0 (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
FitzHughNagumoCell#
- class neuroml.nml.nml.FitzHughNagumoCell(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, I: a Nml2Quantity_none (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseCellFitzHughNagumoCell – Simple dimensionless model of spiking cell from FitzHugh and Nagumo. Superseded by fitzHughNagumo1969Cell ( See NeuroML/NeuroML2#42 )
- Parameters:
I (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
FixedFactorConcentrationModel#
- class neuroml.nml.nml.FixedFactorConcentrationModel(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, ion: a NmlId (required) = None, resting_conc: a Nml2Quantity_concentration (required) = None, decay_constant: a Nml2Quantity_time (required) = None, rho: a Nml2Quantity_rhoFactor (required) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneFixedFactorConcentrationModel – Model of buffering of concentration of an ion ( currently hard coded to be calcium, due to requirement for iCa ) which has a baseline level restingConc and tends to this value with time course decayConstant. A fixed factor rho is used to scale the incoming current independently of the size of the compartment to produce a concentration change.
- Parameters:
restingConc (concentration) –
decayConstant (time) –
rho (rho_factor) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ForwardTransition#
- class neuroml.nml.nml.ForwardTransition(id: a NmlId (required) = None, from_: a NmlId (required) = None, to: a NmlId (required) = None, anytypeobjs_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseForwardTransition – A forward only KSTransition for a gateKS which specifies a rate ( type baseHHRate ) which follows one of the standard Hodgkin Huxley forms ( e. g. HHExpRate , HHSigmoidRate , HHExpLinearRate
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
GapJunction#
- class neuroml.nml.nml.GapJunction(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, conductance: a Nml2Quantity_conductance (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseSynapseGapJunction – Gap junction/single electrical connection
- Parameters:
conductance (conductance) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
GateFractional#
- class neuroml.nml.nml.GateFractional(id: a NmlId (required) = None, instances: a PositiveInteger (required) = None, notes: a string (optional) = None, q10_settings: a Q10Settings (optional) = None, sub_gates: list of GateFractionalSubgate(s) (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseGateFractional – Gate composed of subgates contributing with fractional conductance
- Parameters:
instances (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
GateFractionalSubgate#
- class neuroml.nml.nml.GateFractionalSubgate(id: a NmlId (required) = None, fractional_conductance: a Nml2Quantity_none (required) = None, notes: a string (optional) = None, q10_settings: a Q10Settings (optional) = None, steady_state: a HHVariable (required) = None, time_course: a HHTime (required) = None, gds_collector_=None, **kwargs_)#
Bases:
Base- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
GateHHInstantaneous#
- class neuroml.nml.nml.GateHHInstantaneous(id: a NmlId (required) = None, instances: a PositiveInteger (required) = None, notes: a string (optional) = None, steady_state: a HHVariable (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseGateHHInstantaneous – Gate which follows the general Hodgkin Huxley formalism but is instantaneous, so tau = 0 and gate follows exactly inf value
- Parameters:
instances (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
GateHHRates#
- class neuroml.nml.nml.GateHHRates(id: a NmlId (required) = None, instances: a PositiveInteger (required) = None, notes: a string (optional) = None, q10_settings: a Q10Settings (optional) = None, forward_rate: a HHRate (required) = None, reverse_rate: a HHRate (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseGateHHRates – Gate which follows the general Hodgkin Huxley formalism
- Parameters:
instances (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
GateHHRatesInf#
- class neuroml.nml.nml.GateHHRatesInf(id: a NmlId (required) = None, instances: a PositiveInteger (required) = None, notes: a string (optional) = None, q10_settings: a Q10Settings (optional) = None, forward_rate: a HHRate (required) = None, reverse_rate: a HHRate (required) = None, steady_state: a HHVariable (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseGateHHRatesInf – Gate which follows the general Hodgkin Huxley formalism
- Parameters:
instances (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
GateHHRatesTau#
- class neuroml.nml.nml.GateHHRatesTau(id: a NmlId (required) = None, instances: a PositiveInteger (required) = None, notes: a string (optional) = None, q10_settings: a Q10Settings (optional) = None, forward_rate: a HHRate (required) = None, reverse_rate: a HHRate (required) = None, time_course: a HHTime (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseGateHHRatesTau – Gate which follows the general Hodgkin Huxley formalism
- Parameters:
instances (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
GateHHRatesTauInf#
- class neuroml.nml.nml.GateHHRatesTauInf(id: a NmlId (required) = None, instances: a PositiveInteger (required) = None, notes: a string (optional) = None, q10_settings: a Q10Settings (optional) = None, forward_rate: a HHRate (required) = None, reverse_rate: a HHRate (required) = None, time_course: a HHTime (required) = None, steady_state: a HHVariable (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseGateHHRatesTauInf – Gate which follows the general Hodgkin Huxley formalism
- Parameters:
instances (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
GateHHTauInf#
- class neuroml.nml.nml.GateHHTauInf(id: a NmlId (required) = None, instances: a PositiveInteger (required) = None, notes: a string (optional) = None, q10_settings: a Q10Settings (optional) = None, time_course: a HHTime (required) = None, steady_state: a HHVariable (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseGateHHTauInf – Gate which follows the general Hodgkin Huxley formalism
- Parameters:
instances (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
GateHHUndetermined#
- class neuroml.nml.nml.GateHHUndetermined(id: a NmlId (required) = None, instances: a PositiveInteger (required) = None, type: a gateTypes (required) = None, notes: a string (optional) = None, q10_settings: a Q10Settings (optional) = None, forward_rate: a HHRate (optional) = None, reverse_rate: a HHRate (optional) = None, time_course: a HHTime (optional) = None, steady_state: a HHVariable (optional) = None, sub_gates: list of GateFractionalSubgate(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseGateHHUndetermined – Note all sub elements for gateHHrates, gateHHratesTau, gateFractional etc. allowed here. Which are valid should be constrained by what type is set
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
GateKS#
- class neuroml.nml.nml.GateKS(id: a NmlId (required) = None, instances: a PositiveInteger (required) = None, notes: a string (optional) = None, q10_settings: a Q10Settings (optional) = None, closed_states: list of ClosedState(s) (required) = None, open_states: list of OpenState(s) (required) = None, forward_transition: list of ForwardTransition(s) (required) = None, reverse_transition: list of ReverseTransition(s) (required) = None, tau_inf_transition: list of TauInfTransition(s) (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseGateKS – A gate which consists of multiple KSState s and KSTransition s giving the rates of transition between them
- Parameters:
instances (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
GeneratedsSuper#
- class neuroml.nml.nml.GeneratedsSuper#
Bases:
GeneratedsSuperSuper
GradedSynapse#
- class neuroml.nml.nml.GradedSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, conductance: a Nml2Quantity_conductance (required) = None, delta: a Nml2Quantity_voltage (required) = None, Vth: a Nml2Quantity_voltage (required) = None, k: a Nml2Quantity_pertime (required) = None, erev: a Nml2Quantity_voltage (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseSynapseGradedSynapse – Graded/analog synapse. Based on synapse in Methods of http://www. nature.com/neuro/journal/v7/n12/abs/nn1352.html
- Parameters:
conductance (conductance) –
delta (voltage) – Slope of the activation curve
k (per_time) – Rate constant for transmitter-receptor dissociation rate
Vth (voltage) – The half-activation voltage of the synapse
erev (voltage) – The reversal potential of the synapse
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
GridLayout#
- class neuroml.nml.nml.GridLayout(x_size: a nonNegativeInteger (optional) = None, y_size: a nonNegativeInteger (optional) = None, z_size: a nonNegativeInteger (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutId- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
HHRate#
- class neuroml.nml.nml.HHRate(type: a NmlId (required) = None, rate: a Nml2Quantity_pertime (optional) = None, midpoint: a Nml2Quantity_voltage (optional) = None, scale: a Nml2Quantity_voltage (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutId- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
HHTime#
- class neuroml.nml.nml.HHTime(type: a NmlId (required) = None, rate: a Nml2Quantity_time (optional) = None, midpoint: a Nml2Quantity_voltage (optional) = None, scale: a Nml2Quantity_voltage (optional) = None, tau: a Nml2Quantity_time (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutId- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
HHVariable#
- class neuroml.nml.nml.HHVariable(type: a NmlId (required) = None, rate: a float (optional) = None, midpoint: a Nml2Quantity_voltage (optional) = None, scale: a Nml2Quantity_voltage (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutId- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
HH_cond_exp#
- class neuroml.nml.nml.HH_cond_exp(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, cm: a float (required) = None, i_offset: a float (required) = None, tau_syn_E: a float (required) = None, tau_syn_I: a float (required) = None, v_init: a float (required) = None, v_offset: a float (required) = None, e_rev_E: a float (required) = None, e_rev_I: a float (required) = None, e_rev_K: a float (required) = None, e_rev_Na: a float (required) = None, e_rev_leak: a float (required) = None, g_leak: a float (required) = None, gbar_K: a float (required) = None, gbar_Na: a float (required) = None, gds_collector_=None, **kwargs_)#
Bases:
basePyNNCellHH_cond_exp – Single-compartment Hodgkin-Huxley-type neuron with transient sodium and delayed-rectifier potassium currents using the ion channel models from Traub.
- Parameters:
gbar_K (none) –
gbar_Na (none) –
g_leak (none) –
e_rev_K (none) –
e_rev_Na (none) –
e_rev_leak (none) –
v_offset (none) –
e_rev_E (none) –
e_rev_I (none) –
cm (none) –
i_offset (none) –
tau_syn_E (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
tau_syn_I (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
v_init (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
IF_cond_alpha#
- class neuroml.nml.nml.IF_cond_alpha(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, cm: a float (required) = None, i_offset: a float (required) = None, tau_syn_E: a float (required) = None, tau_syn_I: a float (required) = None, v_init: a float (required) = None, tau_m: a float (required) = None, tau_refrac: a float (required) = None, v_reset: a float (required) = None, v_rest: a float (required) = None, v_thresh: a float (required) = None, e_rev_E: a float (required) = None, e_rev_I: a float (required) = None, gds_collector_=None, **kwargs_)#
Bases:
basePyNNIaFCondCellIF_cond_alpha – Leaky integrate and fire model with fixed threshold and alpha-function-shaped post-synaptic conductance
- Parameters:
e_rev_E (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
e_rev_I (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
tau_refrac (none) –
v_thresh (none) –
tau_m (none) –
v_rest (none) –
v_reset (none) –
cm (none) –
i_offset (none) –
tau_syn_E (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
tau_syn_I (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
v_init (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
IF_cond_exp#
- class neuroml.nml.nml.IF_cond_exp(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, cm: a float (required) = None, i_offset: a float (required) = None, tau_syn_E: a float (required) = None, tau_syn_I: a float (required) = None, v_init: a float (required) = None, tau_m: a float (required) = None, tau_refrac: a float (required) = None, v_reset: a float (required) = None, v_rest: a float (required) = None, v_thresh: a float (required) = None, e_rev_E: a float (required) = None, e_rev_I: a float (required) = None, gds_collector_=None, **kwargs_)#
Bases:
basePyNNIaFCondCellIF_cond_exp – Leaky integrate and fire model with fixed threshold and exponentially-decaying post-synaptic conductance
- Parameters:
e_rev_E (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
e_rev_I (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
tau_refrac (none) –
v_thresh (none) –
tau_m (none) –
v_rest (none) –
v_reset (none) –
cm (none) –
i_offset (none) –
tau_syn_E (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
tau_syn_I (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
v_init (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
IF_curr_alpha#
- class neuroml.nml.nml.IF_curr_alpha(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, cm: a float (required) = None, i_offset: a float (required) = None, tau_syn_E: a float (required) = None, tau_syn_I: a float (required) = None, v_init: a float (required) = None, tau_m: a float (required) = None, tau_refrac: a float (required) = None, v_reset: a float (required) = None, v_rest: a float (required) = None, v_thresh: a float (required) = None, gds_collector_=None, **kwargs_)#
Bases:
basePyNNIaFCellIF_curr_alpha – Leaky integrate and fire model with fixed threshold and alpha-function-shaped post-synaptic current
- Parameters:
tau_refrac (none) –
v_thresh (none) –
tau_m (none) –
v_rest (none) –
v_reset (none) –
cm (none) –
i_offset (none) –
tau_syn_E (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
tau_syn_I (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
v_init (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
IF_curr_exp#
- class neuroml.nml.nml.IF_curr_exp(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, cm: a float (required) = None, i_offset: a float (required) = None, tau_syn_E: a float (required) = None, tau_syn_I: a float (required) = None, v_init: a float (required) = None, tau_m: a float (required) = None, tau_refrac: a float (required) = None, v_reset: a float (required) = None, v_rest: a float (required) = None, v_thresh: a float (required) = None, gds_collector_=None, **kwargs_)#
Bases:
basePyNNIaFCellIF_curr_exp – Leaky integrate and fire model with fixed threshold and decaying-exponential post-synaptic current
- Parameters:
tau_refrac (none) –
v_thresh (none) –
tau_m (none) –
v_rest (none) –
v_reset (none) –
cm (none) –
i_offset (none) –
tau_syn_E (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
tau_syn_I (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
v_init (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
IafCell#
- class neuroml.nml.nml.IafCell(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, leak_reversal: a Nml2Quantity_voltage (required) = None, thresh: a Nml2Quantity_voltage (required) = None, reset: a Nml2Quantity_voltage (required) = None, C: a Nml2Quantity_capacitance (required) = None, leak_conductance: a Nml2Quantity_conductance (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseCellIafCell – Integrate and fire cell with capacitance C, leakConductance and leakReversal
- Parameters:
leakConductance (conductance) –
leakReversal (voltage) –
thresh (voltage) –
reset (voltage) –
C (capacitance) – Total capacitance of the cell membrane
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
IafRefCell#
- class neuroml.nml.nml.IafRefCell(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, leak_reversal: a Nml2Quantity_voltage (required) = None, thresh: a Nml2Quantity_voltage (required) = None, reset: a Nml2Quantity_voltage (required) = None, C: a Nml2Quantity_capacitance (required) = None, leak_conductance: a Nml2Quantity_conductance (required) = None, refract: a Nml2Quantity_time (required) = None, gds_collector_=None, **kwargs_)#
Bases:
IafCellIafRefCell – Integrate and fire cell with capacitance C, leakConductance, leakReversal and refractory period refract
- Parameters:
refract (time) –
leakConductance (conductance) –
leakReversal (voltage) –
thresh (voltage) –
reset (voltage) –
C (capacitance) – Total capacitance of the cell membrane
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
IafTauCell#
- class neuroml.nml.nml.IafTauCell(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, leak_reversal: a Nml2Quantity_voltage (required) = None, thresh: a Nml2Quantity_voltage (required) = None, reset: a Nml2Quantity_voltage (required) = None, tau: a Nml2Quantity_time (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseCellIafTauCell – Integrate and fire cell which returns to its leak reversal potential of leakReversal with a time constant tau
- Parameters:
leakReversal (voltage) –
tau (time) –
thresh (voltage) – The membrane potential at which to emit a spiking event and reset voltage
reset (voltage) – The value the membrane potential is reset to on spiking
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
IafTauRefCell#
- class neuroml.nml.nml.IafTauRefCell(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, leak_reversal: a Nml2Quantity_voltage (required) = None, thresh: a Nml2Quantity_voltage (required) = None, reset: a Nml2Quantity_voltage (required) = None, tau: a Nml2Quantity_time (required) = None, refract: a Nml2Quantity_time (required) = None, gds_collector_=None, **kwargs_)#
Bases:
IafTauCellIafTauRefCell – Integrate and fire cell which returns to its leak reversal potential of leakReversal with a time course tau. It has a refractory period of refract after spiking
- Parameters:
refract (time) –
leakReversal (voltage) –
tau (time) –
thresh (voltage) – The membrane potential at which to emit a spiking event and reset voltage
reset (voltage) – The value the membrane potential is reset to on spiking
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Include#
- class neuroml.nml.nml.Include(segment_groups: a NmlId (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdInclude – Include all members of another segmentGroup in this group
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
IncludeType#
- class neuroml.nml.nml.IncludeType(href: a anyURI (required) = None, gds_collector_=None, **kwargs_)#
Bases:
GeneratedsSuper- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
InhomogeneousParameter#
- class neuroml.nml.nml.InhomogeneousParameter(id: a NmlId (required) = None, variable: a string (required) = None, metric: a Metric (required) = None, proximal: a ProximalDetails (optional) = None, distal: a DistalDetails (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseInhomogeneousParameter – An inhomogeneous parameter specified across the segmentGroup ( see variableParameter for usage ).
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
InhomogeneousValue#
- class neuroml.nml.nml.InhomogeneousValue(inhomogeneous_parameters: a string (required) = None, value: a string (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdInhomogeneousValue – Specifies the value of an inhomogeneousParameter. For usage see variableParameter
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
InitMembPotential#
- class neuroml.nml.nml.InitMembPotential(value: a Nml2Quantity_voltage (required) = None, segment_groups: a NmlId (optional) = 'all', gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdInitMembPotential – Explicitly set initial membrane potential for the cell
- Parameters:
value (voltage) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Input#
- class neuroml.nml.nml.Input(id: a NonNegativeInteger (required) = None, target: a Nml2PopulationReferencePath (required) = None, destination: a NmlId (required) = None, segment_id: a NonNegativeInteger (optional) = None, fraction_along: a ZeroToOne (optional) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseNonNegativeIntegerIdInput – Specifies a single input to a target, optionally giving the segmentId ( default 0 ) and fractionAlong the segment ( default 0. 5 ).
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- get_fraction_along()#
Get fraction along.
Returns 0.5 is fraction_along was not set.
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- get_segment_id()#
Get the ID of the segment.
Returns 0 if segment_id was not set.
- get_target_cell_id()#
Get ID of target cell.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
- validate_Nml2PopulationReferencePath(value)#
- validate_Nml2PopulationReferencePath_patterns_ = [['^((\\.\\./)?([a-zA-Z_][a-zA-Z0-9_]*)((\\[[0-9]+\\])|(/[0-9]+)+((/[a-zA-Z_][a-zA-Z0-9_]*)?)/?))$']]#
InputList#
- class neuroml.nml.nml.InputList(id: a NonNegativeInteger (required) = None, populations: a NmlId (required) = None, component: a NmlId (required) = None, input: list of Input(s) (optional) = None, input_ws: list of InputW(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseInputList – An explicit list of input s to a population.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- exportHdf5(h5file, h5Group)#
Export to HDF5 file.
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
InputW#
- class neuroml.nml.nml.InputW(id: a NonNegativeInteger (required) = None, target: a Nml2PopulationReferencePath (required) = None, destination: a NmlId (required) = None, segment_id: a NonNegativeInteger (optional) = None, fraction_along: a ZeroToOne (optional) = None, weight: a float (required) = None, gds_collector_=None, **kwargs_)#
Bases:
InputInputW – Specifies input lists. Can set weight to scale individual inputs.
- Parameters:
weight (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- get_fraction_along()#
Get fraction along.
Returns 0.5 is fraction_along was not set.
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- get_segment_id()#
Get the ID of the segment.
Returns 0 if segment_id was not set.
- get_target_cell_id()#
Get ID of target cell.
- get_weight()#
Get weight.
If weight is not set, the default value of 1.0 is returned.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
- validate_Nml2PopulationReferencePath(value)#
- validate_Nml2PopulationReferencePath_patterns_ = [['^((\\.\\./)?([a-zA-Z_][a-zA-Z0-9_]*)((\\[[0-9]+\\])|(/[0-9]+)+((/[a-zA-Z_][a-zA-Z0-9_]*)?)/?))$']]#
Instance#
- class neuroml.nml.nml.Instance(id: a nonNegativeInteger (optional) = None, i: a nonNegativeInteger (optional) = None, j: a nonNegativeInteger (optional) = None, k: a nonNegativeInteger (optional) = None, location: a Location (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdInstance – Specifies a single instance of a component in a population ( placed at location ).
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
InstanceRequirement#
- class neuroml.nml.nml.InstanceRequirement(name: a string (required) = None, type: a string (required) = None, gds_collector_=None, **kwargs_)#
Bases:
GeneratedsSuper- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
IntracellularProperties#
- class neuroml.nml.nml.IntracellularProperties(species: list of Species(s) (optional) = None, resistivities: list of Resistivity(s) (optional) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdIntracellularProperties – Biophysical properties related to the intracellular space within the cell , such as the resistivity and the list of ionic species present. caConc and caConcExt are explicitly exposed here to facilitate accessing these values from other Components, even though caConcExt is clearly not an intracellular property
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
IntracellularProperties2CaPools#
- class neuroml.nml.nml.IntracellularProperties2CaPools(species: list of Species(s) (optional) = None, resistivities: list of Resistivity(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
IntracellularPropertiesIntracellularProperties2CaPools – Variant of intracellularProperties with 2 independent Ca pools
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
IonChannel#
- class neuroml.nml.nml.IonChannel(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, q10_conductance_scalings: list of Q10ConductanceScaling(s) (optional) = None, species: a NmlId (optional) = None, type: a channelTypes (optional) = None, conductance: a Nml2Quantity_conductance (optional) = None, gates: list of GateHHUndetermined(s) (optional) = None, gate_hh_rates: list of GateHHRates(s) (optional) = None, gate_h_hrates_taus: list of GateHHRatesTau(s) (optional) = None, gate_hh_tau_infs: list of GateHHTauInf(s) (optional) = None, gate_h_hrates_infs: list of GateHHRatesInf(s) (optional) = None, gate_h_hrates_tau_infs: list of GateHHRatesTauInf(s) (optional) = None, gate_hh_instantaneouses: list of GateHHInstantaneous(s) (optional) = None, gate_fractionals: list of GateFractional(s) (optional) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
IonChannelScalableIonChannel – Note ionChannel and ionChannelHH are currently functionally identical. This is needed since many existing examples use ionChannel, some use ionChannelHH. NeuroML v2beta4 should remove one of these, probably ionChannelHH.
- Parameters:
conductance (conductance) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
IonChannelHH#
- class neuroml.nml.nml.IonChannelHH(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, q10_conductance_scalings: list of Q10ConductanceScaling(s) (optional) = None, species: a NmlId (optional) = None, type: a channelTypes (optional) = None, conductance: a Nml2Quantity_conductance (optional) = None, gates: list of GateHHUndetermined(s) (optional) = None, gate_hh_rates: list of GateHHRates(s) (optional) = None, gate_h_hrates_taus: list of GateHHRatesTau(s) (optional) = None, gate_hh_tau_infs: list of GateHHTauInf(s) (optional) = None, gate_h_hrates_infs: list of GateHHRatesInf(s) (optional) = None, gate_h_hrates_tau_infs: list of GateHHRatesTauInf(s) (optional) = None, gate_hh_instantaneouses: list of GateHHInstantaneous(s) (optional) = None, gate_fractionals: list of GateFractional(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
IonChannelIonChannelHH – Note ionChannel and ionChannelHH are currently functionally identical. This is needed since many existing examples use ionChannel, some use ionChannelHH. NeuroML v2beta4 should remove one of these, probably ionChannelHH.
- Parameters:
conductance (conductance) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
IonChannelKS#
- class neuroml.nml.nml.IonChannelKS(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, species: a NmlId (optional) = None, conductance: a Nml2Quantity_conductance (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, gate_kses: list of GateKS(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneA kinetic scheme based ion channel with multiple gateKS s, each of which consists of multiple KSState s and KSTransition s giving the rates of transition between them IonChannelKS – A kinetic scheme based ion channel with multiple gateKS s, each of which consists of multiple KSState s and KSTransition s giving the rates of transition between them
- Parameters:
conductance (conductance) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
IonChannelScalable#
- class neuroml.nml.nml.IonChannelScalable(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, q10_conductance_scalings: list of Q10ConductanceScaling(s) (optional) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
Standalone- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
IonChannelVShift#
- class neuroml.nml.nml.IonChannelVShift(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, q10_conductance_scalings: list of Q10ConductanceScaling(s) (optional) = None, species: a NmlId (optional) = None, type: a channelTypes (optional) = None, conductance: a Nml2Quantity_conductance (optional) = None, gates: list of GateHHUndetermined(s) (optional) = None, gate_hh_rates: list of GateHHRates(s) (optional) = None, gate_h_hrates_taus: list of GateHHRatesTau(s) (optional) = None, gate_hh_tau_infs: list of GateHHTauInf(s) (optional) = None, gate_h_hrates_infs: list of GateHHRatesInf(s) (optional) = None, gate_h_hrates_tau_infs: list of GateHHRatesTauInf(s) (optional) = None, gate_hh_instantaneouses: list of GateHHInstantaneous(s) (optional) = None, gate_fractionals: list of GateFractional(s) (optional) = None, v_shift: a Nml2Quantity_voltage (required) = None, gds_collector_=None, **kwargs_)#
Bases:
IonChannelIonChannelVShift – Same as ionChannel , but with a vShift parameter to change voltage activation of gates. The exact usage of vShift in expressions for rates is determined by the individual gates.
- Parameters:
vShift (voltage) –
conductance (conductance) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Izhikevich2007Cell#
- class neuroml.nml.nml.Izhikevich2007Cell(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, C: a Nml2Quantity_capacitance (required) = None, v0: a Nml2Quantity_voltage (required) = None, k: a Nml2Quantity_conductancePerVoltage (required) = None, vr: a Nml2Quantity_voltage (required) = None, vt: a Nml2Quantity_voltage (required) = None, vpeak: a Nml2Quantity_voltage (required) = None, a: a Nml2Quantity_pertime (required) = None, b: a Nml2Quantity_conductance (required) = None, c: a Nml2Quantity_voltage (required) = None, d: a Nml2Quantity_current (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseCellMembPotCapIzhikevich2007Cell – Cell based on the modified Izhikevich model in Izhikevich 2007, Dynamical systems in neuroscience, MIT Press
- Parameters:
v0 (voltage) – Initial membrane potential
k (conductance_per_voltage) –
vr (voltage) – Resting membrane potential
vt (voltage) – Spike threshold
vpeak (voltage) – Peak action potential value
a (per_time) – Time scale of recovery variable u
b (conductance) – Sensitivity of recovery variable u to subthreshold fluctuations of membrane potential v
c (voltage) – After-spike reset value of v
d (current) – After-spike increase to u
C (capacitance) – Total capacitance of the cell membrane
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
IzhikevichCell#
- class neuroml.nml.nml.IzhikevichCell(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, v0: a Nml2Quantity_voltage (required) = None, thresh: a Nml2Quantity_voltage (required) = None, a: a Nml2Quantity_none (required) = None, b: a Nml2Quantity_none (required) = None, c: a Nml2Quantity_none (required) = None, d: a Nml2Quantity_none (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseCellIzhikevichCell – Cell based on the 2003 model of Izhikevich, see http://izhikevich.org/publications/spikes.htm
- Parameters:
v0 (voltage) – Initial membrane potential
a (none) – Time scale of the recovery variable U
b (none) – Sensitivity of U to the subthreshold fluctuations of the membrane potential V
c (none) – After-spike reset value of V
d (none) – After-spike increase to U
thresh (voltage) – Spike threshold
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
LEMS_Property#
- class neuroml.nml.nml.LEMS_Property(name: a string (required) = None, dimension: a string (required) = None, description: a string (optional) = None, default_value: a double (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
NamedDimensionalType- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Layout#
- class neuroml.nml.nml.Layout(spaces: a NmlId (optional) = None, random: a RandomLayout (required) = None, grid: a GridLayout (required) = None, unstructured: a UnstructuredLayout (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutId- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
LinearGradedSynapse#
- class neuroml.nml.nml.LinearGradedSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, conductance: a Nml2Quantity_conductance (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseSynapseLinearGradedSynapse – Behaves just like a one way gap junction.
- Parameters:
conductance (conductance) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Location#
- class neuroml.nml.nml.Location(x: a float (required) = None, y: a float (required) = None, z: a float (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdLocation – Specifies the ( x, y, z ) location of a single instance of a component in a population
- Parameters:
x (none) –
y (none) –
z (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Member#
- class neuroml.nml.nml.Member(segments: a NonNegativeInteger (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdMember – A single identified segment which is part of the segmentGroup
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
MembraneProperties#
- class neuroml.nml.nml.MembraneProperties(channel_populations: list of ChannelPopulation(s) (optional) = None, channel_densities: list of ChannelDensity(s) (optional) = None, channel_density_v_shifts: list of ChannelDensityVShift(s) (optional) = None, channel_density_nernsts: list of ChannelDensityNernst(s) (optional) = None, channel_density_ghks: list of ChannelDensityGHK(s) (optional) = None, channel_density_ghk2s: list of ChannelDensityGHK2(s) (optional) = None, channel_density_non_uniforms: list of ChannelDensityNonUniform(s) (optional) = None, channel_density_non_uniform_nernsts: list of ChannelDensityNonUniformNernst(s) (optional) = None, channel_density_non_uniform_ghks: list of ChannelDensityNonUniformGHK(s) (optional) = None, spike_threshes: list of SpikeThresh(s) (optional) = None, specific_capacitances: list of SpecificCapacitance(s) (optional) = None, init_memb_potentials: list of InitMembPotential(s) (optional) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdMembraneProperties – Properties specific to the membrane, such as the populations of channels, channelDensities, specificCapacitance, etc.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
MembraneProperties2CaPools#
- class neuroml.nml.nml.MembraneProperties2CaPools(channel_populations: list of ChannelPopulation(s) (optional) = None, channel_densities: list of ChannelDensity(s) (optional) = None, channel_density_v_shifts: list of ChannelDensityVShift(s) (optional) = None, channel_density_nernsts: list of ChannelDensityNernst(s) (optional) = None, channel_density_ghks: list of ChannelDensityGHK(s) (optional) = None, channel_density_ghk2s: list of ChannelDensityGHK2(s) (optional) = None, channel_density_non_uniforms: list of ChannelDensityNonUniform(s) (optional) = None, channel_density_non_uniform_nernsts: list of ChannelDensityNonUniformNernst(s) (optional) = None, channel_density_non_uniform_ghks: list of ChannelDensityNonUniformGHK(s) (optional) = None, spike_threshes: list of SpikeThresh(s) (optional) = None, specific_capacitances: list of SpecificCapacitance(s) (optional) = None, init_memb_potentials: list of InitMembPotential(s) (optional) = None, channel_density_nernst_ca2s: list of ChannelDensityNernstCa2(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
MembranePropertiesMembraneProperties2CaPools – Variant of membraneProperties with 2 independent Ca pools
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Morphology#
- class neuroml.nml.nml.Morphology(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, segments: list of Segment(s) (required) = None, segment_groups: list of SegmentGroup(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneMorphology – The collection of segment s which specify the 3D structure of the cell, along with a number of segmentGroup s
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- property num_segments#
Get the number of segments included in this cell morphology.
- Returns:
number of segments
- Return type:
int
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
NamedDimensionalType#
- class neuroml.nml.nml.NamedDimensionalType(name: a string (required) = None, dimension: a string (required) = None, description: a string (optional) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutId- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
NamedDimensionalVariable#
- class neuroml.nml.nml.NamedDimensionalVariable(name: a string (required) = None, dimension: a string (required) = None, description: a string (optional) = None, exposure: a string (optional) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutId- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Network#
- class neuroml.nml.nml.Network(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, type: a networkTypes (optional) = None, temperature: a Nml2Quantity_temperature (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, spaces: list of Space(s) (optional) = None, regions: list of Region(s) (optional) = None, extracellular_properties: list of ExtracellularPropertiesLocal(s) (optional) = None, populations: list of Population(s) (required) = None, cell_sets: list of CellSet(s) (optional) = None, synaptic_connections: list of SynapticConnection(s) (optional) = None, projections: list of Projection(s) (optional) = None, electrical_projections: list of ElectricalProjection(s) (optional) = None, continuous_projections: list of ContinuousProjection(s) (optional) = None, explicit_inputs: list of ExplicitInput(s) (optional) = None, input_lists: list of InputList(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneNetwork – Network containing: population s ( potentially of type populationList , and so specifying a list of cell location s ); projection s ( with lists of connection s ) and/or explicitConnection s; and inputList s ( with lists of input s ) and/or explicitInput s. Note: often in NeuroML this will be of type networkWithTemperature if there are temperature dependent elements ( e. g. ion channels ).
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- exportHdf5(h5file, h5Group)#
Export to HDF5 file.
- get_by_id(id)#
Get a component by its ID
- Parameters:
id (str) – ID of component to find
- Returns:
component with specified ID or None if no component with specified ID found
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
NeuroMLDocument#
- class neuroml.nml.nml.NeuroMLDocument(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, includes: list of IncludeType(s) (optional) = None, extracellular_properties: list of ExtracellularProperties(s) (optional) = None, intracellular_properties: list of IntracellularProperties(s) (optional) = None, morphology: list of Morphology(s) (optional) = None, ion_channel: list of IonChannel(s) (optional) = None, ion_channel_hhs: list of IonChannelHH(s) (optional) = None, ion_channel_v_shifts: list of IonChannelVShift(s) (optional) = None, ion_channel_kses: list of IonChannelKS(s) (optional) = None, decaying_pool_concentration_models: list of DecayingPoolConcentrationModel(s) (optional) = None, fixed_factor_concentration_models: list of FixedFactorConcentrationModel(s) (optional) = None, alpha_current_synapses: list of AlphaCurrentSynapse(s) (optional) = None, alpha_synapses: list of AlphaSynapse(s) (optional) = None, exp_one_synapses: list of ExpOneSynapse(s) (optional) = None, exp_two_synapses: list of ExpTwoSynapse(s) (optional) = None, exp_three_synapses: list of ExpThreeSynapse(s) (optional) = None, blocking_plastic_synapses: list of BlockingPlasticSynapse(s) (optional) = None, double_synapses: list of DoubleSynapse(s) (optional) = None, gap_junctions: list of GapJunction(s) (optional) = None, silent_synapses: list of SilentSynapse(s) (optional) = None, linear_graded_synapses: list of LinearGradedSynapse(s) (optional) = None, graded_synapses: list of GradedSynapse(s) (optional) = None, biophysical_properties: list of BiophysicalProperties(s) (optional) = None, cells: list of Cell(s) (optional) = None, cell2_ca_poolses: list of Cell2CaPools(s) (optional) = None, base_cells: list of BaseCell(s) (optional) = None, iaf_tau_cells: list of IafTauCell(s) (optional) = None, iaf_tau_ref_cells: list of IafTauRefCell(s) (optional) = None, iaf_cells: list of IafCell(s) (optional) = None, iaf_ref_cells: list of IafRefCell(s) (optional) = None, izhikevich_cells: list of IzhikevichCell(s) (optional) = None, izhikevich2007_cells: list of Izhikevich2007Cell(s) (optional) = None, ad_ex_ia_f_cells: list of AdExIaFCell(s) (optional) = None, fitz_hugh_nagumo_cells: list of FitzHughNagumoCell(s) (optional) = None, fitz_hugh_nagumo1969_cells: list of FitzHughNagumo1969Cell(s) (optional) = None, pinsky_rinzel_ca3_cells: list of PinskyRinzelCA3Cell(s) (optional) = None, hindmarshRose1984Cell: list of HindmarshRose1984Cell(s) (optional) = None, pulse_generators: list of PulseGenerator(s) (optional) = None, pulse_generator_dls: list of PulseGeneratorDL(s) (optional) = None, sine_generators: list of SineGenerator(s) (optional) = None, sine_generator_dls: list of SineGeneratorDL(s) (optional) = None, ramp_generators: list of RampGenerator(s) (optional) = None, ramp_generator_dls: list of RampGeneratorDL(s) (optional) = None, compound_inputs: list of CompoundInput(s) (optional) = None, compound_input_dls: list of CompoundInputDL(s) (optional) = None, voltage_clamps: list of VoltageClamp(s) (optional) = None, voltage_clamp_triples: list of VoltageClampTriple(s) (optional) = None, spike_arrays: list of SpikeArray(s) (optional) = None, timed_synaptic_inputs: list of TimedSynapticInput(s) (optional) = None, spike_generators: list of SpikeGenerator(s) (optional) = None, spike_generator_randoms: list of SpikeGeneratorRandom(s) (optional) = None, spike_generator_poissons: list of SpikeGeneratorPoisson(s) (optional) = None, spike_generator_ref_poissons: list of SpikeGeneratorRefPoisson(s) (optional) = None, poisson_firing_synapses: list of PoissonFiringSynapse(s) (optional) = None, transient_poisson_firing_synapses: list of TransientPoissonFiringSynapse(s) (optional) = None, IF_curr_alpha: list of IF_curr_alpha(s) (optional) = None, IF_curr_exp: list of IF_curr_exp(s) (optional) = None, IF_cond_alpha: list of IF_cond_alpha(s) (optional) = None, IF_cond_exp: list of IF_cond_exp(s) (optional) = None, EIF_cond_exp_isfa_ista: list of EIF_cond_exp_isfa_ista(s) (optional) = None, EIF_cond_alpha_isfa_ista: list of EIF_cond_alpha_isfa_ista(s) (optional) = None, HH_cond_exp: list of HH_cond_exp(s) (optional) = None, exp_cond_synapses: list of ExpCondSynapse(s) (optional) = None, alpha_cond_synapses: list of AlphaCondSynapse(s) (optional) = None, exp_curr_synapses: list of ExpCurrSynapse(s) (optional) = None, alpha_curr_synapses: list of AlphaCurrSynapse(s) (optional) = None, SpikeSourcePoisson: list of SpikeSourcePoisson(s) (optional) = None, networks: list of Network(s) (optional) = None, ComponentType: list of ComponentType(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
Standalone- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- append(element)#
Append an element
- Parameters:
element (Object) – element to append
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- get_by_id(id)#
Get a component by specifying its ID.
- Parameters:
id (str) – id of Component to get
- Returns:
Component with given ID or None if no Component with provided ID was found
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- summary(show_includes=True, show_non_network=True)#
Get a pretty-printed summary of the complete NeuroMLDocument.
This includes information on the various Components included in the NeuroMLDocument: networks, cells, projections, synapses, and so on.
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
OnCondition#
- class neuroml.nml.nml.OnCondition(test: a string (required) = None, StateAssignment: list of StateAssignment(s) (optional) = None, EventOut: list of EventOut(s) (optional) = None, Transition: a Transition (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
GeneratedsSuper- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
OnEntry#
- class neuroml.nml.nml.OnEntry(StateAssignment: list of StateAssignment(s) (required) = None, gds_collector_=None, **kwargs_)#
Bases:
GeneratedsSuper- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
OnEvent#
- class neuroml.nml.nml.OnEvent(port: a string (required) = None, StateAssignment: list of StateAssignment(s) (optional) = None, EventOut: list of EventOut(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
GeneratedsSuper- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
OnStart#
- class neuroml.nml.nml.OnStart(StateAssignment: list of StateAssignment(s) (required) = None, gds_collector_=None, **kwargs_)#
Bases:
GeneratedsSuper- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
OpenState#
- class neuroml.nml.nml.OpenState(id: a NmlId (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseOpenState – A KSState with relativeConductance of 1
- Parameters:
relativeConductance (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Parameter#
- class neuroml.nml.nml.Parameter(name: a string (required) = None, dimension: a string (required) = None, description: a string (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
NamedDimensionalType- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Path#
- class neuroml.nml.nml.Path(from_: a SegmentEndPoint (optional) = None, to: a SegmentEndPoint (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdPath – Include all the segment s between those specified by from and to , inclusive
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
PinskyRinzelCA3Cell#
- class neuroml.nml.nml.PinskyRinzelCA3Cell(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, i_soma: a Nml2Quantity_currentDensity (required) = None, i_dend: a Nml2Quantity_currentDensity (required) = None, gc: a Nml2Quantity_conductanceDensity (required) = None, g_ls: a Nml2Quantity_conductanceDensity (required) = None, g_ld: a Nml2Quantity_conductanceDensity (required) = None, g_na: a Nml2Quantity_conductanceDensity (required) = None, g_kdr: a Nml2Quantity_conductanceDensity (required) = None, g_ca: a Nml2Quantity_conductanceDensity (required) = None, g_kahp: a Nml2Quantity_conductanceDensity (required) = None, g_kc: a Nml2Quantity_conductanceDensity (required) = None, g_nmda: a Nml2Quantity_conductanceDensity (required) = None, g_ampa: a Nml2Quantity_conductanceDensity (required) = None, e_na: a Nml2Quantity_voltage (required) = None, e_ca: a Nml2Quantity_voltage (required) = None, e_k: a Nml2Quantity_voltage (required) = None, e_l: a Nml2Quantity_voltage (required) = None, qd0: a Nml2Quantity_none (required) = None, pp: a Nml2Quantity_none (required) = None, alphac: a Nml2Quantity_none (required) = None, betac: a Nml2Quantity_none (required) = None, cm: a Nml2Quantity_specificCapacitance (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseCellPinskyRinzelCA3Cell – Reduced CA3 cell model from Pinsky, P. F. , Rinzel, J. Intrinsic and network rhythmogenesis in a reduced traub model for CA3 neurons. J Comput Neurosci 1, 39-60 ( 1994 ). See OpenSourceBrain/PinskyRinzelModel
- Parameters:
iSoma (currentDensity) –
iDend (currentDensity) –
gLs (conductanceDensity) –
gLd (conductanceDensity) –
gNa (conductanceDensity) –
gKdr (conductanceDensity) –
gCa (conductanceDensity) –
gKahp (conductanceDensity) –
gKC (conductanceDensity) –
gc (conductanceDensity) –
eNa (voltage) –
eCa (voltage) –
eK (voltage) –
eL (voltage) –
pp (none) –
cm (specificCapacitance) –
alphac (none) –
betac (none) –
gNmda (conductanceDensity) –
gAmpa (conductanceDensity) –
qd0 (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
PlasticityMechanism#
- class neuroml.nml.nml.PlasticityMechanism(type: a PlasticityTypes (required) = None, init_release_prob: a ZeroToOne (required) = None, tau_rec: a Nml2Quantity_time (required) = None, tau_fac: a Nml2Quantity_time (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutId- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Point3DWithDiam#
- class neuroml.nml.nml.Point3DWithDiam(x: a double (required) = None, y: a double (required) = None, z: a double (required) = None, diameter: a DoubleGreaterThanZero (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdPoint3DWithDiam – Base type for ComponentTypes which specify an ( x, y, z ) coordinate along with a diameter. Note: no dimension used in the attributes for these coordinates! These are assumed to have dimension micrometer ( 10^-6 m ). This is due to micrometers being the default option for the majority of neuronal morphology formats, and dimensions are omitted here to facilitate reading and writing of morphologies in NeuroML.
- Parameters:
x (none) – x coordinate of the point. Note: no dimension used, see description of point3DWithDiam for details.
y (none) – y coordinate of the ppoint. Note: no dimension used, see description of point3DWithDiam for details.
z (none) – z coordinate of the ppoint. Note: no dimension used, see description of point3DWithDiam for details.
diameter (none) – Diameter of the ppoint. Note: no dimension used, see description of point3DWithDiam for details.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- distance_to(other_3d_point)#
Find the distance between this point and another.
- Parameters:
other_3d_point (Point3DWithDiam) – other 3D point to calculate distance to
- Returns:
distance between the two points
- Return type:
float
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
PoissonFiringSynapse#
- class neuroml.nml.nml.PoissonFiringSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, average_rate: a Nml2Quantity_pertime (required) = None, synapse: a string (required) = None, spike_target: a string (required) = None, gds_collector_=None, **kwargs_)#
Bases:
StandalonePoissonFiringSynapse – Poisson spike generator firing at averageRate, which is connected to single synapse that is triggered every time a spike is generated, producing an input current. See also transientPoissonFiringSynapse .
- Parameters:
averageRate (per_time) – The average rate at which spikes are emitted
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Population#
- class neuroml.nml.nml.Population(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, component: a NmlId (required) = None, size: a NonNegativeInteger (optional) = None, type: a populationTypes (optional) = None, extracellular_properties: a NmlId (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, layout: a Layout (optional) = None, instances: list of Instance(s) (required) = None, gds_collector_=None, **kwargs_)#
Bases:
StandalonePopulation – A population of components, with just one parameter for the size, i. e. number of components to create. Note: quite often this is used with type= populationList which means the size is determined by the number of instance s ( with location s ) in the list. The size attribute is still set, and there will be a validation error if this does not match the number in the list.
- Parameters:
size (none) – Number of instances of this Component to create when the population is instantiated
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- exportHdf5(h5file, h5Group)#
Export to HDF5 file.
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- get_size()#
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Projection#
- class neuroml.nml.nml.Projection(id: a NmlId (required) = None, presynaptic_population: a NmlId (required) = None, postsynaptic_population: a NmlId (required) = None, synapse: a NmlId (required) = None, connections: list of Connection(s) (optional) = None, connection_wds: list of ConnectionWD(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseProjectionProjection – Projection from one population, presynapticPopulation to another, postsynapticPopulation, through synapse. Contains lists of connection or connectionWD elements.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- exportHdf5(h5file, h5Group)#
Export to HDF5 file.
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Property#
- class neuroml.nml.nml.Property(tag: a string (required) = None, value: a string (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdProperty – A property ( a tag and value pair ), which can be on any baseStandalone either as a direct child, or within an Annotation . Generally something which helps the visual display or facilitates simulation of a Component, but is not a core physiological property. Common examples include: numberInternalDivisions, equivalent of nseg in NEURON; radius, for a radius to use in graphical displays for abstract cells ( i. e. without defined morphologies ); color, the color to use for a Population or populationList of cells; recommended_dt_ms, the recommended timestep to use for simulating a Network , recommended_duration_ms the recommended duration to use when running a Network
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ProximalDetails#
- class neuroml.nml.nml.ProximalDetails(translation_start: a double (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdProximalDetails – What to do at the proximal point when creating an inhomogeneous parameter
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
PulseGenerator#
- class neuroml.nml.nml.PulseGenerator(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, delay: a Nml2Quantity_time (required) = None, duration: a Nml2Quantity_time (required) = None, amplitude: a Nml2Quantity_current (required) = None, gds_collector_=None, **kwargs_)#
Bases:
StandalonePulseGenerator – Generates a constant current pulse of a certain amplitude for a specified duration after a delay. Scaled by weight, if set
- Parameters:
delay (time) – Delay before change in current. Current is zero prior to this.
duration (time) – Duration for holding current at amplitude. Current is zero after delay + duration.
amplitude (current) – Amplitude of current pulse
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
PulseGeneratorDL#
- class neuroml.nml.nml.PulseGeneratorDL(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, delay: a Nml2Quantity_time (required) = None, duration: a Nml2Quantity_time (required) = None, amplitude: a Nml2Quantity_current (required) = None, gds_collector_=None, **kwargs_)#
Bases:
StandalonePulseGeneratorDL – Dimensionless equivalent of pulseGenerator . Generates a constant current pulse of a certain amplitude for a specified duration after a delay. Scaled by weight, if set
- Parameters:
delay (time) – Delay before change in current. Current is zero prior to this.
duration (time) – Duration for holding current at amplitude. Current is zero after delay + duration.
amplitude (none) – Amplitude of current pulse
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Q10ConductanceScaling#
- class neuroml.nml.nml.Q10ConductanceScaling(q10_factor: a Nml2Quantity_none (required) = None, experimental_temp: a Nml2Quantity_temperature (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdQ10ConductanceScaling – A value for the conductance scaling which varies as a standard function of the difference between the current temperature, temperature, and the temperature at which the conductance was originally determined, experimentalTemp
- Parameters:
q10Factor (none) –
experimentalTemp (temperature) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Q10Settings#
- class neuroml.nml.nml.Q10Settings(type: a NmlId (required) = None, fixed_q10: a Nml2Quantity_none (optional) = None, q10_factor: a Nml2Quantity_none (optional) = None, experimental_temp: a Nml2Quantity_temperature (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
GeneratedsSuper- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
RampGenerator#
- class neuroml.nml.nml.RampGenerator(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, delay: a Nml2Quantity_time (required) = None, duration: a Nml2Quantity_time (required) = None, start_amplitude: a Nml2Quantity_current (required) = None, finish_amplitude: a Nml2Quantity_current (required) = None, baseline_amplitude: a Nml2Quantity_current (required) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneRampGenerator – Generates a ramping current after a time delay, for a fixed duration. During this time the current steadily changes from startAmplitude to finishAmplitude. Scaled by weight, if set
- Parameters:
delay (time) – Delay before change in current. Current is baselineAmplitude prior to this.
duration (time) – Duration for holding current at amplitude. Current is baselineAmplitude after delay + duration.
startAmplitude (current) – Amplitude of linearly varying current at time delay
finishAmplitude (current) – Amplitude of linearly varying current at time delay + duration
baselineAmplitude (current) – Amplitude of current before time delay, and after time delay + duration
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
RampGeneratorDL#
- class neuroml.nml.nml.RampGeneratorDL(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, delay: a Nml2Quantity_time (required) = None, duration: a Nml2Quantity_time (required) = None, start_amplitude: a Nml2Quantity_current (required) = None, finish_amplitude: a Nml2Quantity_current (required) = None, baseline_amplitude: a Nml2Quantity_current (required) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneRampGeneratorDL – Dimensionless equivalent of rampGenerator . Generates a ramping current after a time delay, for a fixed duration. During this time the dimensionless current steadily changes from startAmplitude to finishAmplitude. Scaled by weight, if set
- Parameters:
delay (time) – Delay before change in current. Current is baselineAmplitude prior to this.
duration (time) – Duration for holding current at amplitude. Current is baselineAmplitude after delay + duration.
startAmplitude (none) – Amplitude of linearly varying current at time delay
finishAmplitude (none) – Amplitude of linearly varying current at time delay + duration
baselineAmplitude (none) – Amplitude of current before time delay, and after time delay + duration
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
RandomLayout#
- class neuroml.nml.nml.RandomLayout(number: a nonNegativeInteger (optional) = None, regions: a NmlId (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutId- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
ReactionScheme#
- class neuroml.nml.nml.ReactionScheme(id: a NmlId (required) = None, source: a string (required) = None, type: a string (required) = None, anytypeobjs_=None, gds_collector_=None, **kwargs_)#
Bases:
Base- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Regime#
- class neuroml.nml.nml.Regime(name: a string (required) = None, initial: a TrueOrFalse (optional) = None, TimeDerivative: list of TimeDerivative(s) (optional) = None, OnEntry: a OnEntry (optional) = None, OnCondition: list of OnCondition(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
GeneratedsSuper- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
- validate_TrueOrFalse(value)#
Region#
- class neuroml.nml.nml.Region(id: a NmlId (required) = None, spaces: a NmlId (optional) = None, anytypeobjs_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseRegion – Initial attempt to specify 3D region for placing cells. Work in progress…
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Requirement#
- class neuroml.nml.nml.Requirement(name: a string (required) = None, dimension: a string (required) = None, description: a string (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
NamedDimensionalType- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Resistivity#
- class neuroml.nml.nml.Resistivity(value: a Nml2Quantity_resistivity (required) = None, segment_groups: a NmlId (optional) = 'all', gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdResistivity – The resistivity, or specific axial resistance, of the cytoplasm
- Parameters:
value (resistivity) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
- validate_Nml2Quantity_resistivity(value)#
- validate_Nml2Quantity_resistivity_patterns_ = [['^(-?([0-9]*(\\.[0-9]+)?)([eE]-?[0-9]+)?[\\s]*(ohm_cm|kohm_cm|ohm_m))$']]#
ReverseTransition#
- class neuroml.nml.nml.ReverseTransition(id: a NmlId (required) = None, from_: a NmlId (required) = None, to: a NmlId (required) = None, anytypeobjs_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseReverseTransition – A reverse only KSTransition for a gateKS which specifies a rate ( type baseHHRate ) which follows one of the standard Hodgkin Huxley forms ( e. g. HHExpRate , HHSigmoidRate , HHExpLinearRate
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Segment#
- class neuroml.nml.nml.Segment(id: a NonNegativeInteger (required) = None, name: a string (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, parent: a SegmentParent (optional) = None, proximal: a Point3DWithDiam (optional) = None, distal: a Point3DWithDiam (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseNonNegativeIntegerIdSegment – A segment defines the smallest unit within a possibly branching structure ( morphology ), such as a dendrite or axon. Its id should be a nonnegative integer ( usually soma/root = 0 ). Its end points are given by the proximal and distal points. The proximal point can be omitted, usually because it is the same as a point on the parent segment, see proximal for details. parent specifies the parent segment. The first segment of a cell ( with no parent ) usually represents the soma. The shape is normally a cylinder ( radii of the proximal and distal equal, but positions different ) or a conical frustum ( radii and positions different ). If the x, y, x positions of the proximal and distal are equal, the segment can be interpreted as a sphere, and in this case the radii of these points must be equal. NOTE: LEMS does not yet support multicompartmental modelling, so the Dynamics here is only appropriate for single compartment modelling.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- property length#
Get the length of the segment.
- Returns:
length of the segment
- Return type:
float
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- property surface_area#
Get the surface area of the segment.
- Returns:
surface area of segment
- Return type:
float
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
- property volume#
Get the volume of the segment.
- Returns:
volume of segment
- Return type:
float
SegmentEndPoint#
- class neuroml.nml.nml.SegmentEndPoint(segments: a NonNegativeInteger (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutId- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
SegmentGroup#
- class neuroml.nml.nml.SegmentGroup(id: a NonNegativeInteger (required) = None, neuro_lex_id: a NeuroLexId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, members: list of Member(s) (optional) = None, includes: list of Include(s) (optional) = None, paths: list of Path(s) (optional) = None, sub_trees: list of SubTree(s) (optional) = None, inhomogeneous_parameters: list of InhomogeneousParameter(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseSegmentGroup – A method to describe a group of segment s in a morphology , e. g. soma_group, dendrite_group, axon_group. While a name is useful to describe the group, the neuroLexId attribute can be used to explicitly specify the meaning of the group, e. g. sao1044911821 for ‘Neuronal Cell Body’, sao1211023249 for ‘Dendrite’. The segment s in this group can be specified as: a list of individual member segments; a path , all of the segments along which should be included; a subTree of the cell to include; other segmentGroups to include ( so all segments from those get included here ). An inhomogeneousParameter can be defined on the region of the cell specified by this group ( see variableParameter for usage ).
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
SegmentParent#
- class neuroml.nml.nml.SegmentParent(segments: a NonNegativeInteger (required) = None, fraction_along: a ZeroToOne (optional) = '1', gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutId- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
SilentSynapse#
- class neuroml.nml.nml.SilentSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseSynapseSilentSynapse – Dummy synapse which emits no current. Used as presynaptic endpoint for analog synaptic connection.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
SineGenerator#
- class neuroml.nml.nml.SineGenerator(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, delay: a Nml2Quantity_time (required) = None, phase: a Nml2Quantity_none (required) = None, duration: a Nml2Quantity_time (required) = None, amplitude: a Nml2Quantity_current (required) = None, period: a Nml2Quantity_time (required) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneSineGenerator – Generates a sinusoidally varying current after a time delay, for a fixed duration. The period and maximum amplitude of the current can be set as well as the phase at which to start. Scaled by weight, if set
- Parameters:
phase (none) – Phase ( between 0 and 2*pi ) at which to start the varying current ( i. e. at time given by delay )
delay (time) – Delay before change in current. Current is zero prior to this.
duration (time) – Duration for holding current at amplitude. Current is zero after delay + duration.
amplitude (current) – Maximum amplitude of current
period (time) – Time period of oscillation
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
SineGeneratorDL#
- class neuroml.nml.nml.SineGeneratorDL(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, delay: a Nml2Quantity_time (required) = None, phase: a Nml2Quantity_none (required) = None, duration: a Nml2Quantity_time (required) = None, amplitude: a Nml2Quantity_current (required) = None, period: a Nml2Quantity_time (required) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneSineGeneratorDL – Dimensionless equivalent of sineGenerator . Generates a sinusoidally varying current after a time delay, for a fixed duration. The period and maximum amplitude of the current can be set as well as the phase at which to start. Scaled by weight, if set
- Parameters:
phase (none) – Phase ( between 0 and 2*pi ) at which to start the varying current ( i. e. at time given by delay )
delay (time) – Delay before change in current. Current is zero prior to this.
duration (time) – Duration for holding current at amplitude. Current is zero after delay + duration.
amplitude (none) – Maximum amplitude of current
period (time) – Time period of oscillation
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Space#
- class neuroml.nml.nml.Space(id: a NmlId (required) = None, based_on: a allowedSpaces (optional) = None, structure: a SpaceStructure (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
Base- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
SpaceStructure#
- class neuroml.nml.nml.SpaceStructure(x_spacing: a float (optional) = None, y_spacing: a float (optional) = None, z_spacing: a float (optional) = None, x_start: a float (optional) = 0, y_start: a float (optional) = 0, z_start: a float (optional) = 0, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutId- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Species#
- class neuroml.nml.nml.Species(id: a NmlId (required) = None, concentration_model: a NmlId (required) = None, ion: a NmlId (optional) = None, initial_concentration: a Nml2Quantity_concentration (required) = None, initial_ext_concentration: a Nml2Quantity_concentration (required) = None, segment_groups: a NmlId (optional) = 'all', gds_collector_=None, **kwargs_)#
Bases:
BaseSpecies – Description of a chemical species identified by ion, which has internal, concentration, and external, extConcentration values for its concentration
- Parameters:
initialConcentration (concentration) –
initialExtConcentration (concentration) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
SpecificCapacitance#
- class neuroml.nml.nml.SpecificCapacitance(value: a Nml2Quantity_specificCapacitance (required) = None, segment_groups: a NmlId (optional) = 'all', gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdSpecificCapacitance – Capacitance per unit area
- Parameters:
value (specificCapacitance) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Spike#
- class neuroml.nml.nml.Spike(id: a NonNegativeInteger (required) = None, time: a Nml2Quantity_time (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseNonNegativeIntegerIdSpike – Emits a single spike at the specified time
- Parameters:
time (time) – Time at which to emit one spike event
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
SpikeArray#
- class neuroml.nml.nml.SpikeArray(id: a NonNegativeInteger (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, spikes: list of Spike(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneSpikeArray – Set of spike ComponentTypes, each emitting one spike at a certain time. Can be used to feed a predetermined spike train into a cell
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
SpikeGenerator#
- class neuroml.nml.nml.SpikeGenerator(id: a NonNegativeInteger (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, period: a Nml2Quantity_time (required) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneSpikeGenerator – Simple generator of spikes at a regular interval set by period
- Parameters:
period (time) – Time between spikes. The first spike will be emitted after this time.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
SpikeGeneratorPoisson#
- class neuroml.nml.nml.SpikeGeneratorPoisson(id: a NonNegativeInteger (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, average_rate: a Nml2Quantity_pertime (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneSpikeGeneratorPoisson – Generator of spikes whose ISI is distributed according to an exponential PDF with scale: 1 / averageRate
- Parameters:
averageRate (per_time) – The average rate at which spikes are emitted
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
SpikeGeneratorRandom#
- class neuroml.nml.nml.SpikeGeneratorRandom(id: a NonNegativeInteger (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, max_isi: a Nml2Quantity_time (required) = None, min_isi: a Nml2Quantity_time (required) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneSpikeGeneratorRandom – Generator of spikes with a random interspike interval of at least minISI and at most maxISI
- Parameters:
maxISI (time) – Maximum interspike interval
minISI (time) – Minimum interspike interval
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
SpikeGeneratorRefPoisson#
- class neuroml.nml.nml.SpikeGeneratorRefPoisson(id: a NonNegativeInteger (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, average_rate: a Nml2Quantity_pertime (required) = None, minimum_isi: a Nml2Quantity_time (required) = None, gds_collector_=None, **kwargs_)#
Bases:
SpikeGeneratorPoissonSpikeGeneratorRefPoisson – Generator of spikes whose ISI distribution is the maximum entropy distribution over [ minimumISI, +infinity ) with mean: 1 / averageRate
- Parameters:
minimumISI (time) – The minimum interspike interval
averageRate (per_time) – The average rate at which spikes are emitted
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
SpikeSourcePoisson#
- class neuroml.nml.nml.SpikeSourcePoisson(id: a NonNegativeInteger (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, start: a Nml2Quantity_time (required) = None, duration: a Nml2Quantity_time (required) = None, rate: a Nml2Quantity_pertime (required) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneSpikeSourcePoisson – Spike source, generating spikes according to a Poisson process.
- Parameters:
start (time) –
duration (time) –
rate (per_time) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
SpikeThresh#
- class neuroml.nml.nml.SpikeThresh(value: a Nml2Quantity_voltage (required) = None, segment_groups: a NmlId (optional) = 'all', gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdSpikeThresh – Membrane potential at which to emit a spiking event. Note, usually the spiking event will not be emitted again until the membrane potential has fallen below this value and rises again to cross it in a positive direction
- Parameters:
value (voltage) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Standalone#
- class neuroml.nml.nml.Standalone(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseStandalone – Elements which can stand alone and be referenced by id, e.g. cell, morphology.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
StateAssignment#
- class neuroml.nml.nml.StateAssignment(variable: a string (required) = None, value: a string (required) = None, gds_collector_=None, **kwargs_)#
Bases:
GeneratedsSuper- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
StateVariable#
- class neuroml.nml.nml.StateVariable(name: a string (required) = None, dimension: a string (required) = None, description: a string (optional) = None, exposure: a string (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
NamedDimensionalVariable- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
SubTree#
- class neuroml.nml.nml.SubTree(from_: a SegmentEndPoint (optional) = None, to: a SegmentEndPoint (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdSubTree – Include all the segment s distal to that specified by from in the segmentGroup
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
SynapticConnection#
- class neuroml.nml.nml.SynapticConnection(neuro_lex_id: a NeuroLexId (optional) = None, from_: a Nml2PopulationReferencePath (required) = None, to: a Nml2PopulationReferencePath (required) = None, synapse: a NmlId (required) = None, destination: a NmlId (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutIdSynapticConnection – Explicit event connection between named components, which gets processed via a new instance of a synapse component which is created on the target component
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
- validate_Nml2PopulationReferencePath(value)#
- validate_Nml2PopulationReferencePath_patterns_ = [['^((\\.\\./)?([a-zA-Z_][a-zA-Z0-9_]*)((\\[[0-9]+\\])|(/[0-9]+)+((/[a-zA-Z_][a-zA-Z0-9_]*)?)/?))$']]#
TauInfTransition#
- class neuroml.nml.nml.TauInfTransition(id: a NmlId (required) = None, from_: a NmlId (required) = None, to: a NmlId (required) = None, steady_state: a HHVariable (required) = None, time_course: a HHTime (required) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseTauInfTransition – KS Transition specified in terms of time constant tau and steady state inf
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
TimeDerivative#
- class neuroml.nml.nml.TimeDerivative(variable: a string (required) = None, value: a string (required) = None, gds_collector_=None, **kwargs_)#
Bases:
GeneratedsSuper- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
TimedSynapticInput#
- class neuroml.nml.nml.TimedSynapticInput(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, synapse: a NmlId (required) = None, spike_target: a string (required) = None, spikes: list of Spike(s) (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneTimedSynapticInput – Spike array connected to a single synapse, producing a current triggered by each spike in the array.
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
TransientPoissonFiringSynapse#
- class neuroml.nml.nml.TransientPoissonFiringSynapse(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, average_rate: a Nml2Quantity_pertime (required) = None, delay: a Nml2Quantity_time (required) = None, duration: a Nml2Quantity_time (required) = None, synapse: a string (required) = None, spike_target: a string (required) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneTransientPoissonFiringSynapse – Poisson spike generator firing at averageRate after a delay and for a duration, connected to single synapse that is triggered every time a spike is generated, providing an input current. Similar to ComponentType poissonFiringSynapse .
- Parameters:
averageRate (per_time) –
delay (time) –
duration (time) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
Transition#
- class neuroml.nml.nml.Transition(regime: a string (required) = None, gds_collector_=None, **kwargs_)#
Bases:
GeneratedsSuper- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
TrueOrFalse#
- class neuroml.nml.nml.TrueOrFalse(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)#
Bases:
str,Enum- FALSE = 'false'#
- TRUE = 'true'#
- capitalize()#
Return a capitalized version of the string.
More specifically, make the first character have upper case and the rest lower case.
- casefold()#
Return a version of the string suitable for caseless comparisons.
- center(width, fillchar=' ', /)#
Return a centered string of length width.
Padding is done using the specified fill character (default is a space).
- count(sub[, start[, end]]) int#
Return the number of non-overlapping occurrences of substring sub in string S[start:end]. Optional arguments start and end are interpreted as in slice notation.
- encode(encoding='utf-8', errors='strict')#
Encode the string using the codec registered for encoding.
- encoding
The encoding in which to encode the string.
- errors
The error handling scheme to use for encoding errors. The default is ‘strict’ meaning that encoding errors raise a UnicodeEncodeError. Other possible values are ‘ignore’, ‘replace’ and ‘xmlcharrefreplace’ as well as any other name registered with codecs.register_error that can handle UnicodeEncodeErrors.
- endswith(suffix[, start[, end]]) bool#
Return True if S ends with the specified suffix, False otherwise. With optional start, test S beginning at that position. With optional end, stop comparing S at that position. suffix can also be a tuple of strings to try.
- expandtabs(tabsize=8)#
Return a copy where all tab characters are expanded using spaces.
If tabsize is not given, a tab size of 8 characters is assumed.
- find(sub[, start[, end]]) int#
Return the lowest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.
Return -1 on failure.
- format(*args, **kwargs) str#
Return a formatted version of S, using substitutions from args and kwargs. The substitutions are identified by braces (‘{’ and ‘}’).
- format_map(mapping) str#
Return a formatted version of S, using substitutions from mapping. The substitutions are identified by braces (‘{’ and ‘}’).
- index(sub[, start[, end]]) int#
Return the lowest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.
Raises ValueError when the substring is not found.
- isalnum()#
Return True if the string is an alpha-numeric string, False otherwise.
A string is alpha-numeric if all characters in the string are alpha-numeric and there is at least one character in the string.
- isalpha()#
Return True if the string is an alphabetic string, False otherwise.
A string is alphabetic if all characters in the string are alphabetic and there is at least one character in the string.
- isascii()#
Return True if all characters in the string are ASCII, False otherwise.
ASCII characters have code points in the range U+0000-U+007F. Empty string is ASCII too.
- isdecimal()#
Return True if the string is a decimal string, False otherwise.
A string is a decimal string if all characters in the string are decimal and there is at least one character in the string.
- isdigit()#
Return True if the string is a digit string, False otherwise.
A string is a digit string if all characters in the string are digits and there is at least one character in the string.
- isidentifier()#
Return True if the string is a valid Python identifier, False otherwise.
Call keyword.iskeyword(s) to test whether string s is a reserved identifier, such as “def” or “class”.
- islower()#
Return True if the string is a lowercase string, False otherwise.
A string is lowercase if all cased characters in the string are lowercase and there is at least one cased character in the string.
- isnumeric()#
Return True if the string is a numeric string, False otherwise.
A string is numeric if all characters in the string are numeric and there is at least one character in the string.
- isprintable()#
Return True if the string is printable, False otherwise.
A string is printable if all of its characters are considered printable in repr() or if it is empty.
- isspace()#
Return True if the string is a whitespace string, False otherwise.
A string is whitespace if all characters in the string are whitespace and there is at least one character in the string.
- istitle()#
Return True if the string is a title-cased string, False otherwise.
In a title-cased string, upper- and title-case characters may only follow uncased characters and lowercase characters only cased ones.
- isupper()#
Return True if the string is an uppercase string, False otherwise.
A string is uppercase if all cased characters in the string are uppercase and there is at least one cased character in the string.
- join(iterable, /)#
Concatenate any number of strings.
The string whose method is called is inserted in between each given string. The result is returned as a new string.
Example: ‘.’.join([‘ab’, ‘pq’, ‘rs’]) -> ‘ab.pq.rs’
- ljust(width, fillchar=' ', /)#
Return a left-justified string of length width.
Padding is done using the specified fill character (default is a space).
- lower()#
Return a copy of the string converted to lowercase.
- lstrip(chars=None, /)#
Return a copy of the string with leading whitespace removed.
If chars is given and not None, remove characters in chars instead.
- static maketrans()#
Return a translation table usable for str.translate().
If there is only one argument, it must be a dictionary mapping Unicode ordinals (integers) or characters to Unicode ordinals, strings or None. Character keys will be then converted to ordinals. If there are two arguments, they must be strings of equal length, and in the resulting dictionary, each character in x will be mapped to the character at the same position in y. If there is a third argument, it must be a string, whose characters will be mapped to None in the result.
- partition(sep, /)#
Partition the string into three parts using the given separator.
This will search for the separator in the string. If the separator is found, returns a 3-tuple containing the part before the separator, the separator itself, and the part after it.
If the separator is not found, returns a 3-tuple containing the original string and two empty strings.
- removeprefix(prefix, /)#
Return a str with the given prefix string removed if present.
If the string starts with the prefix string, return string[len(prefix):]. Otherwise, return a copy of the original string.
- removesuffix(suffix, /)#
Return a str with the given suffix string removed if present.
If the string ends with the suffix string and that suffix is not empty, return string[:-len(suffix)]. Otherwise, return a copy of the original string.
- replace(old, new, count=-1, /)#
Return a copy with all occurrences of substring old replaced by new.
- count
Maximum number of occurrences to replace. -1 (the default value) means replace all occurrences.
If the optional argument count is given, only the first count occurrences are replaced.
- rfind(sub[, start[, end]]) int#
Return the highest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.
Return -1 on failure.
- rindex(sub[, start[, end]]) int#
Return the highest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.
Raises ValueError when the substring is not found.
- rjust(width, fillchar=' ', /)#
Return a right-justified string of length width.
Padding is done using the specified fill character (default is a space).
- rpartition(sep, /)#
Partition the string into three parts using the given separator.
This will search for the separator in the string, starting at the end. If the separator is found, returns a 3-tuple containing the part before the separator, the separator itself, and the part after it.
If the separator is not found, returns a 3-tuple containing two empty strings and the original string.
- rsplit(sep=None, maxsplit=-1)#
Return a list of the substrings in the string, using sep as the separator string.
- sep
The separator used to split the string.
When set to None (the default value), will split on any whitespace character (including n r t f and spaces) and will discard empty strings from the result.
- maxsplit
Maximum number of splits (starting from the left). -1 (the default value) means no limit.
Splitting starts at the end of the string and works to the front.
- rstrip(chars=None, /)#
Return a copy of the string with trailing whitespace removed.
If chars is given and not None, remove characters in chars instead.
- split(sep=None, maxsplit=-1)#
Return a list of the substrings in the string, using sep as the separator string.
- sep
The separator used to split the string.
When set to None (the default value), will split on any whitespace character (including n r t f and spaces) and will discard empty strings from the result.
- maxsplit
Maximum number of splits (starting from the left). -1 (the default value) means no limit.
Note, str.split() is mainly useful for data that has been intentionally delimited. With natural text that includes punctuation, consider using the regular expression module.
- splitlines(keepends=False)#
Return a list of the lines in the string, breaking at line boundaries.
Line breaks are not included in the resulting list unless keepends is given and true.
- startswith(prefix[, start[, end]]) bool#
Return True if S starts with the specified prefix, False otherwise. With optional start, test S beginning at that position. With optional end, stop comparing S at that position. prefix can also be a tuple of strings to try.
- strip(chars=None, /)#
Return a copy of the string with leading and trailing whitespace removed.
If chars is given and not None, remove characters in chars instead.
- swapcase()#
Convert uppercase characters to lowercase and lowercase characters to uppercase.
- title()#
Return a version of the string where each word is titlecased.
More specifically, words start with uppercased characters and all remaining cased characters have lower case.
- translate(table, /)#
Replace each character in the string using the given translation table.
- table
Translation table, which must be a mapping of Unicode ordinals to Unicode ordinals, strings, or None.
The table must implement lookup/indexing via __getitem__, for instance a dictionary or list. If this operation raises LookupError, the character is left untouched. Characters mapped to None are deleted.
- upper()#
Return a copy of the string converted to uppercase.
- zfill(width, /)#
Pad a numeric string with zeros on the left, to fill a field of the given width.
The string is never truncated.
UnstructuredLayout#
- class neuroml.nml.nml.UnstructuredLayout(number: a nonNegativeInteger (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
BaseWithoutId- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
VariableParameter#
- class neuroml.nml.nml.VariableParameter(parameter: a string (required) = None, segment_groups: a string (required) = None, inhomogeneous_value: a InhomogeneousValue (optional) = None, gds_collector_=None, **kwargs_)#
Bases:
GeneratedsSuperVariableParameter – Specifies a parameter ( e. g. condDensity ) which can vary its value across a segmentGroup. The value is calculated from value attribute of the inhomogeneousValue subelement. This element is normally a child of channelDensityNonUniform , channelDensityNonUniformNernst or channelDensityNonUniformGHK and is used to calculate the value of the conductance, etc. which will vary on different parts of the cell. The segmentGroup specified here needs to define an inhomogeneousParameter ( referenced from inhomogeneousParameter in the inhomogeneousValue ), which calculates a variable ( e. g. p ) varying across the cell ( e. g. based on the path length from soma ), which is then used in the value attribute of the inhomogeneousValue ( so for example condDensity = f( p ) )
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
VoltageClamp#
- class neuroml.nml.nml.VoltageClamp(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, delay: a Nml2Quantity_time (required) = None, duration: a Nml2Quantity_time (required) = None, target_voltage: a Nml2Quantity_voltage (required) = None, simple_series_resistance: a Nml2Quantity_resistance (required) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneVoltageClamp – Voltage clamp. Applies a variable current i to try to keep parent at targetVoltage. Not yet fully tested!!! Consider using voltageClampTriple!!
- Parameters:
delay (time) – Delay before change in current. Current is zero prior to this.
duration (time) – Duration for attempting to keep parent at targetVoltage. Current is zero after delay + duration.
targetVoltage (voltage) – Current will be applied to try to get parent to this target voltage
simpleSeriesResistance (resistance) – Current will be calculated by the difference in voltage between the target and parent, divided by this value
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
VoltageClampTriple#
- class neuroml.nml.nml.VoltageClampTriple(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, active: a ZeroOrOne (required) = None, delay: a Nml2Quantity_time (required) = None, duration: a Nml2Quantity_time (required) = None, conditioning_voltage: a Nml2Quantity_voltage (required) = None, testing_voltage: a Nml2Quantity_voltage (required) = None, return_voltage: a Nml2Quantity_voltage (required) = None, simple_series_resistance: a Nml2Quantity_resistance (required) = None, gds_collector_=None, **kwargs_)#
Bases:
StandaloneVoltageClampTriple – Voltage clamp with 3 clamp levels. Applies a variable current i ( through simpleSeriesResistance ) to try to keep parent cell at conditioningVoltage until time delay, testingVoltage until delay + duration, and returnVoltage afterwards. Only enabled if active = 1.
- Parameters:
active (none) – Whether the voltage clamp is active ( 1 ) or inactive ( 0 ).
delay (time) – Delay before switching from conditioningVoltage to testingVoltage.
duration (time) – Duration to hold at testingVoltage.
conditioningVoltage (voltage) – Target voltage before time delay
testingVoltage (voltage) – Target voltage between times delay and delay + duration
returnVoltage (voltage) – Target voltage after time duration
simpleSeriesResistance (resistance) – Current will be calculated by the difference in voltage between the target and parent, divided by this value
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
basePyNNCell#
- class neuroml.nml.nml.basePyNNCell(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, cm: a float (required) = None, i_offset: a float (required) = None, tau_syn_E: a float (required) = None, tau_syn_I: a float (required) = None, v_init: a float (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
BaseCellbasePyNNCell – Base type of any PyNN standard cell model. Note: membrane potential v has dimensions voltage, but all other parameters are dimensionless. This is to facilitate translation to and from PyNN scripts in Python, where these parameters have implicit units, see http://neuralensemble.org/trac/PyNN/wiki/StandardModels
- Parameters:
cm (none) –
i_offset (none) –
tau_syn_E (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
tau_syn_I (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
v_init (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
basePyNNIaFCell#
- class neuroml.nml.nml.basePyNNIaFCell(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, cm: a float (required) = None, i_offset: a float (required) = None, tau_syn_E: a float (required) = None, tau_syn_I: a float (required) = None, v_init: a float (required) = None, tau_m: a float (required) = None, tau_refrac: a float (required) = None, v_reset: a float (required) = None, v_rest: a float (required) = None, v_thresh: a float (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
basePyNNCellbasePyNNIaFCell – Base type of any PyNN standard integrate and fire model
- Parameters:
tau_refrac (none) –
v_thresh (none) –
tau_m (none) –
v_rest (none) –
v_reset (none) –
cm (none) –
i_offset (none) –
tau_syn_E (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
tau_syn_I (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
v_init (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid
basePyNNIaFCondCell#
- class neuroml.nml.nml.basePyNNIaFCondCell(id: a NmlId (required) = None, metaid: a MetaId (optional) = None, notes: a string (optional) = None, properties: list of Property(s) (optional) = None, annotation: a Annotation (optional) = None, neuro_lex_id: a NeuroLexId (optional) = None, cm: a float (required) = None, i_offset: a float (required) = None, tau_syn_E: a float (required) = None, tau_syn_I: a float (required) = None, v_init: a float (required) = None, tau_m: a float (required) = None, tau_refrac: a float (required) = None, v_reset: a float (required) = None, v_rest: a float (required) = None, v_thresh: a float (required) = None, e_rev_E: a float (required) = None, e_rev_I: a float (required) = None, extensiontype_=None, gds_collector_=None, **kwargs_)#
Bases:
basePyNNIaFCellbasePyNNIaFCondCell – Base type of conductance based PyNN IaF cell models
- Parameters:
e_rev_E (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
e_rev_I (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
tau_refrac (none) –
v_thresh (none) –
tau_m (none) –
v_rest (none) –
v_reset (none) –
cm (none) –
i_offset (none) –
tau_syn_E (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
tau_syn_I (none) – This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell
v_init (none) –
- add(obj=None, hint=None, force=False, validate=True, **kwargs)#
Generic function to allow easy addition of a new member to a NeuroML object. Without arguments, when obj=None, it simply calls the info() method to provide the list of valid member types for the NeuroML class.
Please use the info() method directly for more information on the current contents of this component object.
When obj is given a string name of a NeuroML class (“NeuroMLDocument”), or the class itself (neuroml.NeuroMLDocument), a new object will be created of this type and added as a member to the calling (parent) component type object.
- Parameters:
obj (Object) – member object or class type (neuroml.NeuroMLDocument) or name of class type (“NeuroMLDocument”), or None
hint (string) – member name to add to when there are multiple members that obj can be added to
force (bool) – boolean to force addition when an obj has already been added previously
validate (bool) – validate component after adding (default: True)
- Returns obj:
the provided or created object
- Raises:
Exception – if a member compatible to obj could not be found
Exception – if multiple members can accept the object and no hint is provided.
- classmethod component_factory(component_type, validate=True, **kwargs)#
Factory function to create a NeuroML Component object.
Users can provide the name of the component as a string or the class variable, along with its named constructor arguments, and this function will create a new object of the Component and return it.
Users can use the add() helper function to further modify components
This factory runs two checks while creating the component object:
that all arguments given do belong to the ComponentType (useful for caching typos)
that the created component is valid NeuroML
It is therefore less error prone than creating Components directly using the ComponentType constructors.
It may be useful to disable validation when starting a model. The validate parameter can be set to False for this.
- Parameters:
component_type (str/type) – component type to create component from: this can either be the name of the component as a string, e.g. “NeuroMLDocument”, or it can be the class type itself: NeuroMLDocument. Note that when providing the class type, one will need to import it, e.g.: import NeuroMLDocument, to ensure that it is defined, whereas this will not be required when using the string.
validate (bool) – toggle validation (default: True)
kwargs (named arguments) – named arguments to be passed to ComponentType constructor
- Returns:
new Component (object) of provided ComponentType
- Return type:
object
- Raises:
ValueError – if validation/checks fail
- classmethod get_class_hierarchy()#
Get the class hierarchy for a component classs.
Reference: https://stackoverflow.com/a/75161393/375067
See the methods in neuroml.utils to use this generated hierarchy.
- Returns:
nested single key dictionaries where the key of each dictionary is the root node of that subtree, and keys are its immediate descendents
- classmethod get_nml2_class_hierarchy()#
Return the NeuroML class hierarchy.
The root here is NeuroMLDocument. This is useful in calculating paths to different components to aid in construction of relative paths.
This caches the value as a class variable so that it is not re-calculated when used multiple times.
- has__content()#
- info(show_contents=False, return_format='string')#
Provide information on NeuroML component.
This is useful to quickly check what members can go into a particular NeuroML class (which will match the Schema definitions). It lists these members and notes whether they are “single” type elements (Child elements) or “List” elements (Children elements). It will also note whether a member is optional or required.
To get a list of possible parents, use the parentinfo() method.
By default, this will only show the members, and not their contents. To see contents that have been set, use show_contents=True. This will not show empty/unset contents. To see all contents, set show_contents=all.
Note that not all members will have ids (since not all NeuroML2 ComponentTypes have ids). For members that do not have ids, the object reference is listed instead.
See http://www.davekuhlman.org/generateDS.html#user-methods for more information on the MemberSpec_ class that generateDS uses.
- Parameters:
show_contents (bool or str) – toggle to print out the contents of the members
return_format (str) –
select what format to return information in “string” (default), or “dict” or “list”.
If “dict” or “list” is provided, the information is returned as a dict/list instead of being printed. Note that if show_contents is False, only a list of members is available and will be returned even if “dict” is supplied. If show_contents is True or “all” but “list” is provided, only the list of members will be returned. If something other than “string”, “list”, or “dict” is provided, the string representation is returned and printed.
- Returns:
info string, or list of members or dict with members as keys and member values as values
- Return type:
str, list/dict
- parentinfo(return_format='string')#
Show the list of possible parents.
This object can then be added to objects of the parents using the add method.
It is similar to the info() method. However, where in the info() method, it is possible to find the contents of members for a component (object) rather easily, it is not so easily possible to get all the objects that may refer to another object.
So, this will provide information on possible parents. It will not provide information on whether the components (objects) of the particular parent have already been instantiated and what their values are. The user should be able to gather this information easily by reading the sources.
Please also note that various component types in NeuroML take ids of components as parameters. For example, an ExplicitInput will take the id of a cell as its target, and the id of a PulseGenerator as input. However, these are string fields, and the cell/pulse generator classes do not currently know that their ids can be used in ExplicitInput. This information does not live in the XSD schema, and so cannot be obtained here either.
- Parameters:
return_format (str) – format in which to return information. If “string” (default), an information string is returned. If “list” or “dict”, a list or dictionary is returned. The list will only contain the parent names, whereas the dict will also include the member of the parent that the component type matches to.
- Returns:
info string, or list of parents or dict with parents as keys and member information as values
- Return type:
str, list/dict
- validate(recursive=False)#
Validate the component.
Throws a Python ValueError if a the component is invalid. You can ignore this by using a try .. except ValueError: pass block.
Note: validating your NeuroML file against the schema, which pynml and jnml do, will also check this.
Note: that this is different from the validate_ method, which does not validate inherited members.
- Parameters:
recursive (bool) – toggle recursive validation (default: False)
- Returns:
None
- Return type:
None
- Raises:
ValueError – if component is invalid