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: object

Super 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

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

class neuroml.nml.generatedscollector.GdsCollector(messages=None)

Bases: object

add_message(msg)

clear_messages()

get_messages()

print_messages()

write_messages(outstream)

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: BaseCellMembPotCap

AdExIaFCell – 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) –

• EL (voltage) –

• VT (voltage) –

• thresh (voltage) –

• reset (voltage) –

• delT (voltage) –

• tauw (time) –

• refract (time) –

• a (conductance) –

• b (current) –

• 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

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: BasePynnSynapse

AlphaCondSynapse – 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

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: BasePynnSynapse

AlphaCurrSynapse – 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

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: BaseCurrentBasedSynapse

AlphaCurrentSynapse – 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

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: BaseConductanceBasedSynapse

AlphaSynapse – 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

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: BaseWithoutId

Annotation – 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

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: BaseWithoutId

Base – 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

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: Standalone

BaseCell – 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

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: BaseCell

BaseCellMembPotCap – 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

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: BaseVoltageDepSynapse

BaseConductanceBasedSynapse – 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

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: BaseVoltageDepSynapse

BaseConductanceBasedSynapseTwo – 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

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: BaseNonNegativeIntegerId

BaseConnection – 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

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: BaseConnection

BaseConnectionNewFormat – 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

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 string (required) = None, pre_segment_id: a NonNegativeInteger (optional) = '0', pre_fraction_along: a ZeroToOne (optional) = '0.5', post_cell_id: a string (required) = None, post_segment_id: a NonNegativeInteger (optional) = '0', post_fraction_along: a ZeroToOne (optional) = '0.5', extensiontype_=None, gds_collector_=None, **kwargs_)

Bases: BaseConnection

BaseConnectionOldFormat – 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

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

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: BaseSynapse

BaseCurrentBasedSynapse – 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

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: BaseWithoutId

BaseNonNegativeIntegerId – 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

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: Base

BaseProjection – 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

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: BaseSynapse

BasePynnSynapse – 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

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: Standalone

BaseSynapse – 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

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: BaseSynapse

BaseVoltageDepSynapse – 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

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: GeneratedsSuper

BaseWithoutId – 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

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: Standalone

BiophysicalProperties – 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

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: Standalone

BiophysicalProperties2CaPools – 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

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

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: ExpTwoSynapse

BlockingPlasticSynapse – 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

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

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: BaseCell

Cell – 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

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

None

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

None

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

None

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)

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 (SegmentParent) – parent segment

• 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.

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

Segment

Raises

ValueError – if seg_id is provided and a segment with this ID already exists

add_segment_group(group_id)

Add a new general segment group.

The segments included in this group do not need to be contiguous. This segment group will not be marked as a section using the required NeuroLex ID.

Parameters

group_id (str) – ID of segment group

Returns

new segment group

Return type

SegmentGroup

add_unbranched_segment_group(group_id)

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.

Parameters

group_id (str) – ID of segment group

Returns

new segment group

Return type

SegmentGroup

add_unbranched_segments(points, parent=None, fraction_along=1.0, group_id=None, use_convention=True, seg_type=None)

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”)

Returns

the segment group containing this new list of segments

Return type

SegmentGroup

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)

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

Returns

modified cell with new section groups

Return type

neuroml.Cell

get_actual_proximal(segment_id)

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_segments_in_group(segment_group, assume_all_means_all=True)

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_ordered_segments_in_groups(group_list, check_parentage=False, include_cumulative_lengths=False, include_path_lengths=False, path_length_metric='Path Length from root')

Get ordered list of segments in specified groups

Parameters

• group_list (str or list) – a group id or list of groups to get segments from

• check_parentage (bool) – verify parentage

• include_commulative_lengths – also include cummulative lengths

• include_path_lengths (bool) – also include path lengths

• path_length_metric (str) – metric to use for path length (“Path Length from root” is currently the only supported option, and the default)

Returns

dictionary of segments with additional information depending on what parameters were used:

Raises

Exception if check_parentage is True and parentage cannot be verified

get_segment(segment_id)

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.

Returns

dict with parent segments as keys and their children as values

Return type

dict

get_segment_group(sg_id)

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_groups_by_substring(substring)

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()

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)

Get the length of the segment.

Parameters

segment_id – ID of segment

Returns

length of segment

get_segment_surface_area(segment_id)

Get the surface area of the segment.

Parameters

segment_id – ID of the segment

Returns

surface area of segment

get_segment_volume(segment_id)

Get volume of segment

Parameters

segment_id – ID of the segment

Returns

volume of the segment

get_segments_by_substring(substring)

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

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

neuro_lex_ids = {'axon': 'GO:0030424', 'dend': 'GO:0030425', 'section': 'sao864921383', 'soma': 'GO:0043025'}

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_nml_cell(use_convention=True, overwrite=False)

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 some default SegmentGroups for convenience:

• “all”, “soma_group”, “dendrite_group”, “axon_group” which are used by other helper functions to include all, soma, dendrite, and axon segments respectively.

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

Returns

None

Return type

None

summary()

Print cell summary.

Currently prints:

• id of cell

• any notes

• number of segments

• number of segment groups

TODO: extend to show more information about the cell that may be useful to users.

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: Cell

Cell2CaPools – 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

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

None

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

None

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

None

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)

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 (SegmentParent) – parent segment

• 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.

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

Segment

Raises

ValueError – if seg_id is provided and a segment with this ID already exists

add_segment_group(group_id)

Add a new general segment group.

The segments included in this group do not need to be contiguous. This segment group will not be marked as a section using the required NeuroLex ID.

Parameters

group_id (str) – ID of segment group

Returns

new segment group

Return type

SegmentGroup

add_unbranched_segment_group(group_id)

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.

Parameters

group_id (str) – ID of segment group

Returns

new segment group

Return type

SegmentGroup

add_unbranched_segments(points, parent=None, fraction_along=1.0, group_id=None, use_convention=True, seg_type=None)

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”)

Returns

the segment group containing this new list of segments

Return type

SegmentGroup

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)

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

Returns

modified cell with new section groups

Return type

neuroml.Cell

get_actual_proximal(segment_id)

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_segments_in_group(segment_group, assume_all_means_all=True)

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_ordered_segments_in_groups(group_list, check_parentage=False, include_cumulative_lengths=False, include_path_lengths=False, path_length_metric='Path Length from root')

Get ordered list of segments in specified groups

Parameters

• group_list (str or list) – a group id or list of groups to get segments from

• check_parentage (bool) – verify parentage

• include_commulative_lengths – also include cummulative lengths

• include_path_lengths (bool) – also include path lengths

• path_length_metric (str) – metric to use for path length (“Path Length from root” is currently the only supported option, and the default)

Returns

dictionary of segments with additional information depending on what parameters were used:

Raises

Exception if check_parentage is True and parentage cannot be verified

get_segment(segment_id)

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.

Returns

dict with parent segments as keys and their children as values

Return type

dict

get_segment_group(sg_id)

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_groups_by_substring(substring)

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()

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)

Get the length of the segment.

Parameters

segment_id – ID of segment

Returns

length of segment

get_segment_surface_area(segment_id)

Get the surface area of the segment.

Parameters

segment_id – ID of the segment

Returns

surface area of segment

get_segment_volume(segment_id)

Get volume of segment

Parameters

segment_id – ID of the segment

Returns

volume of the segment

get_segments_by_substring(substring)

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

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

neuro_lex_ids = {'axon': 'GO:0030424', 'dend': 'GO:0030425', 'section': 'sao864921383', 'soma': 'GO:0043025'}

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_nml_cell(use_convention=True, overwrite=False)

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 some default SegmentGroups for convenience:

• “all”, “soma_group”, “dendrite_group”, “axon_group” which are used by other helper functions to include all, soma, dendrite, and axon segments respectively.

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

Returns

None

Return type

None

summary()

Print cell summary.

Currently prints:

• id of cell

• any notes

• number of segments

• number of segment groups

TODO: extend to show more information about the cell that may be useful to users.

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

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: Base

ChannelDensity – 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

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: Base

ChannelDensityGHK – 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

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: Base

ChannelDensityGHK2 – Time varying conductance density, gDensity, which is distributed on an area of the cel l, 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

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: Base

ChannelDensityNernst – 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

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: ChannelDensityNernst

ChannelDensityNernstCa2 – 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

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: Base

ChannelDensityNonUniform – 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

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: Base

ChannelDensityNonUniformGHK – 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

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: Base

ChannelDensityNonUniformNernst – 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

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: ChannelDensity

ChannelDensityVShift – 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

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: Base

ChannelPopulation – 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

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: Base

ClosedState – 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

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, 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: GeneratedsSuper

ComponentType – 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

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: Standalone

CompoundInput – 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

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: Standalone

CompoundInputDL – 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

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

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: NamedDimensionalVariable

ConditionalDerivedVariable – 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

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 string (required) = None, pre_segment_id: a NonNegativeInteger (optional) = '0', pre_fraction_along: a ZeroToOne (optional) = '0.5', post_cell_id: a string (required) = None, post_segment_id: a NonNegativeInteger (optional) = '0', post_fraction_along: a ZeroToOne (optional) = '0.5', gds_collector_=None, **kwargs_)

Bases: BaseConnectionOldFormat

Connection – 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

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

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

ConnectionWD

class neuroml.nml.nml.ConnectionWD(id: a NonNegativeInteger (required) = None, neuro_lex_id: a NeuroLexId (optional) = None, pre_cell_id: a string (required) = None, pre_segment_id: a NonNegativeInteger (optional) = '0', pre_fraction_along: a ZeroToOne (optional) = '0.5', post_cell_id: a string (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: BaseConnectionOldFormat

ConnectionWD – 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

get_delay_in_ms()

Get connection delay in milli seconds

Returns

connection delay in milli seconds

Return type

float

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

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

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: BaseWithoutId

Constant – 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

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: BaseConnectionNewFormat

ContinuousConnection – 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

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

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: ContinuousConnection

ContinuousConnectionInstance – 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

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

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: ContinuousConnectionInstance

ContinuousConnectionInstanceW – 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

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.

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: BaseProjection

ContinuousProjection – 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.

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: Standalone

DecayingPoolConcentrationModel – 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

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: NamedDimensionalVariable

DerivedVariable – 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

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: 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

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: BaseVoltageDepSynapse

DoubleSynapse – 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

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, gds_collector_=None, **kwargs_)

Bases: GeneratedsSuper

Dynamics – 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

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_ista

EIF_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

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: basePyNNIaFCondCell

EIF_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

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: BaseConnectionNewFormat

ElectricalConnection – 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

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

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: ElectricalConnection

ElectricalConnectionInstance – 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

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

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: ElectricalConnectionInstance

ElectricalConnectionInstanceW – 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

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

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: BaseProjection

ElectricalProjection – 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.

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: BasePynnSynapse

ExpCondSynapse – 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

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: BasePynnSynapse

ExpCurrSynapse – 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

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: BaseConductanceBasedSynapse

ExpOneSynapse – 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

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: BaseConductanceBasedSynapseTwo

ExpThreeSynapse – 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

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: BaseConductanceBasedSynapse

ExpTwoSynapse – 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

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 string (required) = None, input: a string (required) = None, destination: a string (optional) = None, gds_collector_=None, **kwargs_)

Bases: BaseWithoutId

ExplicitInput – 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

get_fraction_along()

Get fraction along.

Returns 0.5 is fraction_along was not set.

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.

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

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: BaseWithoutId

Exposure – 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

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

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

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: BaseCell

FitzHughNagumo1969Cell – 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

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: BaseCell

FitzHughNagumoCell – 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

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: Standalone

FixedFactorConcentrationModel – 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

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: Base

ForwardTransition – 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

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: BaseSynapse

GapJunction – 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

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: Base

GateFractional – 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

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

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: Base

GateHHInstantaneous – 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

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: Base

GateHHRates – 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

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: Base

GateHHRatesInf – 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

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: Base

GateHHRatesTau – 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

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: Base

GateHHRatesTauInf – 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

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: Base

GateHHTauInf – 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

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: Base

GateHHUndetermined – 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

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: Base

GateKS – 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

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: BaseSynapse

GradedSynapse – 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

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

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

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

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

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: basePyNNCell

HH_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

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: basePyNNIaFCondCell

IF_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

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: basePyNNIaFCondCell

IF_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

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: basePyNNIaFCell

IF_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

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: basePyNNIaFCell

IF_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

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: BaseCell

IafCell – 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

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: IafCell

IafRefCell – 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

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: BaseCell

IafTauCell – 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

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: IafTauCell

IafTauRefCell – 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

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: BaseWithoutId

Include – 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

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

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: Base

InhomogeneousParameter – 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

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: BaseWithoutId

InhomogeneousValue – 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

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: BaseWithoutId

InitMembPotential – 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

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 string (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: BaseNonNegativeIntegerId

Input – 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

get_fraction_along()

Get fraction along.

Returns 0.5 is fraction_along was not set.

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.

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

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: Base

InputList – 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.

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 string (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: Input

InputW – 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

get_fraction_along()

Get fraction along.

Returns 0.5 is fraction_along was not set.

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.

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

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: BaseWithoutId

Instance – 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

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

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: BaseWithoutId

IntracellularProperties – 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

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: IntracellularProperties

IntracellularProperties2CaPools – 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

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: IonChannelScalable

IonChannel – 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

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: IonChannel

IonChannelHH – 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

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: Standalone

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 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

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

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: IonChannel

IonChannelVShift – 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

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: BaseCellMembPotCap

Izhikevich2007Cell – Cell based on the modified Izhikevich model in Izhikevich 2007, Dynamical systems in neuroscience, MIT Press

Parameters

• v0 (voltage) –

• k (conductance_per_voltage) –

• vr (voltage) –

• vt (voltage) –

• vpeak (voltage) –

• a (per_time) –

• b (conductance) –

• c (voltage) –

• d (current) –

• 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

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: BaseCell

IzhikevichCell – 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

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

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

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: BaseSynapse

LinearGradedSynapse – 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

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: BaseWithoutId

Location – 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

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: BaseWithoutId

Member – 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

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: BaseWithoutId

MembraneProperties – 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

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: MembraneProperties

MembraneProperties2CaPools – 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

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: Standalone

Morphology – 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

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

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

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: Standalone

Network – 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

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, 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

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

OpenState

class neuroml.nml.nml.OpenState(id: a NmlId (required) = None, gds_collector_=None, **kwargs_)

Bases: Base

OpenState – 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

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

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: BaseWithoutId

Path – 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

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: BaseCell

PinskyRinzelCA3Cell – Reduced CA3 cell model from Pinsky and Rinzel 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

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

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: BaseWithoutId

Point3DWithDiam – 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

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: Standalone

PoissonFiringSynapse – 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

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: Standalone

Population – 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.

get_size()

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: BaseProjection

Projection – 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.

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: BaseWithoutId

Property – 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

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: 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

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: Standalone

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 (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

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: Standalone

PulseGeneratorDL – 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

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: BaseWithoutId

Q10ConductanceScaling – 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

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

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: Standalone

RampGenerator – 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

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: Standalone

RampGeneratorDL – 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

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

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

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

Region

class neuroml.nml.nml.Region(id: a NmlId (required) = None, spaces: a NmlId (optional) = None, anytypeobjs_=None, gds_collector_=None, **kwargs_)

Bases: Base

Region – 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

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

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: BaseWithoutId

Resistivity – 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

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: Base

ReverseTransition – 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

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: BaseNonNegativeIntegerId

Segment – 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

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

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: Base

SegmentGroup – 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

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

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: BaseSynapse

SilentSynapse – 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

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: Standalone

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 (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

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: Standalone

SineGeneratorDL – 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

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

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

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: Base

Species – 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

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: BaseWithoutId

SpecificCapacitance – 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

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: BaseNonNegativeIntegerId

Spike – 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

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: Standalone

SpikeArray – 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

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: Standalone

SpikeGenerator – 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

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: Standalone

SpikeGeneratorPoisson – 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

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: Standalone

SpikeGeneratorRandom – 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

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: SpikeGeneratorPoisson

SpikeGeneratorRefPoisson – 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

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: Standalone

SpikeSourcePoisson – 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

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: BaseWithoutId

SpikeThresh – 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

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: Base

Standalone – 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

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

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: BaseWithoutId

SubTree – 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

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 string (required) = None, to: a string (required) = None, synapse: a string (required) = None, destination: a NmlId (optional) = None, gds_collector_=None, **kwargs_)

Bases: BaseWithoutId

SynapticConnection – 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

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

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: Base

TauInfTransition – 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

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

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: Standalone

TimedSynapticInput – 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

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: Standalone

TransientPoissonFiringSynapse – 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

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

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

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: GeneratedsSuper

VariableParameter – 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

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: Standalone

VoltageClamp – 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

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: Standalone

VoltageClampTriple – 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

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: BaseCell

basePyNNCell – 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

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: basePyNNCell

basePyNNIaFCell – 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

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: basePyNNIaFCell

basePyNNIaFCondCell – 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

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