arraymorph Module

Prototype for object model backend for the libNeuroML project

class neuroml.arraymorph.ArrayMorphology(vertices=[], connectivity=[], id=None, node_types=None, name=None, physical_mask=None, fractions_along=None)

Bases: Morphology

Core of the array-based object model backend.

Provides the core arrays - vertices,connectivity etc. node_types.

The connectivity array is a list of indices pointing to which other element an element is attached. So for instance, connectivity[3] is an integer with the index of the section it refers to in the Backend

• EXAMPLE:

  Vertices[3] and connectivity[3] refer to the vertex and connectivity of the same node.

Note

The root section by convention has connectivity == -1.

children(index)

Returns an array with indexes of children

property num_vertices

parent_id(index)

Return the parent index for the given index

property physical_indices

returns indices of vertices which are physical

pop(index)

TODO:This is failing tests (understandably) - need to fix! Deletes a node from the morphology, its children become children of the deleted node’s parent.

property root_index

property root_vertex

segment_from_vertex_index(index)

to_neuroml_morphology(id='')

to_root(index)

Changes the connectivity matrix so that the node at index becomes the root

property valid_ids

property valid_morphology

vertex(index)

Return vertex corresponding to index in morphology

class neuroml.arraymorph.SegmentList(arraymorph)

Bases: object

This class is a proxy, it returns a segment either from the arraymorph or if it has already been instantiated it returns the relevant segment.

append(segment)

Adds a new segment

TODO: Correct connectivity is currently being ignored - The new segment is always connected to the root node.