neuroml Package

neuroml Package

loaders Module

class neuroml.loaders.ArrayMorphLoader

Bases: object

classmethod load(filepath)

Right now this load method isn’t done in a very nice way. TODO: Complete refactoring.

class neuroml.loaders.JSONLoader

Bases: object

classmethod load(file)
classmethod load_from_mongodb(db, id, host=None, port=None)
class neuroml.loaders.NeuroMLHdf5Loader

Bases: object

classmethod load(src, optimized=False)
class neuroml.loaders.NeuroMLLoader

Bases: object

classmethod load(src)
class neuroml.loaders.SWCLoader

Bases: object

WARNING: Class defunct

classmethod load_swc_single(src, name=None)
neuroml.loaders.print_(text, verbose=True)
neuroml.loaders.read_neuroml2_file(nml2_file_name, include_includes=False, verbose=False, already_included=[], print_method=<function print_>, optimized=False)
neuroml.loaders.read_neuroml2_string(nml2_string, include_includes=False, verbose=False, already_included=[], print_method=<function print_>, optimized=False, base_path=None)

writers Module

class neuroml.writers.ArrayMorphWriter

Bases: object

For now just testing a simple method which can write a morphology, not a NeuroMLDocument.

classmethod write(data, filepath)
class neuroml.writers.JSONWriter

Bases: object

Write a NeuroMLDocument to JSON, particularly useful when dealing with lots of ArrayMorphs.

classmethod write(neuroml_document, file)
classmethod write_to_mongodb(neuroml_document, db, host=None, port=None, id=None)
class neuroml.writers.NeuroMLHdf5Writer

Bases: object

classmethod write(nml_doc, h5_file_name, embed_xml=True, compress=True)
class neuroml.writers.NeuroMLWriter

Bases: object

classmethod write(nmldoc, file, close=True)

Writes from NeuroMLDocument to nml file in future can implement from other types via chain of responsibility pattern.

utils Module

Utilities for checking generated code

neuroml.utils.add_all_to_document(nml_doc_src, nml_doc_tgt, verbose=False)
neuroml.utils.append_to_element(parent, child)
neuroml.utils.get_summary(nml_file_name)
neuroml.utils.has_segment_fraction_info(connections)
neuroml.utils.is_valid_neuroml2(file_name)
neuroml.utils.main()
neuroml.utils.print_summary(nml_file_name)
neuroml.utils.validate_neuroml2(file_name)

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: neuroml.nml.nml.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.