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.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)¶
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.