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