pyneuroml.swc package#

pyneuroml.swc.LoadSWC module#

Module for loading SWC files

Added in version 1.3.9.

Copyright 2024 NeuroML contributors

class pyneuroml.swc.LoadSWC.SWCGraph#

Bases: object

Graph data structure holding SWCNode objects

HEADER_FIELDS = ['ORIGINAL_SOURCE', 'CREATURE', 'REGION', 'FIELD/LAYER', 'TYPE', 'CONTRIBUTOR', 'REFERENCE', 'RAW', 'EXTRAS', 'SOMA_AREA', 'SHRINKAGE_CORRECTION', 'VERSION_NUMBER', 'VERSION_DATE', 'SCALE']#
add_metadata(key: str, value: str)#

Add metadata to the SWC graph.

Parameters:

  • key (str) – The key for the metadata

  • value (str) – The value for the metadata

add_node(node: SWCNode)#

Add a node to the SWC graph.

Parameters:

node (SWCNode) – The node to be added

Raises:

ValueError – If a node with the same ID already exists in the graph or if multiple root nodes are detected

export_to_swc_file(filename: str) → None#

Export the SWCGraph to a new SWC file.

Parameters:

filename (str) – The path to the output SWC file

get_branch_points(types: List[int] | None) → List[SWCNode] | Dict[int, List[SWCNode]]#

Get all branch points (nodes with multiple children) of the given types.

Parameters:

types (int) – One or more node type IDs to filter the branch points by

Returns:

if node types are given, a dictionary with keys as the node type and lists of nodes as values; otherwise a list of all nodes

Return type:

list or dict

get_children(node_id: int) → List[SWCNode]#

Get a list of child nodes for a given node.

Parameters:

node_id (int) – The ID of the node for which to get the children

Returns:

A list of SWCNode objects representing the children of the given node

Return type:

list

Raises:

ValueError – If the provided node_id is not found in the graph

get_node(node_id: int) → SWCNode#

Get a node from the graph by its ID.

Parameters:

node_id (int) – The ID of the node to retrieve

Returns:

The node with the specified ID

Return type:

SWCNode

Raises:

ValueError – If the specified node_id is not found in the SWC tree

get_nodes_by_type(type_id: int) → List[SWCNode]#

Get a list of nodes of a specific type.

Parameters:

type_id (int) – The type ID of the nodes to retrieve

Returns:

A list of SWCNode objects that have the specified type ID

Return type:

list

get_nodes_with_multiple_children(type_id: int | None = None) → List[SWCNode]#

Get nodes with multiple children, optionally filtered by type.

Parameters:

type_id (int or None) – The type ID to filter nodes by (optional)

Returns:

A list of SWCNode objects that have multiple children and match the specified type (if provided)

Return type:

list

get_parent(node_id: int) → SWCNode | None#

Get the parent node of a given node in the SWC tree.

Parameters:

node_id (int) – The ID of the node for which to retrieve the parent

Returns:

The parent node if the node has a parent, otherwise None

Return type:

SWCNode or None

Raises:

ValueError – If the specified node_id is not found in the SWC tree

class pyneuroml.swc.LoadSWC.SWCNode(node_id: str | int, type_id: str | int, x: str | float, y: str | float, z: str | float, radius: str | float, parent_id: str | int)#

Bases: object

Represents a single node in an SWC (Standardized Morphology Data Format) file.

The SWC format is a widely used standard for representing neuronal morphology data. It consists of a series of lines, each representing a single node or sample point along the neuronal structure. For more information on the SWC format, see: https://swc-specification.readthedocs.io/en/latest/swc.html

Parameters:

  • UNDEFINED (int) – ID representing an undefined node type

  • SOMA (int) – ID representing a soma node

  • AXON (int) – ID representing an axon node

  • BASAL_DENDRITE (int) – ID representing a basal dendrite node

  • APICAL_DENDRITE (int) – ID representing an apical dendrite node

  • CUSTOM (int) – ID representing a custom node type

  • UNSPECIFIED_NEURITE (int) – ID representing an unspecified neurite node

  • GLIA_PROCESSES (int) – ID representing a glia process node

  • TYPE_NAMES (dict) – A mapping of node type IDs to their string representations

APICAL_DENDRITE = 4#
AXON = 2#
BASAL_DENDRITE = 3#
CUSTOM = 5#
GLIA_PROCESSES = 7#
SOMA = 1#
TYPE_NAMES = {0: 'Undefined', 1: 'Soma', 2: 'Axon', 3: 'Basal Dendrite', 4: 'Apical Dendrite', 5: 'Custom', 6: 'Unspecified Neurite', 7: 'Glia Processes'}#
UNDEFINED = 0#
UNSPECIFIED_NEURITE = 6#
pyneuroml.swc.LoadSWC.load_swc(filename: str) → SWCGraph#

Load an SWC file and create an SWCGraph object.

Parameters:

filename (str) – The path to the SWC file to be loaded

Returns:

An SWCGraph object representing the loaded SWC file

Return type:

SWCGraph

Raises:

ValueError – If a non header line with more than the required number of fields is found

pyneuroml.swc.LoadSWC.parse_header(line_number: int, line: str) → Tuple[str, str] | None#

Parse a header line from an SWC file.

Parameters:

  • line_number (int) – line number, for logging purposes

  • line (str) – A single line from the SWC file header

Returns:

A tuple containing the matched header field name and corresponding value (or None if no match)

Return type:

tuple

pyneuroml.swc.ExportSWC module#

A script to export SWC files from NeuroML <cell>s

pyneuroml.swc.ExportSWC.convert_to_swc(nml_file_name, add_comments=False, target_dir=None)#

Find all <cell> elements and create one SWC file for each

pyneuroml.swc.ExportNML module#

Module for exporting NeuroML from SWC files.

Added in version 1.3.9.

Copyright 2024 NeuroML contributors

class pyneuroml.swc.ExportNML.NeuroMLWriter(swc_graph: SWCGraph)#

Bases: object

A class to convert SWC graph data to NeuroML format.

This class takes an SWC graph and converts it into a NeuroML representation, handling different neuron segment types and creating appropriate segment groups.

export_to_nml_file(filename: str, standalone_morphology: bool = True, unbranched_segment_groups: bool = True) → None#

Export the NeuroML representation to a file.

Parameters:

  • filename (str) – The name of the file to export to.

  • standalone_morphology (bool) – export morphology as standalone object (not as part of a Cell object)

  • unbranched_segment_groups (bool) – toggle creation of unbranched segment groups

generate_neuroml(standalone_morphology: bool = True, unbranched_segment_groups: bool = True) → NeuroMLDocument#

Generate NeuroML representation.

Main worker function

Parameters:

  • standalone_morphology (bool) – export morphology as standalone object (not as part of a Cell object)

  • unbranched_segment_groups (bool) – toggle creation of unbranched segment groups

Returns:

the NeuroML document

Return type:

NeuroMLDocument

pyneuroml.swc.ExportNML.convert_swc_to_neuroml(swc_file: str, neuroml_file: str | None = None, standalone_morphology: bool = True, unbranched_segment_groups: bool = True) → NeuroMLDocument#

Convert an SWC file to NeuroML.

If neuroml_file is provided, will also write to file.

Parameters:

  • swc_file (str) – SWC input file

  • neuroml_file (str) – output NeuroML file (optional)

  • standalone_morphology (bool) – export morphology as standalone object (not as part of a Cell object)

Returns:

NeuroML document

Return type:

NeuroMLDocument