navis.write_swc

navis.write_swc(x, filepath, header=None, write_meta=True, labels=True, export_connectors=False, return_node_map=False)

Write TreeNeuron(s) to SWC.

Follows the format specified here.

Parameters:

• x (TreeNeuron | Dotprops | NeuronList) – If multiple neurons, will generate a single SWC file for each neuron (see also filepath).

• filepath (str | pathlib.Path | list thereof) – Destination for the SWC files. See examples for options. If x is multiple neurons, filepath must either be a folder, a “formattable” filename, a filename ending in .zip or a list of filenames (one for each neuron in x). Existing files will be overwritten!

• header (str | None, optional) – Header for SWC file. If not provided, will use generic header.

• write_meta (bool | list | dict) –

  If not False, will add meta data as JSON-formatted string to the header:

  True: adds neuron `id`, `name` and `units`
  list: use to set which properties, e.g. ['id', 'units']
  dict: use to set meta data, e.g. {'template': 'JRC2018F'}
  

  This parameter is ignored if custom header is provided.

• labels (str | dict | bool, optional) –

  Node labels. Can be:

  str : column name in node table
  dict: must be of format {node_id: 'label', ...}.
  bool: if True, will generate automatic labels, if False all nodes have label "0".
  

• export_connectors (bool, optional) – If True, will label nodes with pre- (“7”) and postsynapse (“8”). Because only one label can be given this might drop synapses (i.e. in case of multiple pre- and/or postsynapses on a single node)! labels must be True for this to have any effect.

• return_node_map (bool) – If True, will return a dictionary mapping the old node ID to the new reindexed node IDs in the file.

Returns:

node_map – Only if return_node_map=True.

Return type:

dict

See also

navis.read_swc()

Import skeleton from SWC files.

Examples

Save a single neuron to a specific file:

>>> import navis
>>> n = navis.example_neurons(1, kind='skeleton')
>>> navis.write_swc(n, tmp_dir / 'my_neuron.swc')

Save two neurons to specific files:

>>> import navis
>>> nl = navis.example_neurons(2, kind='skeleton')
>>> navis.write_swc(nl, [tmp_dir / 'my_neuron1.swc', tmp_dir / 'my_neuron2.swc'])

Save multiple neurons to a folder (must exist). Filenames will be autogenerated as “{neuron.id}.swc”:

>>> import navis
>>> nl = navis.example_neurons(5, kind='skeleton')
>>> navis.write_swc(nl, tmp_dir)

Save multiple neurons to a folder but modify the pattern for the autogenerated filenames:

>>> import navis
>>> nl = navis.example_neurons(5, kind='skeleton')
>>> navis.write_swc(nl, tmp_dir / 'skel-{neuron.name}.swc')

Save multiple neurons to a zip file:

>>> import navis
>>> nl = navis.example_neurons(5, kind='skeleton')
>>> navis.write_swc(nl, tmp_dir / 'neuronlist.zip')

Save multiple neurons to a zip file but modify the filenames:

>>> import navis
>>> nl = navis.example_neurons(5, kind='skeleton')
>>> navis.write_swc(nl, tmp_dir / 'skel-{neuron.name}.swc@neuronlist.zip')