navis.write_nrrd¶

navis.write_nrrd(x, filepath, compression_level=3, attrs=None)[source]¶

Write VoxelNeurons or Dotprops to NRRD file(s).

Parameters:

x (VoxelNeuron | Dotprops | NeuronList) – If multiple neurons, will generate a NRRD file for each neuron (see also filepath).
filepath (str | pathlib.Path | list thereof) – Destination for the NRRD files. See examples for options. If x is multiple neurons, filepath must either be a folder, a “formattable” filename (see Examples) or a list of filenames (one for each neuron in x). Existing files will be overwritten!
compression_level (int 1-9) – Lower = faster writing but larger files. Higher = slower writing but smaller files.
attrs (dict) – Any additional attributes will be written to NRRD header.

Return type:

Nothing

Examples

Save a single neuron to a specific file:

>>> import navis
>>> n = navis.example_neurons(1, kind='skeleton')
>>> vx = navis.voxelize(n, pitch='2 microns')
>>> navis.write_nrrd(vx, tmp_dir / 'my_neuron.nrrd')

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

>>> import navis
>>> nl = navis.example_neurons(5, kind='skeleton')
>>> dp = navis.make_dotprops(nl, k=5)
>>> navis.write_nrrd(dp, 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')
>>> vx = navis.voxelize(nl, pitch='2 microns')
>>> navis.write_nrrd(vx, tmp_dir / 'voxels-{neuron.name}.nrrd')

Save multiple neurons to a zip file:

>>> import navis
>>> nl = navis.example_neurons(5, kind='skeleton')
>>> vx = navis.voxelize(nl, pitch='2 microns')
>>> navis.write_nrrd(vx, tmp_dir / 'neuronlist.zip')

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

>>> import navis
>>> nl = navis.example_neurons(5, kind='skeleton')
>>> vx = navis.voxelize(nl, pitch='2 microns')
>>> navis.write_nrrd(vx, tmp_dir / 'voxels-{neuron.name}.nrrd@neuronlist.zip')