navis.make_dotprops

navis.make_dotprops(x, k=20, resample=False, threshold=None)

Produce dotprops from neurons or x/y/z points.

This is following the implementation in R’s nat library.

Parameters:

• x (TreeNeuron | MeshNeuron | VoxelNeuron | NeuronList | pandas.DataFrame | numpy.ndarray) – Data/object to generate dotprops from. DataFrame must have ‘x’, ‘y’ and ‘z’ columns.

• k (int (> 1), optional) –

  Number of nearest neighbours to use for tangent vector calculation:

  • k=0 or k=None is possible but only for TreeNeurons where we then use the midpoints between child -> parent nodes and their vectors

  • k is only guaranteed if the input has at least k points

  • k includes self-hits and while k=1 is not strictly forbidden, it makes little sense and will likely produce nonsense dotprops

• resample (float | int | str, optional) –

  If provided will resample neurons to the given resolution:

  • for MeshNeurons, VoxelNeurons and point clouds, we are using trimesh.points.remove_close to remove surface vertices closer than the given resolution. Note that this is only approximate and also means that Mesh/VoxelNeurons can not be up-sampled!

  • if the neuron has .units set you can also provide this as string, e.g. “1 micron”.

• threshold (float, optional) – Only for VoxelNeurons: determines which voxels will be converted to dotprops points.

• parallel (bool) – If True and input is NeuronList, use parallel processing. Requires pathos.

• n_cores (int, optional) – Numbers of cores to use if parallel=True. Defaults to half the available cores.

• progress (bool) – Whether to show a progress bar. Overruled by navis.set_pbars.

• omit_failures (bool) – If True will omit failures instead of raising an exception. Ignored if input is single neuron.

Returns:

If input is multiple neurons, will return a NeuronList of Dotprops.

Return type:

navis.Dotprops

Examples

>>> import navis
>>> n = navis.example_neurons(1)
>>> dp = navis.make_dotprops(n)
>>> dp
type        navis.Dotprops
name             DA1_lPN_R
id              1734350788
k                       20
units          8 nanometer
n_points              4465
dtype: object