navis.smooth_skeleton¶

navis.smooth_skeleton(x, window=5, to_smooth=['x', 'y', 'z'], inplace=False)[source]¶

Smooth skeleton(s) using rolling windows.

Parameters:

x (TreeNeuron | NeuronList) – Neuron(s) to be processed.
window (int, optional) – Size (N observations) of the rolling window in number of nodes.
to_smooth (list) – Columns of the node table to smooth. Should work with any numeric column (e.g. ‘radius’).
inplace (bool, optional) – If False, will use and return copy of original neuron(s).
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:

Smoothed neuron(s).

Return type:

TreeNeuron/List

Examples

Smooth x/y/z locations (default):

>>> import navis
>>> nl = navis.example_neurons(2)
>>> smoothed = navis.smooth_skeleton(nl, window=5)

Smooth only radii:

>>> rad_smoothed = navis.smooth_skeleton(nl, to_smooth='radius')