navis.guess_radius¶

navis.guess_radius(x, method='linear', limit=None, smooth=True, inplace=False)[source]¶

Guess radii for skeleton nodes.

Uses distance between connectors and nodes to guess radii. Interpolate for nodes without connectors. Fills in radius column in node table.

Parameters:

x (TreeNeuron | NeuronList) – Neuron(s) to be processed.
method (str, optional) – Method to be used to interpolate unknown radii. See pandas.DataFrame.interpolate for details.
limit (int, optional) – Maximum number of consecutive missing radii to fill. Must be greater than 0.
smooth (bool | int, optional) – If True, will smooth radii after interpolation using a rolling window. If int, will use to define size of window.
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.

Return type:

TreeNeuron/List

Examples

>>> import navis
>>> nl = navis.example_neurons(2)
>>> nl_radius = navis.guess_radius(nl)