neurom.ezy.Neuron¶

class neurom.ezy.Neuron(neuron, iterable_type=<built-in function array>)¶

Bases: neurom.core.neuron.Neuron

Class with basic analysis and plotting functionality

By default returns iterables as numpy.arrays and applies no filtering.

Parameters:	neuron – neuron-like object iterable_type – type of iterable to return from methods returning collections (e.g list, tuple, numpy.array).
Raises:	neurom.exceptions.SomaError if no soma can be built from the data neurom.exceptions.IDSequenceError if ID sequence invalid

Example

get the segment lengths of all apical dendrites in a neuron morphology.

>>> from neurom import ezy
>>> nrn = ezy.load_neuron('test_data/swc/Neuron.swc')
>>> nrn.get_segment_lengths(ezy.NeuriteType.apical_dendrite)

Example

use lists instead of numpy arrays and get section lengths for the axon. Read an HDF5 v1 file:

>>> from neurom import ezy
>>> nrn = ezy.load_neuron('test_data/h5/v1/Neuron.h5', iterable_type=list)
>>> nrn.get_section_lengths(ezy.NeuriteType.axon)

Example

plot the neuron and save to a file

>>> fig, ax = nrn.plot()
>>> fig.show()
>>> fig.savefig('nrn.png')

Methods

`__init__`
`bounding_box`	Return 3D bounding box of a neuron
`copy`	Return a copy of the Neuron object.
`get_local_bifurcation_angles`	Get local bifircation angles of all segments of a given type
`get_n_neurites`	Get the number of neurites of a given type in a neuron
`get_n_sections`	Get the number of sections of a given type
`get_n_sections_per_neurite`	Get an iterable with the number of sections for a given neurite type
`get_remote_bifurcation_angles`	Get remote bifircation angles of all segments of a given type
`get_section_lengths`	Get an iterable containing the lengths of all sections of a given type
`get_section_path_distances`	Get section path distances of all neurites of a given type The section path distance is measured to the neurite’s root.
`get_section_radial_distances`	Get an iterable containing section radial distances to origin of all neurites of a given type
`get_segment_lengths`	Get an iterable containing the lengths of all segments of a given type
`get_soma_radius`	Get the radius of the soma
`get_soma_surface_area`	Get the surface area of the soma.
`get_trunk_origin_radii`	Get the trunk origin radii of a given type in a neuron
`get_trunk_section_lengths`	Get the trunk section lengths of a given type in a neuron
`i_neurites`	Returns a mapped iterator to all the neuron’s neurites