neurom.io.utils

Utility functions and for loading neurons.

Functions

get_files_by_path	Get a file or set of files from a file path.
get_morph_files	Get a list of all morphology files in a directory.
load_neuron	Build section trees from a neuron or a h5, swc or asc file.
load_neurons	Create a population object.

Classes

Neuron	Class representing a simple neuron.
NeuronLoader	Caching morphology loader.
Population	Neuron Population Class.

Exceptions

NeuroMError

Base class for NeuroM errors.

exception neurom.io.utils.NeuroMError[source]

Bases: Exception

Base class for NeuroM errors.

class neurom.io.utils.Neuron(filename, name=None)[source]

Bases: morphio._morphio.mut.Morphology

Class representing a simple neuron.

transform(trans)[source]

Return a copy of this neuron with a 3D transformation applied.

class neurom.io.utils.NeuronLoader(directory, file_ext=None, cache_size=None)[source]

Bases: object

Caching morphology loader.

Parameters

• directory – path to directory with morphology files

• file_ext – file extension to look for (if not set, will pick any of .swc|.h5|.asc)

• cache_size – size of LRU cache (if not set, no caching done)

get(name)[source]

Get name morphology data.

class neurom.io.utils.Population(neurons, name='Population')[source]

Bases: object

Neuron Population Class.

Features:

• flattened collection of neurites.

• collection of somas, neurons.

• iterable-like iteration over neurons.

neurom.io.utils.get_files_by_path(path)[source]

Get a file or set of files from a file path.

Return list of files with path

neurom.io.utils.get_morph_files(directory)[source]

Get a list of all morphology files in a directory.

Returns

list with all files with extensions ‘.swc’ , ‘h5’ or ‘.asc’ (case insensitive)

neurom.io.utils.load_neuron(neuron, reader=None)[source]

Build section trees from a neuron or a h5, swc or asc file.

Parameters

• neuron (str|Path|Neuron|morphio.Morphology|morphio.mut.Morphology) –

  A neuron representation It can be:

  • a filename with the h5, swc or asc extension

  • a NeuroM Neuron object

  • a morphio mutable or immutable Morphology object

  • a stream that can be put into a io.StreamIO object. In this case, the READER argument must be passed with the corresponding file format (asc, swc and h5)

• reader (str) – Optional, must be provided if neuron is a stream to specify the file format (asc, swc, h5)

Returns

A Neuron object

Examples:

neuron = neurom.load_neuron('my_neuron_file.h5')

neuron = neurom.load_neuron(morphio.Morphology('my_neuron_file.h5'))

neuron = nm.load_neuron(io.StringIO('''((Dendrite)
                                       (3 -4 0 2)
                                       (3 -6 0 2)
                                       (3 -8 0 2)
                                       (3 -10 0 2)
                                       (
                                         (0 -10 0 2)
                                         (-3 -10 0 2)
                                         |
                                         (6 -10 0 2)
                                         (9 -10 0 2)
                                       )
                                       )'''), reader='asc')

neurom.io.utils.load_neurons(neurons, neuron_loader=<function load_neuron>, name=None, population_class=<class 'neurom.core.population.Population'>, ignored_exceptions=())[source]

Create a population object.

From all morphologies in a directory of from morphologies in a list of file names.

Parameters

• neurons – directory path or list of neuron file paths

• neuron_loader – function taking a filename and returning a neuron

• population_class – class representing populations

• name (str) – optional name of population. By default ‘Population’ or filepath basename depending on whether neurons is list or directory path respectively.

• ignored_exceptions (tuple) – NeuroM and MorphIO exceptions that you want to ignore when loading neurons.

Returns

neuron population object