tmd.io.io¶

Python module that contains the functions about reading and writing files.

Functions

`load_neuron`(input_file[, line_delimiter, ...])	I/O method to load an swc or h5 file into a Neuron object.
`load_neuron_from_morphio`(path_or_obj[, ...])	Create Neuron object from morphio object or from path loaded via morphio.
`load_population`(neurons[, user_tree_types, ...])	Load all data of recognised format (swc, h5) into a Population object.
`make_tree`(data)	Make tree structure from loaded data.
`redefine_types`([user_types])	Return tree types depending on the customized types selected by the user.

Exceptions

Captures the exception of failing to load a single neuron.

exception tmd.io.io.LoadNeuronError¶

Bases: TmdError

Captures the exception of failing to load a single neuron.

tmd.io.io.load_neuron(input_file, line_delimiter='\n', soma_type=None, user_tree_types=None, remove_duplicates=True)¶: I/O method to load an swc or h5 file into a Neuron object.

tmd.io.io.load_neuron_from_morphio(path_or_obj, user_tree_types=None)¶

Create Neuron object from morphio object or from path loaded via morphio.

Supported file formats: h5, swc, asc.

Parameters:: path_or_obj (Union[str, morphio.Morphology]) – Filepath or morphio object
Returns:: tmd Neuron object
Return type:: neuron (Neuron)

tmd.io.io.load_population(neurons, user_tree_types=None, name=None, use_morphio=False)¶

Load all data of recognised format (swc, h5) into a Population object.

Takes as input a directory or a list of files to load.

tmd.io.io.redefine_types(user_types=None)¶

Return tree types depending on the customized types selected by the user.