axon_synthesis.inputs

Define the class to store the inputs.

Classes

Inputs(path[, morphology_path, ...])

Class to store the Inputs.

class axon_synthesis.inputs.Inputs(path: str | PathLike, morphology_path: str | PathLike | None = None, *, pop_probability_path: str | PathLike | None = None, proj_probability_path: str | PathLike | None = None, brain_regions_mask_path: str | PathLike | None = None, neuron_density: float | None = None, **kwargs)

Bases: BasePathBuilder

Class to store the Inputs.

property brain_regions_mask_file

Return the brain_regions_mask_file attribute or load if it’s None.

compute_atlas_region_masks()

Compute all region masks of the Atlas.

compute_probabilities(source='WMR', *, export=True)

Compute projection probabilities.

export_probabilities()

Export the computed probabilities.

classmethod load(path: str | PathLike | None, atlas_config: AtlasConfig | AtlasHelper | None = None, **kwargs: dict) → Self

Load all the inputs from the given path.

load_atlas(atlas_config=None)

Load the Atlas.

load_brain_regions_masks()

Load the brain region masks.

load_clustering_data(file_selection=FILE_SELECTION.REQUIRED_ONLY, **kwargs)

Load the Atlas.

load_metadata()

Load the metadata.

load_probabilities(**kwargs)

Load the population and projection probabilities.

load_tuft_params_and_distrs(**kwargs)

Load and validate the parameters and distributions used to generate the tufts.

load_wmr(wmr_config: WmrConfig | None = None)

Load the Atlas.

property metadata: dict

Return the metadata and automatically update them when an atlas is added.

metadata_to_attributes()

Propagate metadata to attributes.

property pop_neuron_numbers

Load the population numbers.

save_metadata()

Save the metadata.

unload_brain_regions_masks()

Unload the brain region masks.