axon_synthesis.validation.mimic

Validation workflow that mimics inputs morphologies.

Functions

create_cell_collection(morphology_dir[, ...])	Create a CellCollection object from a directory containing morphologies.
create_probabilities(cells_df, tuft_properties)	Create the population and projection probabilities.
export_cells_df(cells_df, path)	Export cells DF for future debugging.
merge_result_folders(results, output_path)	Create a new folder with simlinks to all result sub-folders.
mimic_axons(morphology_dir, ...[, ...])	Synthesize mimicking axons.
mimic_preferred_regions_workflow(morph, ...)	Synthesize axons using morphology preferred regions.
run_workflows(data, workflows, ...[, ...])	Run all the workflows on each morphology.
update_cells(cells_df, projection_probabilities)	Update the cell collection according to the computed projection probabilities.
workflow_col_name(name)	Create a column name based on a workflow name.

axon_synthesis.validation.mimic.create_cell_collection(morphology_dir, output_path: str | PathLike | None = None, convert_to: str | PathLike | None = None, *, recenter: bool = True) → CellCollection

Create a CellCollection object from a directory containing morphologies.

axon_synthesis.validation.mimic.create_probabilities(cells_df, tuft_properties)

Create the population and projection probabilities.

axon_synthesis.validation.mimic.export_cells_df(cells_df, path)

Export cells DF for future debugging.

axon_synthesis.validation.mimic.merge_result_folders(results, output_path)

Create a new folder with simlinks to all result sub-folders.

axon_synthesis.validation.mimic.mimic_axons(morphology_dir: str | PathLike, clustering_parameters: dict, *, tuft_parameters_file: str | PathLike | None = None, create_graph_config: CreateGraphConfig | None = None, post_process_config: PostProcessConfig | None = None, output_config: OutputConfig | None = None, workflows: list[str] | None = None, voxel_dimensions: int | None = None, rng: None | int | Sequence[int] | SeedSequence | BitGenerator | Generator = None, debug: bool = False, parallel_config: ParallelConfig | None = None, keep_tmp_atlas: bool = False, merge_results: bool = True)

Synthesize mimicking axons.

axon_synthesis.validation.mimic.mimic_preferred_regions_workflow(morph, voxel_dimensions, synthesis_config, create_graph_config, post_process_config, output_config, rng, *, keep_tmp_atlas=False)

Synthesize axons using morphology preferred regions.

axon_synthesis.validation.mimic.run_workflows(data, workflows, synthesis_config, create_graph_config, post_process_config, output_config, rng, *, voxel_dimensions=None, keep_tmp_atlas=False)

Run all the workflows on each morphology.

axon_synthesis.validation.mimic.update_cells(cells_df, projection_probabilities)

Update the cell collection according to the computed projection probabilities.

axon_synthesis.validation.mimic.workflow_col_name(name)

Create a column name based on a workflow name.