axon_synthesis.white_matter_recipe

Helpers for white matter recipe.

Functions

fetch(url, output_path[, file_path, ...])	Fetch the White Natter Recipe file from an internal repository.
get_atlas_region_id(region_map, pop_row, ...)	Get the ID of an atlas region.
load(white_matter_file)	Load the white matter recipe from YAML file.

Classes

WhiteMatterRecipe(path, *[, load])	Class to store the White Matter Recipe data.
WmrConfig(path, subregion_uppercase, ...)	Class to store the WhiteMatterRecipe configuration.

class axon_synthesis.white_matter_recipe.WhiteMatterRecipe(path, *, load=True)

Bases: BasePathBuilder

Class to store the White Matter Recipe data.

compute_probabilities(atlas: AtlasHelper)

Compute projection probabilities from the White Matter Recipe.

load()

Load the White Matter Recipe from the associated directory.

load_from_raw_wmr(config: WmrConfig, atlas: AtlasHelper)

Process the white matter recipe.

save()

Save the White Matter Recipe into the given directory.

class axon_synthesis.white_matter_recipe.WmrConfig(path, subregion_uppercase: bool, subregion_remove_prefix: bool, sub_region_separator: str)

Bases: object

Class to store the WhiteMatterRecipe configuration.

classmethod from_dict(data: dict) → Self

Create a new AtlasConfig object from a dictionary.

to_dict() → dict

Return all attribute values into a dictionary.

axon_synthesis.white_matter_recipe.fetch(url, output_path, file_path='white_matter_FULL_RECIPE_v1p20.yaml', version_reference=None)

Fetch the White Natter Recipe file from an internal repository.

axon_synthesis.white_matter_recipe.get_atlas_region_id(region_map, pop_row, col_name, second_col_name=None)

Get the ID of an atlas region.

axon_synthesis.white_matter_recipe.load(white_matter_file: str | PathLike) → dict

Load the white matter recipe from YAML file.