axon_synthesis.atlas

Helpers for atlas.

Classes

AtlasConfig(path[, region_filename, ...])

Class to store the Atlas configuration.

AtlasHelper(config[, logger])

Atlas helper.
class axon_synthesis.atlas.AtlasConfig(path, region_filename=PosixPath('brain_regions'), layer_names: list[int | str] | None = None, load_region_map: bool = False, outside_region_id: int = 0, use_boundary: bool = True)

Bases: object

Class to store the Atlas configuration.

path

The path to the directory containing the atlas.

Type:

pathlib.Path

region_filename

The name of the file containing the brain regions.

Type:

pathlib.Path

layer_names

The list of layer names.

Type:

list[int | str] | None

load_region_map

Trigger for region map loading.

Type:

bool

outside_region_id

The brain region ID of the outside of the brain.

Type:

int

use_boundary

Trigger to use the boundary or not.

Type:

bool

classmethod from_dict(data: dict) → Self

Create a new AtlasConfig object from a dictionary.

to_dict() → dict

Return all attribute values into a dictionary.

class axon_synthesis.atlas.AtlasHelper(config: AtlasConfig, logger=None)

Bases: object

Atlas helper.

property brain_regions_and_ascendants: DataFrame

Return the brain regions and their ascendants from the hierarchy.

property brain_regions_and_descendants: DataFrame

Return the brain regions and their descendants from the hierarchy.

build_boundary(logger=None)

Build the boundary orientations.

compute_region_masks(output_path: str | PathLike)

Compute all region masks.

copy()

Return a copy of the current atlas.

get_hemisphere(coord: list[number] | ndarray[Any, dtype[number]], h_axis: int = 2, h_origin: str = 'L') → str

Return the hemisphere of the given coordinate.

Parameters:

  • coord – The coordinate of the point.

  • h_axis – The axis along which to check the hemisphere.

  • h_origin – The origin of the hemisphere (‘L’ or ‘R’).

Returns:

The hemisphere of the given coordinate, ‘L’ or ‘R’.

get_random_voxel_shifts(size, *, rng: None | int | Sequence[int] | SeedSequence | BitGenerator | Generator = None)

Pick random shifts from voxel centers according to the voxel sizes.

get_region_ids(brain_region_names: int | str | list[int | str], *, with_descendants: bool = True) → tuple[list[str | int], list[str | int]]

Find brain region IDs from their names, acronyms or direct IDs.

Parameters:

  • brain_region_names – The names of the brain regions to get IDs.

  • with_descendants – If set to True, all the descendants are included.

get_region_points(brain_region_names: int | str | list[int | str], *, size: int | None = None, random_shifts: bool = False, inverse: bool = False, rng: None | int | Sequence[int] | SeedSequence | BitGenerator | Generator = None) → ndarray | tuple[ndarray, list[str | int]]

Extract region points from the atlas.

If ‘random_shifts’ is set to False (the default), the voxel centers are returned. If ‘random_shifts’ is set to True, one random point inside each of these voxels (chosen using the given Random Number Generator) are returned.

Parameters:

  • brain_region_names – The name of the regions to consider.

  • size – The number of points to return (they are chosen randomly along the possible ones).

  • random_shifts – If True, a random shift is applied to return a random point inside the voxel.

  • inverse – If True, choose points that are NOT located in the given regions.

  • rng – The random number generator (can be an int used as seed or a numpy Generator).

get_region_voxels(brain_region_names: int | str | list[int | str], *, inverse: bool = False) → ndarray | tuple[ndarray, list[str | int]]

Get the coordinates of the voxels located in the given regions from the atlas.

property pia_coord: VoxelData

Return an atlas of the pia coordinate along the principal axis.

place_point_in_hemisphere(coord: list[number] | ndarray[Any, dtype[number]], hemisphere: str, h_axis: int = 2, h_origin: str = 'L') → list[number] | ndarray[Any, dtype[number]]

Place the point in the given hemisphere.

If the point is already in the given hemisphere, nothing is done. If the point is in the opposite hemisphere, an axial symmetry of axis h_axis is performed.

Parameters:

  • coord – The coordinate of the point.

  • hemisphere – The hemisphere where the point should be (‘L’ or ‘R’).

  • h_axis – The axis along which to check the hemisphere.

  • h_origin – The origin of the hemisphere (‘L’ or ‘R’).

Returns:

The coordinate of the point in the given hemisphere.

property region_map

Return the region map.

property region_map_df

Return the DF representation of the region map.

save(path)

Export the atlas to the given directory.