atlannot.merge_original.fine module¶

The fine merging of the annotation atlases.

atlannot.merge_original.fine.explore_voxel(origin, data, count=-1)[source]¶

Explore a given voxel.

Ask Dimitri for more details.

Parameters:

origin (sequence) – A triplet with the (x, y, z) coordinates of the origin voxel.
data (np.ndarray) – A 3D array with the volume data.
count (int) – Maximal number of iterations.

Returns:

value – The value of some voxel in the data volume.

Return type:

int

atlannot.merge_original.fine.fine_merge(annotation, annotation2, brain_regions)[source]¶

Perform the coarse atlas merging.

Parameters:

annotation (np.ndarray) – The first atlas to merge, usually CCFv2
annotation2 (np.ndarray) – The second atlas to merge, usually CCFv3
brain_regions (dict) – The brain regions dictionary. Can be obtained from the “msg” key of the brain_regions.json (1.json) file.

Returns: