atlannot.merge.fine module

The fine merging of the annotation atlases.

This is the refactored and optimized version of atlas_merge.fine. It uses RegionMeta instead of JSONread and greatly speeds up the merging by optimizing a number of steps. The original logic was designed by Dimitri Rodarie.

atlannot.merge.fine.explore_voxel(start_pos: tuple, masked_atlas: MaskedArray, *, count: int = -1) → int[source]

Explore a given voxel.

Ask Dimitri for more details.

Seems like this is a BFS until a voxel with a different value is found or the maximal number of new voxels were seen.

Parameters:

  • start_pos – A triplet with the (x, y, z) coordinates of the starting voxel.

  • masked_atlas – A masked 3D array with the volume data.

  • count – Maximal number of iterations. A negative value means no limit on the number of iterations.

Returns:

The value of some voxel in the data volume.

Return type:

int

atlannot.merge.fine.manual_relabel_1(ids_v2: ndarray, ids_v3: ndarray) → None[source]

Perform a manual re-labeling step on the CCFv2 and CCFv3 atlases.

The replacements were compiled by Dimitri Rodarie.

Parameters:

  • ids_v2 – The (unique) region IDs of the CCFv2 atlas.

  • ids_v3 – The (unique) region IDs of the CCFv3 atlas.

atlannot.merge.fine.manual_relabel_2(ids_v2: ndarray, ids_v3: ndarray) → None[source]

Perform a manual re-labeling step on the CCFv2 and CCFv3 atlases.

The replacements were compiled by Dimitri Rodarie.

Parameters:

  • ids_v2 – The (unique) region IDs of the CCFv2 atlas.

  • ids_v3 – The (unique) region IDs of the CCFv3 atlas.

atlannot.merge.fine.merge(ccfv2: np.ndarray, ccfv3: np.ndarray, rm: RegionMeta) → tuple[np.ndarray, np.ndarray][source]

Perform the coarse atlas merging.

Parameters:

  • ccfv2 – The first atlas to merge, usually CCFv2

  • ccfv3 – The second atlas to merge, usually CCFv3

  • rm – The brain region metadata. Usually constructed as follows: RegionMeta.from_dict(brain_regions), where brain_regions can be obtained from the “msg” key of the brain_regions.json (1.json) file.

Returns:

  • ccfv2_new (np.ndarray) – The merged CCFv2 atlas.

  • ccfv3_new (np.ndarray) – The merged CCFv3 atlas.