get_neighbors_map#

get_neighbors_map(array: ndarray) → dict[source]#

Create map of region ids to lists of neighbors.

Each region id is also assigned a group number, where all regions in a given group are simply connected.

Parameters:

array – Segmentation array.

Returns:

Map of id to group and neighbor ids.

get_bounding_box(array: ndarray) → tuple[int, int, int, int, int, int][source]#

Find bounding box around array.

Bounds are calculated with a one-voxel border, if possible.

Parameters:

array – Segmentation array.

Returns:

The bounding box (xmin, xmax, ymin, ymax, zmin, zmax) indices

get_cropped_array(array: np.ndarray, label: int, labels: np.ndarray | None = None, *, crop_original: bool) → np.ndarray[source]#

Crop array around label region.

Parameters:

  • array – Array to crop.

  • label – Region label.

  • labels – Array of all region labels.

  • crop_original – True to crop the original array keeping all labels, False otherwise.

Returns:

Cropped array.