Delete smaller artifacts from a single object binary image volume

clean_3d_mask.py

from typing import Iterable

from scipy.ndimage import label, find_objects


def volume_from_slices(*slices: Iterable[slice]):
    volume = 1
    for comp_slice in slices:
        volume *= (comp_slice.stop - comp_slice.start)
    return volume


def clean_smaller_artifacts(image_volume):
    labeled, num_features = label(image_volume)

    object_slice_sequence = find_objects(labeled)
    size_to_label = {
        volume_from_slices(*slices): label for label, slices in zip(range(1, num_features + 1), object_slice_sequence)
    }
    max_size = max(size_to_label)
    max_label = size_to_label[max_size]
    return labeled[object_slice_sequence[max_label - 1]] == max_label