Implementation of morphological interpolation along the z-axis for binarized images

morphological_interpolation.py

from typing import Union

import itk
import numpy as np
from yaspin import yaspin
from yaspin.spinners import Spinners

INTERPOLATION_TEXT = "Interpolating for the first time"


@yaspin(Spinners.bouncingBall, text=INTERPOLATION_TEXT)
def morphological_interpolation(
    labeled_stack: np.ndarray, stack_depth_spacing: Union[float, int]
):
    spacing_array = np.zeros(
        (round(stack_depth_spacing), *labeled_stack.shape[1:]),
        dtype=labeled_stack.dtype,
    )

    spaced_stack = []
    for xy_plane in labeled_stack:
        spaced_stack.append(np.expand_dims(xy_plane, axis=0))
        spaced_stack.append(spacing_array)
    spaced_stack.pop(-1)
    spaced_stack = np.concatenate(spaced_stack)
    spaced_stack.astype(labeled_stack.dtype, copy=False)

    return itk.GetArrayFromImage(
        itk.morphological_contour_interpolator(itk.GetImageFromArray(spaced_stack))
    )