Source code for phenotypic.detect._otsu_detector

from __future__ import annotations

from typing import TYPE_CHECKING

if TYPE_CHECKING:
    from phenotypic import Image
from skimage.filters import threshold_otsu
from skimage.segmentation import clear_border

from ..abc_ import ThresholdDetector




class OtsuDetector(ThresholdDetector):
    """Class for applying Otsu's thresholding to an image.

    This class inherits from the `ThresholdDetector` and provides the functionality
    to apply Otsu's thresholding method on the enhance matrix (`enh_gray`) of an
    arr image. The operation generates a binary mask (`objmask`) depending on the
    computed threshold other_image.

    Methods:
        apply: Applies Otsu's thresholding on the arr image object and modifies its
            omask attribute accordingly.

    """

    def __init__(self, ignore_zeros: bool = True, ignore_borders: bool = True):
        self.ignore_zeros = ignore_zeros
        self.ignore_borders = ignore_borders

    def _operate(self, image: Image) -> Image:
        """Binarizes the given image matrix using the Otsu threshold method.

        This function modifies the arr image by applying a binary mask to
        its enhanced matrix (`enh_gray`). The binarization threshold is
        automatically determined using Otsu's method. The resulting binary
        mask is stored in the image's `objmask` attribute.

        Args:
            image (Image): The arr image object. It must have an `enh_gray`
                attribute, which is used as the basis for creating the binary mask.

        Returns:
            Image: The arr image object with its `objmask` attribute updated
                to the computed binary mask other_image.
        """
        enh_matrix = image.enh_gray[:]
        nbins = 2 ** int(image.bit_depth)
        mask = image.enh_gray[:] >= threshold_otsu(
            enh_matrix[enh_matrix != 0] if self.ignore_zeros else enh_matrix,
            nbins=nbins,
        )
        mask = clear_border(mask) if self.ignore_borders else mask
        image.objmask = mask
        return image



# Set the docstring so that it appears in the sphinx documentation
OtsuDetector.apply.__doc__ = OtsuDetector._operate.__doc__