HistoQC/DeconvolutionModule.py at master · Pacific89/HistoQC · GitHub

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import logging
import os
import sys
import numpy as np
from skimage import io, color, img_as_ubyte
from skimage.exposure import rescale_intensity
from skimage.color import separate_stains
from skimage.color import hed_from_rgb, hdx_from_rgb, fgx_from_rgb, bex_from_rgb, rbd_from_rgb
from skimage.color import gdx_from_rgb, hax_from_rgb, bro_from_rgb, bpx_from_rgb, ahx_from_rgb, \
    hpx_from_rgb  # need to load all of these in case the user selects them
from distutils.util import strtobool

import matplotlib.pyplot as plt


def seperateStains(s, params):
    logging.info(f"{s['filename']} - \tseperateStains")
    stain = params.get("stain", "")
    use_mask = strtobool(params.get("use_mask", "True"))

    if stain == "":
        logging.error(f"{s['filename']} - stain not set in DeconvolutionModule.seperateStains")
        sys.exit(1)
        return

    stain_matrix = getattr(sys.modules[__name__], stain, "")

    if stain_matrix == "":
        logging.error(f"{s['filename']} - Unknown stain matrix specified in DeconolutionModule.seperateStains")
        sys.exit(1)
        return

    mask = s["img_mask_use"]

    if use_mask and len(mask.nonzero()[0]) == 0: #-- lets just error check at the top if mask is empty and abort early
        for c in range(3):
            s.addToPrintList(f"deconv_c{c}_std", str(-100))
            s.addToPrintList(f"deconv_c{c}_mean", str(-100))
            io.imsave(s["outdir"] + os.sep + s["filename"] + f"_deconv_c{c}.png", img_as_ubyte(np.zeros(mask.shape)))

        logging.warning(f"{s['filename']} - DeconvolutionModule.seperateStains: NO tissue "
                             f"remains detectable! Saving Black images")
        s["warnings"].append(f"DeconvolutionModule.seperateStains: NO tissue "
                             f"remains detectable! Saving Black images")

        return

    img = s.getImgThumb(s["image_work_size"])
    dimg = separate_stains(img, stain_matrix)

    for c in range(0, 3):
        dc = dimg[:, :, c]

        if use_mask:
            dc_sub = dc[mask]
            dc_min = dc_sub.min()
            dc_max = dc_sub.max()

            s.addToPrintList(f"deconv_c{c}_mean", str(dc_sub.mean()))
            s.addToPrintList(f"deconv_c{c}_std", str(dc_sub.std()))
        else:
            mask = 1.0
            dc_min = dc.min()
            dc_max = dc.max()

            s.addToPrintList(f"deconv_c{c}_mean", str(dc.mean()))
            s.addToPrintList(f"deconv_c{c}_std", str(dc.std()))

        dc = (dc - dc_min) / float(dc_max - dc_min) * mask
        io.imsave(s["outdir"] + os.sep + s["filename"] + f"_deconv_c{c}.png", img_as_ubyte(dc))

    return