mask_histo_images.py

import glob
import matplotlib.pyplot as plt
import numpy as np
import skimage.io as io
import mahotas as mht
import os
import ntpath
import sys


MASK_VAL = 255

def apply_masks(imgtiles,masktiles,outtiles):
    #IMGTILES: folder where the histology img tiles are located
    #MASKTILES: folder where the mask tiles are located
    #OUTTILES: folder where masked images are saved

    files_mask = glob.glob(os.path.join(masktiles,'*.tif'))
    files_img = glob.glob(os.path.join(imgtiles,'*.tif'))

    nMasks = len(files_mask)
    nImgs = len(files_img)

    if nMasks != nImgs:
        print("Error: the number of masks and images must match.")
        return
    else:
        print("Found " + str(nImgs) + " images to mask.")

    for f in range(nMasks):
        img_file = os.path.join(imgtiles,files_img[f])
        base_name = ntpath.basename(img_file)
        mask_file = os.path.join(masktiles,'mask_'+base_name)
        mask = io.imread(mask_file)
        img = io.imread(img_file)
        if not (mask.shape[0] == img.shape[0] and mask.shape[1] == mask.shape[1]):
            tmp = mht.imresize(mask,(img.shape[0],img.shape[1]))
            tmp[tmp < 1] = 0
            tmp[tmp > 0] = 255
            mask = tmp.astype('ubyte')


        size = img.shape[0:2]

        R = img[...,0].copy()
        G = img[...,1].copy()
        B = img[...,2].copy()

        R[mask < MASK_VAL] = 0
        G[mask < MASK_VAL] = 0
        B[mask < MASK_VAL] = 0

        R = R.reshape([size[0],size[1],1])
        G = G.reshape([size[0],size[1],1])
        B = B.reshape([size[0],size[1],1])

        img2 = np.concatenate((R,G,B),axis=2)

        out_file = os.path.join(outtiles,base_name)
        #io.imsave(out_file,img2)
        mht.imsave(out_file,img2)
        print("File " + base_name + " saved.")


def main():

    if len(sys.argv) != 4:
        print('Usage: smask_images <img tiles folder> <mask tiles folder> <segmented tiles folder>')
        print('Example: seg_background /AVID/AV13/AT100#440/tiles AVID/AV13/AT100#440/tiles_mask AVID/AV13/AT100#440/tiles_seg')
        exit()

    imgdir = str(sys.argv[1])
    maskdir = str(sys.argv[2])
    outdir = str(sys.argv[3])

    #maskdir = '/Volumes/SUSHI_HD/SUSHI/AVID/AV13/AT100#440/tiles_mask'
    #imgdir = '/Volumes/SUSHI_HD/SUSHI/AVID/AV13/AT100#440/tiles'
    #outdir = '/Volumes/SUSHI_HD/SUSHI/AVID/AV13/AT100#440/tiles_seg'

    apply_masks(imgdir,maskdir,outdir)

    print('Images were successfully processed.')

if __name__ == '__main__':
    main()