run_seg_background_v2.py

import sys
import skimage.io as io
from skimage import color
from skimage import filters as filt
from skimage import morphology as morph
# import mahotas as mht
import numpy as np
import matplotlib.pyplot as plt
from skimage import img_as_ubyte


def seg_background(img,segname, outname):
    #IMG: RGB image
    #OUTNAME: mask file full path

    #create mask
    #lab = color.rgb2lab(img) #for old tau staining
    #B = lab[...,2] #for old tau staining
    B = img[..., 2] #for new tau staining
    B = np.fabs(B)
    #level = filt.threshold_triangle(B)
    level = filt.threshold_otsu(B) 
    # level = filt.threshold_isodata(B)
    # level = filt.threshold_li(B)
    # level = filt.threshold_mean(B)
    # level = filt.threshold_minimum(B)
    # level = filt.threshold_niblack(B)
    # level = filt.threshold_sauvola(B)
    # level = filt.threshold_yen(B)
    # mask = B > level #for old tau staining
    mask = B < level #for new tau staining
    se = morph.disk(5)
    mask2 = morph.opening(mask,se)
    # mask2 = mht.open(mask,se) 
    se2 = morph.disk(3)
    mask3 = morph.erosion(mask2, se2)
    # mask3 = mht.erode(mask2,se2)
    mask4 = mask3*255
    io.imsave(outname,mask4.astype('ubyte'))
    print('Mask {} successfully saved.'.format(outname))

    if segname: #if segname not empty
        #segment image
        gry = color.rgb2gray(img[:,:,:3])
        gry = img_as_ubyte(gry)
        gry[mask3 == False] = 0
        io.imsave(segname,gry)
        print('BW image {} successfully saved.'.format(segname))




def run_seg_background(imgname,segname, outname):
    img = io.imread(imgname)
    seg_background(img, segname, outname)

def main():

    if len(sys.argv) != 4 and len(sys.argv) != 3:
        print('Usage: seg_background <rescaled histo> [<seg_img>] <mask>')
        print('Example: seg_background /AVID/AV13/AT100#440/res_10.tif /AVID/AV13/AT100#440/seg_res_10.tif /AVID/AV13/AT100#440/mask_res_10.tif')
        exit()

        #imgname = "/Volumes/SUSHI_HD/SUSHI/AVID/AV13/AT100#440/res_10.tif"
        #outname = "/Volumes/SUSHI_HD/SUSHI/AVID/AV13/AT100#440/mask_res_10.tif"

    if len(sys.argv) == 4:
        imgname = str(sys.argv[1]) #abs path to where the images are
        segname = str(sys.argv[2])
        outname = str(sys.argv[3]) #row size
    elif len(sys.argv) == 3:
        imgname = str(sys.argv[1]) #abs path to where the images are
        segname = []
        outname = str(sys.argv[2]) #row size

    # img = io.imread(imgname)
    # seg_background(img, segname, outname)
    run_seg_background(imgname, segname, outname)




if __name__ == '__main__':
    main()