#!/usr/bin/env python

import warnings

import numpy as np

from scipy import linalg

import glob

from skimage.util import dtype

from skimage.exposure import rescale_intensity

from skimage import img_as_ubyte

from multiprocessing import Pool

import os

import argparse

try:

from cv2 import imread

from cv2 import imwrite as imsave

except ImportError:

from skimage.io import imread

from skimage.io import imsave

warnings.filterwarnings('ignore')

# H&E

M2 = np.array([[0.6443186, 0.7166757, 0.26688856],

[0.09283128, 0.9545457, 0.28324],

[0.63595444, 0.001, 0.7717266]])

"""

# H&E2

M2 = np.array([[0.49, 0.760, 0.41],

[0.046, 0.84, 0.54],

[0.76, 0.001, 0.64]])

"""

D = linalg.inv(M2)

def loadData(file_name):

file_data = imread(file_name)

return file_data

def makeDeconv(image):

saveNewFile(np.reshape(stains, rgb.shape), os.path.basename(image))

def saveNewFile(new_file_data, name):

imsave(os.path.join(args.output, name), new_data)

if __name__ == '__main__':

cur_path = os.getcwd()

parser = argparse.ArgumentParser(description="color deconvolution")

parser.add_argument('-c', '--channel', type=str, choices=['h', 'e', 'd', 'hed'],

nargs='?', default='h', help='channel for save: '

'h: hematoxylin, '

'e: eosin, '

'd: dab, '

'hed: h + e + dab. '

'Default: %(default)s')

parser.add_argument('-r', '--regexp', type=str, nargs='?', default='*.png',

help='regulas expression for images name. '

'Default: %(default)s')

parser.add_argument('-o', '--output', type=str,

nargs='?', default=os.path.join(

cur_path, 'output'), help='output dir. '

'Default: %(default)s')

args = parser.parse_args()

images = sorted(glob.glob(os.path.join(cur_path, args.regexp)))

try:

os.makedirs(args.output)

except OSError:

pass

p = Pool(7)

p.map(makeDeconv, images)