view colocalization_viz.py @ 3:9ccf11c11d85 draft default tip

"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 0500f513ee291ae0f6fad32a0b4fad05cd59cb71"

import argparse
import sys

import numpy as np
import skimage.color
import skimage.io
from skimage import img_as_uint
from skimage.exposure import equalize_adapthist


# TODO make importable by python script
def readImg(path):
    img = skimage.io.imread(path)

    if len(img.shape) > 2:
        img = skimage.color.rgb2gray(img)
    img = equalize_adapthist(img, clip_limit=0.03)
    img = img_as_uint(img)
    img = np.reshape(img, [img.shape[0], img.shape[1], 1])
    return img


parser = argparse.ArgumentParser()
parser.add_argument('input_file1', type=argparse.FileType('r'), default=sys.stdin, help='input file (red)')
parser.add_argument('input_file2', type=argparse.FileType('r'), default=sys.stdin, help='input file (green)')
parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
args = parser.parse_args()

im1 = readImg(args.input_file1.name)
im2 = readImg(args.input_file2.name)
res = np.concatenate((im1, im2, np.zeros_like(im1)), axis=-1)
skimage.io.imsave(args.out_file.name, res)