Mercurial > repos > imgteam > colocalization_viz

comparison colocalization_viz.py @ 1:fc85eb253163 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 1453917dfaf4c0922aec82c400015ff7e13ab737
author imgteam
date Mon, 22 Jul 2019 07:08:46 -0400
parents 9ddb11b272ee
children c73332d5c3bb
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0:9ddb11b272ee 1:fc85eb253163
1 import skimage.io 1 import skimage.io
2 import skimage.color 2 import skimage.color
3 from skimage import img_as_uint
4 from skimage.exposure import equalize_adapthist
3 import numpy as np 5 import numpy as np
4 import os 6 import argparse
5 import sys 7 import sys
6 import warnings
7 8
8 #TODO make importable by python script
9 9
10 args = sys.argv 10 # TODO make importable by python script
11
12 def readImg(path): 11 def readImg(path):
13 img = skimage.io.imread(path) 12 img = skimage.io.imread(path)
13
14 if len(img.shape) > 2: 14 if len(img.shape) > 2:
15 img = skimage.color.rgb2gray(img) 15 img = skimage.color.rgb2gray(img)
16 img = np.expand_dims(img > 0, 3) 16 img = equalize_adapthist(img, clip_limit=0.03)
17 img = img_as_uint(img)
18 img = np.reshape(img, [img.shape[0], img.shape[1], 1])
17 return img 19 return img
18 20
19 im1 = readImg(args[1])
20 im2 = readImg(args[2])
21 res = np.concatenate((im1, im2, np.zeros_like(im1)), axis=2) * 1.0
22 21
23 with warnings.catch_warnings(): 22 parser = argparse.ArgumentParser()
24 warnings.simplefilter("ignore") 23 parser.add_argument('input_file1', type=argparse.FileType('r'), default=sys.stdin, help='input file (red)')
25 skimage.io.imsave(args[3], res) 24 parser.add_argument('input_file2', type=argparse.FileType('r'), default=sys.stdin, help='input file (green)')
25 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
26 args = parser.parse_args()
27
28 im1 = readImg(args.input_file1.name)
29 im2 = readImg(args.input_file2.name)
30 res = np.concatenate((im1, im2, np.zeros_like(im1)), axis=-1)
31 skimage.io.imsave(args.out_file.name, res)