Mercurial > repos > imgteam > concat_channels

comparison concat_channels.py @ 0:30517f733f7b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:33:14 -0500
parents
children d42501109c05
comparison
equal deleted inserted replaced
-1:000000000000 0:30517f733f7b
1 import argparse
2 import sys
3 import warnings
4 import numpy as np
5 import skimage.io
6 import skimage.util
7
8 def concat_channels(input_image_paths, output_image_path, axis):
9 images = []
10 for image_path in input_image_paths:
11 raw_image = skimage.io.imread(image_path)
12 if len(raw_image.shape) == 2:
13 if axis == 0:
14 raw_image = [raw_image]
15 else:
16 raw_image = np.expand_dims(raw_image, 2)
17 images.append(raw_image)
18 res = np.concatenate(images, axis)
19 with warnings.catch_warnings():
20 warnings.simplefilter("ignore")
21 res = skimage.util.img_as_uint(res) #Attention: precision loss
22 skimage.io.imsave(output_image_path, res, plugin='tifffile')
23
24 if __name__ == "__main__":
25 parser = argparse.ArgumentParser()
26 parser.add_argument('input_files', type=argparse.FileType('r'), nargs='+', help='input file')
27 parser.add_argument('-o', dest='out_file', type=argparse.FileType('w'), help='out file (TIFF)')
28 parser.add_argument('--axis', dest='axis', type=int, default=0, choices=[0,2], help='concatenation axis')
29 args = parser.parse_args()
30
31 # print([x.name for x in args.input_files], args.out_file.name, args.axis)
32 concat_channels([x.name for x in args.input_files], args.out_file.name, args.axis)
33 # concat_channels(args.input_files, args.out_file, args.axis)