Mercurial > repos > imgteam > concat_channels

comparison concat_channels.py @ 2:212627bfb759 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:10:47 +0000
parents d42501109c05
children 4c43875c790c
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1:d42501109c05 2:212627bfb759
1 import argparse 1 import argparse
2 import sys
3 import warnings 2 import warnings
3
4 import numpy as np 4 import numpy as np
5 import skimage.io 5 import skimage.io
6 import skimage.util 6 import skimage.util
7
7 8
8 def concat_channels(input_image_paths, output_image_path, axis): 9 def concat_channels(input_image_paths, output_image_path, axis):
9 images = [] 10 images = []
10 for image_path in input_image_paths: 11 for image_path in input_image_paths:
11 raw_image = skimage.io.imread(image_path) 12 raw_image = skimage.io.imread(image_path)
12 if len(raw_image.shape) == 2: 13 if len(raw_image.shape) == 2:
13 if axis == 0: 14 if axis == 0:
14 raw_image = [raw_image] 15 raw_image = [raw_image]
15 else: 16 else:
16 raw_image = np.expand_dims(raw_image, 2) 17 raw_image = np.expand_dims(raw_image, 2)
17 images.append(raw_image) 18 images.append(raw_image)
18 res = np.concatenate(images, axis) 19 res = np.concatenate(images, axis)
19 with warnings.catch_warnings(): 20 with warnings.catch_warnings():
20 warnings.simplefilter("ignore") 21 warnings.simplefilter("ignore")
21 res = skimage.util.img_as_uint(res) #Attention: precision loss 22 res = skimage.util.img_as_uint(res) # Attention: precision loss
22 skimage.io.imsave(output_image_path, res, plugin='tifffile') 23 skimage.io.imsave(output_image_path, res, plugin='tifffile')
24
23 25
24 if __name__ == "__main__": 26 if __name__ == "__main__":
25 parser = argparse.ArgumentParser() 27 parser = argparse.ArgumentParser()
26 parser.add_argument('input_files', type=argparse.FileType('r'), nargs='+', help='input file') 28 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)') 29 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') 30 parser.add_argument('--axis', dest='axis', type=int, default=0, choices=[0, 2], help='concatenation axis')
29 args = parser.parse_args() 31 args = parser.parse_args()
30 32
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([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)