Mercurial > repos > imgteam > concat_channels

comparison concat_channels.py @ 2:ad1caf2331c6 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
author imgteam
date Sun, 07 Dec 2025 16:15:54 +0000
parents 31c8c700d98d
children 01c1d5af33be
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1:31c8c700d98d 2:ad1caf2331c6
1 import argparse 1 import argparse
2 import sys 2
3 import warnings 3 import giatools
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 def concat_channels(input_image_paths, output_image_path, axis): 8
9 normalized_axes = 'QTZYXC'
10
11
12 def concat_channels(
13 input_image_paths: list[str],
14 output_image_path: str,
15 axis: str,
16 preserve_values: bool,
17 ):
18 # Create list of arrays to be concatenated
9 images = [] 19 images = []
10 for image_path in input_image_paths: 20 for image_path in input_image_paths:
11 raw_image = skimage.io.imread(image_path) 21
12 if len(raw_image.shape) == 2: 22 img = giatools.Image.read(image_path, normalize_axes=normalized_axes)
13 if axis == 0: 23 arr = img.data
14 raw_image = [raw_image] 24
15 else: 25 # Preserve values: Convert to `float` dtype without changing the values
16 raw_image = np.expand_dims(raw_image, 2) 26 if preserve_values:
17 images.append(raw_image) 27 arr = arr.astype(float)
18 res = np.concatenate(images, axis) 28
19 with warnings.catch_warnings(): 29 # Preserve brightness: Scale values to 0..1
20 warnings.simplefilter("ignore") 30 else:
21 res = skimage.util.img_as_uint(res) #Attention: precision loss 31 arr = skimage.util.img_as_float(arr)
22 skimage.io.imsave(output_image_path, res, plugin='tifffile') 32
33 images.append(arr)
34
35 # Do the concatenation
36 axis_pos = normalized_axes.index(axis)
37 arr = np.concatenate(images, axis_pos)
38 res = giatools.Image(arr, normalized_axes)
39
40 # Squeeze singleton axes and save
41 squeezed_axes = ''.join(np.array(list(res.axes))[np.array(arr.shape) > 1])
42 res = res.squeeze_like(squeezed_axes)
43 res.write(output_image_path, backend='tifffile')
44
23 45
24 if __name__ == "__main__": 46 if __name__ == "__main__":
25 parser = argparse.ArgumentParser() 47 parser = argparse.ArgumentParser()
26 parser.add_argument('input_files', type=argparse.FileType('r'), nargs='+', help='input file') 48 parser.add_argument('input_files', type=str, nargs='+')
27 parser.add_argument('-o', dest='out_file', type=argparse.FileType('w'), help='out file (TIFF)') 49 parser.add_argument('out_file', type=str)
28 parser.add_argument('--axis', dest='axis', type=int, default=0, choices=[0,2], help='concatenation axis') 50 parser.add_argument('axis', type=str)
51 parser.add_argument('--preserve_values', default=False, action='store_true')
29 args = parser.parse_args() 52 args = parser.parse_args()
30 53
31 # print([x.name for x in args.input_files], args.out_file.name, args.axis) 54 concat_channels(
32 concat_channels([x.name for x in args.input_files], args.out_file.name, args.axis) 55 args.input_files,
33 # concat_channels(args.input_files, args.out_file, args.axis) 56 args.out_file,
57 args.axis,
58 args.preserve_values,
59 )