Mercurial > repos > imgteam > concat_channels

annotate 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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24d64e0a405f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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diff changeset
1 import argparse
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ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
imgteam
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ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
imgteam
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3 import giatools
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24d64e0a405f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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4 import numpy as np
24d64e0a405f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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5 import skimage.io
24d64e0a405f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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6 import skimage.util
24d64e0a405f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
imgteam
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9 normalized_axes = 'QTZYXC'
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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12 def concat_channels(
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
imgteam
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13 input_image_paths: list[str],
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
imgteam
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14 output_image_path: str,
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
imgteam
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15 axis: str,
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
imgteam
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16 preserve_values: bool,
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
imgteam
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17 ):
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
imgteam
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18 # Create list of arrays to be concatenated
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24d64e0a405f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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19 images = []
24d64e0a405f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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20 for image_path in input_image_paths:
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ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
imgteam
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22 img = giatools.Image.read(image_path, normalize_axes=normalized_axes)
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
imgteam
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23 arr = img.data
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
imgteam
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25 # Preserve values: Convert to `float` dtype without changing the values
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
imgteam
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26 if preserve_values:
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
imgteam
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27 arr = arr.astype(float)
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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29 # Preserve brightness: Scale values to 0..1
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
imgteam
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30 else:
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
imgteam
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31 arr = skimage.util.img_as_float(arr)
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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33 images.append(arr)
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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35 # Do the concatenation
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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36 axis_pos = normalized_axes.index(axis)
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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37 arr = np.concatenate(images, axis_pos)
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
imgteam
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38 res = giatools.Image(arr, normalized_axes)
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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40 # Squeeze singleton axes and save
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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41 squeezed_axes = ''.join(np.array(list(res.axes))[np.array(arr.shape) > 1])
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
imgteam
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42 res = res.squeeze_like(squeezed_axes)
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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43 res.write(output_image_path, backend='tifffile')
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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24d64e0a405f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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24d64e0a405f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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46 if __name__ == "__main__":
24d64e0a405f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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47 parser = argparse.ArgumentParser()
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ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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48 parser.add_argument('input_files', type=str, nargs='+')
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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49 parser.add_argument('out_file', type=str)
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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50 parser.add_argument('axis', type=str)
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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51 parser.add_argument('--preserve_values', default=False, action='store_true')
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24d64e0a405f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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52 args = parser.parse_args()
24d64e0a405f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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54 concat_channels(
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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55 args.input_files,
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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56 args.out_file,
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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57 args.axis,
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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58 args.preserve_values,
ad1caf2331c6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
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59 )