Mercurial > repos > imgteam > concat_channels

annotate concat_channels.py @ 3:4c43875c790c draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:25:29 +0000
parents 212627bfb759
children 2592a29a785e
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30517f733f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
1 import argparse
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212627bfb759 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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30517f733f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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3 import numpy as np
30517f733f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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4 import skimage.io
30517f733f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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5 import skimage.util
30517f733f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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212627bfb759 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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4c43875c790c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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8 def concat_channels(input_image_paths, output_image_path, axis, preserve_values):
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30517f733f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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9 images = []
30517f733f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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10 for image_path in input_image_paths:
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4c43875c790c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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30517f733f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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12 raw_image = skimage.io.imread(image_path)
30517f733f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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13 if len(raw_image.shape) == 2:
30517f733f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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14 if axis == 0:
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212627bfb759 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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15 raw_image = [raw_image]
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30517f733f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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16 else:
30517f733f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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17 raw_image = np.expand_dims(raw_image, 2)
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4c43875c790c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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4c43875c790c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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19 # Preserve values: Convert to `float` dtype without changing the values
4c43875c790c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 2
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20 if preserve_values:
4c43875c790c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 2
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21 raw_image = raw_image.astype(float)
4c43875c790c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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4c43875c790c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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23 # Preserve brightness: Scale values to 0..1
4c43875c790c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 2
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24 else:
4c43875c790c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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25 raw_image = skimage.util.img_as_float(raw_image)
4c43875c790c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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30517f733f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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27 images.append(raw_image)
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4c43875c790c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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4c43875c790c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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29 # Do the concatenation and save
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30517f733f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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30 res = np.concatenate(images, axis)
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4c43875c790c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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31 skimage.io.imsave(output_image_path, res, plugin='tifffile')
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30517f733f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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212627bfb759 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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30517f733f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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34 if __name__ == "__main__":
30517f733f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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35 parser = argparse.ArgumentParser()
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4c43875c790c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 2
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36 parser.add_argument('input_files', type=argparse.FileType('r'), nargs='+')
4c43875c790c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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37 parser.add_argument('-o', dest='out_file', type=argparse.FileType('w'))
4c43875c790c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 2
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38 parser.add_argument('--axis', dest='axis', type=int, default=0, choices=[0, 2])
4c43875c790c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 2
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39 parser.add_argument('--preserve_values', default=False, action='store_true')
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30517f733f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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40 args = parser.parse_args()
30517f733f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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4c43875c790c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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42 concat_channels([x.name for x in args.input_files], args.out_file.name, args.axis, args.preserve_values)