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annotate repeat_channels.py @ 0:7cdb50fee601 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
author imgteam
date Thu, 25 Apr 2024 10:57:53 +0000
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7cdb50fee601 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
imgteam
parents:
diff changeset
1 import argparse
7cdb50fee601 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
imgteam
parents:
diff changeset
2
7cdb50fee601 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
imgteam
parents:
diff changeset
3 import giatools.io
7cdb50fee601 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
imgteam
parents:
diff changeset
4 import numpy as np
7cdb50fee601 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
imgteam
parents:
diff changeset
5 import skimage.io
7cdb50fee601 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
imgteam
parents:
diff changeset
6
7cdb50fee601 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
imgteam
parents:
diff changeset
7
7cdb50fee601 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
imgteam
parents:
diff changeset
8 if __name__ == '__main__':
7cdb50fee601 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
imgteam
parents:
diff changeset
9
7cdb50fee601 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
imgteam
parents:
diff changeset
10 parser = argparse.ArgumentParser()
7cdb50fee601 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
imgteam
parents:
diff changeset
11 parser.add_argument('input', type=str)
7cdb50fee601 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
imgteam
parents:
diff changeset
12 parser.add_argument('count', type=int)
7cdb50fee601 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
imgteam
parents:
diff changeset
13 parser.add_argument('output', type=str)
7cdb50fee601 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
imgteam
parents:
diff changeset
14 args = parser.parse_args()
7cdb50fee601 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
imgteam
parents:
diff changeset
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7cdb50fee601 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
imgteam
parents:
diff changeset
16 im = giatools.io.imread(args.input)
7cdb50fee601 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
imgteam
parents:
diff changeset
17 im = np.squeeze(im)
7cdb50fee601 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
imgteam
parents:
diff changeset
18 im = np.dstack([im] * args.count)
7cdb50fee601 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ commit 60cf803236ef94f414056823688e6fd008b7a1b6
imgteam
parents:
diff changeset
19 skimage.io.imsave(args.output, im)