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annotate orientationpy-cli.py @ 0:214f548481eb draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
author imgteam
date Tue, 12 Mar 2024 10:54:40 +0000
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214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
parents:
diff changeset
1 import argparse
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
parents:
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2 import csv
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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4 import numpy as np
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
parents:
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5 import orientationpy
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
parents:
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6 import skimage.io
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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7 import skimage.util
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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10 if __name__ == '__main__':
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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12 parser = argparse.ArgumentParser()
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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13 parser.add_argument('input', type=str)
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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14 parser.add_argument('--mode', type=str, required=True)
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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15 parser.add_argument('--sigma', type=float, required=True)
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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16 parser.add_argument('--min_coherency', type=float, required=True)
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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17 parser.add_argument('--min_energy', type=float, required=True)
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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18 parser.add_argument('--max_precision', type=int, required=True)
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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19 parser.add_argument('--output_angle_tsv', type=str, default=None)
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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20 args = parser.parse_args()
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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22 im = skimage.io.imread(args.input)
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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23 im = skimage.util.img_as_float(im)
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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24 im = np.squeeze(im)
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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25 assert im.ndim == 2
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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27 Gy, Gx = orientationpy.computeGradient(im, mode=args.mode)
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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28 structureTensor = orientationpy.computeStructureTensor([Gy, Gx], sigma=args.sigma)
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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29 orientations = orientationpy.computeOrientation(structureTensor, computeEnergy=True, computeCoherency=True)
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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31 # Compute angle according to https://bigwww.epfl.ch/demo/orientationj/#dist:
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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32 mask = np.logical_and(
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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33 orientations['coherency'] >= args.min_coherency,
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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34 orientations['energy'] >= args.min_energy * orientations['energy'].max(),
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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35 )
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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36 angles = orientations['theta'][mask]
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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37 weights = orientations['coherency'][mask]
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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38 bin_size = 1 if args.max_precision == 0 else pow(10, -args.max_precision)
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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39 hist, bin_edges = np.histogram(
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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40 angles,
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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41 range=(-90, +90),
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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42 weights=weights,
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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43 bins=round(180 / bin_size),
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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44 )
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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45 hidx = np.argmax(hist)
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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46 angle = (bin_edges[hidx] + bin_edges[hidx + 1]) / 2
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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47 angle = round(angle, args.max_precision)
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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48
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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49 # Write results
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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50 if args.output_angle_tsv:
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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51 with open(args.output_angle_tsv, 'w') as fp:
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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52 writer = csv.writer(fp, delimiter='\t', lineterminator='\n')
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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53 writer.writerow(['Angle'])
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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54 writer.writerow([angle])