Mercurial > repos > imgteam > orientationpy
annotate orientationpy-cli.py @ 1:df211f6b5cf2 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit c045f067a57e8308308cf6329060c7ccd3fc372f
author | imgteam |
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date | Thu, 04 Apr 2024 15:25:49 +0000 |
parents | 214f548481eb |
children | cc8fe984ec3e |
rev | line source |
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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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1 import argparse |
214f548481eb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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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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3 |
214f548481eb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
parents:
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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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8 |
214f548481eb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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9 |
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
imgteam
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11 |
214f548481eb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
parents:
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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
parents:
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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
parents:
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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
parents:
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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
parents:
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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
parents:
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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
parents:
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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
parents:
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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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21 |
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
imgteam
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26 |
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
parents:
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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
imgteam
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30 |
214f548481eb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
parents:
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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
parents:
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35 ) |
214f548481eb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
parents:
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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
parents:
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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
parents:
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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
imgteam
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48 |
214f548481eb
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
imgteam
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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
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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
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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
imgteam
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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]) |