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comparison 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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children cc8fe984ec3e
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-1:000000000000 0:214f548481eb
1 import argparse
2 import csv
3
4 import numpy as np
5 import orientationpy
6 import skimage.io
7 import skimage.util
8
9
10 if __name__ == '__main__':
11
12 parser = argparse.ArgumentParser()
13 parser.add_argument('input', type=str)
14 parser.add_argument('--mode', type=str, required=True)
15 parser.add_argument('--sigma', type=float, required=True)
16 parser.add_argument('--min_coherency', type=float, required=True)
17 parser.add_argument('--min_energy', type=float, required=True)
18 parser.add_argument('--max_precision', type=int, required=True)
19 parser.add_argument('--output_angle_tsv', type=str, default=None)
20 args = parser.parse_args()
21
22 im = skimage.io.imread(args.input)
23 im = skimage.util.img_as_float(im)
24 im = np.squeeze(im)
25 assert im.ndim == 2
26
27 Gy, Gx = orientationpy.computeGradient(im, mode=args.mode)
28 structureTensor = orientationpy.computeStructureTensor([Gy, Gx], sigma=args.sigma)
29 orientations = orientationpy.computeOrientation(structureTensor, computeEnergy=True, computeCoherency=True)
30
31 # Compute angle according to https://bigwww.epfl.ch/demo/orientationj/#dist:
32 mask = np.logical_and(
33 orientations['coherency'] >= args.min_coherency,
34 orientations['energy'] >= args.min_energy * orientations['energy'].max(),
35 )
36 angles = orientations['theta'][mask]
37 weights = orientations['coherency'][mask]
38 bin_size = 1 if args.max_precision == 0 else pow(10, -args.max_precision)
39 hist, bin_edges = np.histogram(
40 angles,
41 range=(-90, +90),
42 weights=weights,
43 bins=round(180 / bin_size),
44 )
45 hidx = np.argmax(hist)
46 angle = (bin_edges[hidx] + bin_edges[hidx + 1]) / 2
47 angle = round(angle, args.max_precision)
48
49 # Write results
50 if args.output_angle_tsv:
51 with open(args.output_angle_tsv, 'w') as fp:
52 writer = csv.writer(fp, delimiter='\t', lineterminator='\n')
53 writer.writerow(['Angle'])
54 writer.writerow([angle])