Mercurial > repos > thomaswollmann > slice_image
comparison slice_image.py @ 0:ef763552586d draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
author | thomaswollmann |
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date | Mon, 07 Jan 2019 05:40:17 -0500 |
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-1:000000000000 | 0:ef763552586d |
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1 import argparse | |
2 import sys | |
3 import warnings | |
4 import numpy as np | |
5 import random | |
6 import os.path | |
7 import skimage.io | |
8 import skimage.util | |
9 import skimage.feature | |
10 from scipy.stats import entropy as scipy_entropy | |
11 | |
12 def slice_image(input_file, out_folder, label=None, label_out_folder=None, window_size=64, stride=1, bg_thresh=1, limit_slices=False, n_thresh=5000): | |
13 #TODO NOT Implemented:process labels | |
14 | |
15 img_raw = skimage.io.imread(input_file) | |
16 if len(img_raw.shape) == 2: | |
17 img_raw = np.expand_dims(img_raw, 3) | |
18 | |
19 patches_raw = skimage.util.view_as_windows(img_raw, (window_size, window_size, img_raw.shape[2]), step=stride) | |
20 patches_raw = patches_raw.reshape([-1, window_size, window_size, img_raw.shape[2]]) | |
21 | |
22 filename = os.path.splitext(os.path.basename(input_file))[0] | |
23 new_path = out_folder+"/"+filename+"_%d.tiff" | |
24 | |
25 #samples for thresholding the amount of slices | |
26 sample = random.sample(range(patches_raw.shape[0]), n_thresh) | |
27 | |
28 with warnings.catch_warnings(): | |
29 warnings.simplefilter("ignore") | |
30 | |
31 for i in range(0, patches_raw.shape[0]): | |
32 # TODO improve | |
33 sum_image = np.sum(patches_raw[i], 2)/img_raw.shape[2] | |
34 total_entr = np.var(sum_image.reshape([-1])) | |
35 | |
36 if bg_thresh > 0: | |
37 sum_image = skimage.util.img_as_uint(sum_image) | |
38 g = skimage.feature.greycomatrix(sum_image, [1,2], [0, np.pi/2], nnormed=True, symmetric=True) | |
39 hom = np.var(skimage.feature.greycoprops(g, prop='homogeneity')) | |
40 if hom > bg_thresh: #0.0005 | |
41 continue | |
42 | |
43 if limit_slices == True: | |
44 if i in sample: | |
45 res = skimage.util.img_as_uint(patches_raw[i]) #Attention: precision loss | |
46 skimage.io.imsave(new_path % i, res, plugin='tifffile') | |
47 else: | |
48 res = skimage.util.img_as_uint(patches_raw[i]) #Attention: precision loss | |
49 skimage.io.imsave(new_path % i, res, plugin='tifffile') | |
50 | |
51 | |
52 | |
53 if __name__ == "__main__": | |
54 parser = argparse.ArgumentParser() | |
55 parser.add_argument('input_file', type=argparse.FileType('r'), help='input file') | |
56 parser.add_argument('out_folder', help='out folder') | |
57 parser.add_argument('--label', dest='label_file', default=None, help='auxiliary label file to split in the same way') | |
58 parser.add_argument('--label_out_folder', dest='label_out_folder', default=None, help='label out folder') | |
59 parser.add_argument('--stride', dest='stride', type=int, default=1, help='applied stride') | |
60 parser.add_argument('--window_size', dest='window_size', type=int, default=64, help='size of resulting patches') | |
61 parser.add_argument('--bg_thresh', dest='bg_thresh', type=float, default=0, help='skip patches without information using a treshold') | |
62 parser.add_argument('--limit_slices', dest='limit_slices', type=bool, default=False, help='limit amount of slices') | |
63 parser.add_argument('--n_thresh', dest='n_thresh', type=int, default=5000, help='amount of slices') | |
64 args = parser.parse_args() | |
65 | |
66 slice_image(args.input_file.name, args.out_folder, | |
67 label=args.label_file, label_out_folder=args.label_out_folder, | |
68 stride=args.stride, window_size=args.window_size, bg_thresh=args.bg_thresh, limit_slices=args.limit_slices, n_thresh=args.n_thresh) |