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comparison slice_image.py @ 3:1faa7e3c94ff draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:26:38 +0000
parents f312d414f234
children a72590196440
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2:f312d414f234 3:1faa7e3c94ff
7 import skimage.feature 7 import skimage.feature
8 import skimage.io 8 import skimage.io
9 import skimage.util 9 import skimage.util
10 10
11 11
12 def slice_image(input_file, out_folder, label=None, label_out_folder=None, window_size=64, 12 def slice_image(input_file, out_folder, window_size=64, stride=1, bg_thresh=1, limit_slices=False, n_thresh=5000, seed=None):
13 stride=1, bg_thresh=1, limit_slices=False, n_thresh=5000, seed=None):
14 # TODO NOT Implemented:process labels
15 # --> label and label_out_folder useless so far
16 13
17 # primarily for testing purposes: 14 # Primarily for testing purposes
18 if seed is not None: 15 if seed is not None:
19 random.seed(seed) 16 random.seed(seed)
20 17
21 img_raw = skimage.io.imread(input_file) 18 img_raw = skimage.io.imread(input_file)
22 if len(img_raw.shape) == 2: 19 if len(img_raw.shape) == 2:
38 35
39 if bg_thresh > 0: 36 if bg_thresh > 0:
40 sum_image = skimage.util.img_as_uint(sum_image) 37 sum_image = skimage.util.img_as_uint(sum_image)
41 g = skimage.feature.greycomatrix(sum_image, [1, 2], [0, np.pi / 2], nnormed=True, symmetric=True) 38 g = skimage.feature.greycomatrix(sum_image, [1, 2], [0, np.pi / 2], nnormed=True, symmetric=True)
42 hom = np.var(skimage.feature.greycoprops(g, prop='homogeneity')) 39 hom = np.var(skimage.feature.greycoprops(g, prop='homogeneity'))
43 if hom > bg_thresh: # 0.0005 40 if hom > bg_thresh:
44 continue 41 continue
45 42
46 if limit_slices: 43 if limit_slices:
47 if i in sample: 44 if i in sample:
48 res = skimage.util.img_as_uint(patches_raw[i]) # Attention: precision loss 45 res = skimage.util.img_as_uint(patches_raw[i]) # Attention: precision loss
52 skimage.io.imsave(new_path % i, res, plugin='tifffile') 49 skimage.io.imsave(new_path % i, res, plugin='tifffile')
53 50
54 51
55 if __name__ == "__main__": 52 if __name__ == "__main__":
56 parser = argparse.ArgumentParser() 53 parser = argparse.ArgumentParser()
57 parser.add_argument('input_file', type=argparse.FileType('r'), help='input file') 54 parser.add_argument('input_file', type=argparse.FileType('r'), help='Input file')
58 parser.add_argument('out_folder', help='out folder') 55 parser.add_argument('out_folder', help='Output directory')
59 parser.add_argument('--label', dest='label_file', default=None, help='auxiliary label file to split in the same way') 56 parser.add_argument('--stride', dest='stride', type=int, default=1, help='Applied stride')
60 parser.add_argument('--label_out_folder', dest='label_out_folder', default=None, help='label out folder') 57 parser.add_argument('--window_size', dest='window_size', type=int, default=64, help='Size of resulting patches')
61 parser.add_argument('--stride', dest='stride', type=int, default=1, help='applied stride') 58 parser.add_argument('--bg_thresh', dest='bg_thresh', type=float, default=0, help='Skip background patches without information using a treshold')
62 parser.add_argument('--window_size', dest='window_size', type=int, default=64, help='size of resulting patches') 59 parser.add_argument('--n_thresh', dest='n_thresh', type=int, default=5000, help='Maximum number of slices to retain')
63 parser.add_argument('--bg_thresh', dest='bg_thresh', type=float, default=0, help='skip patches without information using a treshold') 60 parser.add_argument('--seed', dest='seed', type=int, default=None, help='Seed for random choice of slices')
64 parser.add_argument('--limit_slices', dest='limit_slices', type=bool, default=False, help='limit amount of slices')
65 parser.add_argument('--n_thresh', dest='n_thresh', type=int, default=5000, help='amount of slices')
66 parser.add_argument('--seed', dest='seed', type=int, default=None, help='seed for random choice of limited slices')
67 args = parser.parse_args() 61 args = parser.parse_args()
68 62
69 slice_image(args.input_file.name, args.out_folder, 63 slice_image(
70 label=args.label_file, label_out_folder=args.label_out_folder, 64 args.input_file.name,
71 stride=args.stride, window_size=args.window_size, bg_thresh=args.bg_thresh, 65 args.out_folder,
72 limit_slices=args.limit_slices, n_thresh=args.n_thresh, seed=args.seed) 66 stride=args.stride,
67 window_size=args.window_size,
68 bg_thresh=args.bg_thresh,
69 limit_slices=args.n_thresh > 0,
70 n_thresh=args.n_thresh,
71 seed=args.seed,
72 )