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