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annotate auto_local_threshold.py @ 3:0bbcb6a31a20 draft default tip

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
author imgteam
date Sat, 19 Feb 2022 15:16:20 +0000
parents d070576c6286
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81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
parents:
diff changeset
1 import argparse
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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2 import sys
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0bbcb6a31a20 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
parents: 2
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0bbcb6a31a20 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
parents: 2
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4 import numpy as np
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81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
parents:
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5 import skimage.filters
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0bbcb6a31a20 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
parents: 2
diff changeset
6 import skimage.io
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81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
parents:
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7 import skimage.util
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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9 threshOptions = {
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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10 'gaussian': lambda img_raw, bz: skimage.filters.threshold_local(img_raw, bz, method='gaussian'),
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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11 'mean': lambda img_raw, bz: skimage.filters.threshold_local(img_raw, bz, method='mean'),
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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12 'median': lambda img_raw, bz: skimage.filters.threshold_local(img_raw, bz, method='median')
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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13 }
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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15 if __name__ == "__main__":
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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16 parser = argparse.ArgumentParser(description='Segment Foci')
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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17 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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18 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
parents:
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19 parser.add_argument('block_size', type=int, default=5, help='Odd size of pixel neighborhood which is used to calculate the threshold value')
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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20 parser.add_argument('thresh_type', choices=threshOptions.keys(), help='thresholding method')
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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21 parser.add_argument('dark_background', default=True, type=bool, help='True if background is dark')
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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22 args = parser.parse_args()
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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24 img_in = skimage.io.imread(args.input_file.name)
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f03398bea281 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit 8a2a5763d1ac38b3c7974bd7c2da4d5c1101a0a9
imgteam
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25 img_in = np.reshape(img_in, [img_in.shape[0], img_in.shape[1]])
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81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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26 thresh = threshOptions[args.thresh_type](img_in, args.block_size)
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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0bbcb6a31a20 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
parents: 2
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28 if args.dark_background:
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81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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29 res = img_in > thresh
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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30 else:
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
imgteam
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31 res = img_in <= thresh
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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33 res = skimage.util.img_as_uint(res)
81b3d18678ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_local_threshold/ commit f3903c908786b9b0ea5a46e9cc35ee025770ecda
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34 skimage.io.imsave(args.out_file.name, res, plugin="tifffile")