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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
author imgteam
date Sat, 19 Feb 2022 15:16:52 +0000
parents f40e5d11eb47
children
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3
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
parents: 2
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1 """
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
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2 Copyright 2017-2022 Biomedical Computer Vision Group, Heidelberg University.
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
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3
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
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4 Distributed under the MIT license.
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
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5 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
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6
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
parents: 2
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7 """
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
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9 import argparse
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5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
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11 import skimage.filters
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6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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12 import skimage.io
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
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13 import skimage.util
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5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
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14 import tifffile
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6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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16 thOptions = {
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
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17 'otsu': lambda img_raw, bz: skimage.filters.threshold_otsu(img_raw),
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
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18 'li': lambda img_raw, bz: skimage.filters.threshold_li(img_raw),
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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19 'yen': lambda img_raw, bz: skimage.filters.threshold_yen(img_raw),
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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20 'isodata': lambda img_raw, bz: skimage.filters.threshold_isodata(img_raw),
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
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22 'loc_gaussian': lambda img_raw, bz: skimage.filters.threshold_local(img_raw, bz, method='gaussian'),
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
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23 'loc_median': lambda img_raw, bz: skimage.filters.threshold_local(img_raw, bz, method='median'),
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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24 'loc_mean': lambda img_raw, bz: skimage.filters.threshold_local(img_raw, bz, method='mean')
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6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
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25 }
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
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28 def auto_thresholding(in_fn, out_fn, th_method, block_size=5, dark_bg=True):
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
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29 img = skimage.io.imread(in_fn)
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
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30 th = thOptions[th_method](img, block_size)
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
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31 if dark_bg:
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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32 res = img > th
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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33 else:
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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34 res = img <= th
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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35 tifffile.imwrite(out_fn, skimage.util.img_as_ubyte(res))
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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38 if __name__ == "__main__":
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5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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39 parser = argparse.ArgumentParser(description='Automatic Image Thresholding')
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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40 parser.add_argument('im_in', help='Path to the input image')
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
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41 parser.add_argument('im_out', help='Path to the output image (TIFF)')
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
imgteam
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42 parser.add_argument('th_method', choices=thOptions.keys(), help='Thresholding method')
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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43 parser.add_argument('block_size', type=int, default=5, help='Odd size of pixel neighborhood for calculating the threshold')
5224cc463a97 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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44 parser.add_argument('dark_bg', default=True, type=bool, help='True if background is dark')
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6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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45 args = parser.parse_args()
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
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46
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47 auto_thresholding(args.im_in, args.im_out, args.th_method, args.block_size, args.dark_bg)