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annotate auto_threshold.py @ 5:7db4fc31dbee draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
author imgteam
date Mon, 11 Mar 2024 17:12:33 +0000
parents 0c777d708acc
children 8bccb36e055a
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0c777d708acc "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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1 """
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7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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2 Copyright 2017-2024 Biomedical Computer Vision Group, Heidelberg University.
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0c777d708acc "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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4 Distributed under the MIT license.
0c777d708acc "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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5 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
0c777d708acc "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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6 """
0c777d708acc "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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8 import argparse
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7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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10 import numpy as np
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11 import skimage.filters
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d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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12 import skimage.io
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 import skimage.util
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0c777d708acc "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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14 import tifffile
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d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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16 th_methods = {
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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17 'manual': lambda thres, **kwargs: thres,
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7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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19 'otsu': lambda img_raw, **kwargs: skimage.filters.threshold_otsu(img_raw),
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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20 'li': lambda img_raw, **kwargs: skimage.filters.threshold_li(img_raw),
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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21 'yen': lambda img_raw, **kwargs: skimage.filters.threshold_yen(img_raw),
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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22 'isodata': lambda img_raw, **kwargs: skimage.filters.threshold_isodata(img_raw),
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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24 'loc_gaussian': lambda img_raw, bz, **kwargs: skimage.filters.threshold_local(img_raw, bz, method='gaussian'),
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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25 'loc_median': lambda img_raw, bz, **kwargs: skimage.filters.threshold_local(img_raw, bz, method='median'),
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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26 'loc_mean': lambda img_raw, bz, **kwargs: skimage.filters.threshold_local(img_raw, bz, method='mean')
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d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 }
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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30 def do_thresholding(in_fn, out_fn, th_method, block_size=5, threshold=0, invert_output=False):
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0c777d708acc "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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31 img = skimage.io.imread(in_fn)
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7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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32 th = th_methods[th_method](img_raw=img, bz=block_size, thres=threshold)
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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33 res = img > th
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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34 if invert_output:
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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35 res = np.logical_not(res)
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36 tifffile.imwrite(out_fn, skimage.util.img_as_ubyte(res))
0c777d708acc "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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39 if __name__ == "__main__":
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40 parser = argparse.ArgumentParser(description='Automatic Image Thresholding')
0c777d708acc "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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41 parser.add_argument('im_in', help='Path to the input image')
0c777d708acc "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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42 parser.add_argument('im_out', help='Path to the output image (TIFF)')
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7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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43 parser.add_argument('th_method', choices=th_methods.keys(), help='Thresholding method')
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0c777d708acc "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('block_size', type=int, default=5, help='Odd size of pixel neighborhood for calculating the threshold')
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7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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45 parser.add_argument('threshold', type=float, default=0, help='Manual thresholding value')
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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46 parser.add_argument('invert_output', default=False, type=bool, help='Values below/above the threshold are labeled with 0/255 if False, and with 255/0 otherwise')
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d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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47 args = parser.parse_args()
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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49 do_thresholding(args.im_in, args.im_out, args.th_method, args.block_size, args.threshold, args.invert_output)