annotate auto_threshold.py @ 8:699a5e9146b3 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
author imgteam
date Wed, 24 Apr 2024 08:11:33 +0000
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1 """
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2 Copyright 2017-2024 Biomedical Computer Vision Group, Heidelberg University.
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4 Distributed under the MIT license.
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5 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
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6 """
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8 import argparse
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10 import giatools.io
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11 import numpy as np
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12 import skimage.filters
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13 import skimage.util
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14 import tifffile
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17 th_methods = {
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18 'manual': lambda thres, **kwargs: thres,
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20 'otsu': lambda img_raw, **kwargs: skimage.filters.threshold_otsu(img_raw),
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21 '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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22 'yen': lambda img_raw, **kwargs: skimage.filters.threshold_yen(img_raw),
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23 'isodata': lambda img_raw, **kwargs: skimage.filters.threshold_isodata(img_raw),
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25 'loc_gaussian': lambda img_raw, bz, **kwargs: skimage.filters.threshold_local(img_raw, bz, method='gaussian'),
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26 'loc_median': lambda img_raw, bz, **kwargs: skimage.filters.threshold_local(img_raw, bz, method='median'),
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27 'loc_mean': lambda img_raw, bz, **kwargs: skimage.filters.threshold_local(img_raw, bz, method='mean')
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28 }
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31 def do_thresholding(in_fn, out_fn, th_method, block_size, offset, threshold, invert_output=False):
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32 img = giatools.io.imread(in_fn)
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33 img = np.squeeze(img)
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34 assert img.ndim == 2
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36 th = offset + th_methods[th_method](img_raw=img, bz=block_size, thres=threshold)
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37 res = img > th
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38 if invert_output:
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39 res = np.logical_not(res)
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41 tifffile.imwrite(out_fn, skimage.util.img_as_ubyte(res))
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44 if __name__ == "__main__":
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45 parser = argparse.ArgumentParser(description='Automatic image thresholding')
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46 parser.add_argument('im_in', help='Path to the input image')
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47 parser.add_argument('im_out', help='Path to the output image (uint8)')
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48 parser.add_argument('th_method', choices=th_methods.keys(), help='Thresholding method')
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49 parser.add_argument('block_size', type=int, default=5, help='Odd size of pixel neighborhood for calculating the threshold')
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50 parser.add_argument('offset', type=float, default=0, help='Offset of automatically determined threshold value')
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51 parser.add_argument('threshold', type=float, default=0, help='Manual threshold value')
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52 parser.add_argument('--invert_output', default=False, action='store_true', help='Values below/above the threshold are labeled with 0/255 by default, and with 255/0 if this argument is used')
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53 args = parser.parse_args()
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55 do_thresholding(args.im_in, args.im_out, args.th_method, args.block_size, args.offset, args.threshold, args.invert_output)