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annotate auto_threshold.py @ 0:d4da97f51700 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:27:36 -0500
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children 4853fc2b50bf
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d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
1 import argparse
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
2 import numpy as np
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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3 import os
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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4 import sys
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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5 import warnings
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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6 import skimage.io
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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7 import skimage.filters
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
8 import skimage.util
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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9
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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10 threshOptions = {
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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11 'otsu' : lambda img_raw: skimage.filters.threshold_otsu(img_raw),
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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12 'gaussian_adaptive' : lambda img_raw: skimage.filters.threshold_local(img_raw.reshape(img_raw.shape[0], img_raw.shape[1]), 3, method='gaussian'), # todo reshape 2d
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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13 'mean_adaptive' : lambda img_raw: skimage.filters.threshold_local(img_raw.reshape(img_raw.shape[0], img_raw.shape[1]), 3, method='mean'), # todo reshape 2d
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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14 'isodata' : lambda img_raw: skimage.filters.threshold_isodata(img_raw),
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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15 'li' : lambda img_raw: skimage.filters.threshold_li(img_raw),
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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16 'yen' : lambda img_raw: skimage.filters.threshold_yen(img_raw),
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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17 }
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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19 if __name__ == "__main__":
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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20 parser = argparse.ArgumentParser(description='Segment Foci')
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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21 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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22 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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23 parser.add_argument('thresh_type', choices=threshOptions.keys(), help='thresholding method')
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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24 parser.add_argument('dark_background', default=True, type=bool, help='True if background is dark')
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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25 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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d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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27 img_in = skimage.io.imread(args.input_file.name)
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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28 thresh = threshOptions[args.thresh_type](img_in)
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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30 if args.dark_background:
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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31 res = img_in > thresh
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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32 else:
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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33 res = img_in <= thresh
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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34
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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35 with warnings.catch_warnings():
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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36 warnings.simplefilter("ignore")
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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37 res = skimage.util.img_as_uint(res)
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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38 skimage.io.imsave(args.out_file.name, res, plugin="tifffile")