Mercurial > repos > imgteam > 2d_auto_threshold

annotate auto_threshold.py @ 2:81f0cbca04a7 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 05:00:41 -0500
parents 4853fc2b50bf
children 0c777d708acc
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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
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2 import numpy as np
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4853fc2b50bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit 8a2a5763d1ac38b3c7974bd7c2da4d5c1101a0a9
imgteam
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3 import sys
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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 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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5 import skimage.filters
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.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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d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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8 threshOptions = {
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4853fc2b50bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit 8a2a5763d1ac38b3c7974bd7c2da4d5c1101a0a9
imgteam
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9 'otsu': lambda img_raw: skimage.filters.threshold_otsu(img_raw),
4853fc2b50bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit 8a2a5763d1ac38b3c7974bd7c2da4d5c1101a0a9
imgteam
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10 'gaussian_adaptive': lambda img_raw: skimage.filters.threshold_local(img_raw, 3, method='gaussian'),
4853fc2b50bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit 8a2a5763d1ac38b3c7974bd7c2da4d5c1101a0a9
imgteam
parents: 0
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11 'mean_adaptive': lambda img_raw: skimage.filters.threshold_local(img_raw, 3, method='mean'),
4853fc2b50bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit 8a2a5763d1ac38b3c7974bd7c2da4d5c1101a0a9
imgteam
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12 'isodata': lambda img_raw: skimage.filters.threshold_isodata(img_raw),
4853fc2b50bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit 8a2a5763d1ac38b3c7974bd7c2da4d5c1101a0a9
imgteam
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13 'li': lambda img_raw: skimage.filters.threshold_li(img_raw),
4853fc2b50bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit 8a2a5763d1ac38b3c7974bd7c2da4d5c1101a0a9
imgteam
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14 'yen': lambda img_raw: skimage.filters.threshold_yen(img_raw),
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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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15 }
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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17 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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18 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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19 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
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20 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
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21 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
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22 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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23 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
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25 img_in = skimage.io.imread(args.input_file.name)
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4853fc2b50bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit 8a2a5763d1ac38b3c7974bd7c2da4d5c1101a0a9
imgteam
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26 img_in = np.reshape(img_in, [img_in.shape[0], img_in.shape[1]])
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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 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
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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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29 if args.dark_background:
d4da97f51700 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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30 res = img_in > thresh
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81f0cbca04a7 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
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31 else:
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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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32 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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33
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4853fc2b50bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit 8a2a5763d1ac38b3c7974bd7c2da4d5c1101a0a9
imgteam
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34 res = skimage.util.img_as_uint(res)
4853fc2b50bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit 8a2a5763d1ac38b3c7974bd7c2da4d5c1101a0a9
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35 skimage.io.imsave(args.out_file.name, res, plugin="tifffile")