Mercurial > repos > imgteam > 2d_filter_segmentation_by_features
annotate 2d_filter_segmentation_by_features.py @ 3:9d47aabda459 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
author | imgteam |
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date | Wed, 24 Apr 2024 08:11:47 +0000 |
parents | 6ad1d3cfdea1 |
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e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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1 import argparse |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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2 import sys |
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6ad1d3cfdea1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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3 |
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9d47aabda459
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
imgteam
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4 import giatools.io |
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6ad1d3cfdea1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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5 import pandas as pd |
6ad1d3cfdea1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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6 import skimage.io |
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e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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7 import skimage.util |
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6ad1d3cfdea1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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8 |
0
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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9 |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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10 if __name__ == "__main__": |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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11 parser = argparse.ArgumentParser(description='Filter segmentation by features') |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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12 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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13 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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14 parser.add_argument('feature_file', type=argparse.FileType('r'), default=sys.stdin, help='feature file (cols: label, f1, f2)') |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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15 parser.add_argument('rule_file', type=argparse.FileType('r'), default=sys.stdin, help='file with rules per feature (cols: ,f1,2, rows: feature_name, min, max)') |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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16 args = parser.parse_args() |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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17 |
3
9d47aabda459
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
imgteam
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18 img_in = giatools.io.imread(args.input_file.name) |
0
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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19 features = pd.read_csv(args.feature_file, delimiter="\t") |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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20 rules = pd.read_csv(args.rule_file, delimiter="\t") |
1
6ad1d3cfdea1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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21 |
6ad1d3cfdea1
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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22 cols = [a for a in rules.columns if 'Unnamed' not in a] |
0
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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23 for a_c in cols: |
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9d47aabda459
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
imgteam
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24 a_min = rules[rules.iloc[:, 0] == 'min'][a_c] |
9d47aabda459
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
imgteam
parents:
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25 a_max = rules[rules.iloc[:, 0] == 'max'][a_c] |
0
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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26 for a_l in features.label: |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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27 a_val = float(features[features['label'] == a_l][a_c]) |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff
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28 if a_val < float(a_min) or a_val > float(a_max): |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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29 img_in[img_in == int(a_l)] = 0 |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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30 |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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31 res = skimage.util.img_as_uint(img_in) |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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32 skimage.io.imsave(args.out_file.name, res, plugin="tifffile") |