Mercurial > repos > imgteam > 2d_filter_segmentation_by_features
annotate 2d_filter_segmentation_by_features.py @ 0:e576b73a2e2f draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
author | imgteam |
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date | Mon, 22 Jul 2019 05:00:03 -0400 |
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children | 6ad1d3cfdea1 |
rev | line source |
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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
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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 |
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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3 import skimage.io |
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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4 import skimage.util |
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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5 import pandas as pd |
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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6 |
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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7 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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8 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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9 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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10 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
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11 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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12 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
parents:
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13 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
parents:
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14 |
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 img_in = skimage.io.imread(args.input_file.name) |
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 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
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17 rules = pd.read_csv(args.rule_file, delimiter="\t") |
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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18 |
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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19 cols = [a for a in rules.columns if not 'Unnamed' in a] |
e576b73a2e2f
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff
changeset
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20 for a_c in cols: |
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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21 a_min = rules[rules.ix[:, 0] == 'min'][a_c] |
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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22 a_max = rules[rules.ix[:, 0] == 'max'][a_c] |
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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changeset
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23 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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24 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
changeset
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25 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:
diff
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26 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
parents:
diff
changeset
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27 |
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 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
parents:
diff
changeset
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29 skimage.io.imsave(args.out_file.name, res, plugin="tifffile") |