| Next changeset 1:6ad1d3cfdea1 (2023-11-13) |
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Commit message:
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d |
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added:
2d_filter_segmentation_by_features.py 2d_filter_segmentation_by_features.xml test-data/features.tabular test-data/in.tif test-data/out.tif test-data/rules.tabular |
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| diff -r 000000000000 -r e576b73a2e2f 2d_filter_segmentation_by_features.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/2d_filter_segmentation_by_features.py Mon Jul 22 05:00:03 2019 -0400 |
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| @@ -0,0 +1,29 @@ +import argparse +import sys +import skimage.io +import skimage.util +import pandas as pd + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description='Filter segmentation by features') + parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') + parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') + parser.add_argument('feature_file', type=argparse.FileType('r'), default=sys.stdin, help='feature file (cols: label, f1, f2)') + 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)') + args = parser.parse_args() + + img_in = skimage.io.imread(args.input_file.name) + features = pd.read_csv(args.feature_file, delimiter="\t") + rules = pd.read_csv(args.rule_file, delimiter="\t") + + cols = [a for a in rules.columns if not 'Unnamed' in a] + for a_c in cols: + a_min = rules[rules.ix[:, 0] == 'min'][a_c] + a_max = rules[rules.ix[:, 0] == 'max'][a_c] + for a_l in features.label: + a_val = float(features[features['label'] == a_l][a_c]) + if a_val < float(a_min) or a_val > float(a_max): + img_in[img_in == int(a_l)] = 0 + + res = skimage.util.img_as_uint(img_in) + skimage.io.imsave(args.out_file.name, res, plugin="tifffile") |
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| diff -r 000000000000 -r e576b73a2e2f 2d_filter_segmentation_by_features.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/2d_filter_segmentation_by_features.xml Mon Jul 22 05:00:03 2019 -0400 |
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| @@ -0,0 +1,37 @@ +<tool id="ip_2d_filter_segmentation_by_features" name="Filter segmentation" version="0.0.1"> + <description>Filter segmentation by rules</description> + <requirements> + <requirement type="package" version="0.14.2">scikit-image</requirement> + <requirement type="package" version="5.3.0">pillow</requirement> + <requirement type="package" version="0.23.4">pandas</requirement> + <requirement type="package" version="0.15.1">tifffile</requirement> + </requirements> + <command detect_errors="aggressive"> + <![CDATA[ + python '$__tool_directory__/2d_filter_segmentation_by_features.py' '$input' '$output' '$feature_file' '$rule_file' + ]]> + </command> + <inputs> + <param name="input" type="data" format="tiff" label="Source file" /> + <param name="feature_file" type="data" format="tabular" label="Feature file" /> + <param name="rule_file" type="data" format="tabular" label="Rules file" /> + </inputs> + <outputs> + <data format="tiff" name="output" /> + </outputs> + <tests> + <test> + <param name="input" value="in.tif"/> + <param name="feature_file" value="features.tabular"/> + <param name="rule_file" value="rules.tabular"/> + <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/> + </test> + </tests> + <help> + Filter label image by rules (e.g., remove large or deformed objects). + Rules file has a specific format (cols: ,f1,2, rows: feature_name, min, max). The features have to be also profived in a specific format (cols: label, f1, f2). + </help> + <citations> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r e576b73a2e2f test-data/features.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features.tabular Mon Jul 22 05:00:03 2019 -0400 |
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| @@ -0,0 +1,5 @@ +label area eccentricity +1 344 0.42521053699241596 +2 434 0.47679001553231926 +3 907 0.9973539531125177 +4 14320 0.17131009631035327 |
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| diff -r 000000000000 -r e576b73a2e2f test-data/in.tif |
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| Binary file test-data/in.tif has changed |
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| diff -r 000000000000 -r e576b73a2e2f test-data/out.tif |
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| Binary file test-data/out.tif has changed |
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| diff -r 000000000000 -r e576b73a2e2f test-data/rules.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rules.tabular Mon Jul 22 05:00:03 2019 -0400 |
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| @@ -0,0 +1,3 @@ + area eccentricity +min 500 0. +max 100000 0.5 |