Mercurial > repos > imgteam > 2d_filter_segmentation_by_features
diff 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 |
parents | |
children | 6ad1d3cfdea1 |
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--- /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 @@ -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")