Mercurial > repos > imgteam > 2d_filter_segmentation_by_features
diff 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 |
|---|---|
| date | Wed, 24 Apr 2024 08:11:47 +0000 |
| parents | 6ad1d3cfdea1 |
| children |
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--- a/2d_filter_segmentation_by_features.py Thu Apr 04 15:23:28 2024 +0000 +++ b/2d_filter_segmentation_by_features.py Wed Apr 24 08:11:47 2024 +0000 @@ -1,6 +1,7 @@ import argparse import sys +import giatools.io import pandas as pd import skimage.io import skimage.util @@ -14,14 +15,14 @@ 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) + img_in = giatools.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 'Unnamed' not 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] + a_min = rules[rules.iloc[:, 0] == 'min'][a_c] + a_max = rules[rules.iloc[:, 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):