Update 2d_filter_segmentation_by_features tool

BMCV · Apr 23, 2024 · a28c820 · a28c820
1 parent 8772c79
commit a28c820
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Showing 2 changed files with 9 additions and 8 deletions.
diff --git a/tools/2d_filter_segmentation_by_features/2d_filter_segmentation_by_features.py b/tools/2d_filter_segmentation_by_features/2d_filter_segmentation_by_features.py
@@ -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):

diff --git a/tools/2d_filter_segmentation_by_features/2d_filter_segmentation_by_features.xml b/tools/2d_filter_segmentation_by_features/2d_filter_segmentation_by_features.xml
@@ -1,4 +1,4 @@
-<tool id="ip_2d_filter_segmentation_by_features" name="Filter label map by rules" version="0.0.1-3" profile="20.05">
+<tool id="ip_2d_filter_segmentation_by_features" name="Filter label map by rules" version="0.0.1-4" profile="20.05">
     <description></description>
     <macros>
         <import>creators.xml</import>
@@ -14,10 +14,10 @@
         <xref type="bio.tools">galaxy_image_analysis</xref>
     </xrefs>
     <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>
+        <requirement type="package" version="0.18.1">scikit-image</requirement> 
+        <requirement type="package" version="2.2.2">pandas</requirement>
+        <requirement type="package" version="2020.10.1">tifffile</requirement>
+        <requirement type="package" version="0.1">giatools</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[