Update 2d_feature_extraction tool

BMCV · Apr 23, 2024 · 8772c79 · 8772c79
1 parent 14e6d71
commit 8772c79
Show file tree

Hide file tree

Showing 2 changed files with 9 additions and 8 deletions.
diff --git a/tools/2d_feature_extraction/2d_feature_extraction.py b/tools/2d_feature_extraction/2d_feature_extraction.py
@@ -1,9 +1,9 @@
 import argparse
 
+import giatools.io
 import numpy as np
 import pandas as pd
 import skimage.feature
-import skimage.io
 import skimage.measure
 import skimage.morphology
 import skimage.segmentation
@@ -57,9 +57,9 @@
 
     raw_image = None
     if args.raw_file is not None:
-        raw_image = skimage.io.imread(args.raw_file.name)
+        raw_image = giatools.io.imread(args.raw_file.name)
 
-    raw_label_image = skimage.io.imread(label_file)
+    raw_label_image = giatools.io.imread(label_file)
 
     df = pd.DataFrame()
     if label_file_binary:
@@ -124,4 +124,4 @@
         df['convexity'] = area / (perimeter * perimeter)
 
     del df['it']
-    df.to_csv(out_file, sep='\t', line_terminator='\n', index=False)
+    df.to_csv(out_file, sep='\t', lineterminator='\n', index=False)
diff --git a/tools/2d_feature_extraction/2d_feature_extraction.xml b/tools/2d_feature_extraction/2d_feature_extraction.xml
@@ -2,7 +2,7 @@
     <description>with scikit-image</description>
     <macros>
         <import>creators.xml</import>
-        <token name="@TOOL_VERSION@">0.14.2</token>
+        <token name="@TOOL_VERSION@">0.18.1</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <creator>
@@ -17,9 +17,10 @@
     </xrefs>
     <requirements> 
         <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
-        <requirement type="package" version="0.23.4">pandas</requirement>
-        <requirement type="package" version="1.15.4">numpy</requirement>
-        <requirement type="package" version="0.15.1">tifffile</requirement>
+        <requirement type="package" version="2.2.2">pandas</requirement>
+        <requirement type="package" version="1.23.3">numpy</requirement>
+        <requirement type="package" version="2020.10.1">tifffile</requirement>
+        <requirement type="package" version="0.1">giatools</requirement>
     </requirements>
     <command detect_errors="aggressive">
     <![CDATA[