Mercurial > repos > imgteam > 2d_histogram_equalization

changeset 1:77f7159d775a draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:10:25 +0000
parents 70316d792fc9
children 3f3783846dc0
files histogram_equalization.py histogram_equalization.xml
diffstat 2 files changed, 20 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/histogram_equalization.py	Tue Jul 23 14:07:07 2019 -0400
+++ b/histogram_equalization.py	Mon Nov 13 22:10:25 2023 +0000
@@ -1,13 +1,13 @@
 import argparse
-import os
 import sys
+
+import skimage.exposure
 import skimage.io
-import skimage.exposure
 import skimage.util
 
 hOptions = {
-    'default' : lambda img_raw: skimage.exposure.equalize_hist(img_raw),
-    'clahe' : lambda img_raw: skimage.exposure.equalize_adapthist(img_raw)
+    'default': lambda img_raw: skimage.exposure.equalize_hist(img_raw),
+    'clahe': lambda img_raw: skimage.exposure.equalize_adapthist(img_raw)
 }
 
 if __name__ == "__main__":
--- a/histogram_equalization.xml	Tue Jul 23 14:07:07 2019 -0400
+++ b/histogram_equalization.xml	Mon Nov 13 22:10:25 2023 +0000
@@ -1,17 +1,23 @@
-<tool id="ip_histogram_equalization" name="Histogram equalization" version="0.0.1">
-   <description>automatic histogram equalization</description>
-   <requirements> 
+<tool id="ip_histogram_equalization" name="Perform histogram equalization" version="0.0.1-2">
+   <description>with scikit-image</description>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">galaxy_image_analysis</xref>
+    </xrefs>
+    <requirements> 
         <requirement type="package" version="0.14.2">scikit-image</requirement>
         <requirement type="package" version="1.15.4">numpy</requirement>
         <requirement type="package" version="5.3.0">pillow</requirement>
         <requirement type="package" version="0.15.1">tifffile</requirement>
-   </requirements>
-   <command detect_errors="aggressive">
-   <![CDATA[
-   python '$__tool_directory__/histogram_equalization.py' '$input' '$output' $h_type
-   ]]>
-   </command>
-   <inputs>
+    </requirements>
+    <command detect_errors="aggressive">
+    <![CDATA[
+    python '$__tool_directory__/histogram_equalization.py' '$input' '$output' $h_type
+    ]]>
+    </command>
+    <inputs>
         <param name="input" type="data" format="tiff" label="Source file" />
         <param name="h_type" type="select" label="Histogram Equalization Algorithm">
           <option value="default">Stretching</option>