Mercurial > repos > imgteam > 2d_histogram_equalization

changeset 1:77455af98d88 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 558152251d5d7a1bf77db91aa5388aca7a68ae62
author imgteam
date Fri, 20 Feb 2026 09:56:36 +0000
parents d54f14727f77
children
files creators.xml histogram_equalization.py histogram_equalization.xml test-data/out.tif test-data/out.tiff test-data/out_clahe.tiff test-data/sample.tif test-data/sample.tiff tests.xml
diffstat 9 files changed, 194 insertions(+), 24 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/creators.xml	Fri Feb 20 09:56:36 2026 +0000
@@ -0,0 +1,43 @@
+<macros>
+
+    <xml name="creators/bmcv">
+        <organization name="Biomedical Computer Vision Group, Heidelberg Universtiy" alternateName="BMCV" url="http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html" />
+        <yield />
+    </xml>
+
+    <xml name="creators/kostrykin">
+        <person givenName="Leonid" familyName="Kostrykin"/>
+        <yield/>
+    </xml>
+
+    <xml name="creators/rmassei">
+        <person givenName="Riccardo" familyName="Massei"/>
+        <yield/>
+    </xml>
+
+    <xml name="creators/alliecreason">
+        <person givenName="Allison" familyName="Creason"/>
+        <yield/>
+    </xml>
+
+    <xml name="creators/bugraoezdemir">
+        <person givenName="Bugra" familyName="Oezdemir"/>
+        <yield/>
+    </xml>
+
+    <xml name="creators/thawn">
+        <person givenName="Till" familyName="Korten"/>
+        <yield/>
+    </xml>
+
+    <xml name="creators/pavanvidem">
+        <person givenName="Pavan" familyName="Videm"/>
+        <yield/>
+    </xml>
+
+    <xml name="creators/tuncK">
+        <person givenName="Tunc" familyName="Kayikcioglu"/>
+        <yield/>
+    </xml>
+
+</macros>
--- a/histogram_equalization.py	Tue Jul 23 14:06:42 2019 -0400
+++ b/histogram_equalization.py	Fri Feb 20 09:56:36 2026 +0000
@@ -1,13 +1,22 @@
 import argparse
-import os
 import sys
+
+import giatools.io
+import numpy as np
+import skimage.exposure
 import skimage.io
-import skimage.exposure
 import skimage.util
 
+
+def rescale(img):
+    assert np.issubdtype(img.dtype, np.floating), str(img.dtype)  # sanity check
+    img = img - img.min()
+    return img / img.max() if img.max() != 0 else 1
+
+
 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: rescale(skimage.exposure.equalize_hist(img_raw)),  # rescale needed for values to be in [0, 1]
+    'clahe': lambda img_raw: skimage.exposure.equalize_adapthist(img_raw),  # produces image with values in [0, 1]
 }
 
 if __name__ == "__main__":
@@ -17,7 +26,7 @@
     parser.add_argument('h_type', choices=hOptions.keys(), help='histogram equalization method')
     args = parser.parse_args()
 
-    img_in = skimage.io.imread(args.input_file.name)
+    img_in = giatools.io.imread(args.input_file.name)
     res = hOptions[args.h_type](img_in)
     res = skimage.util.img_as_uint(res)
     skimage.io.imsave(args.out_file.name, res, plugin="tifffile")
--- a/histogram_equalization.xml	Tue Jul 23 14:06:42 2019 -0400
+++ b/histogram_equalization.xml	Fri Feb 20 09:56:36 2026 +0000
@@ -1,19 +1,35 @@
-<tool id="ip_histogram_equalization" name="Histogram equalization" version="0.0.1">
-   <description>automatic histogram equalization</description>
-   <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' $h_type
-   ]]>
-   </command>
-   <inputs>
-        <param name="input" type="data" format="tiff" label="Source file" />
-        <param name="h_type" type="select" label="Histogram Equalization Algorithm">
+<tool id="ip_histogram_equalization" name="Perform histogram equalization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
+    <description>with scikit-image</description>
+    <macros>
+        <import>creators.xml</import>
+        <import>tests.xml</import>
+        <token name="@TOOL_VERSION@">0.25.2</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <creator>
+        <expand macro="creators/bmcv" />
+    </creator>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">scikit-image</xref>
+        <xref type="biii">scikit-image</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
+        <requirement type="package" version="2.3.5">numpy</requirement>
+        <requirement type="package" version="2025.5.10">tifffile</requirement>
+        <requirement type="package" version="0.1.2">giatools</requirement>
+    </requirements>
+    <command detect_errors="aggressive">
+    <![CDATA[
+    python '$__tool_directory__/histogram_equalization.py' '$input' '$output' $h_type
+    ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="tiff" label="Input image" />
+        <param name="h_type" type="select" label="Histogram equalization algorithm">
           <option value="default">Stretching</option>
           <option value="clahe" selected="True">CLAHE</option>
         </param>
@@ -23,13 +39,20 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" value="sample.tif"/>
-            <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
+            <param name="input" value="sample.tiff"/>
             <param name="h_type" value="default"/>
+            <expand macro="tests/intensity_image_diff" name="output" value="out.tiff" ftype="tiff"/>
+        </test>
+        <test>
+            <param name="input" value="sample.tiff"/>
+            <param name="h_type" value="clahe"/>
+            <expand macro="tests/intensity_image_diff" name="output" value="out_clahe.tiff" ftype="tiff"/>
         </test>
     </tests>
     <help>
-        Applies histogram equalization to an image.
+
+        **Applies histogram equalization to an image.**
+
     </help>
     <citations>
         <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
Binary file test-data/out.tif has changed
Binary file test-data/out.tiff has changed
Binary file test-data/out_clahe.tiff has changed
Binary file test-data/sample.tif has changed
Binary file test-data/sample.tiff has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tests.xml	Fri Feb 20 09:56:36 2026 +0000
@@ -0,0 +1,95 @@
+<macros>
+
+    <!-- Macros for verification of image outputs -->
+
+    <xml
+        name="tests/binary_image_diff"
+        tokens="name,value,ftype,metric,eps"
+        token_metric="mae"
+        token_eps="0.01">
+
+        <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="0">
+            <assert_contents>
+                <has_image_n_labels n="2"/>
+                <yield/>
+            </assert_contents>
+        </output>
+
+    </xml>
+
+    <xml
+        name="tests/label_image_diff"
+        tokens="name,value,ftype,metric,eps,pin_labels"
+        token_metric="iou"
+        token_eps="0.01"
+        token_pin_labels="0">
+
+        <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="@PIN_LABELS@">
+            <assert_contents>
+                <yield/>
+            </assert_contents>
+        </output>
+
+    </xml>
+
+    <xml
+        name="tests/intensity_image_diff"
+        tokens="name,value,ftype,metric,eps"
+        token_metric="rms"
+        token_eps="0.01">
+
+        <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@">
+            <assert_contents>
+                <yield/>
+            </assert_contents>
+        </output>
+
+    </xml>
+
+    <!-- Variants of the above for verification of collection elements -->
+
+    <xml
+        name="tests/binary_image_diff/element"
+        tokens="name,value,ftype,metric,eps"
+        token_metric="mae"
+        token_eps="0.01">
+
+        <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="0">
+            <assert_contents>
+                <has_image_n_labels n="2"/>
+                <yield/>
+            </assert_contents>
+        </element>
+
+    </xml>
+
+    <xml
+        name="tests/label_image_diff/element"
+        tokens="name,value,ftype,metric,eps"
+        token_metric="iou"
+        token_eps="0.01"
+        token_pin_labels="0">
+
+        <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="@PIN_LABELS@">
+            <assert_contents>
+                <yield/>
+            </assert_contents>
+        </element>
+
+    </xml>
+
+    <xml
+        name="tests/intensity_image_diff/element"
+        tokens="name,value,ftype,metric,eps"
+        token_metric="rms"
+        token_eps="0.01">
+
+        <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@">
+            <assert_contents>
+                <yield/>
+            </assert_contents>
+        </element>
+
+    </xml>
+
+</macros>