updates "Perform local thresholding" tool

Also fixes a bug in the tests of the tool.
BMCV · Nov 1, 2023 · 5f280ca · 5f280ca
1 parent ffd1a33
commit 5f280ca
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Showing 3 changed files with 32 additions and 25 deletions.
diff --git a/deprecated/tools/2d_auto_local_threshold/auto_local_threshold.xml b/deprecated/tools/2d_auto_local_threshold/auto_local_threshold.xml
@@ -1,17 +1,24 @@
-<tool id="ip_localthreshold" name="Local Threshold" version="0.0.3" profile="20.05"> 
-   <description>applies a local threshold algorithm to an image</description> 
-   <requirements>
+<tool id="ip_localthreshold" name="Perform local thresholding" version="0.0.3-2" profile="20.05">
+    <description>scikit-image</description> 
+    <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="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 '$__tool_directory__/auto_local_threshold.py' '$input' '$output' $block_size $thresh_type $dark_background
-   ]]>
-   </command>
-   <inputs>
+    </requirements>
+    <command detect_errors="aggressive">
+    <![CDATA[
+    python '$__tool_directory__/auto_local_threshold.py' '$input' '$output' $block_size $thresh_type $dark_background
+    ]]>
+    </command>
+    <inputs>
         <param name="input" type="data" format="tiff" label="Source file" />
         <param name="thresh_type" type="select" label="Threshold Algorithm">
           <option value="gaussian" selected="True">Gaussian</option>
@@ -30,7 +37,7 @@
             <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
             <param name="thresh_type" value="gaussian"/>
             <param name="block_size" value="429"/>
-            <param name="dark_backgroud" value="True"/>
+            <param name="dark_background" value="True"/>
         </test>
     </tests>
     <help>

diff --git a/deprecated/tools/2d_auto_local_threshold/test-data/out.tif b/deprecated/tools/2d_auto_local_threshold/test-data/out.tif
diff --git a/tools/2d_auto_threshold/auto_threshold.xml b/tools/2d_auto_threshold/auto_threshold.xml
@@ -1,27 +1,27 @@
 <tool id="ip_threshold" name="Threshold image" version="0.0.5-2" profile="20.05">
-   <description>scikit-image</description>
+    <description>scikit-image</description>
     <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> 
+    <requirements> 
         <requirement type="package" version="0.18.1">scikit-image</requirement>
         <requirement type="package" version="2020.10.1">tifffile</requirement>
-   </requirements>
-   <command detect_errors="aggressive">
-   <![CDATA[
-   python '$__tool_directory__/auto_threshold.py'
-   '$input'
-   ./out.tif
-   '$th_method'
-   '$block_size'
-   '$dark_bg'
-   ]]>
-   </command>
-   <inputs>
+    </requirements>
+    <command detect_errors="aggressive">
+    <![CDATA[
+    python '$__tool_directory__/auto_threshold.py'
+    '$input'
+    ./out.tif
+    '$th_method'
+    '$block_size'
+    '$dark_bg'
+    ]]>
+    </command>
+    <inputs>
         <param name="input" type="data" format="tiff,png" label="Input image" />
         <param name="th_method" type="select" label="Thresholding method">
           <option value="otsu" selected="True">Otsu</option>