Mercurial > repos > imgteam > 2d_auto_threshold

diff auto_threshold.xml @ 9:50fa6150e340 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
author imgteam
date Sat, 07 Jun 2025 18:38:31 +0000
parents 699a5e9146b3
children 2ee04d2ebdcf
line wrap: on
line diff
--- a/auto_threshold.xml	Wed Apr 24 08:11:33 2024 +0000
+++ b/auto_threshold.xml	Sat Jun 07 18:38:31 2025 +0000
@@ -3,8 +3,8 @@
     <macros>
         <import>creators.xml</import>
         <import>tests.xml</import>
-        <token name="@TOOL_VERSION@">0.18.1</token>
-        <token name="@VERSION_SUFFIX@">3</token>
+        <token name="@TOOL_VERSION@">0.25.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
         <xml name="inputs/offset">
             <param name="offset" type="float" value="0" label="Offset" help="Offset to be added to the automatically determined threshold value. Positive values will increase the threshold (and thus reduce the amount of values above the threshold)." />
         </xml>
@@ -19,21 +19,28 @@
         <xref type="bio.tools">scikit-image</xref>
         <xref type="biii">scikit-image</xref>
     </xrefs>
-    <requirements> 
+    <requirements>
         <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
-        <requirement type="package" version="2020.10.1">tifffile</requirement>
-        <requirement type="package" version="0.1">giatools</requirement>
+        <requirement type="package" version="0.4.1">giatools</requirement>
     </requirements>
     <command detect_errors="aggressive">
     <![CDATA[
-    python '$__tool_directory__/auto_threshold.py'
-    '$input'
-    ./out.tif
-    '$th_method.method_id'
-    '$th_method.block_size'
-    '$th_method.offset'
-    '$th_method.threshold'
-    $invert_output
+
+        python '$__tool_directory__/auto_threshold.py'
+
+        '$input'
+        ./out.tiff
+
+        '$th_method.method_id'
+        '$th_method.block_size'
+        '$th_method.offset'
+        '$th_method.threshold1'
+         $invert_output
+
+        #if str($th_method.threshold2) != '':
+            --threshold2 '$th_method.threshold2'
+        #end if
+
     ]]>
     </command>
     <inputs>
@@ -50,42 +57,50 @@
                 <option value="loc_mean">Locally adaptive / Mean</option>
             </param>
             <when value="manual">
-                <param name="threshold" type="float" value="0" label="Threshold value" />
+                <param name="threshold1" type="float" value="0" label="Threshold value" />
+                <param name="threshold2" type="float" value="" optional="true" label="Second threshold value for hysteresis thresholding" />
                 <param name="block_size" type="hidden" value="0" />
                 <param name="offset" type="hidden" value="0" />
             </when>
             <when value="otsu">
-                <param name="threshold" type="hidden" value="0" />
+                <param name="threshold1" type="hidden" value="0" />
+                <param name="threshold2" type="hidden" value="" />
                 <param name="block_size" type="hidden" value="0" />
                 <expand macro="inputs/offset" />
             </when>
             <when value="li">
-                <param name="threshold" type="hidden" value="0" />
+                <param name="threshold1" type="hidden" value="0" />
+                <param name="threshold2" type="hidden" value="" />
                 <param name="block_size" type="hidden" value="0" />
                 <expand macro="inputs/offset" />
             </when>
             <when value="isodata">
-                <param name="threshold" type="hidden" value="0" />
+                <param name="threshold1" type="hidden" value="0" />
+                <param name="threshold2" type="hidden" value="" />
                 <param name="block_size" type="hidden" value="0" />
                 <expand macro="inputs/offset" />
             </when>
             <when value="yen">
-                <param name="threshold" type="hidden" value="0" />
+                <param name="threshold1" type="hidden" value="0" />
+                <param name="threshold2" type="hidden" value="" />
                 <param name="block_size" type="hidden" value="0" />
                 <expand macro="inputs/offset" />
             </when>
             <when value="loc_gaussian">
-                <param name="threshold" type="hidden" value="0" />
+                <param name="threshold1" type="hidden" value="0" />
+                <param name="threshold2" type="hidden" value="" />
                 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
                 <expand macro="inputs/offset" />
             </when>
             <when value="loc_median">
-                <param name="threshold" type="hidden" value="0" />
+                <param name="threshold1" type="hidden" value="0" />
+                <param name="threshold2" type="hidden" value="" />
                 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
                 <expand macro="inputs/offset" />
             </when>
             <when value="loc_mean">
-                <param name="threshold" type="hidden" value="0" />
+                <param name="threshold1" type="hidden" value="0" />
+                <param name="threshold2" type="hidden" value="" />
                 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
                 <expand macro="inputs/offset" />
             </when>
@@ -93,48 +108,67 @@
         <param name="invert_output" type="boolean" checked="false" truevalue="--invert_output" falsevalue="" label="Invert output labels" help="Pixels are usually assigned the label 0 if the pixel value is below (or equal to) the threshold, and 255 if it is above the threshold. If this option is activated, pixels are assigned the label 255 if the pixel value is below (or equal to) the threshold, and 0 if it is above the threshold." />
     </inputs>
     <outputs>
-       <data format="tiff" name="output" from_work_dir="out.tif" />
+       <data format="tiff" name="output" from_work_dir="out.tiff" />
     </outputs>
     <tests>
-        <!-- Tests for single-channel images -->
+        <!-- Tests for single-channel images (TIFF) -->
         <test>
-            <param name="input" value="sample.tif"/>
-            <param name="method_id" value="loc_gaussian"/>
-            <param name="block_size" value="51"/>
-            <param name="invert_output" value="False"/>
-            <expand macro="tests/binary_image_diff" name="output" value="out1.tif" ftype="tiff"/>
+            <param name="input" value="sample.tiff"/>
+            <conditional name="th_method">
+                <param name="method_id" value="loc_gaussian"/>
+                <param name="block_size" value="51"/>
+            </conditional>
+            <expand macro="tests/binary_image_diff" name="output" value="out1.tiff" ftype="tiff"/>
+        </test>
+        <test>
+            <param name="input" value="sample.tiff"/>
+            <conditional name="th_method">
+                <param name="method_id" value="loc_gaussian"/>
+                <param name="block_size" value="51"/>
+                <param name="offset" value="1"/>
+            </conditional>
+            <expand macro="tests/binary_image_diff" name="output" value="out2.tiff" ftype="tiff"/>
         </test>
         <test>
-            <param name="input" value="sample.tif"/>
-            <param name="method_id" value="loc_gaussian"/>
-            <param name="block_size" value="51"/>
-            <param name="offset" value="1"/>
-            <param name="invert_output" value="False"/>
-            <expand macro="tests/binary_image_diff" name="output" value="out2.tif" ftype="tiff"/>
+            <param name="input" value="sample.tiff"/>
+            <conditional name="th_method">
+                <param name="method_id" value="otsu"/>
+            </conditional>
+            <expand macro="tests/binary_image_diff" name="output" value="out3.tiff" ftype="tiff"/>
+        </test>
+        <test>
+            <param name="input" value="sample.tiff"/>
+            <param name="invert_output" value="True"/>
+            <conditional name="th_method">
+                <param name="method_id" value="manual"/>
+                <param name="threshold1" value="64"/>
+            </conditional>
+            <expand macro="tests/binary_image_diff" name="output" value="out4.tiff" ftype="tiff"/>
         </test>
         <test>
-            <param name="input" value="sample.tif"/>
-            <param name="method_id" value="otsu"/>
-            <param name="invert_output" value="False"/>
-            <expand macro="tests/binary_image_diff" name="output" value="out3.tif" ftype="tiff"/>
+            <param name="input" value="sample.tiff"/>
+            <conditional name="th_method">
+                <param name="method_id" value="manual"/>
+                <param name="threshold1" value="180"/>
+                <param name="threshold2" value="240"/>
+            </conditional>
+            <expand macro="tests/binary_image_diff" name="output" value="sample_manual_180_240.tiff" ftype="tiff"/>
         </test>
+        <!-- Tests for multi-channel images (PNG) -->
         <test>
-            <param name="input" value="sample.tif"/>
-            <param name="method_id" value="manual"/>
-            <param name="threshold" value="64"/>
-            <param name="invert_output" value="True"/>
-            <expand macro="tests/binary_image_diff" name="output" value="out4.tif" ftype="tiff"/>
+            <param name="input" value="rgb.png"/>
+            <conditional name="th_method">
+                <param name="method_id" value="otsu"/>
+            </conditional>
+            <expand macro="tests/binary_image_diff" name="output" value="rgb_otsu.tiff" ftype="tiff"/>
         </test>
         <!-- Tests for irregular files -->
         <test>
-            <param name="input" value="sample2.tif"/>
-            <param name="method_id" value="otsu"/>
-            <param name="invert_output" value="False"/>
-            <expand macro="tests/binary_image_diff" name="output" value="out5.tif" ftype="tiff"/>
-        </test>
-        <!-- Tests for multi-channel images -->
-        <test expect_failure="true">
-            <param name="input" value="rgb.png"/>
+            <param name="input" value="sample2.tiff"/>
+            <conditional name="th_method">
+                <param name="method_id" value="otsu"/>
+            </conditional>
+            <expand macro="tests/binary_image_diff" name="output" value="out5.tiff" ftype="tiff"/>
         </test>
     </tests>
     <help>