Mercurial > repos > imgteam > colorize_labels

changeset 2:3aa2d054848a draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:25:22 +0000
parents 43c80f3c3b60
children 2d1de6e7b113
files colorize_labels.xml creators.xml tests.xml
diffstat 3 files changed, 134 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/colorize_labels.xml	Wed Mar 13 19:08:34 2024 +0000
+++ b/colorize_labels.xml	Thu Apr 04 15:25:22 2024 +0000
@@ -1,14 +1,19 @@
 <tool id="colorize_labels" name="Colorize label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
     <description>with NetworkX</description>
     <macros>
+        <import>creators.xml</import>
+        <import>tests.xml</import>
         <token name="@TOOL_VERSION@">3.2.1</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
+    <creator>
+        <expand macro="creators/bmcv" />
+    </creator>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
     </edam_operations>
     <requirements>
-        <requirement type="package" version="3.2.1">networkx</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">networkx</requirement>
         <requirement type="package" version="1.22">numpy</requirement>
         <requirement type="package" version="0.18.1">scikit-image</requirement>
     </requirements>
@@ -42,18 +47,23 @@
             <param name="radius" value="1" />
             <param name="bg_label" value="0" />
             <param name="bg_color" value="#5a5a5a" />
-            <output name="output" value="output1.png" ftype="png" compare="sim_size" delta_frac="0.1" />
+            <expand macro="tests/intensity_image_diff" name="output" value="output1.png" ftype="png">
+                <has_image_channels channels="3"/>
+            </expand>
         </test>
         <test>
             <param name="input" value="input2.tif" />
             <param name="radius" value="10" />
             <param name="bg_label" value="0" />
             <param name="bg_color" value="#ffffff" />
-            <output name="output" value="output2.png" ftype="png" compare="sim_size" delta_frac="0.1" />
+            <expand macro="tests/intensity_image_diff" name="output" value="output2.png" ftype="png">
+                <has_image_channels channels="3"/>
+            </expand>
         </test>
     </tests>
     <help>
-        Colorize a 2-D label map for visualization using greedy coloring.
+
+        **Colorizes a 2-D label map for visualization using greedy coloring.**
 
         Label maps are produced by segmentation and other image analysis steps.
         Direct inspection of label maps can be difficult,
@@ -61,6 +71,7 @@
         distinguish visually from each other and from the image background.
         To facilitate the visual inspection of label maps, this tools converts
         label maps to color images, by assigning each label a unique color.
+
     </help>
     <citations>
         <citation type="bibtex">
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/creators.xml	Thu Apr 04 15:25:22 2024 +0000
@@ -0,0 +1,23 @@
+<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/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>
+    
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tests.xml	Thu Apr 04 15:25:22 2024 +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>