Mercurial > repos > imgteam > visceral_evaluatesegmentation

changeset 0:8c1a805c2fc5 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:48:18 -0500
parents
children d098aed00229
files test-data/out.xml test-data/sample.png visceral-evaluatesegmentation.xml
diffstat 3 files changed, 69 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.xml	Sat Feb 09 14:48:18 2019 -0500
@@ -0,0 +1,35 @@
+<measurement>
+  <fixed-image filename="/tmp/tmpjybJID/files/000/dataset_1.dat" nonzeropoints="0" intersection="50477"/>
+  <moving-image filename="/tmp/tmpjybJID/files/000/dataset_1.dat" nonzeropoints="0" intersection="50477"/>
+  <metrics>
+    <DICE name="Dice Coefficient (F1-Measure)" symbol="DICE" type="similarity" value="1.000000"/>
+    <JACRD name="Jaccard Coefficient" symbol="JACRD" type="similarity" value="1.000000"/>
+    <AUC name="Area under ROC Curve" symbol="AUC" type="similarity" value="1.000000"/>
+    <KAPPA name="Cohen Kappa" symbol="KAPPA" type="similarity" value="1.000000"/>
+    <RNDIND name="Rand Index" symbol="RNDIND" type="similarity" value="1.000000"/>
+    <ADJRIND name="Adjusted Rand Index" symbol="ADJRIND" type="similarity" value="1.000000"/>
+    <ICCORR name="Interclass Correlation" symbol="ICCORR" type="similarity" value="1.000000"/>
+    <VOLSMTY name="Volumetric Similarity Coefficient" symbol="VOLSMTY" type="similarity" value="1.000000"/>
+    <MUTINF name="Mutual Information" symbol="MUTINF" type="similarity" value="0.984545"/>
+    <HDRFDST name="Hausdorff Distance" symbol="HDRFDST" type="distance" value="0.000000" executiontime="16" unit="voxel"/>
+    <AVGDIST name="Average Hausdorff Distance" symbol="AVGDIST" type="distance" value="0.000000" executiontime="5" unit="voxel"/>
+    <MAHLNBS name="Mahanabolis Distance" symbol="MAHLNBS" type="distance" value="0.000000"/>
+    <VARINFO name="Variation of Information" symbol="VARINFO" type="distance" value="-0.000000"/>
+    <GCOERR name="Global Consistency Error" symbol="GCOERR" type="distance" value="0.000000"/>
+    <PROBDST name="Probabilistic Distance" symbol="PROBDST" type="distance" value="0.000000"/>
+    <SNSVTY name="Sensitivity (Recall, true positive rate)" symbol="SNSVTY" type="similarity" value="1.000000"/>
+    <SPCFTY name="Specificity (true negative rate)" symbol="SPCFTY" type="similarity" value="1.000000"/>
+    <PRCISON name="Precision (Confidence)" symbol="PRCISON" type="similarity" value="1.000000"/>
+    <FMEASR name="F-Measure" symbol="FMEASR" type="similarity" value="1.000000"/>
+    <ACURCY name="Accuracy" symbol="ACURCY" type="similarity" value="1.000000"/>
+    <FALLOUT name="Fallout (false positive rate)" symbol="FALLOUT" type="distance" value="0.000000"/>
+    <TP name="true positive" symbol="TP" type="similarity" value="49962" unit="voxel"/>
+    <FP name="false positive" symbol="FP" type="similarity" value="0" unit="voxel"/>
+    <TN name="true negative" symbol="TN" type="similarity" value="37223" unit="voxel"/>
+    <FN name="false negative" symbol="FN" type="similarity" value="0" unit="voxel"/>
+    <REFVOL name="reference volume" symbol="REFVOL" type="similarity" value="49962" unit="voxel"/>
+    <SEGVOL name="segmented volume" symbol="SEGVOL" type="similarity" value="49962" unit="voxel"/>
+  </metrics>
+  <time total-executiontime="51"/>
+  <dimention max_x="328" max_y="264" max_z="0" voxelspacing_x="1.000000" voxelspacing_y="1.000000" voxelspacing_z="1.000000"/>
+</measurement>
Binary file test-data/sample.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/visceral-evaluatesegmentation.xml	Sat Feb 09 14:48:18 2019 -0500
@@ -0,0 +1,34 @@
+<tool id="ip_visceral_evaluatesegmentation" name="Visceral" version="0.5">
+    <description>Evaluate Segmentation</description>
+    <requirements>
+        <!--requirement type="package" version="9c">jpeg</requirement-->
+        <!--requirement type="package" version="4.13.0">libitk</requirement-->
+        <requirement type="package" version="2015.07.03">visceral-evaluatesegmentation</requirement>
+    </requirements>
+    <command>
+        <![CDATA[
+        EvaluateSegmentation '$gt_path' '$seg_path' -xml '$output'
+        ]]>
+    </command>
+    <inputs>
+        <param name="gt_path" type="data" format="tiff,png,jpg,bmp" label="Ground Truth Image"/>
+        <param name="seg_path" type="data" format="tiff,png,jpg,bmp" label="Segmented Image"/>
+    </inputs>
+    <outputs>
+        <data format="xml" name="output"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="gt_path" value="sample.png" />
+            <param name="seg_path" value="sample.png" />
+            <output name="output" value="out.xml" ftype="xml" lines_diff="15" />
+        </test>
+    </tests>
+    <help>
+    **What it does**
+
+    Calculates Metrics for Evaluating Image Segmentation</help>
+    <citations>
+        <citation type="doi">10.1186/s12880-015-0068-x</citation>
+    </citations>
+</tool>