| Next changeset 1:d098aed00229 (2019-03-20) |
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Commit message:
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit c3f4b766f03770f094fda6bda0a5882c0ebd4581 |
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test-data/out.xml test-data/sample.png visceral-evaluatesegmentation.xml |
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| diff -r 000000000000 -r 8c1a805c2fc5 test-data/out.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.xml Sat Feb 09 14:48:18 2019 -0500 |
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| @@ -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> |
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| diff -r 000000000000 -r 8c1a805c2fc5 test-data/sample.png |
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| Binary file test-data/sample.png has changed |
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| diff -r 000000000000 -r 8c1a805c2fc5 visceral-evaluatesegmentation.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/visceral-evaluatesegmentation.xml Sat Feb 09 14:48:18 2019 -0500 |
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| @@ -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> |
