Mercurial > repos > thomaswollmann > visceral_evaluatesegmentation
changeset 0:cc77c9bf7b4a draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit 84957f4ad2994ba9bf594d835e5ddd6bcb98c59f
| author | thomaswollmann |
|---|---|
| date | Thu, 16 Feb 2017 05:18:42 -0500 |
| parents | |
| children | e542633095b7 |
| files | test-data/out.xml test-data/sample.png visceral-evaluatesegmentation.xml |
| diffstat | 3 files changed, 66 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.xml Thu Feb 16 05:18:42 2017 -0500 @@ -0,0 +1,29 @@ +<measurement> + <fixed-image filename="sample.tif" nonzeropoints="0" intersection="86495"/> + <moving-image filename="sample.tif" nonzeropoints="0" intersection="86495"/> + <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="10"/> + <AVGDIST name="Average Hausdorff Distance" symbol="AVGDIST" type="distance" value="0.000000" executiontime="10"/> + <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"/> + </metrics> + <time total-executiontime="80"/> + <dimention max_x="328" max_y="264" max_z="0"/> +</measurement>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/visceral-evaluatesegmentation.xml Thu Feb 16 05:18:42 2017 -0500 @@ -0,0 +1,37 @@ +<tool id="visceral_evaluatesegmentation" name="Visceral - Evaluate Segmentation" version="0.4"> + <description>Evaluate Segmentation</description> + <requirements> + <requirement type="package">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="10" /> + </test> + </tests> + <help>Calculates Metrics for Evaluating Image Segmentation</help> + <citations> + <citation type="bibtex">@article{TA2015, + author = {Abdel Aziz Taha and Allan Hanbury}, + title = {Metrics for Evaluating 3{D} Medical Image Segmentation: analysis, selection, and tool}, + journal = {BMC Medical Imaging}, + year = {2015}, + volume = {15}, + pages = {29}, + month = {August}, +}</citation> + </citations> +</tool>