<tool id="ip_segmetrics" name="SegMetrics" version="0.11.3" profile="20.05">
   <description>image segmentation and object detection performance measures</description>
   <requirements> 
        <requirement type="package" version="0.11.3">segmetrics</requirement>
        <requirement type="package" version="0.18.1">scikit-image</requirement>
   </requirements>
   <command detect_errors="aggressive">
   <![CDATA[
   python '$__tool_directory__/run-segmetrics.py'
   '$input_seg'
   '$input_gt'
   ./results.csv
   $unzip
   $is_seg_unique
   $is_gt_unique
   $measures.dice
   $measures.seg
   $measures.jc
   $measures.ji
   $measures.ri
   $measures.ari
   $measures.hsd_sym
   $measures.hsd_e2a
   $measures.hsd_a2e
   $measures.nsd
   $measures.o_hsd_sym
   $measures.o_hsd_e2a
   $measures.o_hsd_a2e
   $measures.o_nsd
   $measures.fs
   $measures.fm
   $measures.fp
   $measures.fn
   ]]>
   </command>
   <inputs>

        <param name="input_seg" type="data" format="tiff,png,zip" label="Segmented images" />
        <param name="input_gt"  type="data" format="tiff,png,zip" label="Ground truth images" />

        <param name="unzip" type="boolean" checked="false" truevalue="-unzip" falsevalue="" label="Unzip" />

        <param name="is_seg_unique" type="boolean" checked="false" truevalue="-seg_unique" falsevalue="" label="Segmentation is uniquely labeled" />
        <param name="is_gt_unique"  type="boolean" checked="false" truevalue="-gt_unique"  falsevalue="" label="Ground truth is uniquely labeled" />

        <section name="measures" title="Performance measures" >
            <param name="dice" type="boolean" checked="true"  truevalue="-measure-dice" falsevalue="" label="Dice" />
            <param name="seg"  type="boolean" checked="true"  truevalue="-measure-seg"  falsevalue="" label="SEG" />
            <param name="jc"   type="boolean" checked="false" truevalue="-measure-jc"   falsevalue="" label="Jaccard coefficient" />
            <param name="ji"   type="boolean" checked="true"  truevalue="-measure-ji"   falsevalue="" label="Jaccard index" />
            <param name="ri"   type="boolean" checked="false" truevalue="-measure-ri"   falsevalue="" label="Rand index" />
            <param name="ari"  type="boolean" checked="false" truevalue="-measure-ari"  falsevalue="" label="Adjusted Rand index" />
            <param name="hsd_sym" type="boolean" checked="false" truevalue="-measure-hsd_sym" falsevalue="" label="Hausdorff distance (symmetric)" />
            <param name="hsd_e2a" type="boolean" checked="false" truevalue="-measure-hsd_e2a" falsevalue="" label="Hausdorff distance (ground truth to segmented)" />
            <param name="hsd_a2e" type="boolean" checked="false" truevalue="-measure-hsd_a2e" falsevalue="" label="Hausdorff distance (segmented to ground truth)" />
            <param name="nsd"     type="boolean" checked="false" truevalue="-measure-nsd"     falsevalue="" label="Normalized sum of distances" />
            <param name="o_hsd_sym" type="boolean" checked="true"  truevalue="-measure-o_hsd_sym" falsevalue="" label="Object-based Hausdorff distance (symmetric)" />
            <param name="o_hsd_e2a" type="boolean" checked="false" truevalue="-measure-o_hsd_e2a" falsevalue="" label="Object-based Hausdorff distance (ground truth to segmented)" />
            <param name="o_hsd_a2e" type="boolean" checked="false" truevalue="-measure-o_hsd_a2e" falsevalue="" label="Object-based Hausdorff distance (segmented to ground truth)" />
            <param name="o_nsd"     type="boolean" checked="true"  truevalue="-measure-o_nsd"     falsevalue="" label="Object-based normalized sum of distances" />
            <param name="fs" type="boolean" checked="true" truevalue="-measure-fs" falsevalue="" label="Falsely split objects per image" />
            <param name="fm" type="boolean" checked="true" truevalue="-measure-fm" falsevalue="" label="Falsely merged objects per image" />
            <param name="fp" type="boolean" checked="true" truevalue="-measure-fp" falsevalue="" label="Spurious objects per image" />
            <param name="fn" type="boolean" checked="true" truevalue="-measure-fn" falsevalue="" label="Missing objects per image" />
        </section>

    </inputs>
    <outputs>
       <data format="csv" name="results" from_work_dir="results.csv" />
    </outputs>
    <tests>
        <test>
            <param name="input_seg" value="input2.png"/>
            <param name="input_gt"  value="input1.png"/>
            <output name="results" value="results1.csv" ftype="csv" compare="diff"/>
            <param name="is_seg_unique" value="True"/>
            <param name="is_gt_unique"  value="True"/>
        </test>
        <test>
            <param name="input_seg" value="input1.zip"/>
            <param name="input_gt"  value="input2.zip"/>
            <output name="results" value="results2.csv" ftype="csv" compare="diff"/>
            <param name="is_seg_unique" value="True"/>
            <param name="is_gt_unique"  value="True"/>
            <param name="unzip" value="True"/>
        </test>
    </tests>
    <help>
        Image segmentation and object detection performance measures for 2-D image data.
    </help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btu080</citation>
        <citation type="doi">10.1109/ISBI.2009.5193098</citation>
        <citation type="doi">10.1109/ICIP.2003.1246871</citation>
    </citations>
</tool>