<tool id="ip_segmetrics" name="SegMetrics" version="0.11.3-1" 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>
        This tool permits the computation of image segmentation and object detection performance measures for 2-D image data.

        You can either use a pair of individual input images (a segmented and a ground truth image), or a pair of ZIP archives which contain the segmented and the correspondiong ground truth images. When using a pair of individual images, remember to turn off the "Unzip" option. When using ZIP archives, turn it on instead and make sure that the directory structure is the same for the segmented and the ground truth images. Correspondences are estbalished based on the file names, which should be *identical* for a pair of corresponding images.

        If all objects within your segmented images are *uniquely* labeled, you can turn on the "Segmentation is uniquely labeled" switch to speed up the computations. Leave it off otherwise, or if you are unsure. The same accounts for the "Ground truth is uniquely labeled" switch and your ground turth 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>