<?xml version='1.0' encoding='UTF-8'?>
<tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="1.0.0">
    <description>with ImageJ2</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <expand macro="fiji_20141125_requirements" />
    <command>
<![CDATA[
    python $__tool_directory__/imagej2_analyze_skeleton.py
    --input "$input"
    --input_datatype $input.ext
    --prune_cycle_method $prune_cycle_method
    --prune_ends $prune_ends
    --calculate_largest_shortest_path $calculate_largest_shortest_path
    --show_detailed_info $show_detailed_info
    @max_heap_size_args@
    --jython_script $__tool_directory__/jython_script.py
    --output "$output"
]]>
    </command>
    <inputs>
        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select grayscale image"/>
        <param name="prune_cycle_method" type="select" label="Prune cycle method">
            <option value="none" selected="True">None</option>
            <option value="shortest_branch">Shortest branch</option>
            <option value="lowest_intensity_voxel">Lowest intensity voxel</option>
            <option value="lowest_intensity_branch">Lowest intensity branch</option>
        </param>
        <param name="prune_ends" type="select" label="Prune ends">
            <option value="no" selected="True">No</option>
            <option value="yes">Yes</option>
        </param>
        <param name="calculate_largest_shortest_path" type="select" label="Calculate largest shortest path">
            <option value="no" selected="True">No</option>
            <option value="yes">Yes</option>
        </param>
        <param name="show_detailed_info" type="select" label="Show detailed info">
            <option value="no" selected="True">No</option>
            <option value="yes">Yes</option>
        </param>
        <expand macro="max_heap_size_type_conditional" />
    </inputs>
    <outputs>
        <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="skeletonized_blobs.gif" />
            <param name="input_datatype" value="gif" />
            <output name="output" file="basic.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="input" value="skeletonized_clown.jpg" />
            <param name="input_datatype" value="jpg" />
            <param name="prune_cycle_method" value="shortest_branch" />
            <output name="output" file="shortest_branch_basic.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="input" value="skeletonized_blobs.gif" />
            <param name="input_datatype" value="gif" />
            <param name="calculate_largest_shortest_path" value="yes" />
            <output name="output" file="largest_shortest_path_basic.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="input" value="skeletonized_blobs.gif" />
            <param name="input_datatype" value="gif" />
            <param name="show_detailed_info" value="yes" />
            <output name="output" file="detailed.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="input" value="skeletonized_clown.jpg" />
            <param name="input_datatype" value="jpg" />
            <param name="prune_cycle_method" value="shortest_branch" />
            <param name="calculate_largest_shortest_path" value="yes" />
            <param name="show_detailed_info" value="yes" />
            <output name="output" file="shortest_branch_all_yes.tabular" ftype="tabular" />
        </test>
    </tests>
    <help>
**What it does**

<![CDATA[
Tags all pixel/voxels in a skeleton image and then counts all its junctions, triple and quadruple
points and branches, and measures their average and maximum length.  The "Skeletonize images" tool
produces skeleton images that can be used as input to this tool.  Images that have not been
skeletonized will not result in errors, but the results may or may not be useful.  The underlying
AnalyzeSkeleton Fiji plugin works on grayscale images, so other image types will automatically be
converted to grayscale before they are analyzed.  This step is performed using the ImageJ **Make
Binary** command.

The voxels are classified into three different categories depending on their 26 neighbors:

- **End-point** voxels: if they have less than 2 neighbors.
- **Junction** voxels: if they have more than 2 neighbors.
- **Slab** voxels: if they have exactly 2 neighbors.

-----

**Options**

- **Prune cycle method**: prune the possible loops in the skeleton.
- **Prune ends**: prunes any branch that ends in an end-point.
- **Calculate largest shortest path**: calculate the largest shortest path of each skeleton using the APSP (all pairs shortest path).
- **Show detailed info**: produces information about the branches of each skeleton in the image.
]]>
    </help>
    <citations>
        <citation type="doi">10.1002/jemt.20829</citation>
        <citation type="doi">10.1038/nmeth.2102</citation>
    </citations>
</tool>