<tool id="ip_slice_image" name="Slice image into patches" version="0.3-3">
    <description></description>
    <macros>
        <import>creators.xml</import>
        <import>tests.xml</import>
    </macros>
    <creator>
        <expand macro="creators/bmcv" />
    </creator>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">galaxy_image_analysis</xref>
    </xrefs>
    <requirements> 
        <requirement type="package" version="0.14.2">scikit-image</requirement>
        <requirement type="package" version="1.15.4">numpy</requirement>
        <requirement type="package" version="1.1.0">scipy</requirement>
        <requirement type="package" version="0.15.1">tifffile</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[

        mkdir ./out &&

        python '$__tool_directory__/slice_image.py'
        '$input_file' ./out

        --stride '$stride'
        --window_size '$patch_size'
        --bg_thresh '$bg_thresh'

        #if $n_thresh > 0:
            --n_thresh '$n_thresh'
        #end if

        #if len('$seed') > 0:
            --seed '$seed'
        #end if

        && ls -l ./out

    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="tiff,png" label="Input image"/> 
        <param name="stride" type="integer" optional="true" value="16" min="1" label="Stride" help="Minimum offset between any two patches in pixels."/>
        <param name="patch_size" type="integer" optional="true" value="64" label="Patch size" help="Width of the patches in pixels (the height is identical)."/>
        <param name="bg_thresh" type="float" optional="true" value="0" min="0" label="Maximum patch homogeneity" help="If larger than 0, patches with a homogeneity above this threshold will be considered as purely background and discarded."/>
        <param name="n_thresh" type="integer" optional="true" label="Maximum number of patches" value="0" min="0" help="If larger than 0, only the specified number of patches will be retained (or less). Those will be selected randomly."/>
        <param name="seed" type="hidden" value=""/>
    </inputs>
    <outputs>
        <collection name="slices" type="list" label="Slices obtained from input">
            <discover_datasets directory="out" format="tiff" pattern="__name__"/>
        </collection>
    </outputs>
    <tests>
        <!-- Tests for TIFF input -->
        <test>
            <param name="input_file" value="input.tiff"/>
            <param name="n_thresh" value="5"/>
            <param name="seed" value="17"/>
            <output_collection name="slices" type="list">
                <expand macro="tests/intensity_image_diff/element" name="148.tiff" value="input_148.tiff" ftype="tiff"/>
                <expand macro="tests/intensity_image_diff/element" name="155.tiff" value="input_155.tiff" ftype="tiff"/>
                <expand macro="tests/intensity_image_diff/element" name="187.tiff" value="input_187.tiff" ftype="tiff"/>
                <expand macro="tests/intensity_image_diff/element" name="212.tiff" value="input_212.tiff" ftype="tiff"/>
                <expand macro="tests/intensity_image_diff/element" name="267.tiff" value="input_267.tiff" ftype="tiff"/>
            </output_collection>
        </test>
        <!-- TODO: Add tests for PNG input -->
    </tests>
    <help>

        **Slices an image into multiple smaller, square-shaped patches.**

        For overlapping patches, set the stride to a value smaller than the patch size.
        For non-overlapping patches, set the stride to a value identical to the patch size (or larger).
        If the stride is set to a value larger than the patch size, parts of the original image will be skipped.

        Optionally, patches entirely corresponding to image background are discarded.
        To decide whether a patch corresponds to image background, the `homogeneity`_ of its `gray-level co-occurrence matrix`_ is considered.

        .. _homogeneity: https://scikit-image.org/docs/stable/api/skimage.feature.html#skimage.feature.graycoprops
        .. _gray-level co-occurrence matrix: https://scikit-image.org/docs/stable/api/skimage.feature.html#skimage.feature.graycomatrix

        In addition, the number of the remaining patches can be reduced by specifying a maximum number of patches to retain.
        Those will be selected randomly.

    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>