<tool id="3dtrees_potree" name="3Dtrees: Potree Converter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
    <description>Convert LAS/LAZ point clouds to Potree octree format for web visualization</description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.0</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <requirements>
        <container type="docker">ghcr.io/3dtrees-earth/3dtrees_potree:@TOOL_VERSION@</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p data &&
        #for $f in $input
            ln -s '$f' data/'${f.element_identifier}.laz' &&
        #end for
        python /src/run.py
        --source data
        --outdir output
        --encoding '$encoding'
        --method '$method'
        #if $attributes
            --attributes '$attributes'
        #end if
        $keep_chunks
        $no_chunking
        $no_indexing
        $generate_page
        #if $generate_page
            &&

            ## Setup HTML with extra files for Galaxy viewing
            cp output/potree-vis.html '$viewer_html' &&
            mkdir -p '$viewer_html.files_path' &&
            cp -r /opt/PotreeConverter/resources/page_template/libs '$viewer_html.files_path/' &&
            cp -r output/pointclouds '$viewer_html.files_path/' &&
            chmod -R a+rX '$viewer_html.files_path'
        #end if
        2>&1
        ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="laz" multiple="true" label="Point Cloud Files" help="Input LAS/LAZ files to convert to Potree format" />
        <param argument="--generate-page" type="boolean" truevalue="-p potree-vis" falsevalue="" checked="false" label="Generate interactive Viewer" help="Generate a ready-to-use HTML viewer page for in-Galaxy visualization" />
        <param argument="--encoding" type="select" label="Encoding" help="Compression encoding for output">
            <option value="BROTLI" selected="true">Brotli</option>
            <option value="UNCOMPRESSED">Uncompressed</option>
        </param>
        <param argument="--method" type="select" label="Sampling Method" help="Point sampling method for octree generation">
            <option value="poisson" selected="true">Poisson</option>
            <option value="poisson_average">Poisson Average</option>
            <option value="random">Random</option>
        </param>
        <param argument="--attributes" type="text" optional="true" label="Attributes" help="Comma-separated list of attributes to include in output (e.g., 'rgb,intensity,classification'). Leave empty to use defaults." >
             <validator type="regex" message="Only letters and commas are allowed">^[a-zA-Z,]+$</validator>
        </param>
        <param argument="--keep-chunks" type="boolean" truevalue="--keep-chunks" falsevalue="" checked="false" label="Keep Chunks" help="Skip deleting temporary chunks during conversion" />
        <param argument="--no-chunking" type="boolean" truevalue="--no-chunking" falsevalue="" checked="false" label="No Chunking" help="Disable chunking phase" />
        <param argument="--no-indexing" type="boolean" truevalue="--no-indexing" falsevalue="" checked="false" label="No Indexing" help="Disable indexing phase" />
    </inputs>
    <outputs>
        <!-- HTML viewer for in-Galaxy viewing (when generate_page is specified) -->
        <data name="viewer_html" format="html" label="Potree Visualization">
            <filter>generate_page</filter>
        </data>
        <!-- Collection output - discovers files in output directory -->
        <collection name="potree_output" type="list" label="Potree Output">
            <discover_datasets pattern="(?P&lt;designation&gt;metadata)\.json$" directory="output" format="json" recurse="true"/>
            <discover_datasets pattern="(?P&lt;designation&gt;hierarchy)\.bin$" directory="output" format="binary" recurse="true"/>
            <discover_datasets pattern="(?P&lt;designation&gt;octree)\.bin$" directory="output" format="binary" recurse="true"/>
            <discover_datasets pattern="(?P&lt;designation&gt;log)\.txt$" directory="output" format="txt" recurse="true"/>
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="input" value="mikro.laz" ftype="laz"/>
            <param name="generate_page" value="true"/>
            <!-- HTML viewer for Galaxy -->
            <output name="viewer_html" ftype="html">
                <assert_contents>
                    <has_text text='Potree.loadPointCloud("./pointclouds/potree-vis/metadata.json", "potree-vis"'/>
                </assert_contents>
            </output>
            <!-- Collection output for octree data -->
            <output_collection name="potree_output" type="list" count="4">
                <element name="metadata" ftype="json">
                    <assert_contents>
                        <has_json_property_with_value property="points" value="12917" />
                    </assert_contents>
                </element>
                <element name="hierarchy" ftype="binary">
                    <assert_contents>
                        <has_size value="2500" delta="500"/>
                    </assert_contents>
                </element>
                <element name="octree" ftype="binary">
                    <assert_contents>
                        <has_size value="135000" delta="50000"/>
                    </assert_contents>
                </element>
                <element name="log" ftype="txt">
                    <assert_contents>
                        <has_text text="counting mikro.laz"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help>

**What it does**

This tool converts LAS/LAZ point cloud files to the Potree octree format for efficient web-based visualization using the Potree viewer.

**Key features:**

1. **Octree Level-of-Detail (LOD)**: Creates an efficient hierarchical structure for progressive rendering
2. **Multiple compression options**: Supports BROTLI compression for smaller file sizes
3. **Flexible sampling methods**: Choose between Poisson, Poisson Average, or Random sampling
4. **Web-ready output**: Generates files that can be directly served for Potree viewer visualization
5. **Optional web page generation**: Can generate a ready-to-use HTML viewer page

-----

**Input**

- **Point Cloud Files**: Input LAS/LAZ files to convert
- **Encoding**: Compression type (BROTLI for compression, UNCOMPRESSED for raw data, DEFAULT)
- **Sampling Method**: Algorithm for point sampling during octree generation (Poisson, Poisson Average, Random)
- **Attributes**: Optional comma-separated list of point attributes to include in output
- **Keep Chunks**: Preserve temporary chunk files after conversion
- **No Chunking**: Disable the chunking phase
- **No Indexing**: Disable the indexing phase
- **Generate Page**: Create a web viewer page with the specified name

-----

**Output**

The tool produces a collection containing:

- **metadata** (JSON): Metadata file describing the octree structure and point cloud properties
- **hierarchy** (binary): Binary file containing the octree hierarchy
- **octree** (binary): Binary file containing the point data
- **log** (text): Conversion log file

When **Generate Page** is specified (e.g., "viewer"):

- **{name} Potree Viewer** (HTML): Interactive viewer that can be viewed directly in Galaxy
  - Note: This tool is meant for visualization - other tools (eg. measurements, camera) may not work properly
  - Includes libs/ and pointclouds/ as extra files

- **{name} Potree Viewer Package (Download)** (ZIP): Self-contained package for local use
  - Download, extract, and open files in PotreeViewer.

-----

**Workflow Integration**

This tool converts point cloud data to an optimized web visualization format using PotreeConverter's octree algorithm.
The output can be downloaded and visualized using the Potree viewer.

    </help>
    <creator>
        <organization name="3Dtrees-Team, University of Freiburg" url="https://github.com/3dTrees-earth"/>
    </creator>
    <citations>
        <citation type="bibtex">@misc{potreeconverter, title = {PotreeConverter: Create multi-resolution octree structure}, author = {Markus Schütz}, year = {2024}, url = {https://github.com/potree/PotreeConverter}}</citation>
        <citation type="bibtex">
            @misc{3dtrees_potree, title = {3Dtrees: Potree Converter}, author = {3Dtrees-Project}, year = {2025}}
        </citation>
    </citations>
</tool>