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Update 3dtrees_standardization v1.1 (#1747)
* Update standard.xml to use conditional mode selector and fix Docker image * naming consistency * Refactor standard.xml to improve command paths and update input collection parameter. Changed output expectations for tests and clarified documentation for collection mode validation. * add second test file * remove mikro2; add single file test; fix multiple=true issue * update to include mikro2 * Update tools/3dtrees_standardization/standard.xml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Update tools/3dtrees_standardization/standard.xml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * add proper json tests * add suggestions * fix typo * Update standard.xml --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
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‎tools/3dtrees_standardization/standard.xml‎

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<tool id="3dtrees_standardization" name="3Dtrees: LAZ Standardization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
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<description>
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laz file checks and standardization.
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</description>
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<tool id="3dtrees_standardization" name="3DTrees: LAS/LAZ Standardization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
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<description>Standardize LAS/LAZ files or validate collections for consistency</description>
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<macros>
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<token name="@TOOL_VERSION@">1.0.1</token>
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<token name="@TOOL_VERSION@">1.1.0</token>
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<token name="@VERSION_SUFFIX@">0</token>
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</macros>
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<requirements>
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<container type="docker">ghcr.io/3dtrees-earth/3dtrees-pc-standard:@TOOL_VERSION@</container>
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</requirements>
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<command detect_errors="exit_code"><![CDATA[
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## needed because the Rscript is following symlinks
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cp '$input' /in/input.laz &&
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cd /src &&
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Rscript run.R
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--dataset-path /in/input.laz
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--output-dir .
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--min-density
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$min_density &&
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mv /src/pc_standardized.laz '$pc_standardized'
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]]>
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</command>
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#if $mode.task == 'single_file':
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cp '$mode.input' input.laz &&
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Rscript /src/run.R
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--dataset-path ./input.laz
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--output-dir ./
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--method single_file
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--min-density '$mode.min_density'
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#if $mode.removeable_attributes:
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--removeable_attributes '$mode.removeable_attributes'
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#end if
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#else:
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mkdir -p ./input_files &&
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#for $f in $mode.input_collection
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cp '$f' ./input_files/'${f.element_identifier}.laz' &&
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#end for
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Rscript /src/run.R
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--dataset-path ./input_files/
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--output-dir ./
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--method collection
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#end if
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]]></command>
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<inputs>
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<param name="input" type="data" format="laz" label="Point Cloud Dataset" help="LAZ point cloud to process"/>
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<param name="min_density" type="integer" value="500" min="1" max="10000" label="Minimum Point Density (points/m²)" help="Minimum required point density in points per square meter. Default: 500 for TLS data. Use lower values (e.g., 10-50) for ALS data."/>
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<conditional name="mode">
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<param name="task" type="select" label="Mode">
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<option value="single_file">Single File Standardization</option>
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<option value="collection">Collection Validation</option>
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</param>
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<when value="single_file">
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<param name="input" type="data" format="laz" label="Point Cloud File"
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help="LAS/LAZ point cloud file to standardize (CRS validation, density check, format normalization)"/>
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<param argument="--min-density" type="integer" min="1" max="10000" value="10"
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label="Minimum Point Density"
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help="Minimum acceptable point density in points per square meter. Default: 10 pts/m²"/>
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<param argument="--removeable_attributes" type="text" value="" optional="true"
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label="Attributes to Remove"
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help="Space-separated list of attribute names to remove (e.g., 'Intensity UserData'). Leave empty for auto-detection."/>
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</when>
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<when value="collection">
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<param name="input_collection" type="data" format="laz" multiple="true" label="Point Cloud Collection"
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help="Multiple LAZ/LAS files to validate for consistency (CRS homogeneity, attribute consistency, overlaps)"/>
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</when>
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</conditional>
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</inputs>
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<outputs>
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<data name="pc_standardized" format="laz" label="Standardized Point Cloud"/>
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<data name="pc_standardized" format="laz" label="standardized" from_work_dir="input.laz">
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<filter>mode['task'] == "single_file"</filter>
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</data>
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<data name="metadata_json" format="json" label="metadata" from_work_dir="input.json">
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<filter>mode['task'] == "single_file"</filter>
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</data>
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<data name="convex_hull" format="geojson" label="convex_hull" from_work_dir="input_convex_hull_wgs84.GeoJSON">
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<filter>mode['task'] == "single_file"</filter>
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</data>
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<data name="collection_summary" format="json" label="collection_summary" from_work_dir="collection_summary.json">
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<filter>mode['task'] == "collection"</filter>
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</data>
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</outputs>
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<tests>
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<test>
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<param name="input" value="mikro.laz" ftype="laz"/>
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<param name="min_density" value="10"/>
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<output name="pc_standardized">
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<test expect_num_outputs="3">
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<conditional name="mode">
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<param name="task" value="single_file"/>
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<param name="input" value="mikro.laz" ftype="laz"/>
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<param name="min_density" value="10"/>
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</conditional>
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<output name="pc_standardized" ftype="laz">
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<assert_contents>
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<has_size min="1000"/>
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</assert_contents>
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</output>
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<output name="convex_hull" ftype="geojson">
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<assert_contents>
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<has_size value="100000" delta="50000"/>
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<has_json_property_with_text property="type" text="FeatureCollection"/>
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</assert_contents>
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</output>
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<output name="metadata_json" ftype="json">
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<assert_contents>
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<has_text text='"point_count":[12917]'/>
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<has_text text='"standardized":[true]'/>
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</assert_contents>
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</output>
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</test>
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<test expect_num_outputs="1">
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<conditional name="mode">
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<param name="task" value="collection"/>
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<param name="input_collection" value="mikro.laz,mikro2.laz" ftype="laz"/>
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</conditional>
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<output name="collection_summary" ftype="json">
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<assert_contents>
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<has_json_property_with_value property="n_tiles" value="2"/>
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<has_json_property_with_value property="homogeneous_crs" value="true"/>
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<has_json_property_with_value property="homogeneous_attribute_names" value="true"/>
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</assert_contents>
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</output>
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</test>
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</tests>
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<help>
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**What it does**
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This tool performs a series of checks and standardizations on a LAS/LAZ point cloud file. It checks:
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<help><![CDATA[
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**What it does**
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This tool supports two modes:
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1. **Basic LAS Validation**
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- Validates the object using las_check()
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- Ensures the file has at least 100 points
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**Single File Mode** (standardization):
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Standardizes a single LAS/LAZ file:
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2. **Bounding Box Consistency**
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- Updates header if bounding box doesn't match points
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- Validates spatial extent (all dimensions &gt; 1 meter)
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- Checks Z range is plausible (-100 to 5500 meters)
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1. **LAS Validation**: Runs ``las_check()`` and fixes header issues
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2. **Bounding Box**: Validates and corrects header bounding box
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3. **Point Density**: Checks density meets minimum threshold
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4. **CRS Validation**: Verifies CRS is defined and transformable to EPSG:4978
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5. **Land Check**: Confirms centroid is on land (using Natural Earth data)
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6. **Format Normalization**: Downgrades Point Data Format to ≤7 for compatibility
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7. **Attribute Cleanup**: Optionally removes specified attributes
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3. **Point Density Check**
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- Calculates point density using convex hull
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- Requires minimum point density (configurable, default: 500 points/m² for TLS)
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**Outputs (single file mode):**
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- Standardized ``.laz`` file
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- Metadata JSON with pre/post standardization info
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- Convex hull GeoJSON in WGS84
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4. **Extra Byte Data Type Check**
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- Validates extra byte attribute data types
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- Corrects mismatches if found
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**Collection Mode** (validation):
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Validates consistency of multiple LAS/LAZ files:
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5. **CRS Validation**
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- Ensures CRS is specified
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- Validates transformation to EPSG:3857
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- **CRS Homogeneity**: Checks if all files share the same coordinate reference system
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- **Attribute Consistency**: Verifies attribute names and types across files
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- **Tile Geometry**: Detects overlaps and gaps between tiles
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- **Global Statistics**: Computes aggregated statistics across all files
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- **Removeable Attributes**: Identifies attributes that are all-NA or constant-zero
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6. **Point Data Format Check**
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- Downgrades format to 7 if necessary
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- Preserves NIR channel as extra attribute
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**Outputs (collection mode):**
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- ``collection_summary.json`` containing collection-level checks and flags, per-file metadata (CRS, attributes, point counts, convex hulls), and suggested removeable attributes for standardization
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7. **Land Coverage Validation**
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- Validates centroid is on land using Natural Earth data
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**Workflow Usage**
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For collection-based workflows:
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1. Run this tool with **Collection Validation** first to check consistency
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2. Use the suggested ``removeable_attributes`` from the collection summary
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3. Then run this tool with **Single File Standardization** (Galaxy maps over collection automatically) for standardization
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]]></help>
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8. **Output Writing**
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- Writes standardized LAZ file with Point Format ≤ 7
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</help>
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<creator>
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<person name="Julian Frey" email="julian.frey@wwd.uni-freiburg.de" url="https://orcid.org/0000-0001-7895-702X"/>
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<person name="Janusch Vajna-Jehle" email="janusch.jehle@geosense.uni-freiburg.de" url="https://orcid.org/0009-0002-0034-9387"/>
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<person name="Kilian Gerberding" email="kilian.gerberding@geosense.uni-freiburg.de" url="https://orcid.org/0009-0002-5001-2571"/>
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<person name="Mirko Mälicke" identifier="0000-0002-0424-2651"/>
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<organization name="3Dtrees-Team, University of Freiburg" url="https://github.com/3dTrees-earth"/>
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</creator>
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<citations>
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<citation type="bibtex">
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@misc{3dtrees_standard, title = {3D Trees Standardization}, author = {3D Trees Project}, year = {2025}}

‎tools/3dtrees_standardization/test-data/mikro2.laz‎

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