From a79dbec2bb5e6b5d035fe4d36cae0a2e2185dae3 Mon Sep 17 00:00:00 2001
From: Hannah Greven <greven.hannah@gmail.com>
Date: Mon, 12 Jan 2026 17:17:54 +0100
Subject: [PATCH 1/2] Add xml file for raycloudtools

---
 tools/raycloudtools.xml | 90 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 90 insertions(+)
 create mode 100644 tools/raycloudtools.xml

diff --git a/tools/raycloudtools.xml b/tools/raycloudtools.xml
new file mode 100644
index 0000000..56feac6
--- /dev/null
+++ b/tools/raycloudtools.xml
@@ -0,0 +1,90 @@
+<tool id="3dtrees_raycloudtools" name="3DTrees: RayCloudTools" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.1" license="BSD-3-Clause">
+    <description>Tree instance segmentation</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <container type="docker">
+            ghcr.io/3dtrees-earth/3dtrees_rct:@TOOL_VERSION@
+        </container>
+    </requirements>
+    
+    <command detect_errors="exit_code"><![CDATA[
+        python3 -u /src/run.py 
+        --dataset-path '$input'
+        --output-dir .
+        # other params defined in parameters.py
+        ]]>
+    </command>
+
+    <inputs>
+        <param name="input" type="data" format="laz" label="Input Dataset (.laz)" 
+                help="Input file to process"/>
+        <!-- Add your specific parameters from parameters.py -->
+    </inputs>
+    
+    <outputs>
+        <data name="output" format="laz" label="Output" from_work_dir="final_results.laz"/>
+    </outputs>
+    
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="Example_Tree_RCT.laz"/>
+            <output name="output" file="final_results.laz">
+                <assert_contents>
+                    <has_size value="20k" delta="10k"/>  <!-- 10-30KB -->
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+
+    <help format="markdown">
+**What it does**
+
+This tool performs graph-based tree instance segmentation on LiDAR point clouds using the **RayExtract** algorithm (Devereux et al., 2026) implemented as part of **RayCloudTools** (Lowe &amp; Stepanas, 2021). 
+It is platform-agnostic and works across airborne (ULS), terrestrial (TLS), and mobile (MLS) laser scanning data, as long as trees are well-represented by points along the entire tree length.
+  
+-----
+
+**Processing Steps**
+
+- Convert input point cloud to LAZ 1.2
+- Import point cloud as ray cloud
+- Extract terrain
+- Extract trees
+- Convert point color (segmentation result) to instance IDs
+- Add instance IDs back to input point cloud  
+
+-----
+
+**Output**
+
+Original LAZ point cloud + instance IDs in extra dimension 'PredInstance'.
+
+***Tip:** We recommend using the [3DTrees: Tile and Merge](https://usegalaxy.eu/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2F3dtrees_tile_merge%2F3dtrees_tile_merge%2F1.0.1%2Bgalaxy0&amp;version=latest) tool to process large point clouds (workflow: tile → segment → merge)!*
+
+-----
+
+**Third-Party Components**  
+
+You agree to comply with the licence terms for these components as part of accessing the tool.
+
+**RayCloudTools:** Copyright (c) 2020, Commonwealth Scientific and Industrial Research Organisation (CSIRO) ABN 41 687 119 230 | [CSIRO-Open Source Software License (variation of the BSD / MIT License)](https://github.com/csiro-robotics/raycloudtools); 
+**PDAL:** Copyright (c) 2025, Hobu, Inc. (howard@hobu.co) | [pdal License (BSD)](https://github.com/PDAL/PDAL?tab=License-1-ov-file#readme);
+**NumPy:** Copyright (c) 2005-2025, NumPy Developers | [numpy License (BSD)](https://github.com/numpy/numpy?tab=License-1-ov-file#readme); 
+**LasPy:** Copyright (c) 2012, Grant Brown, grant.brown73 at gmail.com, Copyright (c) 2012, Howard Butler, hobu.inc at gmail.com, Copyright (c) 2020, Thomas Montaigu, thomas.montaigu@laposte.net | [laspy License](https://github.com/laspy/laspy?tab=License-1-ov-file#readme); 
+**Open3D:** Copyright (c) 2018-2023 www.open3d.org | [Open3D License (MIT)](https://github.com/isl-org/Open3D?tab=License-1-ov-file#readme).
+    </help>
+    <creator>
+        <person name="Hannah Greven" email="hannah.greven@hnee.de"/>
+        <organization name="3Dtrees-Team, University of Freiburg" url="https://github.com/3dTrees-earth"/>
+    </creator>
+    <citations>
+        <citation type="doi">10.1016/j.rse.2025.115162</citation>
+        <citation type="doi">10.1109/ACCESS.2021.3084954</citation>
+        <citation type="bibtex">
+            @misc{3dtrees_raycloudtools, title = {3Dtrees: RayCloudTools}, author = {3Dtrees-Project}, year = {2025}}
+        </citation>
+    </citations>
+</tool>
\ No newline at end of file

From 77d0a8fd6e821343964e1cf9415eb4636c9078ed Mon Sep 17 00:00:00 2001
From: Hannah Greven <greven.hannah@gmail.com>
Date: Thu, 2 Apr 2026 16:23:28 +0200
Subject: [PATCH 2/2] Update raycloudtools.xml

Updates tool to v1.1.0. Introduces full parameter control, output collection with segmented point cloud, terrain mesh, treefile, and tree meshes. Extra dimension name for instance IDs in the point cloud changes to 'PredInstance_RCT'.
---
 tools/raycloudtools.xml | 85 ++++++++++++++++++++++++++++++++++-------
 1 file changed, 71 insertions(+), 14 deletions(-)

diff --git a/tools/raycloudtools.xml b/tools/raycloudtools.xml
index 56feac6..6272189 100644
--- a/tools/raycloudtools.xml
+++ b/tools/raycloudtools.xml
@@ -1,7 +1,7 @@
-<tool id="3dtrees_raycloudtools" name="3DTrees: RayCloudTools" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.1" license="BSD-3-Clause">
+<tool id="3dtrees_raycloudtools" name="3Dtrees: RayCloudTools" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.1" license="BSD-3-Clause">
     <description>Tree instance segmentation</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.0.0</token>
+        <token name="@TOOL_VERSION@">1.1.1</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
@@ -11,10 +11,30 @@
     </requirements>
     
     <command detect_errors="exit_code"><![CDATA[
+        mkdir 'in' &&
+        mkdir 'out' &&
+        ln -s '$input' 'in/$input.element_identifier' &&
         python3 -u /src/run.py 
-        --dataset-path '$input'
-        --output-dir .
-        # other params defined in parameters.py
+        --dataset-path 'in/$input.element_identifier'
+        --output-dir 'out'
+        --gradient '$gradient'
+        --max-diameter '$max_diameter'
+        --crop-length '$crop_length'
+        --distance-limit '$distance_limit'
+        --height-min '$height_min'
+        --girth-height-ratio '$girth_height_ratio'
+        --global-taper '$global_taper'
+        --global-taper-factor '$global_taper_factor'
+        --gravity-factor '$gravity_factor'
+        #if $branch_segmentation:
+        --branch-segmentation
+        #end if
+        #if $treeinfo:
+        --treeinfo
+        #end if
+        #if $branch_data:
+        --branch_data
+        #end if
         ]]>
     </command>
 
@@ -22,20 +42,57 @@
         <param name="input" type="data" format="laz" label="Input Dataset (.laz)" 
                 help="Input file to process"/>
         <!-- Add your specific parameters from parameters.py -->
+        <!-- rayextract terrain -->
+        <param argument="--gradient" type="float" min="0.001" max="1000" value="1" label="Gradient" help="Gradient threshold for terrain extraction"/>
+        <!-- rayextract trees -->
+        <param argument="--max-diameter" type="float" min="0.01" max="100" value="0.9" label="Maximum diameter" help="maximum trunk diameter in segmenting trees (m)"/>
+        <param argument="--crop-length" type="float" min="0.01" max="100" value="1" label="Crop length" help="Crops branches up to this distance from tip (m)."/>
+        <param argument="--distance-limit" type="float" min="0.01" max="10" value="1" label="Distance limit" help="Maximum distance between neighbour points in a tree (m)"/>
+        <param argument="--height-min" type="float" min="0.01" max="1000" value="2" label="Minimum tree height" help="Minimum height counted as a tree (m)"/>
+        <param argument="--girth-height-ratio" type="float" min="0.001" max="0.5" value="0.12" label="Girth height ratio" help="Amount up tree's height to estimate trunk girth"/>
+        <param argument="--global-taper" type="float" min="0" max="1" value="0.024" label="Global taper" help="Force taper value (diameter per length) for trees under global_taper_factor of max tree height - use 0 to estimate global taper from the data"/>
+        <param argument="--global-taper-factor" type="float" min="0" max="1" value="0.3" label="Global taper factor" help="1 estimates same taper for whole scan, 0 is per-tree tapering, values between 0 and 1 produce soft cutoff at this amount of max tree height"/>
+        <param argument="--gravity-factor" type="float" min="0" max="1" value="0.3" label="Gravity factor" help="Larger values preference vertical trees"/>
+        <param argument="--branch-segmentation" type="boolean" checked="false" label="Branch segmentation" help="Segments per branch segment - assigns IDs per branch segment instead of per tree instance"/>
+        <!-- treeinfo -->
+        <param argument="--treeinfo" type="boolean" checked="false" label="Treeinfo" help="Calculate tree attributes - dbh, height, crown radius, volume, ..."/>
+        <param argument="--branch-data" type="boolean" checked="false" label="Branch data" help="Calculate branch attributes - branch number, segment_length, branch order number, extension and position in branch integers per-segment"/>
     </inputs>
     
     <outputs>
-        <data name="output" format="laz" label="Output" from_work_dir="final_results.laz"/>
+        <!-- collection with terrain, segmented point cloud, and treefile -->
+        <collection name="raycloudtools_outputs_default" type="list" label="RayCloudTools">
+            <!--to exclude tree meshes pattern="(?P&lt;designation&gt;.*_segmented|.*_trees|^(?!.*trees).*_mesh)\.(?P&lt;ext&gt;laz|txt|(?&lt;=_mesh\.)ply)"-->
+            <discover_datasets pattern="(?P&lt;designation&gt;.*_segmented|.*_trees|.*_mesh)\.(?P&lt;ext&gt;laz|txt|(?&lt;=_mesh\.)ply)" directory="out" ext="$ext"/>
+            <filter>not treeinfo</filter>
+        </collection>
+        <!-- collection with terrain, segmented point cloud, and treefile with tree attributes -->
+        <collection name="raycloudtools_outputs_treeinfo" type="list" label="RayCloudTools (treeinfo)">
+            <!-- to exclude tree meshes pattern="(?P&lt;designation&gt;.*_segmented|.*_trees_info|^(?!.*trees).*_mesh)\.(?P&lt;ext&gt;laz|txt|(?&lt;=_mesh\.)ply)"-->
+            <discover_datasets pattern="(?P&lt;designation&gt;.*_segmented|.*_trees_info|.*_mesh)\.(?P&lt;ext&gt;laz|txt|(?&lt;=_mesh\.)ply)" directory="out" ext="$ext"/>
+            <filter>treeinfo</filter>
+        </collection>
     </outputs>
-    
+
     <tests>
         <test expect_num_outputs="1">
             <param name="input" value="Example_Tree_RCT.laz"/>
-            <output name="output" file="final_results.laz">
-                <assert_contents>
-                    <has_size value="20k" delta="10k"/>  <!-- 10-30KB -->
-                </assert_contents>
-            </output>
+            <output_collection name="raycloudtools_outputs_default" count="4" type="list">
+                <element name="Example_Tree_RCT_mesh" file="Example_Tree_RCT_mesh.ply" compare="contains"/>
+                <element name="Example_Tree_RCT_segmented" file="Example_Tree_RCT_segmented.laz" compare="contains"/>
+                <element name="Example_Tree_RCT_trees" file="Example_Tree_RCT_trees.txt" compare="contains"/>
+                <element name="Example_Tree_RCT_trees_mesh" file="Example_Tree_RCT_trees_mesh.ply" compare="contains"/>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="Example_Tree_RCT.laz"/>
+            <param name="treeinfo" value="true"/>
+            <output_collection name="raycloudtools_outputs_treeinfo" count="4" type="list">
+                <element name="Example_Tree_RCT_mesh" file="Example_Tree_RCT_mesh.ply" compare="contains"/>
+                <element name="Example_Tree_RCT_segmented" file="Example_Tree_RCT_segmented.laz" compare="contains"/>
+                <element name="Example_Tree_RCT_trees_info" file="Example_Tree_RCT_trees_info.txt" compare="contains"/>
+                <element name="Example_Tree_RCT_trees_mesh" file="Example_Tree_RCT_trees_mesh.ply" compare="contains"/>
+            </output_collection>
         </test>
     </tests>
 
@@ -60,9 +117,9 @@ It is platform-agnostic and works across airborne (ULS), terrestrial (TLS), and
 
 **Output**
 
-Original LAZ point cloud + instance IDs in extra dimension 'PredInstance'.
+Original LAZ point cloud + instance IDs in extra dimension 'PredInstance_RCT'.
 
-***Tip:** We recommend using the [3DTrees: Tile and Merge](https://usegalaxy.eu/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2F3dtrees_tile_merge%2F3dtrees_tile_merge%2F1.0.1%2Bgalaxy0&amp;version=latest) tool to process large point clouds (workflow: tile → segment → merge)!*
+***Tip:** We recommend using the '3DTrees: Tile and Merge' or '3DTrees: Smart Tile' tool to process large point clouds (workflow: tile → segment → merge)!*
 
 -----