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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3dtrees_segmentanytree commit 7540181d97a24b5bf07dde308f6d79bee5f18c9c
author bgruening
date Thu, 30 Oct 2025 14:37:55 +0000
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1 <tool id="3dtrees_segmentanytree" name="3Dtrees: SegmentAnyTree" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
2 <description>
3 Forest instance segmentation.
4 </description>
5 <macros>
6 <token name="@TOOL_VERSION@">1.1.0</token>
7 <token name="@VERSION_SUFFIX@">0</token>
8 </macros>
9 <requirements>
10 <container type="docker">
11 ghcr.io/3dtrees-earth/3dtrees_sat:@TOOL_VERSION@
12 </container>
13 </requirements>
14 <command detect_errors="exit_code"><![CDATA[
15 export NUMBA_CACHE_DIR=\$TMPDIR &&
16 #if $input.ext == "zip":
17 ln -s '$input' input.zip &&
18 python3.8 -u /src/run.py
19 --dataset-path input.zip
20 --output-dir .
21 --log_file '$log_file' &&
22 mv processed_files.zip '$output'
23 #if $log_file:
24 && mv resource_usage.log '$resource_usage'
25 #end if
26 #else:
27 ln -s '$input' input.laz &&
28 python3.8 -u /src/run.py
29 --dataset-path input.laz
30 --output-dir .
31 --log_file '$log_file' &&
32 mv segmented_pc.laz '$output'
33 #if $log_file:
34 && mv resource_usage.log '$resource_usage'
35 #end if
36 #end if
37 ]]>
38 </command>
39 <inputs>
40 <param argument="--input" type="data" format="zip,laz" label="Input Dataset" help="ZIP file containing point cloud data with required folder structure / single LAZ/LAS point cloud file."/>
41 <param argument="--log_file" type="boolean" label="Resource log" help="If set to true, it returns a log file containing the CPU, RAM and GPU usage statistics"/>
42 </inputs>
43 <outputs>
44 <data name="output" format="zip" label="Processed Files">
45 <change_format>
46 <when input="input.ext" value="laz" format="laz"/>
47 </change_format>
48 </data>
49 <data name="resource_usage" format="txt" label="Resource Usage">
50 <filter>log_file</filter>
51 </data>
52 </outputs>
53 <tests>
54 <test expect_num_outputs="2">
55 <param name="input" value="prepared_files_mikro.zip"/>
56 <param name="log_file" value="true"/>
57 <output name="resource_usage">
58 <assert_contents>
59 <has_line line="timestamp,cpu_percent,cpu_cores_used,cpu_cores_total,mem_used_mb,mem_total_mb,gpu_mem_used_mb,gpu_mem_total_mb" n="1"/>
60 </assert_contents>
61 </output>
62 <assert_stdout>
63 <has_text text="Loading checkpoint from /src/SegmentAnyTree/model_file/PointGroup-PAPER.pt"/>
64 <has_text text="Segmentation complete"/>
65 </assert_stdout>
66 </test>
67 <test expect_exit_code="1" expect_failure="true">
68 <param name="input" value="mikro.laz"/>
69 <param name="log_file" value="false"/>
70 <assert_stderr>
71 <has_text text="RuntimeError: Found no NVIDIA driver"/>
72 </assert_stderr>
73 <assert_stdout>
74 <has_text text="Loading checkpoint from /src/SegmentAnyTree/model_file/PointGroup-PAPER.pt"/>
75 </assert_stdout>
76 </test>
77 </tests>
78 <help format="markdown">
79 **What it does**
80
81 This tool performs deep learning-based tree segmentation on LiDAR point clouds using the **SegmentAnyTree** algorithm (Wielgosz et al., 2024). It is sensor- and platform-agnostic, working across airborne (ALS/ULS), terrestrial (TLS), and mobile (MLS) laser scanning data.
82
83 -----
84
85
86 **Input**
87 - A **ZIP file** containing the following directory structure:
88
89 00_original/
90 input.laz
91 01_subsampled/
92 input_subsampled.laz
93 02_input_SAT/
94 tile_1.laz
95 tile_2.laz
96 ...
97
98 - A single **LAZ/LAS file** containing a point cloud
99
100 -----
101
102 **Output**
103
104 The output depends on the input type:
105 - **ZIP input** → ZIP output containing the complete processed folder structure.
106 - **LAZ input** → Single LAZ output file `segmented_pc.laz` containing the segmented point cloud with tree instance IDs.
107
108 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 preprocess and remap the segmented point cloud back to original resolution.
109
110 </help>
111 <creator>
112 <person name="Marc Wielgosz" email="maciej.wielgosz@nibio.no" url="https://maciej.wielgosz.info/"/>
113 <person name="Kilian Gerberding" email="kilian.gerberding@geosense.uni-freiburg.de" url="https://orcid.org/0009-0002-5001-2571"/>
114 <organization name="3Dtrees-Team, University of Freiburg" url="https://github.com/3dTrees-earth"/>
115 </creator>
116 <citations>
117 <citation type="doi">10.1016/j.rse.2024.114367</citation>
118 <citation type="bibtex">
119 @misc{3dtrees_segmentanytree, title = {3Dtrees: SegmentAnyTree}, author = {3Dtrees-Project}, year = {2025}}
120 </citation>
121 </citations>
122 </tool>