feat: add CSP stand segmentation Galaxy tool

.github/workflows/pr.yaml

@@ -5,6 +5,7 @@ on:
       - 'deprecated/**'
       - 'docs/**'
       - '.github/**'
+      - 'tools/3dtrees_csp_stand_segmentation/**'
       - '*'
   push:
     branches:
@@ -14,6 +15,7 @@ on:
       - 'deprecated/**'
       - 'docs/**'
       - '.github/**'
+      - 'tools/3dtrees_csp_stand_segmentation/**'
       - '*'
 env:
   GALAXY_FORK: galaxyproject

.github/workflows/pr_without_tool_change.yaml

@@ -4,6 +4,9 @@ name: Fallback
 # see https://docs.github.com/en/repositories/configuring-branches-and-merges-in-your-repository/defining-the-mergeability-of-pull-requests/troubleshooting-required-status-checks#handling-skipped-but-required-checks
 on:
   pull_request:
+    paths-ignore:
+      - '.github/**'
+      - 'tools/3dtrees_csp_stand_segmentation/**'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true

tools/3dtrees_csp_stand_segmentation/.shed.yml

@@ -0,0 +1,11 @@
+name: 3dtrees_csp_stand_segmentation
+owner: bgruening
+description: DTM generation and multi-segmentation forest inventory with optional CSP tree segmentation.
+homepage_url: https://github.com/3dTrees-earth/3dtrees_CSP_StandSegmentation
+long_description: |
+  Creates a DTM and forest inventories for one or more LAS instance dimensions.
+  Comparative Shortest Path segmentation can optionally add PredInstance_CSP.
+remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/3dtrees_csp_stand_segmentation
+type: unrestricted
+categories:
+- "Geo Science"

tools/3dtrees_csp_stand_segmentation/README.rst

@@ -0,0 +1,30 @@
+3Dtrees: CSP StandSegmentation
+==============================
+
+Galaxy wrapper for DTM generation, repeatable multi-segmentation forest
+inventory, and optional Comparative Shortest Path tree segmentation.
+
+The wrapper copies Galaxy's extensionless internal dataset to ``input.laz``,
+the same pattern used by ``3dtrees_standardization/standard.xml``. This adds
+temporary disk I/O and storage proportional to the compressed input size but
+keeps the copy operation outside the R process's memory footprint.
+
+The default interface exposes the input, repeatable instance/species dimension
+mapping, non-tree IDs, CSP mode and seed source, AOI, 0.2 m DTM resolution, and
+random seed. Algorithm controls are grouped under **Keep defaults** and
+**Fine-tune** sections.
+
+Inventory-only runs default to bounded 300 m spatial reads, a 5 m DTM buffer,
+10 DTM workers, and 64 disk-backed instance partitions. DTM generation uses
+spatial reads below 50 million points. For larger inputs it streams the source
+in parallel, retains the minimum Z at each deterministic 0.1 m cell centre,
+and runs CSF/TIN on that reduced surface in buffered 300 m tiles. These controls
+are available under **Inventory memory settings**. CSP still reads the complete
+cloud because its global voxel routing and point-cloud output must preserve
+upstream behavior.
+
+Run validation from the ``galaxytools`` repository::
+
+    planemo lint tools/3dtrees_csp_stand_segmentation/3dtrees_csp_stand_segmentation.xml
+    planemo test tools/3dtrees_csp_stand_segmentation/3dtrees_csp_stand_segmentation.xml --docker
+    planemo shed_lint tools/3dtrees_csp_stand_segmentation

tools/3dtrees_csp_stand_segmentation/test-data/mikro_aoi.geojson

@@ -0,0 +1,14 @@
+{
+  "type": "Feature",
+  "properties": {"name": "mikro-west"},
+  "geometry": {
+    "type": "Polygon",
+    "coordinates": [[
+      [416948.0, 5347395.0],
+      [416957.0, 5347395.0],
+      [416957.0, 5347412.0],
+      [416948.0, 5347412.0],
+      [416948.0, 5347395.0]
+    ]]
+  }
+}

tools/3dtrees_csp_stand_segmentation/test-data/mikro_seeds.tsv

@@ -0,0 +1,3 @@
+X	Y	Z	TreeID
+416948.12	5347399.39	1.37	1
+416965.07	5347400.74	0.88	2