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feat: add CSP stand segmentation Galaxy tool - #9

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codex/csp-stand-segmentation-wrapper
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feat: add CSP stand segmentation Galaxy tool#9
kgerb wants to merge 19 commits into
masterfrom
codex/csp-stand-segmentation-wrapper

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@kgerb

@kgerb kgerb commented Jul 15, 2026

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What changed

  • add 3Dtrees: CSP StandSegmentation (3dtrees_csp_stand_segmentation)
  • expose common inventory/CSP controls by default and group algorithm controls under Keep defaults / Fine-tune
  • add hidden DTM/inventory controls with defaults of 300 m tiles, 5 m buffer, 10 DTM workers, automatic streaming above 50 million points, 0.1 m candidates, and 64 instance partitions
  • add conditional DTM, inventory, species, seed, CSP point-cloud, metadata, and resource outputs
  • add real LAZ, FM/species, supplied-seed, and native-coordinate AOI fixtures
  • increment the wrapper revision to 0.2.0+galaxy2

Why

The wrapper provides a single Galaxy entry point for DTM generation and repeatable inventories over SAT, ForestMamba, and optional CSP segmentation dimensions. A point cloud is emitted only when CSP is created.

Validation

  • XML validation and planemo lint pass with four functional tests discovered
  • previous local Planemo Docker run: 4/4 integration tests pass
  • local ToolShed packaging/YAML/README checks pass; the current shed_lint run reaches only the network version check before DNS is blocked
  • final CLI/image smoke test uses the same Fine-tune flags and returns DTM/tables without a CSP point cloud
  • dependent tool DTM path validated on dataset 2056 at 1.14 billion points under 10 CPUs/50 GB

The command copies Galaxy's extensionless dataset to input.laz, matching the existing 3dtrees standardization wrapper.

Depends on 3dTrees-earth/3dtrees_CSP_StandSegmentation#1.

CI note

CI is intentionally disabled for tools/3dtrees_csp_stand_segmentation/**. Review should use the local validation evidence above.

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