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[codex] Add ForestMamba Galaxy wrapper - #5

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[codex] Add ForestMamba Galaxy wrapper#5
kgerb wants to merge 20 commits into
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codex/forestmamba-galaxy-wrapper

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@kgerb

@kgerb kgerb commented Jun 22, 2026

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Summary

Adds a Galaxy wrapper for ForestMamba under tools/3dtrees_forestmamba.

  • adds forestmamba.xml modeled after the existing 3Dtrees SegmentAnyTree wrapper
  • sets tool version 1.0.0+galaxy0
  • uses the local Docker image forestmamba-3dtrees-runtime-readable:latest for now
  • calls /workspace/src/run.py with parameters from the Galaxy XML
  • does not pin CUDA_VISIBLE_DEVICES; GPU allocation is left to the Galaxy/runtime scheduler
  • exposes only the user-facing bluepoint controls; operational defaults such as chunk size, dimension names, checkpoint, config path, and spatial matching tolerance are hidden
  • includes mikro.laz as test data and a deterministic missing-checkpoint failure test

Visible Parameters

  • Input LAZ/LAS point cloud: the point cloud to segment.
  • Bluepoint iterations: 0 runs normal one-pass inference; 2 enables the dense-forest bluepoint flow.
  • Bluepoint score threshold: optional model confidence threshold override for bluepoint runs.
  • Second pass threshold: fraction of first-pass non-ground points with raw instance_pred == -1 required before the second bluepoint pass runs. Default 0.01 means more than 1%.

WANDB_MODE=disabled is set internally to prevent upstream Weights & Biases experiment logging during Galaxy jobs.

Related PRs

Validation

  • XML parse check with xml.etree.ElementTree
  • planemo lint tools/3dtrees_forestmamba/forestmamba.xml passed

Runtime Note

A GPU0 Docker run against mikro.laz was attempted with forestmamba-3dtrees-runtime-readable:latest, but Docker startup/exec hung before the wrapper command produced output. The GPU test still needs to be rerun once the local Docker runtime is responsive.

@kgerb
kgerb force-pushed the codex/forestmamba-galaxy-wrapper branch from aff3458 to 79b7518 Compare June 22, 2026 20:06
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