ENH: Master tracking — Remote-module ingestion, archival, and consolidation

[hjmjohnson]

Primary tracking issue for all remote-module work in ITK 6. Supersedes #3371, #6060, #5174, #4263, #4786, #5557, and is related to #990. The v3 ingestion strategy is documented at Utilities/Maintenance/RemoteModuleIngest/INGESTION_STRATEGY.md.

Goal

Reduce the ~57 entries in Modules/Remote/*.remote.cmake to a small, well-curated set, by either (a) ingesting active modules into the main ITK tree under their natural group (Modules/<Group>/<Name>/) preserving upstream git blame, or (b) archiving unmaintained / superseded upstream repos read-only. Every disposition must be intentional; no module remains as a configure-time fetch unless that is the documented best fit.

Action checklist (live)

Phase 0 — infrastructure (DONE)

• Document the v3 whitelist + filter-repo merge strategy (INGESTION_STRATEGY.md)
• ingest-remote-module.sh with --audit-only and --dry-run
• normalize-ingest-commits.py (per-commit pre-commit replay; subject-prefix normalization) — deprecated 2026-04-28 as linearizing the upstream merge graph; replacement merge-preserving rewriter in COMP: Deprecate linearizing ingest helper; add merge-preserving rewriter #6162 (OPEN)
• cid-normalize.sh (md5 → IPFS CID baseline migration)
• verify-cid-access.sh, verify-whitelist-history.sh
• PruneSupersededCiCaches.py (CI cache hygiene; PR COMP: Prune superseded GitHub Actions ccache entries from CI #6151)

Phase 1 — completed ingests

• AnisotropicDiffusionLBR → Modules/Filtering/ (ENH: Ingest AnisotropicDiffusionLBR into Modules/Filtering #6093, merged 2026-04-23)
• Montage → Modules/Registration/Montage/ (ENH: Ingest ITKMontage remote module into Modules/Registration/Montage #6103, merged 2026-04-25)
• GenericLabelInterpolator → Modules/Filtering/ (ENH: Ingest ITKGenericLabelInterpolator into Modules/Filtering #6135, merged 2026-04-27)
• MGHIO → Modules/IO/MGHIO/ (ENH: Ingest ITKMGHIO into Modules/IO #6137, merged 2026-04-28)
• FastBilateral → Modules/Filtering/ (ENH: Ingest ITKFastBilateral into Modules/Filtering (supersedes #5134) #6159, merged 2026-04-29; supersedes ENH: Integrate FastBilateralImageFilter from remote module #5134)
• MeshNoise → Modules/Filtering/MeshNoise/ (ENH: Ingest ITKMeshNoise into Modules/Filtering (closes #5174) #6161, merged 2026-04-29; closes Compile error in MeshNoise/test/itkAdditiveGaussianNoiseMeshFilterTest.cxx:56 #5174)
• LabelErodeDilate → Modules/Filtering/ (ENH: Ingest ITKLabelErodeDilate into Modules/Filtering #6171, merged 2026-04-30)

Phase 2 — upstream archival (post-ingest follow-up PRs)

For each merged ingest, an archival PR on the original upstream repo deletes the whitelisted files, adds MIGRATION_README.md, and the repo is marked Archived in GitHub settings.

• ITKAnisotropicDiffusionLBR — archive
• ITKMontage — archive
• ITKGenericLabelInterpolator — archival PR open: #43
• ITKMGHImageIO — archival PR open: #50
• ITKFastBilateral — archival PR open: #16
• ITKMeshNoise — archival PR open: #37
• ITKNeuralNetworks — already archived upstream (subsumes NeuralNetworks (Numerics) module missing in recent versions #5557; close that issue with this resolution)
• ITKTBBImageToImageFilter — archive without ingestion (superseded by ITK's built-in TBB threading via PoolMultiThreader)

Phase 3 — Tier A ingest queue (pure ITK, no external deps)

The order below is the proposed ingest sequence. Modify each commit's checklist as PRs land.

Wave 1 (Filtering / IO, smallest footprint, fastest review). ⭐ = open user-filed issue or high upstream-stars community-demand signal raises priority.

Next up: ⭐ MorphologicalContourInterpolation — by far the highest community-demand signal in the Wave 1 queue (34 upstream stars vs. 1–9 for the rest), actively maintained (push 2026-04-23), 3.5 MB repo, owned by @dzenanz. Used heavily for slice-gap filling in 3D medical-image segmentation. Recommend ingesting next.

• LabelErodeDilate → Modules/Filtering/ (ENH: Ingest ITKLabelErodeDilate into Modules/Filtering #6171, merged 2026-04-30; 5★ upstream)
• ⭐ MorphologicalContourInterpolation → Modules/Filtering/ (34★, recently maintained — next)
• IOMeshSTL → Modules/IO/ (9★, dominant 3D-mesh interchange format)
• Cuberille → Modules/Filtering/ (6★, isosurface mesh extraction)
• SplitComponents → Modules/Filtering/ (5★)
• SubdivisionQuadEdgeMeshFilter → Modules/Filtering/ (4★)
• ParabolicMorphology → Modules/Filtering/ (3★)
• SmoothingRecursiveYvvGaussianFilter → Modules/Filtering/ (2★)
• IOMeshMZ3 → Modules/IO/ (2★)
• IOFDF → Modules/IO/ (2★)
• HigherOrderAccurateGradient → Modules/Filtering/ (1★)
• PolarTransform → Modules/Filtering/ (1★)
• MultipleImageIterator → Modules/Filtering/ (1★)

Wave 2 (richer or external-data-heavy). ⭐ = recent user-filed issue raises priority.

• ⭐ IOScanco → Modules/IO/ — wrapping bug IOScanco wrapping fails do to fatal error: 'itkCommand.h' file not found #5920 (closed 2026-03-11) signals active user dependency
• BoneEnhancement → Modules/Filtering/
• BoneMorphometry → Modules/Filtering/
• TextureFeatures → Modules/Filtering/
• IsotropicWavelets → Modules/Filtering/
• GrowCut → Modules/Segmentation/
• RANSAC → Modules/Registration/
• VariationalRegistration → Modules/Registration/
• Thickness3D → Modules/Filtering/
• Strain → Modules/Filtering/
• PhaseSymmetry → Modules/Filtering/
• SimpleITKFilters → Modules/Filtering/
• IOScanco → Modules/IO/

Phase 4 — Tier B (external-dependency or ABI-sensitive; remain remote pending design)

These are explicitly NOT in the ingest queue without further discussion. They depend on optional external libraries, large data caches, or carry niche scope:

• CudaCommon, RTK, VkFFTBackend — GPU/CUDA stacks, separate licensing/build matrix
• SCIFIO, IOOpenSlide, IOTransformDCMTK — large external libraries (Bio-Formats, OpenSlide, DCMTK)
• TubeTK, Ultrasound, LesionSizingToolkit, HASI, SkullStrip, Cleaver — domain-specific toolkits with their own release cadences
• TractographyTRX, MeshToPolyData, PerformanceBenchmarking, SphinxExamples, WebAssemblyInterface, PrincipalComponentsAnalysis, FixedPointInverseDisplacementField, BSplineGradient, AdaptiveDenoising, AnalyzeObjectLabelMap, BioCell, RLEImage, Shape, FPFH, IOMeshSWC, MinimalPathExtraction, TwoProjectionRegistration, TotalVariation — review case-by-case in Phase 5

Phase 5 — discoverability & docs

• Auto-generated remote-module catalog page with status (Updated, self-maintained resource to list exhaustively existing remote modules #4786 — addressed by this issue's status table once it is mirrored to the docs site)
• Re-enable Doxygen processing for in-tree modules now that the historic Modules/Remote/ Doxygen disablement reason no longer applies module-by-module (Re-enable doxygen processing of the "Remote" directories. #990)
• Update Documentation/docs/migration_guides/itk_6_migration_guide.md with the consolidated remote-module disposition table

Status table — every entry under Modules/Remote/ today

(L = Wave 1 ingest queue · 2 = Wave 2 ingest queue · A = archive without ingest · K = keep remote, Tier B · ✓ = ingested · ? = decide in Phase 5)

Module	Disposition	Notes
AdaptiveDenoising	?
AnalyzeObjectLabelMap	?
BioCell	?
BoneEnhancement	2
BoneMorphometry	2
BSplineGradient	?
Cleaver	K	external Cleaver dep
Cuberille	L
CudaCommon	K	CUDA stack
FastBilateral	✓	merged via #6159 (2026-04-29)
FixedPointInverseDisplacementField	?
FPFH	?
GrowCut	2
HASI	K	hierarchical anatomy stack
HigherOrderAccurateGradient	L
IOFDF	L
IOMeshMZ3	L
IOMeshSTL	L
IOMeshSWC	?
IOOpenSlide	K	OpenSlide dep
IOScanco	2
IOTransformDCMTK	K	DCMTK dep
IsotropicWavelets	2
LabelErodeDilate	✓	merged via #6171 (2026-04-30)
LesionSizingToolkit	K	toolkit scope
MeshNoise	✓	merged via #6161 (2026-04-29); closed #5174
MeshToPolyData	?
MinimalPathExtraction	?
MorphologicalContourInterpolation	L⭐	next ingest target — 34★ upstream, actively maintained
MultipleImageIterator	L
ParabolicMorphology	L
PerformanceBenchmarking	K	benchmark harness, separate cadence
PhaseSymmetry	2
PolarTransform	L
PrincipalComponentsAnalysis	?
RANSAC	2
RLEImage	?
RTK	K	reconstruction toolkit
SCIFIO	K	Bio-Formats dep
Shape	?
SimpleITKFilters	2
SkullStrip	K	toolkit scope
SmoothingRecursiveYvvGaussianFilter	L
SphinxExamples	K	docs harness
SplitComponents	L
Strain	2
SubdivisionQuadEdgeMeshFilter	L
TextureFeatures	2
Thickness3D	2
TotalVariation	?
TractographyTRX	?
TubeTK	K	toolkit scope
TwoProjectionRegistration	?
Ultrasound	K	toolkit scope
VariationalRegistration	2
VkFFTBackend	K	VkFFT dep
WebAssemblyInterface	K	wasm build harness

Also tracked outside Modules/Remote/:

Repo	Disposition	Notes
ITKNeuralNetworks	✓ archived	already archived; resolves #5557
ITKTBBImageToImageFilter	A	archive without ingest; superseded by built-in TBB threading

Subsumed and related issues

• Integrate some remote modules into ITK proper #3371 (dzenanz, 2022-04-12) — original "integrate some remote modules" tracker; superseded.
• ENH: Consolidate remote modules into hierarchical category repos #6060 (hjmjohnson, 2026-04-14) — "Consolidate remote modules into hierarchical category repos"; superseded — the per-module disposition table here is the canonical work plan.
• NeuralNetworks (Numerics) module missing in recent versions #5557 (Laurent-777, 2025-10-16) — "NeuralNetworks module missing in recent versions"; resolution: ITKNeuralNetworks already archived upstream, NeuralNetworks is intentionally not migrating into ITK 6. Close.
• Compile error in MeshNoise/test/itkAdditiveGaussianNoiseMeshFilterTest.cxx:56 #5174 (seanm, 2025-01-24) — MeshNoise compile error; resolved by ENH: Ingest ITKMeshNoise into Modules/Filtering (closes #5174) #6161 (merged 2026-04-29).
• Re-evaluate modules in the ITK repository and remote modules for ITK 6 #4263 (thewtex, 2023-10-18) — "Re-evaluate modules for ITK 6"; this issue is the ITK-6 disposition outcome.
• Updated, self-maintained resource to list exhaustively existing remote modules #4786 (jhlegarreta, 2024-07-20) — "self-maintained list of remote modules"; addressed by the status table above plus the Phase 5 docs auto-generation item.
• Re-enable doxygen processing of the "Remote" directories. #990 (hjmjohnson, 2019-06-03) — Doxygen processing of Modules/Remote/; folded into Phase 5.

Recent PR activity (past three weeks)

PR	State	Title
#6093	merged 2026-04-23	ENH: Ingest ITKAnisotropicDiffusionLBR into Modules/Filtering
#6103	merged 2026-04-25	ENH: Ingest ITKMontage remote module into Modules/Registration/Montage
#6135	merged 2026-04-27	ENH: Ingest ITKGenericLabelInterpolator into Modules/Filtering
#6137	merged 2026-04-28	ENH: Ingest ITKMGHIO into Modules/IO
#6159	merged 2026-04-29	ENH: Ingest ITKFastBilateral into Modules/Filtering (supersedes #5134)
#6161	merged 2026-04-29	ENH: Ingest ITKMeshNoise into Modules/Filtering (closes #5174)
#6162	open	COMP: Deprecate linearizing ingest helper; add merge-preserving rewriter
#6151	open	COMP: Prune superseded GitHub Actions ccache entries from CI
#6085	closed	ENH: Add Modules/Beta/ container (alternative approach abandoned in favor of natural-group ingest)
#6086	closed	WIP: Ingest 10 beta modules under Modules/Beta/ (stacked on #6085, abandoned)
#6072	closed	WIP: REMOTE_MODULE_TEST DCMTK external module compatibility (parked)
#6061	closed	WIP: Combine many remote to few remote module groups (alternative approach abandoned)
#5134	closed	dzenanz's original FastBilateral integration (superseded by #6159)

[hjmjohnson]

Wave-1 progress: MeshNoise ingest in flight as #6161. Closes #5174 in the same PR.

[hjmjohnson]

Phase-0 infrastructure follow-up: #6162 deprecates normalize-ingest-commits.py (which linearized history on PRs #6135, #6137, #6159, #6161) and adds rewrite-history-merge-preserving.py, the merge-preserving replacement implementing the Phase 1 / Phase 2 / Phase 3 / Phase 4 architecture from ~/.claude/rules/ingest-merge-topology.md.