ENH: Ingest ITKMorphologicalContourInterpolation (stacked on #6208)

[hjmjohnson]

Ingests MorphologicalContourInterpolation from the standalone remote module KitwareMedical/ITKMorphologicalContourInterpolation into ITK at Modules/Filtering/MorphologicalContourInterpolation/. Stacked on PR #6208 (RLEImage ingest) — that PR provides MCI's TEST_DEPENDS RLEImage and the CTAD deduction guides that MCI's RLE-flavored test exercises.

Local validation: pre-commit run --all-files clean; MorphologicalContourInterpolationTestDriver builds; 368/368 MCI tests pass locally (plain + RLE-flavored, all algorithms B/C/T, all axis/label combinations).

BUG fix: thread_local SmartPointers removed (latest commit)

The upstream module used thread_local ITK SmartPointers in template functions as a per-thread filter cache. On MSVC, thread_local objects in template functions are destroyed when ITK's thread-pool workers exit at program shutdown — after ITK's reference-count infrastructure is partially torn down — causing SEGFAULTs. This manifested as 26 test failures on windows-2022 CI (GridSeg, GridSeg2, AccidentalMiddleSliceSeg, SevenLabels, FullEnd, ThreeAxisFourLabelConflict images). The fix replaces all 8 thread_local SmartPointer declarations with ordinary local variables; the per-thread caching is unnecessary under ITKv5's threading model and the allocation overhead is negligible.

What this provides

MorphologicalContourInterpolation provides filters that interpolate manually-segmented anatomical contours through volumetric label data using morphological reconstruction. Given a sparse set of 2D contours on arbitrary slices, the filter reconstructs a complete 3D label mask. The flagship class is itk::MorphologicalContourInterpolator.

Path: Modules/Filtering/MorphologicalContourInterpolation/ (alongside the existing Modules/Filtering/RLEImage/ from the stacked PR #6208).

Pipeline metrics

Metric	Value
Upstream commits → rewritten	327 → 225
Upstream merges → preserved	77 → 46 (no linearization)
Blobs scanned in sanitize	1765 (cxx=266, py=0, cmake=63, text=369, skip=1067)
Blobs reformatted	317 (clang-format / gersemi / trailing-ws / EOF)
Commit subjects auto-prefixed	144
Subjects truncated to 78 chars	14
Blank lines inserted	131
Subtree merges visible after rebase	1

The relatively high commit count comes from MCI's long history (327 upstream commits since 2016) — reflects the maturity of this module.

Dependencies

• DEPENDS (library): ITKBinaryMathematicalMorphology, ITKDistanceMap — both ITK core (always available)
• TEST_DEPENDS: ITKTestKernel (core), RLEImage (provided by stacked PR ENH: Ingest ITKRLEImage into Modules/Filtering #6208)

EXCLUDE_FROM_DEFAULT is set on the module so it does not auto-build unless Module_MorphologicalContourInterpolation:BOOL=ON is passed.

Stack relationship to PR #6208

This PR stacks on PR #6208 (RLEImage ingest) for two reasons:

1. TEST_DEPENDS RLEImage — MCI's itkMorphologicalContourInterpolationTestWithRLEImage.cxx instantiates the morphological filter against RLEImage types. Without RLEImage as an in-tree module, the test directory is not configured.

2. CTAD deduction guides — when MCI's test code includes itkImageFileWriter.h (which transitively pulls in itkImageAlgorithm.hxx) and instantiates the writer's templates against an RLEImage, ITK core's CTAD-using calls (e.g. ImageRegionConstIterator it(inImage, inRegion);) need explicit deduction guides on the ImageRegionConstIterator<RLEImage<...>> partial specialization. Those guides were added in 8dcb1e8fe3 on PR ENH: Ingest ITKRLEImage into Modules/Filtering #6208. Without them, MCI's RLEImage-flavored test fails to compile.

If reviewers prefer to land MCI without the RLEImage dependency in this cycle, the alternative is to disable the itkMorphologicalContourInterpolationTestWithRLEImage.cxx source from test/CMakeLists.txt until RLEImage lands. The plain (non-RLE) MCI test suite does not need PR #6208.

Follow-up commits in this PR

After the merge commit (ENH: Ingest ITKMorphologicalContourInterpolation into Modules/Filtering):

• DOC: Add Modules/Filtering/MorphologicalContourInterpolation/README.md pointing at the archived upstream.
• COMP: Remove Modules/Remote/MorphologicalContourInterpolation.remote.cmake (now in-tree).
• ENH: Enable Module_MorphologicalContourInterpolation:BOOL=ON in pyproject.toml configure-ci.
• BUG: Replace thread_local SmartPointers with local variables (fixes 26 Windows CI SEGFAULTs).

Phase B (upstream archival) — deferred

Per the v4 design (PR #6204), the upstream archival step is intentionally separated. After this PR merges into ITK main, run:

~/src/ITK/Utilities/Maintenance/RemoteModuleIngest/archive-remote-module.sh \
    MorphologicalContourInterpolation --itk-pr-number <THIS-PR>

Note the upstream is KitwareMedical/ITKMorphologicalContourInterpolation (not the InsightSoftwareConsortium org); confirm push permission before flipping archived=true.

AI assistance

• Tool: Claude Code (claude-sonnet-4-6)
• Role: root-cause analysis of 26 Windows CI SEGFAULTs and authoring the thread_local fix
• Contribution: identified that thread_local ITK SmartPointers in template functions crash on MSVC at thread-pool shutdown by inspecting CI logs, tracing the thread_local introduction through git history to commit 017a693c5d (ITKv5 threading model switch), and confirming the fix compiles and all 368 MCI tests pass locally
• All code was reviewed and tested locally before committing

[hjmjohnson]

Closing temporarily — this PR is stacked on #6208 (RLEImage ingest) and will be reopened (or re-submitted) once #6208 lands on main. MCI's tests use itk::RLEImage so the dependency must merge first.

The 11 missing CIDs are now published (ITKTestingData PR #47, merged), and the rerun of "Populate shared ExternalData cache" went green at ok=2457 fail=0. No work is lost; this is purely a queue-management close.

[dzenanz]

PR generally looks good. Modules/Filtering/MorphologicalContourInterpolation/CMakeLists.txt needs cleanup, like many recent ingestions.

[hjmjohnson]

Rebased on upstream/main (now that #6208 has merged) and addressed @dzenanzs CMakeLists cleanup comment in c38495c9ea (drop cmake_minimum_required, the CXX_STANDARD policing block, and the if(NOT ITK_SOURCE_DIR) standalone-build wrapper). The v4 ingest pipeline (#6204) strips this boilerplate automatically going forward.

[greptile-apps]

Too many files changed for review. (421 files found, 100 file limit)