Ingest ITKAdaptiveDenoising into Modules/Filtering

[hjmjohnson]

Ingest the standalone remote module
ntustison/ITKAdaptiveDenoising
into Modules/Filtering/AdaptiveDenoising/. Patch-based adaptive
non-local-means denoising is now in-tree under
EXCLUDE_FROM_DEFAULT.

Built directly on upstream/main; the v4 ingestion guidelines
defined in #6204 (sanitize-history pass, deny-pattern pass,
whitelist-only paths, ghostflow-clean per-commit subjects) were
applied locally to produce this PR's content, but this PR does
not depend on #6204 merging first.

Test data is gated on
InsightSoftwareConsortium/ITKTestingData#48,
which uploads the 3 fixture blobs the new tests fetch via .cid
stubs. Closes the consolidation work of issue #6060 for this
module.

Stacked on #6236 (pixi 0.68 multi-line cmd compatibility fix). The visible diff includes #6236's pyproject.toml line-continuation changes until that PR merges; once it lands, this branch can be rebased onto main (using git rebase --rebase-merges to keep the 9 ingest merges intact) and the pyproject.toml hunks will drop out.

No raw binary blobs in ITK history

The upstream module shipped its 3 test fixtures
(r16slice.nrrd, r16denoised_mean_squares.nrrd,
r16denoised_pearson_correlation.nrrd) inline in git rather than
via the ITK ExternalData / content-link convention. AGENTS.md
decision 3 forbids merging an ingest with raw binary test/
assets.

Rather than carry the binaries through the merge and then swap
them at the tip, the rewritten upstream history was passed
through git filter-repo --path-glob '*.nrrd' --invert-paths
so that no commit reachable from this PR's HEAD adds a raw
.nrrd file:

$ git log --diff-filter=A --name-only HEAD -- '*.nrrd' | grep -c '\.nrrd$'
0

The .cid stubs are added in a single dedicated commit at the
tip and point at the CID blobs published in
ITKTestingData PR #48.

Ingest results

Aspect	Value
Upstream commits → after sanitize	62 → 34
Merge commits preserved	8 in the rewritten upstream branch (no linearization)
Final tree merge count	9 (incl. ingest merge)
Whitelisted files	17 (include/, src/, test/, wrapping/, CMakeLists.txt, itk-module.cmake, LICENSE)
Raw .nrrd files in history reachable from HEAD	0
Content-links at HEAD	3 .cid, 0 .md5, 0 .shaNNN, 0 raw binaries
examples/ directory	Auto-excluded; remains in archived upstream
License	Apache-2.0
git blame	Walks back to original upstream contributors (Nicholas Tustison and others)

Local validation

• pre-commit run --all-files: clean
• cmake -DModule_AdaptiveDenoising:BOOL=ON .: configures clean
• Compile check: new itkAdaptiveNonLocalMeansDenoisingImageFilterTest.cxx.o
  and itkNonLocalPatchBasedImageFilterEnums.cxx.o build clean
  (16 pre-existing warnings about long subject lines from the
  upstream's itkGetConstMacro-generated names — not new).
• Test execution gated on
  ITKTestingData#48
  merging so the 3 .cid blobs are reachable through the standard
  mirror at fetch time.

Commits at PR tip (top → bottom)

1. ENH: Enable Module_AdaptiveDenoising in configure-ci
2. COMP: Remove AdaptiveDenoising .remote.cmake (in-tree)
3. DOC: Add AdaptiveDenoising README pointing at upstream
4. ENH: Add AdaptiveDenoising test data .cid stubs
   (3 stub files pointing at ITKTestingData PR ENH: Update CircleCI CMake version to 3.11.2 #48 blobs)
5. ENH: Ingest ITKAdaptiveDenoising into Modules/Filtering
   (merge commit --no-ff --allow-unrelated-histories to
   sanitized + .nrrd-stripped filter-repo'd upstream history;
   preserves 8 upstream merges and git blame to original authors)

Phase B (post-merge) — upstream archival

After this PR merges, run Phase B from a fresh worktree:

Utilities/Maintenance/RemoteModuleIngest/archive-remote-module.sh \
    AdaptiveDenoising

Phase B publishes the upstream removal commit, promotes
MIGRATION_README.md to README.md so the GitHub landing page
renders the migration notice (per the
ingest-archive-readme rule), and flips
archived=true. No upstream side-effects happen until that step.

Refs: #6060

[greptile-apps]

Greptile Summary

This PR ingests the standalone remote module ntustison/ITKAdaptiveDenoising into Modules/Filtering/AdaptiveDenoising/ under EXCLUDE_FROM_DEFAULT, removes the corresponding .remote.cmake descriptor, replaces the upstream's raw .nrrd test fixtures with .cid content-link stubs, and enables the module in the CI configure command.

• itkAdaptiveNonLocalMeansDenoisingImageFilter — the flagship patch-based adaptive non-local-means denoiser — is ingested along with its base class itkNonLocalPatchBasedImageFilter and a local itkVarianceImageFilter; Python wrapping and two regression tests are included.
• Two code-correctness issues carried over from the upstream need attention before or shortly after merge: a thread-safety race in ThreadedGenerateData (writes to shared output pixels outside the per-thread region without synchronization) and a normalization fallthrough in VectorizeImagePatch (near-zero std-dev path zeroes then immediately overwrites with −mean/ε).
• Style: itkAdaptiveNonLocalMeansDenoisingImageFilter.h and itkVarianceImageFilter.h use typedef throughout while the base-class header already uses using; the VarianceImageFilter Doxygen block misdescribes the filter as "averaging" and "linear".

Confidence Score: 3/5

The ingestion infrastructure (CMake, wrapping, content links, CI config) is correct, but the core filter implementation carries two pre-existing upstream bugs that affect correctness on multi-core builds.

The flagship filter's ThreadedGenerateData writes accumulated output values and contribution counts to arbitrary pixel locations shared across threads without any synchronization. On any machine with more than one core, the read-modify-write sequences on outputImage and m_ThreadContributionCountImage are data races that silently corrupt the denoised result. Separately, VectorizeImagePatch's near-zero standard-deviation branch zeroes the patch but immediately overwrites those zeros with -mean/tiny_stddev, defeating the guard entirely for any subclass calling the method with normalize=true. Both issues were present in the upstream remote module and are inherited here unchanged.

itkAdaptiveNonLocalMeansDenoisingImageFilter.hxx (thread-safety in ThreadedGenerateData) and itkNonLocalPatchBasedImageFilter.hxx (normalization fallthrough in VectorizeImagePatch).

Important Files Changed

Filename	Overview
Modules/Filtering/AdaptiveDenoising/include/itkAdaptiveNonLocalMeansDenoisingImageFilter.hxx	Flagship filter implementation; contains a thread-safety race condition where ThreadedGenerateData writes output and count-image pixels outside its assigned sub-region without synchronization, producing nondeterministic results on multi-core systems.
Modules/Filtering/AdaptiveDenoising/include/itkNonLocalPatchBasedImageFilter.hxx	Base class implementation; VectorizeImagePatch normalization falls through after zeroing elements when std-dev is near-zero, producing large/infinite values instead of zeros for any normalize=true caller.
Modules/Filtering/AdaptiveDenoising/include/itkAdaptiveNonLocalMeansDenoisingImageFilter.h	Filter header; uses old typedef style throughout while base class uses modern using aliases — inconsistent with ITK coding standards.
Modules/Filtering/AdaptiveDenoising/include/itkVarianceImageFilter.h	Local variance filter header; has incorrect Doxygen ("averaging filter", "linear filter"), a typo ("variacne"), and uses typedef instead of using aliases.
Modules/Filtering/AdaptiveDenoising/include/itkNonLocalPatchBasedImageFilter.h	Base class header; clean modern using aliases, enum class with streaming support, legacy aliases guarded by ITK_LEGACY_REMOVE — no issues found.
Modules/Filtering/AdaptiveDenoising/itk-module.cmake	Module declaration with correct DEPENDS, COMPILE_DEPENDS, TEST_DEPENDS, EXCLUDE_FROM_DEFAULT, and ENABLE_SHARED — looks correct.
Modules/Filtering/AdaptiveDenoising/test/CMakeLists.txt	Two test cases registered with DATA{} content-link references for .cid stubs — correctly follows ITK ExternalData convention.
Modules/Remote/AdaptiveDenoising.remote.cmake	Remote module descriptor correctly removed now that the module is in-tree; deletion is the right action.
pyproject.toml	Adds -DModule_AdaptiveDenoising:BOOL=ON to the CI configure command so the new module is exercised in CI builds.
Modules/Filtering/AdaptiveDenoising/wrapping/CMakeLists.txt	Wrapping order declared correctly: VarianceImageFilter → NonLocalPatchBasedImageFilter → AdaptiveNonLocalMeansDenoisingImageFilter.
Modules/Filtering/AdaptiveDenoising/test/itkAdaptiveNonLocalMeansDenoisingImageFilterTest.cxx	Test exercises both similarity metrics, verifies all public API getters/setters, and uses ITK_TRY_EXPECT_NO_EXCEPTION — good coverage of the public interface.

_{Reviews (1): Last reviewed commit: "ENH: Enable Module_AdaptiveDenoising in ..." | Re-trigger Greptile}

[dzenanz]

Mostly looks good.