VV: Multi-Threshold Objects

[mmarineBlueQuartz]

• Add tests for untested code coverage.
• Add V&V documentation.
• Fix bug regarding thresholding over ThresholdSets.
• Fix bug where inverting mask values does not work.

Naming Conventions

Naming of variables should descriptive where needed. Loop Control Variables can use i if warranted. Most of these conventions are enforced through the clang-tidy and clang-format configuration files. See the file simplnx/docs/Code_Style_Guide.md for a more in depth explanation.

Filter Checklist

The help file simplnx/docs/Porting_Filters.md has documentation to help you port or write new filters. At the top is a nice checklist of items that should be noted when porting a filter.

Unit Testing

The idea of unit testing is to test the filter for proper execution and error handling. How many variations on a unit test each filter needs is entirely dependent on what the filter is doing. Generally, the variations can fall into a few categories:

• 1 Unit test to test output from the filter against known exemplar set of data
• 1 Unit test to test invalid input code paths that are specific to a filter. Don't test that a DataPath does not exist since that test is already performed as part of the SelectDataArrayAction.

Code Cleanup

• No commented out code (rare exceptions to this is allowed..)
• No API changes were made (or the changes have been approved)
• No major design changes were made (or the changes have been approved)
• Added test (or behavior not changed)
• Updated API documentation (or API not changed)
• Added license to new files (if any)
• Added example pipelines that use the filter
• Classes and methods are properly documented

[imikejackson]

Full V&V review of this PR: every claim in the V&V documents was re-verified against head 909bff118, plus an adversarial algorithm review, a CPU/memory review, and an independent legacy 6.5.171 A/B run (which this PR's own deviations doc lists as outstanding).

Independent A/B validation (run for this review)

Shared legacy-format input (100 tuples, Int32 = 0..99, Float32 = 0.01*(i+1)); PipelineRunner 6.5.171 vs this branch's nxrunner vs an independent numpy oracle:

Case	Config	Legacy filter	Result
AB1	Int32 > 42 AND Float32 < 0.70 (flat)	MultiThresholdObjects	MATCH (legacy = NX = oracle)
AB2	Int32 > 20 AND (Float32 < 0.60 OR Int32 == 55) (nested set)	MultiThresholdObjects2	MATCH
AB3	Int32 < 80 OR NOT(Int32 > 30 AND Float32 < 0.95) (inverted nested set)	MultiThresholdObjects2	MATCH

Same three configs at 50M random tuples: this branch matches the oracle exactly. All 17 ctest entries pass locally.

The same pipelines run against develop (pre-PR): AB2 yields an all-false mask (38/100 wrong) and AB3 differs in 51/100 values. Both bug-fix claims in the PR description are real and the fix restores legacy semantics — legacy's invertThreshold() flips values element-wise; the old NX std::reverse was a misport, and the old per-item functor dispatch broke nested-set combination entirely.

Also confirmed from legacy source: MultiThresholdObjects2::dataCheck() rejects non-scalar arrays (error -11003), so component-index selection is NX-only.

Actionable items

Correctness / behavior

• Restore the cancel check. operator()() no longer checks m_ShouldCancel anywhere (the member is now unused). This reverts the cancel check deliberately added by ENH: Add missing cancel checks to lots of filters #1582 and makes large thresholding runs uncancellable. A per-threshold check inside ThresholdSet's loop (or per-chunk) would restore it.
• Restore the SIMPL backwards-compatibility test. TEST_CASE "SIMPL Backwards Compatibility" was deleted, reverting coverage re-enabled by BUG: Fix SIMPL JSON conversion segfault and re-enable backwards-compatibility checks #1605. The 6.4/6.5 fixtures still exist under test/simpl_conversion/ but nothing exercises them now — and the V&V report cites them as evidence.
• Restore valid-execution coverage for custom TRUE/FALSE values. TEMPLATE_TEST_CASE "Valid Execution - Custom Values" (10 types) was deleted; only the out-of-bounds/boolean error paths remain. The rewritten InsertThreshold combines via == trueValue / == falseValue, so custom values interact directly with the new logic and currently have zero execution coverage.
• Decide the fate of ErrorCodes::UnequalComponents (-4001) (MultiThresholdObjectsFilter.hpp:40) — dead after the preflight component-count check removal. Remove it or mark it retired (removing changes the public enum; either way the report should note the relaxed preflight behavior).

V&V document corrections (each verified against head)

• Bug flags: None identified is wrong — this PR itself fixes two user-facing bugs, confirmed by the A/B above (develop produces an all-false mask for a plain nested set). Document both bugs in the report, with a note for users of earlier NX releases whose nested-set masks were silently wrong.
• Legacy comparison is no longer outstanding — fold in the A/B results above (flat vs MultiThresholdObjects, nested + inverted vs MultiThresholdObjects2, all match at head). The deviations file can move past "comparison not yet run"; expected entry count stays 0 for these configs.
• Resolve the open question on component-index: legacy Advanced rejects non-scalar arrays (-11003), so it had no equivalent — the feature is NX-only.
• Status fields are inconsistent: header says READY FOR REVIEW, Sign-off says pending — DRAFT, At-a-glance lists "promotion DRAFT → READY FOR REVIEW" as outstanding.
• Test inventory lists every test as kept/new but omits the two removed TEST_CASEs (Valid Execution - Custom Values, SIMPL Backwards Compatibility). Removals must appear as retired with a reason.
• Stale note: k_MismatchingComponentsArrayPath "leftover at line 31 worth deleting" — it no longer exists on this branch.
• "Mask DataType — 11 SECTIONs, one per mask-output DataType": the TEST_CASE has 10 SECTIONs (boolean is not a SECTION; it's covered via defaults elsewhere, as the same sentence says).
• Material-PRs-since-baseline should include ENH: Add missing cancel checks to lots of filters #1582 (cancel checks — reverted here) and BUG: Fix SIMPL JSON conversion segfault and re-enable backwards-compatibility checks #1605 (SIMPL conversion test — deleted here).
• Code-path table should enumerate the custom TRUE/FALSE execution path (currently uncovered per above), so the "23 of 24" figure is accurate after the fix.

CPU / memory

Measured on 50M tuples (3 threshold filters per pipeline, Release): develop 18.2s / 774MB peak RSS → this PR 21.9s / 861MB. Filter-only time roughly +50%; peak temp usage is now (nesting depth + 2) full-size stores vs 1 std::vector before.

• Drop the functor-level temp + copy loop (ThresholdSetFunctor, Algorithms/MultiThresholdObjects.cpp:197-216). ThresholdSet already produces the complete result; pre-fill the output store with falseValue and pass it directly — saves one N-size allocation and two full passes.
• The std::fill in ThresholdValue (line 147) is redundant — ThresholdFilterHelper writes every element.
• Hoist the if(inverse) per-element branch out of InsertThreshold's loop.
• Temps moved from std::vector to AbstractDataStore — every hot-loop access is now a virtual call, which is where the measured slowdown comes from. If OOC-capable temps are the goal, consider bulk/chunked access; per-element operator[] on a chunked HDF5-backed temp will thrash. Also worth confirming temp stores created via DataStoreUtilities::CreateDataStore under force-large-data prefs are cleaned up.

Test quality / cleanup

• Dead debug locals in CheckThresholdSet2 (test cpp 607-608): value and expected computed then ignored.
• maskArray dereferenced without a null check (test cpp 1133-1134); project convention is REQUIRE_NOTHROW + getDataRefAs.
• 6 of 9 TEST_CASEs are missing UnitTest::CheckArraysInheritTupleDims(dataStructure) (project testing convention) — all the new Valid Single Thresholds / Threshold Sets / Input Array DataType cases.
• operator()() leftovers: firstValueFound only feeds a constant !false, and the thresholdSet local (line 249) is unused.
• Doxygen on InsertThreshold / ApplyThresholdValues is stale (parameter names no longer exist; "threshould" typo).

Verified good

• UUID mapping (both legacy UUIDs → this filter), FromSIMPLJson dual-converter branching, filter UUID, and the recursive component-index preflight check all match the report.
• 9 TEST_CASE groups / 17 ctest entries, all passing locally; CI green on all platforms.
• Class 1 analytical oracle with in-memory fixtures and no exemplar archive — complies with the no-circular-oracle policy; the test matrix genuinely enumerates operator x invert x union x nesting x both DataType axes.
• The algorithm restructure itself is semantically correct against both legacy filters (A/B above), including the forced-OR seeding of each set's accumulator.

[imikejackson]

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