VV/BUG: Identify Sample Full V&V and Minor patches

src/Plugins/SimplnxCore/src/SimplnxCore/Filters/Algorithms/IdentifySample.cpp

@@ -133,7 +133,10 @@ struct IdentifySampleFunctor
 
             if(!checked[voxelIndex] && !goodVoxels.getValue(voxelIndex))
             {
-              bool touchesBoundary = false;
+              // The following is only initialized as true for SingleVoxelImage,
+              // the intention being to flag the voxel as a boundary for proper handling
+              // since the loop that would flag it will not execute with empty lists
+              bool touchesBoundary = k_NeighborCount == 0;
               currentVList.push_back(voxelIndex);
               usize count = 0;
               while(count < currentVList.size())
@@ -286,7 +289,7 @@ struct IdentifySampleSliceBySliceFunctor
               count++;
             }
 
-            if(static_cast<int64>(currentVList.size()) > biggestBlock)
+            if(static_cast<int64>(currentVList.size()) >= biggestBlock)
             {
               biggestBlock = currentVList.size();
               sample.assign(planeDim1 * planeDim2, false);

src/Plugins/SimplnxCore/test/IdentifySampleTest.cpp

@@ -13,7 +13,6 @@
 
 #include <catch2/catch.hpp>
 #include <filesystem>
-#include <fstream>
 
 using namespace nx::core;
 using namespace nx::core::UnitTest;

src/Plugins/SimplnxCore/vv/IdentifySampleFilter.md

@@ -0,0 +1,87 @@
+# V&V Report: IdentifySampleFilter
+
+| | |
+|---|---|
+| Plugin | `SimplnxCore` |
+| SIMPLNX UUID | `94d47495-5a89-4c7f-a0ee-5ff20e6bd273` |
+| DREAM3D 6.5.171 equivalent | `IdentifySample` — UUID `0e8c0818-a3fb-57d4-a5c8-7cb8ae54a40a` |
+| Verified commit | *pending* |
+| Status | COMPLETE |
+| Sign-off | Nathan Young, 06-17-2026 |
+
+## At a glance
+
+| Aspect | State |
+|---|---|
+| Algorithm relationship | **Port** (3D mode) + **1 deviation** (dimensionality dispatch) + new features (`SliceBySlice`, cancel checks) |
+| Oracle | **Class 1 (Analytical)** for 3 non-square 2D tests; **Validated-circular** for 12 archive tests (not legacy-equivalent) |
+| Code paths | **14 of 17** exercised; 3 gaps (1D dispatch, single-voxel, cancel-check) |
+| Tests | **5 TEST_CASEs** (16 functional scenarios) — all pass |
+| External archive | `identify_sample_v2.tar.gz` (active) + `identify_sample.tar.gz` (v1, orphaned) |
+| Deviations | **1 active** (`IdentifySample-D1`): dimensionality dispatch — legacy correctness on degenerate geometries unverified/suspected wrong |
+| Confirmed parity | `checked`-reset between BFS phases verified identical and correct in both versions (source-compared against legacy tag `v6.5.171`) |
+| Open bugs | None |
+
+## Summary
+
+`IdentifySampleFilter` isolates the largest connected component of "good" voxels in an `ImageGeom`, clearing all smaller components. An optional `FillHoles` pass then closes interior holes — bad-voxel components that don't touch the volume boundary are flipped to good. `SliceBySlice` mode (new in SIMPLNX) applies the same two-pass logic independently per 2D slice. The algorithm is purely boolean/integer, so no floating-point precision drift is possible. The genuinely-3D path is a confirmed port of legacy `IdentifySample::execute()`, including an exact-match BFS `checked`-reset behavior between phases. One deviation is open: SIMPLNX's dimensionality-aware dispatch for degenerate (2D/1D/single-voxel) geometries has no verified legacy counterpart — legacy used a single fixed 3D-stride formula whose correctness on such inputs was never established and is suspected wrong.
+
+## Algorithm Relationship
+
+**Port** of the 3D BFS two-pass algorithm; **deviation** in dimensionality handling; **new** SliceBySlice mode.
+
+- **3D mode**: identical two-pass structure (largest-component isolation, then optional hole fill) to legacy. The `checked`-tracker reset between phases — a historically fragile point (see Deviations) — is confirmed correct and identical in both versions.
+- **Dimensionality dispatch** (`ProcessVoxels<>`): routes to `Image3D`, `EmptyZ/Y/XImage2D`, `Z/Y/XImage1D`, or `SingleVoxelImage` neighbor templates based on which dims equal 1. Legacy always used the fixed 3D-stride formula regardless of shape. Classified as deviation `IdentifySample-D1` (not a plain new feature) because degenerate inputs were always legal in legacy — its behavior on them just was never validated. See deviations file.
+- **New, no legacy path to compare against**: `SliceBySlice` mode (gated behind a parameter absent from DREAM3D 6.5.171 and unmapped by `FromSIMPLJson`); cancel checks (`m_ShouldCancel`); rate-limited progress messages.
+
+## Oracle
+
+| Test group | Class | Basis |
+|---|---|---|
+| 3 non-square 2D tests | **1 (Analytical)** | 12-voxel hand-built mask, expected output hard-coded; one fixture per `EmptyZ/Y/XImage2D` dispatch path |
+| 12 archive tests (`identify_sample_v2.tar.gz`) | **Validated-circular** | Exemplars generated by SIMPLNX's own filter (confirmed via `Generate_Exemplars.py`) over a hand-designed, human-reviewed `16×14×12` feature layout. Stronger than bare-circular (documented features, human review) but **not** Class 2 — no legacy parity claim possible. None of the 12 exercise degenerate geometry, so they provide no coverage for `IdentifySample-D1`. |
+
+Full provenance detail, including the feature-layout table and the resolved "checked-reset" question, in `vv/provenance/IdentifySampleFilter.md`.
+
+## Code path coverage
+
+14 of 17 paths exercised. Source: `Algorithms/IdentifySample.cpp`.
+
+| # | Path | Exercised by |
+|---|---|---|
+| 1 | Dispatch: `SliceBySlice=false` → `ProcessVoxels` | `whole_*` + 3 non-square 2D tests |
+| 2 | Dispatch: `SliceBySlice=true` → slice functor | `sliced_*` |
+| 3 | Dim dispatch: `emptyDimCount==0` → `Image3D` | `whole_*` |
+| 4–6 | Dim dispatch: `emptyDimCount==1` → `EmptyZ/Y/XImage2D` | 3 non-square 2D tests (one each) |
+| 7 | Dim dispatch: `emptyDimCount==2` → 1D variants | *Not tested. Impractical/unused in practice; gap acceptable.* |
+| 8 | Dim dispatch: `emptyDimCount==3` → `SingleVoxelImage` | *Not tested. Degenerate case; gap acceptable.* |
+| 9–11 | BFS expansion, valid-neighbor add, boundary skip | All BFS tests |
+| 12 | Clear non-largest component | `whole_*` + 3 non-square 2D tests |
+| 13 | `FillHoles=false` → hole-fill skipped | `*_nofill` |
+| 14 | `FillHoles=true`, enclosed → filled | `*_fill` |
+| 15 | `FillHoles=true`, touches boundary → stays bad | `*_fill` |
+| 16 | Cancel mid-scan → early return | *Not tested. Cancel disregard would hang any test; low-value gap.* |
+| 17 | Slice plane selection (XY/XZ/YZ) | `sliced_xy/xz/yz_*` |
+
+## Test inventory
+
+| Test case | Notes |
+|---|---|
+| `IdentifySampleFilter` (12 sections) | Validated-circular; all SliceBySlice × plane × FillHoles combos |
+| `SIMPL Backwards Compatibility` | 6.4 + 6.5 fixtures; UUID + arg-key + param decoding |
+| `2D Empty Z/Y/X Non-Square` (×3) | Class 1; one per dimensionality dispatch path |
+
+5 TEST_CASEs, all pass (16 functional scenarios total).
+
+## Exemplar archive
+
+- **Active:** `identify_sample_v2.tar.gz` — SHA512 `a7ffac3e...848ac31`. Provenance: `vv/provenance/IdentifySampleFilter.md`.
+- **Orphaned:** `identify_sample.tar.gz` (v1) — no active test references it; recommend removing its `download_test_data()` entry from `CMakeLists.txt`.
+
+## Deviations from DREAM3D 6.5.171
+
+**3D mode:** No deviations — confirmed identical two-pass BFS structure, including the `checked`-reset between phases (source-compared against legacy tag `v6.5.171`, line 254; matches SIMPLNX `IdentifySample.cpp:112` and `:325`).
+
+**`IdentifySample-D1` (active):** Dimensionality dispatch for degenerate geometries. Legacy's fixed 3D-stride neighbor formula was never validated against 2D/1D/single-voxel inputs and is suspected incorrect; SIMPLNX's dispatch is explicit and Class 1 tested. Recommend trusting SIMPLNX. Full entry in `vv/deviations/IdentifySampleFilter.md`.
+
+**`SliceBySlice` and cancel checks:** Genuinely new, no legacy path to deviate from.

src/Plugins/SimplnxCore/vv/deviations/IdentifySampleFilter.md

@@ -0,0 +1,55 @@
+# Deviations from DREAM3D 6.5.171: IdentifySample
+
+This file lists every documented behavioral difference between this SIMPLNX filter and its DREAM3D 6.5.171 equivalent.
+
+Entries are referenced by stable ID (`IdentifySample-D<N>`) from the V&V report and from public migration guidance. The ID is stable across renames; the Filter UUID field is the permanent cross-reference anchor.
+
+---
+
+## 3D mode — no deviations
+
+Source-inspection comparison of the genuinely-3D path (`IdentifySampleFunctor<Image3D>`) against DREAM3D 6.5.171 `IdentifySample::execute()` confirmed identical algorithmic structure:
+
+- **Phase 1 (largest-component isolation):** BFS flood-fill over all good voxels; tracks the largest connected component; all good voxels outside that component are set to false/0.
+- **Phase 2 (hole fill, optional):** BFS flood-fill over all bad voxels; connected components that do not reach the volume boundary are flipped to good.
+
+The algorithm is purely boolean/integer — no floating-point arithmetic — so precision drift cannot occur between two correct implementations of the same 3D logic.
+
+**Confirmed parity — `checked` reset between phases:** `vv/provenance/IdentifySampleFilter.md` documents an "Internal cluster" fixture in `identify_sample_v2.tar.gz`, purpose-built to catch a bug where the `checked` BFS-visited tracker is not reset between Phase 1 and Phase 2 — voxels visited (and marked `checked=true`) while being absorbed into a non-largest component during Phase 1 would then be skipped entirely during Phase 2's hole-fill scan, since `checked` would already be `true` for them, leaving them permanently un-filled even when they qualify as an enclosed hole.
+
+Direct source comparison confirms **both versions reset correctly and this is not a deviation**:
+
+- **Legacy** (`DREAM3D/Source/Plugins/Processing/ProcessingFilters/IdentifySample.cpp:254`, checked out at tag `v6.5.171`): `checked.assign(totalPoints, false);` immediately before the `m_FillHoles` block.
+- **SIMPLNX 3D mode** (`Algorithms/IdentifySample.cpp:112`): `checked.assign(totalPoints, false);` immediately before the `if(fillHoles)` block.
+- **SIMPLNX SliceBySlice mode** (`Algorithms/IdentifySample.cpp:325`): `checked.assign(planeDim1 * planeDim2, false);` immediately before its own `if(fillHoles)` block, scoped per-slice.
+
+The bug referenced in the test data's `generated_data/ReadMe.md` was a SIMPLNX-only regression at some prior point in development (already fixed in current source, as shown above) — it never existed in DREAM3D 6.5.171. The "Internal cluster" fixture remains in the archive as a guard against reintroducing it, not as evidence of any current or legacy deviation.
+
+---
+
+## IdentifySample-D1
+
+| Field | Value |
+|---|---|
+| **Deviation ID** | `IdentifySample-D1` |
+| **Filter UUID** | `94d47495-5a89-4c7f-a0ee-5ff20e6bd273` |
+| **Status** | Active — SIMPLNX defines correct behavior; legacy behavior for this input class is unverified and suspected incorrect |
+
+**Symptom:** For `ImageGeom` inputs with one or more dimensions equal to 1 (2D, 1D, or single-voxel geometries), `IdentifySampleFilter` output may differ from DREAM3D 6.5.171 `IdentifySample`.
+
+**Root cause:** Legacy `IdentifySample::execute()` always computes face-neighbor offsets from a single fixed 3D-stride formula (`±1`, `±dims[0]`, `±dims[0]·dims[1]`) sized for a true 3D volume. SIMPLNX's `ProcessVoxels<>` dispatch (`Algorithms/IdentifySample.cpp:393-440`) detects degenerate dimensions via `emptyDimCount` and routes to dimensionality-specific neighbor templates (`EmptyZ/Y/XImage2D`, `Z/Y/XImage1D`, `SingleVoxelImage`), each with neighbor-offset and boundary-validity logic sized for the actual number of non-flat axes.
+
+**Affected users:** Anyone running `IdentifySampleFilter` on a 2D, 1D, or single-voxel `ImageGeom` (e.g., a single-slice EBSD scan, a line scan, a single-point dataset) who expects numeric parity with a DREAM3D 6.5.171 pipeline run on the same degenerate input.
+
+**Recommendation:** Trust SIMPLNX. The dimensionality-aware dispatch is purpose-built and Class 1 tested (3 non-square 2D fixtures in `IdentifySampleTest.cpp`, one per `EmptyZ/Y/XImage2D` path) to produce correct face connectivity regardless of geometry shape.
+
+---
+
+## New features (no legacy code path to compare against — not deviations)
+
+These differ from `IdentifySample-D1` in that no input could have triggered the corresponding legacy behavior at all — there is nothing to deviate from.
+
+- **`SliceBySlice` mode** (`IdentifySampleSliceBySliceFunctor`): gated behind a parameter (`SliceBySlice`) that does not exist in DREAM3D 6.5.171 and is not mapped by `FromSIMPLJson`. No legacy pipeline could have exercised this path.
+- **Cancel checks** (`m_ShouldCancel`): UX-only; no algorithmic effect on a run that completes.
+
+*If a future run against DREAM3D 6.5.171 confirms (or refutes) the suspected incorrectness in `IdentifySample-D1`, update its Status field accordingly.*