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FILT: Create MTRSimFilter that wraps the primary functionality of the MTRSim app and library#1

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FILT: Create MTRSimFilter that wraps the primary functionality of the MTRSim app and library#1
imikejackson wants to merge 41 commits into
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topic/create_mtr_sim_filter

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@imikejackson imikejackson commented Jun 1, 2026

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imikejackson and others added 14 commits June 1, 2026 14:02
@imikejackson @claude
docs: add Milestone AK design spec
c7d11fc 
Integration of MTR representation codes into DREAM3D-NX filters:
MTRSimFilter (algorithm MTRSim, "Generate Synthetic Microtexture"),
filter-focused + statistical test strategy, and CI validation.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
docs: revise AK spec per review (seed pattern, output names, voxel or…
71bc698 
…der)

- Random seed uses standard simplnx UseSeed/SeedValue/SeedArray pattern
- Output defaults: geometry "MTR Microstructure", arrays "MTRIds"/"Eulers"
- Clarify voxel remap target is SIMPLNX z,y,x (slowest->fastest)

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
docs: add Milestone AK implementation plan
7d56898 
TDD plan for MTRSimFilter: LibMTRSim driver (buildUniformODF,
gridToODFComponent, remapSimToZYX, simulateMTR), the filter +
algorithm, deterministic + statistical tests, and CI validation.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
feat(lib): add buildUniformODF grid helper to MTRSimDriver
b8e5ef8 
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
feat(lib): add gridToODFComponent reconstruction helper
c27c1f6 
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
feat(lib): add remapSimToZYX voxel-order helper
40bfe04 
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
feat(lib): add simulateMTR end-to-end driver; main.cpp uses it
f331a9e 
Declares MTRSimResult struct and simulateMTR() in MTRSimDriver.hpp/.cpp.
The function consolidates PGRF assignment, per-component ODF sampling, and
per-voxel orientation assignment into a single call that returns results
already remapped into SIMPLNX z,y,x voxel order.

Refactors src/app/main.cpp to call simulateMTR() and removes the now-
redundant local buildUniformODF() from the anonymous namespace.

Adds a statistical end-to-end test (6x6 mm domain, seed=42) that verifies
volume fractions land within 0.05 of targets (0.30/0.35/0.35) and that all
output Euler angles are within their valid ranges.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
fix(lib): correct main.cpp voxel ordering + harden simulateMTR per re…
6a79b63 
…view

FIX 1: Rebuild spatialCoords in SIMPLNX z,y,x order (iz outer, iy middle,
ix inner) so row k matches sim.phi*/mtrIndex[k]. The old loop used z-x-y
order which mismatched coordinates with orientations for non-square grids.

FIX 2: Replace magic literals 72, 36, 72 in the simulateMTR call with
named constants (k_OdfBinsPhi1/PHI/Phi2) documenting the fixed 5-degree
Bunge-Euler MATLAB ODF grid layout (186624 bins).

FIX 3: Guard in simulateMTR that pgrf_result.mtrIndex.size() == N; throws
std::runtime_error if the PGRF result dimensions are inconsistent.

FIX 4: CSV loop now uses sim.nx*sim.ny*sim.nz to tie the bound to the
actual result rather than the pre-call N.

FIX 5: Add phi2 range check and phi1/phi/phi2 size-equality checks to the
statistical driver test.

FIX 6: Remove unused <numbers> include from main.cpp; ODFSampler.hpp
retained (ODFComponent is used directly).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
feat(filter): scaffold MTRSimFilter + MTRSim algorithm, params, prefl…
14fbb90 
…ight validation + error tests

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
fix(filter): harden MTRSimFilter preflight + conventions per review
38bb3e0 
- Add zero-spacing guard (-13006) before dim() divisions in preflightImpl
- Update Physical Size help text to document the 2D (Z=0) mode
- Change physicalSize/physicalSpacing members from std::vector<float> to
  std::vector<float32> to match what executeImpl reads from filterArgs
- Change outputs separator label to "Output Data Object(s)" (matches ReadMTRSimODFFilter)
- Remove premature #include "simplnx/DataStructure/DataArray.hpp" from stub MTRSim.cpp
- Add preflight test for Theta List rows with wrong column count (-13005)

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
feat(filter): implement MTRSim algorithm execute + statistical wiring…
b107269 
… test

Wire MTRSimFilter to the LibMTRSim simulateMTR entry point: reconstruct
ODFComponents from the selected Float64 cell arrays, build SimulationParams
from filter inputs, run the simulation, and write MTRIds + Eulers into the
output geometry cell AttributeMatrix. Polar coloring (Task 8) is deferred.

Add preflight non-negativity/range hardening (error -13007) requiring each
Volume Fraction value to lie in [0, 1].

Add an end-to-end execute test (100x100 = 10000 voxels, seed 42, 3 components)
that verifies array contract (types/components/tuples), id set {1,2,3},
finite Bunge-bounded Eulers, recorded seed, and loose volume fractions.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
fix(filter): drop dead seed write, reorder VF checks, tidy per review
3c70392 
- Remove params.seed = m_InputValues->seed (dead write; rng is seeded directly)
- Add clarifying comment noting simulateMTR uses the rng, not SimulationParams::seed
- Remove unused #include <cmath> from MTRSim.cpp
- Move per-element VF range check (-13007) before sum check (-13003) so
  out-of-range values produce the precise diagnostic rather than the misleading
  sum message
- Remove redundant size/spacing/VF args.insertOrAssign calls in execute test
  that duplicated what MakeValidArgs already sets; keep seed overrides

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson
ENH: Add optional polar coloring output to MTRSimFilter
0f46063 
* Implement MTRSim::applyPolarColoring using IPFMapper with the MatLab
  HCP colour scheme and Z-axis reference direction
* Call applyPolarColoring from operator() when generatePolarColoring is true;
  short-circuits on error; leaves no array when the flag is false
* Add two unit tests: polar ON verifies array shape (3 components, 10000
  tuples) and non-zero content; polar OFF asserts array is absent

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>
@imikejackson @claude
docs: add MTRSimFilter (Generate Synthetic Microtexture) documentation
4f41e57 
Documents all parameters, output arrays, preflight error codes, the units
consistency requirement for Physical Size / Spacing / Theta List, and the
expected single-stage progress behaviour for large volumes.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

clang-format

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/Algorithms/MTRSim.cpp

Lines 91 to 95 in 4f5504c

const DataPath cellAm = m_InputValues->outputGeometryPath.createChildPath(m_InputValues->cellAttrMatName);
auto& mtrIds = m_DataStructure.getDataRefAs<Int32Array>(cellAm.createChildPath(m_InputValues->mtrIdsArrayName));
auto& eulers = m_DataStructure.getDataRefAs<Float32Array>(cellAm.createChildPath(m_InputValues->eulersArrayName));
auto& mtrStore = mtrIds.getDataStoreRef();
auto& eulerStore = eulers.getDataStoreRef();

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/Algorithms/MTRSim.cpp

Lines 98 to 99 in 4f5504c

for(std::size_t i = 0; i < N; ++i)
{

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/Algorithms/MTRSim.cpp

Lines 108 to 110 in 4f5504c

if(m_InputValues->generatePolarColoring)
{
m_MessageHandler(IFilter::Message::Type::Info, "Computing polar coloring...");

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/Algorithms/MTRSim.cpp

Lines 112 to 113 in 4f5504c

if(colorResult.invalid())
{

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/Algorithms/MTRSim.cpp

Lines 122 to 123 in 4f5504c

Result<> MTRSim::applyPolarColoring(const mtrsim::MTRSimResult& sim, const DataPath& cellAttrMatPath)
{

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/Algorithms/MTRSim.cpp

Lines 125 to 127 in 4f5504c

Eigen::VectorXd phi1 = Eigen::Map<const Eigen::VectorXd>(sim.phi1.data(), static_cast<Eigen::Index>(N));
Eigen::VectorXd phi = Eigen::Map<const Eigen::VectorXd>(sim.phi.data(), static_cast<Eigen::Index>(N));
Eigen::VectorXd phi2 = Eigen::Map<const Eigen::VectorXd>(sim.phi2.data(), static_cast<Eigen::Index>(N));

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/Algorithms/MTRSim.cpp

Line 130 in 4f5504c

const std::vector<mtrsim::RGBColor> colors = mapper.eulerToColors(phi1, phi, phi2, {0.0, 0.0, 1.0}, mtrsim::IPFColorScheme::MatLab);

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/Algorithms/MTRSim.cpp

Lines 132 to 135 in 4f5504c

auto& rgb = m_DataStructure.getDataRefAs<UInt8Array>(cellAttrMatPath.createChildPath(m_InputValues->polarColorsArrayName));
auto& store = rgb.getDataStoreRef();
for(std::size_t i = 0; i < N; ++i)
{

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/Algorithms/MTRSim.hpp

Lines 13 to 14 in 4f5504c

namespace nx::core
{

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/Algorithms/MTRSim.hpp

Lines 16 to 17 in 4f5504c

struct MTRSIM_EXPORT MTRSimInputValues
{

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/Algorithms/MTRSim.hpp

Lines 36 to 37 in 4f5504c

* from an input ODF and a set of simulation parameters. The output ImageGeom and
* its cell arrays are created by the filter's preflight; this algorithm fills them.

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/Algorithms/MTRSim.hpp

Lines 39 to 40 in 4f5504c

class MTRSIM_EXPORT MTRSim
{

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/Algorithms/MTRSim.hpp

Line 42 in 4f5504c

MTRSim(DataStructure& dataStructure, const IFilter::MessageHandler& mesgHandler, const std::atomic_bool& shouldCancel, MTRSimInputValues* inputValues);

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/Algorithms/MTRSim.hpp

Lines 45 to 48 in 4f5504c

MTRSim(const MTRSim&) = delete;
MTRSim(MTRSim&&) noexcept = delete;
MTRSim& operator=(const MTRSim&) = delete;
MTRSim& operator=(MTRSim&&) noexcept = delete;

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/Algorithms/MTRSim.hpp

Lines 53 to 57 in 4f5504c

Result<> applyPolarColoring(const mtrsim::MTRSimResult& sim, const DataPath& cellAttrMatPath);
DataStructure& m_DataStructure;
const MTRSimInputValues* m_InputValues = nullptr;
const std::atomic_bool& m_ShouldCancel;
const IFilter::MessageHandler& m_MessageHandler;

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 29 to 30 in 4f5504c

namespace nx::core
{

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 32 to 33 in 4f5504c

std::string MTRSimFilter::name() const
{

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 38 to 39 in 4f5504c

std::string MTRSimFilter::className() const
{

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 44 to 47 in 4f5504c

Uuid MTRSimFilter::uuid() const
{
return FilterTraits<MTRSimFilter>::uuid;
}

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 50 to 51 in 4f5504c

std::string MTRSimFilter::humanName() const
{

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 56 to 57 in 4f5504c

std::vector<std::string> MTRSimFilter::defaultTags() const
{

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 62 to 63 in 4f5504c

Parameters MTRSimFilter::parameters() const
{

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 67 to 71 in 4f5504c

params.insert(std::make_unique<GeometrySelectionParameter>(k_InputOdfGeometry_Key, "Input ODF Geometry", "Image Geometry holding the ODF (from the Read/Compute ODF filters).", DataPath{},
GeometrySelectionParameter::AllowedTypes{IGeometry::Type::Image}));
params.insert(std::make_unique<MultiArraySelectionParameter>(k_OdfComponentArrays_Key, "ODF Component Arrays", "Ordered list of per-component ODF cell arrays. Order maps to Volume Fraction columns.",
MultiArraySelectionParameter::ValueType{}, MultiArraySelectionParameter::AllowedTypes{IArray::ArrayType::DataArray}, GetAllNumericTypes(),
MultiArraySelectionParameter::AllowedComponentShapes{{1}}));

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Line 78 in 4f5504c

params.insert(std::make_unique<DynamicTableParameter>(k_VolumeFractions_Key, "Volume Fraction", "One value per ODF component; must match the component count and sum to 1.0.", vfInfo));

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 82 to 87 in 4f5504c

thetaInfo.setRowsInfo(DynamicTableInfo::DynamicVectorInfo(1, 2, "Gaussian {}"));
thetaInfo.setColsInfo(DynamicTableInfo::StaticVectorInfo(DynamicTableInfo::HeadersListType{"theta_x", "theta_y", "theta_z"}));
params.insert(std::make_unique<DynamicTableParameter>(k_ThetaList_Key, "Theta List",
"Correlation lengths [theta_x, theta_y, theta_z] per latent Gaussian. Needs >= (components - 1) rows. Same length unit as Physical "
"Size/Spacing.",
thetaInfo));

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 89 to 97 in 4f5504c

params.insert(std::make_unique<VectorFloat32Parameter>(k_PhysicalSize_Key, "Physical Size (microns)", "Domain extent X, Y, Z in microns. Set Z = 0 to generate a single-layer (2D) microstructure.", std::vector<float32>{38.1f, 12.7f, 0.0f},
std::vector<std::string>{"X", "Y", "Z"}));
params.insert(std::make_unique<VectorFloat32Parameter>(k_PhysicalSpacing_Key, "Physical Spacing (microns)", "Voxel spacing X,Y,Z.", std::vector<float32>{0.02f, 0.02f, 0.02f},
std::vector<std::string>{"X", "Y", "Z"}));
params.insertSeparator(Parameters::Separator{"Random Number Seed Parameters"});
params.insertLinkableParameter(std::make_unique<BoolParameter>(k_UseSeed_Key, "Use Seed for Random Generation", "When true the user can supply a fixed seed.", false));
params.insert(std::make_unique<NumberParameter<uint64>>(k_SeedValue_Key, "Seed Value", "The seed fed into the random generator.", std::mt19937::default_seed));
params.insert(std::make_unique<DataObjectNameParameter>(k_SeedArrayName_Key, "Stored Seed Value Array Name", "Top-level array recording the seed used.", "MTRSim SeedValue"));

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 100 to 106 in 4f5504c

params.insertLinkableParameter(
std::make_unique<BoolParameter>(k_GeneratePolarColoring_Key, "Generate Polar Coloring", "Create a 3-component UInt8 RGB array using the MATLAB polar color mapping.", false));
params.insert(std::make_unique<DataGroupCreationParameter>(k_OutputGeometry_Key, "Output Image Geometry", "Path of the new microstructure Image Geometry.", DataPath({"MTR Microstructure"})));
params.insert(std::make_unique<DataObjectNameParameter>(k_CellAttrMatName_Key, "Cell Attribute Matrix Name", "Name of the created cell AttributeMatrix.", "Cell Data"));
params.insert(std::make_unique<DataObjectNameParameter>(k_MtrIdsArrayName_Key, "MTR Ids Array Name", "Int32 per-voxel MTR component id (1-based).", "MTRIds"));
params.insert(std::make_unique<DataObjectNameParameter>(k_EulersArrayName_Key, "Euler Angles Array Name", "Float32 3-component Bunge Euler angles [rad].", "Eulers"));
params.insert(std::make_unique<DataObjectNameParameter>(k_PolarColorsArrayName_Key, "Polar Colors Array Name", "UInt8 3-component RGB polar coloring.", "Polar Colors"));

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Line 109 in 4f5504c

params.linkParameters(k_GeneratePolarColoring_Key, k_PolarColorsArrayName_Key, true);

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 115 to 118 in 4f5504c

IFilter::VersionType MTRSimFilter::parametersVersion() const
{
return 1;
}

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 121 to 122 in 4f5504c

IFilter::UniquePointer MTRSimFilter::clone() const
{

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 127 to 132 in 4f5504c

IFilter::PreflightResult MTRSimFilter::preflightImpl(const DataStructure& dataStructure, const Arguments& filterArgs, const MessageHandler& messageHandler, const std::atomic_bool& shouldCancel,
const ExecutionContext& executionContext) const
{
auto pOdfArrays = filterArgs.value<MultiArraySelectionParameter::ValueType>(k_OdfComponentArrays_Key);
auto pVolumeFractions = filterArgs.value<DynamicTableParameter::ValueType>(k_VolumeFractions_Key);
auto pThetaList = filterArgs.value<DynamicTableParameter::ValueType>(k_ThetaList_Key);

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 147 to 149 in 4f5504c

if(numComponents < 2)
{
return {MakeErrorResult<OutputActions>(-13001, "MTRSim requires at least 2 ODF component arrays.")};

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 151 to 153 in 4f5504c

if(pVolumeFractions.size() != 1 || pVolumeFractions[0].size() != numComponents)
{
return {MakeErrorResult<OutputActions>(-13002, fmt::format("Volume Fraction must be 1 row x {} columns (one per ODF component).", numComponents))};

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 155 to 159 in 4f5504c

for(double v : pVolumeFractions[0])
{
if(v < 0.0 || v > 1.0)
{
return {MakeErrorResult<OutputActions>(-13007, fmt::format("Each Volume Fraction value must be in the range [0, 1] (got {:.4f}).", v))};

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 163 to 164 in 4f5504c

for(double v : pVolumeFractions[0])
{

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 167 to 169 in 4f5504c

if(std::abs(vfSum - 1.0) > 1.0e-3)
{
return {MakeErrorResult<OutputActions>(-13003, fmt::format("Volume Fraction values must sum to 1.0 (got {:.4f}).", vfSum))};

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 171 to 173 in 4f5504c

if(pThetaList.size() < numComponents - 1)
{
return {MakeErrorResult<OutputActions>(-13004, fmt::format("Theta List needs at least {} rows (components - 1).", numComponents - 1))};

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 175 to 179 in 4f5504c

for(const auto& row : pThetaList)
{
if(row.size() != 3)
{
return {MakeErrorResult<OutputActions>(-13005, "Each Theta List row must have exactly 3 columns.")};

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 183 to 185 in 4f5504c

if(pSpacing[0] <= 0.0f || pSpacing[1] <= 0.0f)
{
return {MakeErrorResult<OutputActions>(-13006, "Physical Spacing X and Y must be greater than 0.")};

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Line 188 in 4f5504c

const auto dim = [](float len, float sp) { return static_cast<usize>(std::max(std::lround(len / sp), 1L)); };

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Line 195 in 4f5504c

const std::vector<float32> spacingXYZ = {pSpacing[0], pSpacing[1], pSpacing[2]};

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 198 to 205 in 4f5504c

resultOutputActions.value().appendAction(std::make_unique<CreateImageGeometryAction>(pOutGeomPath, imageGeomDimsXYZ, origin, spacingXYZ, pCellAttrMatName));
const DataPath cellAttrMatPath = pOutGeomPath.createChildPath(pCellAttrMatName);
resultOutputActions.value().appendAction(std::make_unique<CreateArrayAction>(DataType::int32, tupleShapeZYX, std::vector<usize>{1}, cellAttrMatPath.createChildPath(pMtrIdsName)));
resultOutputActions.value().appendAction(std::make_unique<CreateArrayAction>(DataType::float32, tupleShapeZYX, std::vector<usize>{3}, cellAttrMatPath.createChildPath(pEulersName)));
if(pGenPolar)
{
resultOutputActions.value().appendAction(std::make_unique<CreateArrayAction>(DataType::uint8, tupleShapeZYX, std::vector<usize>{3}, cellAttrMatPath.createChildPath(pPolarName)));

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Line 207 in 4f5504c

resultOutputActions.value().appendAction(std::make_unique<CreateArrayAction>(DataType::uint64, std::vector<usize>{1}, std::vector<usize>{1}, DataPath({pSeedArrayName})));

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 209 to 210 in 4f5504c

preflightUpdatedValues.push_back({"Output Grid (X, Y, Z)", fmt::format("{} x {} x {}", nx, ny, nz)});
preflightUpdatedValues.push_back({"Number of ODF Components", std::to_string(numComponents)});

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 216 to 218 in 4f5504c

Result<> MTRSimFilter::executeImpl(DataStructure& dataStructure, const Arguments& filterArgs, const PipelineFilter* pipelineNode, const MessageHandler& messageHandler, const std::atomic_bool& shouldCancel,
const ExecutionContext& executionContext) const
{

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 220 to 231 in 4f5504c

inputValues.inputOdfGeometryPath = filterArgs.value<DataPath>(k_InputOdfGeometry_Key);
inputValues.odfComponentPaths = filterArgs.value<MultiArraySelectionParameter::ValueType>(k_OdfComponentArrays_Key);
inputValues.volumeFractions = filterArgs.value<DynamicTableParameter::ValueType>(k_VolumeFractions_Key);
inputValues.thetaList = filterArgs.value<DynamicTableParameter::ValueType>(k_ThetaList_Key);
inputValues.physicalSize = filterArgs.value<std::vector<float32>>(k_PhysicalSize_Key);
inputValues.physicalSpacing = filterArgs.value<std::vector<float32>>(k_PhysicalSpacing_Key);
inputValues.generatePolarColoring = filterArgs.value<bool>(k_GeneratePolarColoring_Key);
inputValues.outputGeometryPath = filterArgs.value<DataPath>(k_OutputGeometry_Key);
inputValues.cellAttrMatName = filterArgs.value<std::string>(k_CellAttrMatName_Key);
inputValues.mtrIdsArrayName = filterArgs.value<std::string>(k_MtrIdsArrayName_Key);
inputValues.eulersArrayName = filterArgs.value<std::string>(k_EulersArrayName_Key);
inputValues.polarColorsArrayName = filterArgs.value<std::string>(k_PolarColorsArrayName_Key);

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 234 to 236 in 4f5504c

if(!filterArgs.value<bool>(k_UseSeed_Key))
{
seed = static_cast<uint64>(std::chrono::steady_clock::now().time_since_epoch().count());

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Line 238 in 4f5504c

dataStructure.getDataRefAs<UInt64Array>(DataPath({filterArgs.value<std::string>(k_SeedArrayName_Key)}))[0] = seed;

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Lines 245 to 246 in 4f5504c

Result<Arguments> MTRSimFilter::FromSIMPLJson(const nlohmann::json& json)
{

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.cpp

Line 255 in 4f5504c

return ConvertResultTo<Arguments>(std::move(conversionResult), std::move(args));

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.hpp

Lines 9 to 10 in 4f5504c

namespace nx::core
{

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.hpp

Lines 17 to 18 in 4f5504c

class MTRSIM_EXPORT MTRSimFilter : public IFilter
{

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.hpp

Lines 23 to 24 in 4f5504c

MTRSimFilter(const MTRSimFilter&) = delete;
MTRSimFilter(MTRSimFilter&&) noexcept = delete;

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.hpp

Lines 26 to 27 in 4f5504c

MTRSimFilter& operator=(const MTRSimFilter&) = delete;
MTRSimFilter& operator=(MTRSimFilter&&) noexcept = delete;

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.hpp

Lines 30 to 32 in 4f5504c

static inline constexpr StringLiteral k_InputOdfGeometry_Key = "input_odf_geometry";
static inline constexpr StringLiteral k_OdfComponentArrays_Key = "odf_component_arrays";
static inline constexpr StringLiteral k_VolumeFractions_Key = "volume_fractions";

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.hpp

Line 35 in 4f5504c

static inline constexpr StringLiteral k_PhysicalSpacing_Key = "physical_spacing";

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.hpp

Lines 39 to 44 in 4f5504c

static inline constexpr StringLiteral k_GeneratePolarColoring_Key = "generate_polar_coloring";
static inline constexpr StringLiteral k_OutputGeometry_Key = "output_geometry";
static inline constexpr StringLiteral k_CellAttrMatName_Key = "cell_attribute_matrix_name";
static inline constexpr StringLiteral k_MtrIdsArrayName_Key = "mtr_ids_array_name";
static inline constexpr StringLiteral k_EulersArrayName_Key = "eulers_array_name";
static inline constexpr StringLiteral k_PolarColorsArrayName_Key = "polar_colors_array_name";

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.hpp

Line 51 in 4f5504c

static Result<Arguments> FromSIMPLJson(const nlohmann::json& json);

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.hpp

Lines 105 to 107 in 4f5504c

* @brief Takes in a DataStructure and checks that the filter can be run on it with the given arguments.
* Returns any warnings/errors. Also returns the changes that would be applied to the DataStructure.
* Some parts of the actions may not be completely filled out if all the required information is not available at preflight time.

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.hpp

Line 109 in 4f5504c

* @param filterArgs These are the input values for each parameter that is required for the filter

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.hpp

Lines 111 to 113 in 4f5504c

* @param shouldCancel Atomic boolean value that can be checked to cancel the filter
* @param executionContext The ExecutionContext that can be used to determine the correct absolute path from a relative path
* @return Returns a Result object with error or warning values if any of those occurred during execution of this function

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.hpp

Lines 115 to 116 in 4f5504c

PreflightResult preflightImpl(const DataStructure& dataStructure, const Arguments& filterArgs, const MessageHandler& messageHandler, const std::atomic_bool& shouldCancel,
const ExecutionContext& executionContext) const override;

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.hpp

Lines 119 to 120 in 4f5504c

* @brief Applies the filter's algorithm to the DataStructure with the given arguments. Returns any warnings/errors.
* On failure, there is no guarantee that the DataStructure is in a correct state.

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.hpp

Line 122 in 4f5504c

* @param filterArgs These are the input values for each parameter that is required for the filter

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.hpp

Lines 125 to 127 in 4f5504c

* @param shouldCancel Atomic boolean value that can be checked to cancel the filter
* @param executionContext The ExecutionContext that can be used to determine the correct absolute path from a relative path
* @return Returns a Result object with error or warning values if any of those occurred during execution of this function

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.hpp

Lines 129 to 130 in 4f5504c

Result<> executeImpl(DataStructure& dataStructure, const Arguments& filterArgs, const PipelineFilter* pipelineNode, const MessageHandler& messageHandler, const std::atomic_bool& shouldCancel,
const ExecutionContext& executionContext) const override;

[clang-format] reported by reviewdog 🐶

MTRSim/src/MTRSim/Filters/MTRSimFilter.hpp

Line 134 in 4f5504c

SIMPLNX_DEF_FILTER_TRAITS(nx::core, MTRSimFilter, "f7f7a330-4bff-4a42-a573-09117a89a0a0");

[clang-format] reported by reviewdog 🐶

MTRSim/src/app/main.cpp

Line 249 in 4f5504c

mtrsim::MTRSimResult sim = mtrsim::simulateMTR(params, odfComponents, rng, k_OdfBinsPhi1, k_OdfBinsPHI, k_OdfBinsPhi2);

[clang-format] reported by reviewdog 🐶

MTRSim/src/app/main.cpp

Lines 252 to 254 in 4f5504c

Eigen::VectorXd phi1Vec = Eigen::Map<Eigen::VectorXd>(sim.phi1.data(), static_cast<Eigen::Index>(sim.phi1.size()));
Eigen::VectorXd phiVec = Eigen::Map<Eigen::VectorXd>(sim.phi.data(), static_cast<Eigen::Index>(sim.phi.size()));
Eigen::VectorXd phi2Vec = Eigen::Map<Eigen::VectorXd>(sim.phi2.data(), static_cast<Eigen::Index>(sim.phi2.size()));

[clang-format] reported by reviewdog 🐶

MTRSim/src/app/main.cpp

Line 289 in 4f5504c

<< phi2Vec[i] << ',' << sim.mtrIndex[static_cast<std::size_t>(i)] << '\n';

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Line 10 in 4f5504c

* 5. Theta List rows with wrong column count (2 instead of 3) -> invalid (-13005).

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 33 to 34 in 4f5504c

namespace
{

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 45 to 47 in 4f5504c

std::vector<DataPath> BuildOdfDataStructure(DataStructure& dataStructure, usize numComponents)
{
ImageGeom* imageGeom = ImageGeom::Create(dataStructure, k_OdfGeomPath.getTargetName());

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Line 50 in 4f5504c

imageGeom->setDimensions({k_NPhi2, k_NPHI, k_NPhi1}); // X(phi2), Y(PHI), Z(phi1)

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Line 55 in 4f5504c

AttributeMatrix* cellAM = AttributeMatrix::Create(dataStructure, k_CellAttrMatName, tupleShape, imageGeom->getId());

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 58 to 60 in 4f5504c

const DataPath cellAttrMatPath = k_OdfGeomPath.createChildPath(k_CellAttrMatName);
for(usize c = 0; c < numComponents; ++c)
{

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Line 62 in 4f5504c

CreateTestDataArray<float64>(dataStructure, name, tupleShape, {1}, cellAM->getId());

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 69 to 70 in 4f5504c

Arguments MakeValidArgs(const std::vector<DataPath>& compPaths)
{

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 74 to 77 in 4f5504c

args.insertOrAssign(MTRSimFilter::k_VolumeFractions_Key, DynamicTableParameter::ValueType{{0.30, 0.35, 0.35}});
args.insertOrAssign(MTRSimFilter::k_ThetaList_Key, DynamicTableParameter::ValueType{{0.1, 0.45, 0.1}, {0.08, 0.37, 0.08}});
args.insertOrAssign(MTRSimFilter::k_PhysicalSize_Key, std::vector<float32>{2.0f, 2.0f, 0.0f});
args.insertOrAssign(MTRSimFilter::k_PhysicalSpacing_Key, std::vector<float32>{0.02f, 0.02f, 0.02f});

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Line 80 in 4f5504c

args.insertOrAssign(MTRSimFilter::k_SeedArrayName_Key, std::string("MTRSim SeedValue"));

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 82 to 86 in 4f5504c

args.insertOrAssign(MTRSimFilter::k_OutputGeometry_Key, DataPath({"MTR Microstructure"}));
args.insertOrAssign(MTRSimFilter::k_CellAttrMatName_Key, std::string("Cell Data"));
args.insertOrAssign(MTRSimFilter::k_MtrIdsArrayName_Key, std::string("MTRIds"));
args.insertOrAssign(MTRSimFilter::k_EulersArrayName_Key, std::string("Eulers"));
args.insertOrAssign(MTRSimFilter::k_PolarColorsArrayName_Key, std::string("Polar Colors"));

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 91 to 92 in 4f5504c

TEST_CASE("MTRSim::MTRSimFilter: Valid preflight builds actions", "[MTRSim][MTRSimFilter]")
{

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Line 96 in 4f5504c

const std::vector<DataPath> compPaths = BuildOdfDataStructure(dataStructure, 3);

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 105 to 106 in 4f5504c

TEST_CASE("MTRSim::MTRSimFilter: Rejects mismatched Volume Fraction column count", "[MTRSim][MTRSimFilter][ErrorPath]")
{

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Line 110 in 4f5504c

const std::vector<DataPath> compPaths = BuildOdfDataStructure(dataStructure, 3);

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Line 115 in 4f5504c

args.insertOrAssign(MTRSimFilter::k_VolumeFractions_Key, DynamicTableParameter::ValueType{{0.5, 0.5}});

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 121 to 122 in 4f5504c

TEST_CASE("MTRSim::MTRSimFilter: Execute wires simulation to output arrays", "[MTRSim][MTRSimFilter]")
{

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 126 to 130 in 4f5504c

const std::vector<DataPath> compPaths = BuildOdfDataStructure(dataStructure, 3);
// Fill every component array with a uniform value so ODF sampling is well-defined.
for(const auto& path : compPaths)
{
auto& arr = dataStructure.getDataRefAs<Float64Array>(path);

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Line 154 in 4f5504c

auto& mtrIds = dataStructure.getDataRefAs<Int32Array>(cellAm.createChildPath("MTRIds"));

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Line 159 in 4f5504c

auto& eulers = dataStructure.getDataRefAs<Float32Array>(cellAm.createChildPath("Eulers"));

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 163 to 165 in 4f5504c

// MTR ids in {1,2,3}; at least 2 distinct ids appear. Also accumulate empirical
// volume fractions for a loose wiring check.
const auto& mtrStore = mtrIds.getDataStoreRef();

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 167 to 168 in 4f5504c

for(usize i = 0; i < mtrStore.getSize(); ++i)
{

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 175 to 178 in 4f5504c

for(usize id = 1; id <= 3; ++id)
{
if(counts[id] > 0)
{

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 187 to 189 in 4f5504c

const auto& eulerStore = eulers.getDataStoreRef();
for(usize t = 0; t < expectedTuples; ++t)
{

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Line 205 in 4f5504c

auto& seedArray = dataStructure.getDataRefAs<UInt64Array>(DataPath({"MTRSim SeedValue"}));

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 212 to 214 in 4f5504c

for(usize id = 1; id <= 3; ++id)
{
const double empirical = static_cast<double>(counts[id]) / static_cast<double>(expectedTuples);

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 219 to 220 in 4f5504c

TEST_CASE("MTRSim::MTRSimFilter: Rejects too few Theta List rows", "[MTRSim][MTRSimFilter][ErrorPath]")
{

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Line 224 in 4f5504c

const std::vector<DataPath> compPaths = BuildOdfDataStructure(dataStructure, 3);

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Line 229 in 4f5504c

args.insertOrAssign(MTRSimFilter::k_ThetaList_Key, DynamicTableParameter::ValueType{{0.1, 0.45, 0.1}});

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 235 to 236 in 4f5504c

TEST_CASE("MTRSim::MTRSimFilter: Rejects Volume Fraction not summing to 1.0", "[MTRSim][MTRSimFilter][ErrorPath]")
{

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Line 240 in 4f5504c

const std::vector<DataPath> compPaths = BuildOdfDataStructure(dataStructure, 3);

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Line 245 in 4f5504c

args.insertOrAssign(MTRSimFilter::k_VolumeFractions_Key, DynamicTableParameter::ValueType{{0.2, 0.2, 0.2}});

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 251 to 252 in 4f5504c

TEST_CASE("MTRSim::MTRSimFilter: Execute with polar coloring ON fills Polar Colors array", "[MTRSim][MTRSimFilter]")
{

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 256 to 259 in 4f5504c

const std::vector<DataPath> compPaths = BuildOdfDataStructure(dataStructure, 3);
for(const auto& path : compPaths)
{
auto& arr = dataStructure.getDataRefAs<Float64Array>(path);

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Line 275 in 4f5504c

const DataPath cellAm = DataPath({"MTR Microstructure"}).createChildPath("Cell Data");

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Line 278 in 4f5504c

auto& rgb = dataStructure.getDataRefAs<UInt8Array>(cellAm.createChildPath("Polar Colors"));

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 282 to 283 in 4f5504c

for(usize i = 0; i < rgb.getSize(); ++i)
{

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 289 to 290 in 4f5504c

TEST_CASE("MTRSim::MTRSimFilter: Execute with polar coloring OFF omits Polar Colors array", "[MTRSim][MTRSimFilter]")
{

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 294 to 297 in 4f5504c

const std::vector<DataPath> compPaths = BuildOdfDataStructure(dataStructure, 3);
for(const auto& path : compPaths)
{
auto& arr = dataStructure.getDataRefAs<Float64Array>(path);

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 313 to 314 in 4f5504c

const DataPath cellAm = DataPath({"MTR Microstructure"}).createChildPath("Cell Data");
REQUIRE(dataStructure.getDataAs<UInt8Array>(cellAm.createChildPath("Polar Colors")) == nullptr);

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 317 to 318 in 4f5504c

TEST_CASE("MTRSim::MTRSimFilter: Rejects Theta List rows with wrong column count", "[MTRSim][MTRSimFilter][ErrorPath]")
{

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Line 322 in 4f5504c

const std::vector<DataPath> compPaths = BuildOdfDataStructure(dataStructure, 3);

[clang-format] reported by reviewdog 🐶

MTRSim/test/MTRSimTest.cpp

Lines 326 to 329 in 4f5504c

// 2 rows supplied (enough for 3 components: needs >= 2), but each row has only 2
// columns instead of 3 — must trigger the column-count check (-13005), not the
// row-count check (-13004).
args.insertOrAssign(MTRSimFilter::k_ThetaList_Key, DynamicTableParameter::ValueType{{0.1, 0.45}, {0.08, 0.37}});

[clang-format] reported by reviewdog 🐶

MTRSim/tests/test_mtrsim_driver.cpp

Line 24 in 4f5504c

TEST_CASE("gridToODFComponent derives bin centres in radians and normalizes", "[mtrsim_driver]") {

[clang-format] reported by reviewdog 🐶

MTRSim/tests/test_mtrsim_driver.cpp

Line 40 in 4f5504c

TEST_CASE("remapSimToZYX moves y-fastest data to x-fastest layout", "[mtrsim_driver]") {

[clang-format] reported by reviewdog 🐶

MTRSim/tests/test_mtrsim_driver.cpp

Line 44 in 4f5504c

for (int i = 0; i < nx * ny * nz; ++i) { in[i] = i; }

[clang-format] reported by reviewdog 🐶

MTRSim/tests/test_mtrsim_driver.cpp

Line 64 in 4f5504c

TEST_CASE("simulateMTR reproduces target volume fractions (statistical)", "[mtrsim_driver][statistical]") {

[clang-format] reported by reviewdog 🐶

MTRSim/tests/test_mtrsim_driver.cpp

Lines 66 to 67 in 4f5504c

params.xLen = 6.0; params.yLen = 6.0; params.zLen = 0.0;
params.dx = 0.02; params.dy = 0.02; params.dz = 0.02;

[clang-format] reported by reviewdog 🐶

MTRSim/tests/test_mtrsim_driver.cpp

Lines 73 to 74 in 4f5504c

mtrsim::buildUniformODF(72, 36, 72),
mtrsim::buildUniformODF(72, 36, 72),

[clang-format] reported by reviewdog 🐶

MTRSim/tests/test_mtrsim_driver.cpp

Line 78 in 4f5504c

const mtrsim::MTRSimResult r = mtrsim::simulateMTR(params, comps, rng, 72, 36, 72);

[clang-format] reported by reviewdog 🐶

MTRSim/tests/test_mtrsim_driver.cpp

Line 83 in 4f5504c

for (int v : r.mtrIndex) { REQUIRE(v >= 1); REQUIRE(v <= 3); }

[clang-format] reported by reviewdog 🐶

MTRSim/tests/test_mtrsim_driver.cpp

Line 86 in 4f5504c

for (int v : r.mtrIndex) { counts[static_cast<std::size_t>(v - 1)]++; }

[clang-format] reported by reviewdog 🐶

MTRSim/tests/test_mtrsim_driver.cpp

Lines 95 to 97 in 4f5504c

for (double a : r.phi1) { REQUIRE(a >= 0.0); REQUIRE(a <= 2.0 * std::numbers::pi); }
for (double a : r.phi) { REQUIRE(a >= 0.0); REQUIRE(a <= std::numbers::pi); }
for (double a : r.phi2) { REQUIRE(a >= 0.0); REQUIRE(a <= 2.0 * std::numbers::pi); }

@imikejackson imikejackson force-pushed the topic/create_mtr_sim_filter branch 2 times, most recently from 125eab7 to f5aabb0 Compare June 1, 2026 20:41
@imikejackson
docs: record AK plan execution corrections; ignore CTest Testing/ dir
dea7856 
Plan updated with the Approx (not Catch::Approx) and
src/LibMTRSim/CMakeLists.txt corrections discovered during execution.
@imikejackson imikejackson force-pushed the topic/create_mtr_sim_filter branch from f5aabb0 to dea7856 Compare June 1, 2026 20:49
@imikejackson @claude
docs: add MTRSimFilter overview/algorithm/ODF figures
78e6d53 
Embed the conceptual "what it generates" and "how it works" slides
(converted from output/avatar_slides) plus an ODF Euler-space figure into
the filter documentation. Also correct the Execute error code in the table
to -13050 to match the algorithm source.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson imikejackson force-pushed the topic/create_mtr_sim_filter branch from 10bac67 to 78e6d53 Compare June 1, 2026 21:04
imikejackson and others added 9 commits June 2, 2026 07:49
@imikejackson @claude
fix(filters): parameter keys must end with _path / _index (FilterVali…
b9c696d 
…dationTest)

simplnx's FilterValidationTest requires path-type parameter keys to end
with '_path' and ChoicesParameter keys with '_index'. Rename the offending
key strings across MTRSimFilter, ComputeODFFilter, ReadMTRSimODFFilter, and
WriteMTRSimODFFilter (C++ constant names unchanged, so .cpp/tests are
unaffected) and update the avtr12 example pipeline to match.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson
STY: Add clang-format file and format all sources.
62636dc
@imikejackson @claude
feat(pipelines): add NX pipelines recreating the LibMTRSim configs
0449e71 
Add scripts/generate_nx_pipelines.py which turns each configs/*.json into a
ReadMTRSimODF -> MTRSim -> WriteDREAM3D pipeline, and the 20 generated
.d3dpipeline files. All 20 preflight cleanly via nxrunner.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
fix(lib): add missing .eval() in GPGenerator + tiny smoke-test config
038bf57 
GPGenerator::buildCovarianceMatrix did `gamma += gamma.transpose()`, which
aliases (Eigen throws an assertion in Debug builds). Materialize the transpose
with .eval() before the in-place add.

Also add a 1500-voxel smoke_test config + pipeline that exercises the full
MTRSim execute path quickly; verified clean end-to-end in the Debug build
(nxrunner_d --execute), confirming no remaining debug-only Eigen issues.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
chore: ignore generated output/*.dream3d run artifacts
7a0c5fd 
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
docs: add design spec for simulation observer + config-file input
63daece 
ISimulationObserver (progress + cancel) threaded through simulateMTR/sampleN,
and an optional MTRSim config-JSON input on MTRSimFilter gated by a linked
boolean (config mode vs manual mode).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
docs: add implementation plan for observer + config-file input
d1d2b14 
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson
ENH: Add ISimulationObserver interface with Null and Console implemen…
80eb2a9 
…tations

* Add ISimulationObserver pure-virtual interface (updateProgress + shouldCancel)
  to give callers a clean hook for progress reporting and cancellation
* Add NullObserver (no-op default) and ConsoleObserver (spdlog-throttled)
  concrete implementations in SimulationObservers.hpp
* Register both headers in src/LibMTRSim/CMakeLists.txt and MTRSimPlugin.cmake
* Add Catch2 tests covering NullObserver and a RecordingObserver test double
  that verifies cancel-after-K-updates behaviour

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>
@imikejackson @claude
feat(lib): thread ISimulationObserver through simulateMTR, PGRFSimula…
5444c48 
…tion, ODFSampler

Tasks A2 + A3: observer (nullable, default nullptr) is now propagated from
simulateMTR -> PGRFSimulation::run -> ODFSampler::sampleN.

- MTRSimResult gains `cancelled` flag; simulateMTR returns early with it set
  when the observer vetoes the run.
- PGRFSimulation::run checks shouldCancel() before each latent field and
  reports progress via updateProgress(); returns empty PGRFResult on cancel.
- ODFSampler::sampleN checks shouldCancel() every 4096 iterations in both
  the sampling loop and the assignment loop without consuming the RNG on the
  non-cancel path (bit-stability preserved).
- Python bindings updated to wrap the new signatures with observer=nullptr
  so existing Python callers are unaffected.
- New tests: cancel-early and nullptr-observer in test_mtrsim_driver.cpp;
  immediate-cancel bail-out in test_odf_sampler.cpp.

All 441 tests pass; [mtrsim_driver][statistical] seed-fixed regression guard
continues to pass unchanged.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
imikejackson and others added 15 commits June 2, 2026 13:19
@imikejackson @claude
docs(lib): clarify cancel-check rationale comments (review nits)
f751f65 
- Added documentation for kCheck constant: explains the 4096 poll interval,
  latency rationale, and that modulo check short-circuits before RNG draw.
- Clarified PGRFSimulation return comment to specify the cancelled lambda.
- Documented sampleOne call: n=1 case doesn't need observer (latency negligible).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
feat(app): standalone driver reports progress via ConsoleObserver
15c7d98 
Pass a ConsoleObserver to simulateMTR so the CLI emits spdlog
percentage-progress lines during the simulation, and guard the
CSV/PNG-writing block against a cancelled result.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson
ENH: Add shared parseConfigJson config reader to LibMTRSim
b891954 
* Add ConfigIO.hpp and ConfigIO.cpp with parseConfigJson() function
* Parses xLen/yLen/zLen, dx/dy/dz, volumeFractions, thetaList,
  nuggetVariance, and seed from config JSON; unknown keys are ignored
* Register ConfigIO in LibMTRSim/CMakeLists.txt and MTRSimPlugin.cmake
* Add tests/test_config_io.cpp covering round-trip read, missing-file
  error, and malformed-JSON error (3 test cases, 9 assertions)
* All 444 tests pass

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>
@imikejackson @claude
docs(lib): correct parseConfigJson key list (nuggetVariance is parsed)
bfa3717 
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson
REV: Standalone driver uses shared parseConfigJson helper
ab5446f 
* Replace inline nlohmann JSON-parsing block with mtrsim::parseConfigJson
* Preserve CLI semantics: --seed non-zero overrides JSON seed; outputDir
  from -o flag survives config load
* Read odfInputPath from JSON separately after parseConfigJson (the shared
  helper intentionally omits that field; keep nlohmann include for this)

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>
@imikejackson @claude
refactor(lib): parseConfigJson reads odfInputPath; drop CLI double-parse
9aeab88 
Teach `mtrsim::parseConfigJson` to populate `SimulationParams::odfInputPath`
so callers no longer need a second JSON read.  The standalone CLI's redundant
re-open/re-parse block and its `#include <nlohmann/json.hpp>` are removed.
The round-trip test is updated to assert the field is now populated.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
feat(filter): report progress + honor cancel via FilterObserver
62b2eb9 
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
feat(filter): optional MTRSim config-file input (linked show/hide, co…
55da08c 
…nfig-mode preflight/execute)

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson
REV: Resolve config in the filter once; algorithm is config-agnostic
fd74649 
* executeImpl now parses the config file at most once and populates
  all MTRSimInputValues fields (VF, theta, size, spacing, seed) from
  whichever source is active (config file or manual UI)
* MTRSim::operator() no longer calls parseConfigJson; it always builds
  SimulationParams directly from m_InputValues — the algorithm has no
  knowledge of the config file
* Removed useConfigFile and configFilePath from MTRSimInputValues and
  the <filesystem> include from MTRSim.hpp (no longer needed there)
* Removed #include "LibMTRSim/ConfigIO.hpp" from MTRSim.cpp
* Execute-time config parse failures use error code -13521 (distinct
  from preflight's -13520) so the two phases can be told apart
* WriteTempConfig helper in the test hardened with REQUIRE(is_open)
  and REQUIRE(good) so temp-write failures surface clearly

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>
@imikejackson @claude
docs: document config-file mode and progress/cancel in MTRSimFilter
a8ce172 
Add a "Configuration Source" section describing the optional JSON config-file
input (what it reads, what it ignores, seed-zero behaviour, units caveat).
Update the Performance section to reflect continuous progress reporting and
mid-run cancellation support (replacing the old "start/completion only; no
cancel" text). Add error codes -13520 (preflight config parse failure) and
-13521 (execute config parse failure) to the Errors table in numeric order.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
chore(pipelines): regenerate with use_config_file/config_file_path keys
3ab1ec3 
The MTRSimFilter gained config-file params; regenerate the example pipelines
(and the generator) so each MTRSim step carries use_config_file=false +
config_file_path explicitly.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson @claude
docs/test: correct theta error-code comments and cancel wording (fina…
c79ed1e 
…l review nits)

Fixed stale error-code references in test comments (-13005 -> -13505 for column-count check,
-13004 -> -13504 for row-count check). Clarified cancel behavior in Performance section
to note that output arrays are created by preflight but remain unfilled on cancellation.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@imikejackson
ENH: Route PGRFSimulation logging through observer info() method
1355be6 
* Add defaulted virtual info() to ISimulationObserver — no-op by
  default so existing test doubles need no changes
* ConsoleObserver overrides info() to emit via spdlog (CLI output
  unchanged)
* FilterObserver overrides info() to forward through the simplnx
  IFilter::MessageHandler with Type::Info (no raw console lines
  from the DREAM3D-NX filter)
* Convert all five direct spdlog::info() calls in PGRFSimulation::run
  to observer->info() with nullptr guard; drop the redundant
  per-field spdlog line that duplicated the updateProgress message
* Remove unused #include <spdlog/spdlog.h> from PGRFSimulation.cpp

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>
@imikejackson
Update all example pipelines to generate the proper IPF Coloring.
1fb3b4e
@imikejackson @claude
fix(win): export embedded LibMTRSim symbols from the plugin DLL on MSVC
1d6a567 
The plugin-build shim hard-coded LIBMTRSIM_EXPORT to empty. On Unix that is
fine (default visibility exports the symbols), but on MSVC nothing is exported
from the plugin DLL, so external consumers (MTRSimUnitTest, the Python
bindings) fail to link mtrsim:: free functions (readODFComponents,
readODFMetadata, tryReadFixtureVersion) with LNK2019/LNK1120. Key the macro on
MTRSim_EXPORTS (dllexport when building the plugin, dllimport when consuming),
matching the plugin's own export macro. macOS build + 42/42 tests unaffected.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
github-actions[bot]
github-actions Bot reviewed Jun 3, 2026
View reviewed changes
Comment thread test/MTRSimTest.cpp Outdated
Comment thread test/MTRSimTest.cpp
@imikejackson imikejackson force-pushed the topic/create_mtr_sim_filter branch from 9f4c0cf to 1d6a567 Compare June 3, 2026 23:51
@imikejackson
COMP: Fix compiler errors on Windows (MSVC)
2d72d3e 
Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>
@imikejackson imikejackson force-pushed the topic/create_mtr_sim_filter branch from 9f4c0cf to 2d72d3e Compare June 3, 2026 23:55
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