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ENH: Face-neighbor filters OoC Optimization #1561

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f869a6c
ENH: Split BadDataNeighborOrientationCheck into in-core and OOC algor…
joeykleingers Feb 28, 2026
27be616
ENH: Split Group B face-neighbor filters into Direct/Scanline OOC dis…
joeykleingers Mar 5, 2026
c838f62
FIX: Wire DispatchAlgorithm calls into base algorithm classes
joeykleingers Mar 5, 2026
0aabf6d
FIX: PR review fixes for Group B face-neighbor filters
joeykleingers Mar 5, 2026
6f45328
STYLE: Run clang-format on Group B PR files
joeykleingers Mar 6, 2026
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2 changes: 2 additions & 0 deletions src/Plugins/OrientationAnalysis/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -168,6 +168,8 @@ set(filter_algorithms
AlignSectionsMisorientation
AlignSectionsMutualInformation
BadDataNeighborOrientationCheck
BadDataNeighborOrientationCheckScanline
BadDataNeighborOrientationCheckWorklist
CAxisSegmentFeatures
ComputeAvgCAxes
ComputeAvgOrientations
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181 changes: 9 additions & 172 deletions ...onAnalysis/src/OrientationAnalysis/Filters/Algorithms/BadDataNeighborOrientationCheck.cpp
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@@ -1,13 +1,10 @@
#include "BadDataNeighborOrientationCheck.hpp"

#include "simplnx/Common/Numbers.hpp"
#include "simplnx/DataStructure/DataArray.hpp"
#include "simplnx/DataStructure/Geometry/ImageGeom.hpp"
#include "simplnx/Utilities/MaskCompareUtilities.hpp"
#include "simplnx/Utilities/MessageHelper.hpp"
#include "simplnx/Utilities/NeighborUtilities.hpp"
#include "BadDataNeighborOrientationCheckScanline.hpp"
#include "BadDataNeighborOrientationCheckWorklist.hpp"

#include <EbsdLib/LaueOps/LaueOps.h>
#include "simplnx/DataStructure/DataArray.hpp"
#include "simplnx/Utilities/AlgorithmDispatch.hpp"

using namespace nx::core;

Expand All @@ -33,170 +30,10 @@ const std::atomic_bool& BadDataNeighborOrientationCheck::getCancel()
// -----------------------------------------------------------------------------
Result<> BadDataNeighborOrientationCheck::operator()()
{
const float misorientationTolerance = m_InputValues->MisorientationTolerance * numbers::pi_v<float> / 180.0f;

const auto* imageGeomPtr = m_DataStructure.getDataAs<ImageGeom>(m_InputValues->ImageGeomPath);
SizeVec3 udims = imageGeomPtr->getDimensions();
const auto& cellPhases = m_DataStructure.getDataRefAs<Int32Array>(m_InputValues->CellPhasesArrayPath);
const auto& quats = m_DataStructure.getDataRefAs<Float32Array>(m_InputValues->QuatsArrayPath);
const auto& crystalStructures = m_DataStructure.getDataRefAs<UInt32Array>(m_InputValues->CrystalStructuresArrayPath);
const usize totalPoints = quats.getNumberOfTuples();

std::unique_ptr<MaskCompareUtilities::MaskCompare> maskCompare;
try
{
maskCompare = MaskCompareUtilities::InstantiateMaskCompare(m_DataStructure, m_InputValues->MaskArrayPath);
} catch(const std::out_of_range& exception)
{
// This really should NOT be happening as the path was verified during preflight, BUT we may be calling this from
// somewhere else that is NOT going through the normal nx::core::IFilter API of Preflight and Execute
return MakeErrorResult(-54900, fmt::format("Mask Array DataPath does not exist or is not of the correct type (Bool | UInt8) {}", m_InputValues->MaskArrayPath.toString()));
}

std::array<int64, 3> dims = {
static_cast<int64>(udims[0]),
static_cast<int64>(udims[1]),
static_cast<int64>(udims[2]),
};

std::array<int64, 6> neighborVoxelIndexOffsets = initializeFaceNeighborOffsets(dims);
std::array<FaceNeighborType, 6> faceNeighborInternalIdx = initializeFaceNeighborInternalIdx();

std::vector<ebsdlib::LaueOps::Pointer> orientationOps = ebsdlib::LaueOps::GetAllOrientationOps();

std::vector<int32> neighborCount(totalPoints, 0);

MessageHelper messageHelper(m_MessageHandler);
ThrottledMessenger throttledMessenger = messageHelper.createThrottledMessenger();
// Loop over every point finding the number of neighbors that fall within the
// user defined angle tolerance.
for(int64 voxelIndex = 0; voxelIndex < totalPoints; voxelIndex++)
{
throttledMessenger.sendThrottledMessage([&] { return fmt::format("Processing Data {:.2f}% completed", CalculatePercentComplete(voxelIndex, totalPoints)); });
// If the mask was set to false, then we check this voxel
if(!maskCompare->isTrue(voxelIndex))
{
// We precalculate the positive voxel quaternion and laue class here to prevent reading and recalculating it for each face below
ebsdlib::QuatD quat1(quats[voxelIndex * 4], quats[voxelIndex * 4 + 1], quats[voxelIndex * 4 + 2], quats[voxelIndex * 4 + 3]);
quat1.positiveOrientation();
const uint32 laueClass1 = crystalStructures[cellPhases[voxelIndex]];

int64 xIdx = voxelIndex % dims[0];
int64 yIdx = (voxelIndex / dims[0]) % dims[1];
int64 zIdx = voxelIndex / (dims[0] * dims[1]);

// Loop over the 6 face neighbors of the voxel
std::array<bool, 6> isValidFaceNeighbor = computeValidFaceNeighbors(xIdx, yIdx, zIdx, dims);
for(const auto& faceIndex : faceNeighborInternalIdx)
{
if(!isValidFaceNeighbor[faceIndex])
{
continue;
}
const int64 neighborPoint = voxelIndex + neighborVoxelIndexOffsets[faceIndex];

// Now compare the mask of the neighbor. If the mask is TRUE, i.e., that voxel
// did not fail the threshold filter that most likely produced the mask array,
// then we can look at that voxel.
if(maskCompare->isTrue(neighborPoint))
{
// Both Cell Phases MUST be the same and be a valid Phase
if(cellPhases[voxelIndex] == cellPhases[neighborPoint] && cellPhases[voxelIndex] > 0)
{
ebsdlib::QuatD quat2(quats[neighborPoint * 4], quats[neighborPoint * 4 + 1], quats[neighborPoint * 4 + 2], quats[neighborPoint * 4 + 3]);
quat2.positiveOrientation();
// Compute the Axis_Angle misorientation between those 2 quaternions
ebsdlib::AxisAngleDType axisAngle = orientationOps[laueClass1]->calculateMisorientation(quat1, quat2);
// if the angle is less than our tolerance, then we increment the neighbor count
// for this voxel
if(axisAngle[3] < misorientationTolerance)
{
neighborCount[voxelIndex]++;
}
}
}
}
}
}

constexpr int32 startLevel = 6;
int32 currentLevel = startLevel;
int32 counter = 0;

// Now we loop over all the points again, but this time we do it as many times
// as the user has requested to iteratively flip voxels
while(currentLevel >= m_InputValues->NumberOfNeighbors)
{
counter = 1;
int32 loopNumber = 0;
while(counter > 0)
{
counter = 0; // Set this while control variable to zero
for(usize voxelIndex = 0; voxelIndex < totalPoints; voxelIndex++)
{
throttledMessenger.sendThrottledMessage([&] {
return fmt::format("Level '{}' of '{}' || Processing Data ('{}') {:.2f}% completed", (startLevel - currentLevel) + 1, startLevel - m_InputValues->NumberOfNeighbors, loopNumber,
CalculatePercentComplete(voxelIndex, totalPoints));
});

// We are comparing the number-of-neighbors of the current voxel, and if it
// is > the current level and the mask is FALSE, then we drop into this
// conditional. The first thing that happens in the conditional is that
// the current voxel's mask value is set to TRUE.
if(neighborCount[voxelIndex] >= currentLevel && !maskCompare->isTrue(voxelIndex))
{
maskCompare->setValue(voxelIndex, true); // the current voxel's mask value is set to TRUE.
counter++; // Increment the `counter` to force the loop to iterate again

// We precalculate the positive voxel quaternion and laue class here to prevent reading and recalculating it for each face below
ebsdlib::QuatD quat1(quats[voxelIndex * 4], quats[voxelIndex * 4 + 1], quats[voxelIndex * 4 + 2], quats[voxelIndex * 4 + 3]);
quat1.positiveOrientation();
const uint32 laueClass1 = crystalStructures[cellPhases[voxelIndex]];

// This whole section below is to now look at the neighbor voxels of the
// current voxel that just got flipped to true. This is needed because
// if any of those neighbor's mask was `false`, then its neighbor count
// is now not correct and will be off-by-one. So we run _almost_ the same
// loop code as above but checking the specific neighbors of the current
// voxel. This part should be termed the "Update Neighbor's Neighbor Count"
int64 xIdx = voxelIndex % dims[0];
int64 yIdx = (voxelIndex / dims[0]) % dims[1];
int64 zIdx = voxelIndex / (dims[0] * dims[1]);

// Loop over the 6 face neighbors of the voxel
std::array<bool, 6> isValidFaceNeighbor = computeValidFaceNeighbors(xIdx, yIdx, zIdx, dims);
for(const auto& faceIndex : faceNeighborInternalIdx)
{
if(!isValidFaceNeighbor[faceIndex])
{
continue;
}

int64 neighborPoint = voxelIndex + neighborVoxelIndexOffsets[faceIndex];

// If the neighbor voxel's mask is false, then ....
if(!maskCompare->isTrue(neighborPoint))
{
// Make sure both cells phase values are identical and valid
if(cellPhases[voxelIndex] == cellPhases[neighborPoint] && cellPhases[voxelIndex] > 0)
{
ebsdlib::QuatD quat2(quats[neighborPoint * 4], quats[neighborPoint * 4 + 1], quats[neighborPoint * 4 + 2], quats[neighborPoint * 4 + 3]);
quat2.positiveOrientation();
// Quaternion Math is not commutative so do not reorder
ebsdlib::AxisAngleDType axisAngle = orientationOps[laueClass1]->calculateMisorientation(quat1, quat2);
if(axisAngle[3] < misorientationTolerance)
{
neighborCount[neighborPoint]++;
}
}
}
}
}
}
++loopNumber;
}
currentLevel = currentLevel - 1;
}
auto* quatsArray = m_DataStructure.getDataAs<IDataArray>(m_InputValues->QuatsArrayPath);
auto* maskArray = m_DataStructure.getDataAs<IDataArray>(m_InputValues->MaskArrayPath);
auto* phasesArray = m_DataStructure.getDataAs<IDataArray>(m_InputValues->CellPhasesArrayPath);

return {};
return DispatchAlgorithm<BadDataNeighborOrientationCheckWorklist, BadDataNeighborOrientationCheckScanline>({quatsArray, maskArray, phasesArray}, m_DataStructure, m_MessageHandler, m_ShouldCancel,
m_InputValues);
}
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