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clean up and renaming
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@nyoungbq
nyoungbq committed Feb 18, 2025
1 parent 75abbcb commit f8177a6
Showing 1 changed file with 32 additions and 37 deletions.
69 changes: 32 additions & 37 deletions .../OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/ComputeTwinBoundaries.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ using namespace nx::core;
namespace
{
template <typename T>
bool IsTwinBoundary(const Eigen::Quaternion<T>& quat1, const Eigen::Quaternion<T>& quat2, const std::vector<LaueOps::Pointer>& orientationOps, uint32 targetPhaseIndex, float32 angTolerance,
bool IsTwinBoundary(const Eigen::Quaternion<T>& quat1, const Eigen::Quaternion<T>& quat2, const std::vector<LaueOps::Pointer>& orientationOps, uint32 crystalStructure, float32 angTolerance,
float32 axisTolerance)
{
T real = std::numeric_limits<T>::max();
Expand All @@ -32,13 +32,13 @@ bool IsTwinBoundary(const Eigen::Quaternion<T>& quat1, const Eigen::Quaternion<T
Eigen::Quaternion<T> s1_misq;
Eigen::Quaternion<T> s2_misq;

const int32 nsym = orientationOps[targetPhaseIndex]->getNumSymOps();
const int32 nsym = orientationOps[crystalStructure]->getNumSymOps();
const Eigen::Quaternion<T> q2 = quat2.conjugate();
misq = quat1 * q2;

for(int32 j = 0; j < nsym; j++)
{
Quaternion<T> jQuat = orientationOps[targetPhaseIndex]->getQuatSymOp(j);
Quaternion<T> jQuat = orientationOps[crystalStructure]->getQuatSymOp(j);
sym_q = Eigen::Quaterniond(jQuat.w(), jQuat.x(), jQuat.y(), jQuat.z());

// calculate crystal direction parallel to normal
Expand All @@ -47,7 +47,7 @@ bool IsTwinBoundary(const Eigen::Quaternion<T>& quat1, const Eigen::Quaternion<T
for(int32 k = j + 1; k < nsym; k++)
{
// calculate the symmetric misorienation
Quaternion<T> kQuat = orientationOps[targetPhaseIndex]->getQuatSymOp(k);
Quaternion<T> kQuat = orientationOps[crystalStructure]->getQuatSymOp(k);
sym_q = Eigen::Quaterniond(kQuat.w(), kQuat.x(), kQuat.y(), kQuat.z());
sym_q = sym_q.conjugate();
s2_misq = sym_q * s1_misq;
Expand All @@ -69,7 +69,7 @@ bool IsTwinBoundary(const Eigen::Quaternion<T>& quat1, const Eigen::Quaternion<T

template <typename T>
std::optional<T> FindTwinBoundaryIncoherence(const Eigen::Vector3d& xstl_norm, const Eigen::Quaternion<T>& quat1, const Eigen::Quaternion<T>& quat2,
const std::vector<LaueOps::Pointer>& orientationOps, uint32 targetPhaseIndex, float32 angTolerance, float32 axisTolerance)
const std::vector<LaueOps::Pointer>& orientationOps, uint32 crystalStructure, float32 angTolerance, float32 axisTolerance)
{
T real = std::numeric_limits<T>::max();
T axisdiff111;
Expand All @@ -85,14 +85,14 @@ std::optional<T> FindTwinBoundaryIncoherence(const Eigen::Vector3d& xstl_norm, c
Eigen::Quaternion<T> s1_misq;
Eigen::Quaternion<T> s2_misq;

const int32 nsym = orientationOps[targetPhaseIndex]->getNumSymOps();
const int32 nsym = orientationOps[crystalStructure]->getNumSymOps();
const Eigen::Quaternion<T> q2 = quat2.conjugate();
misq = quat1 * q2;

bool valid = false;
for(int32 j = 0; j < nsym; j++)
{
Quaternion<T> jQuat = orientationOps[targetPhaseIndex]->getQuatSymOp(j);
Quaternion<T> jQuat = orientationOps[crystalStructure]->getQuatSymOp(j);
j_sym_q = Eigen::Quaterniond(jQuat.w(), jQuat.x(), jQuat.y(), jQuat.z());

// calculate crystal direction parallel to normal
Expand All @@ -101,7 +101,7 @@ std::optional<T> FindTwinBoundaryIncoherence(const Eigen::Vector3d& xstl_norm, c
for(int32 k = j + 1; k < nsym; k++)
{
// calculate the symmetric misorienation
Quaternion<T> kQuat = orientationOps[targetPhaseIndex]->getQuatSymOp(k);
Quaternion<T> kQuat = orientationOps[crystalStructure]->getQuatSymOp(k);
sym_q = Eigen::Quaterniond(kQuat.w(), kQuat.x(), kQuat.y(), kQuat.z());
sym_q = sym_q.conjugate();
s2_misq = sym_q * s1_misq;
Expand Down Expand Up @@ -183,26 +183,24 @@ class CalculateTwinBoundaryWithIncoherenceImpl

const int32 feature1 = m_FaceLabels[2 * i];
const int32 feature2 = m_FaceLabels[(2 * i) + 1];
if(feature1 > 0 && feature2 > 0 && m_FeaturePhases[feature1] == m_FeaturePhases[feature2])
const int32 phase = m_FeaturePhases[feature1]; // Feature1 was arbitrarily selected the feature phase index is identical
if(feature1 > 0 && feature2 > 0 && phase == m_FeaturePhases[feature2])
{
const uint32 phase1 = m_CrystalStructures[m_FeaturePhases[feature1]];
const uint32 phase2 = m_CrystalStructures[m_FeaturePhases[feature2]];
if(phase1 == phase2)
{
// Avg Quats is stored Vector Scalar but the Quaternion Constructor is Scalar-Vector
const Eigen::Quaterniond q1(m_AvgQuats[(feature1 * 4) + 3], m_AvgQuats[feature1 * 4], m_AvgQuats[(feature1 * 4) + 1], m_AvgQuats[(feature1 * 4) + 2]); // W X Y Z
Eigen::Quaterniond q2(m_AvgQuats[(feature2 * 4) + 3], m_AvgQuats[feature2 * 4], m_AvgQuats[(feature2 * 4) + 1], m_AvgQuats[(feature2 * 4) + 2]); // W X Y Z
const uint32 crystalStructure = m_CrystalStructures[phase];

// Avg Quats is stored Vector Scalar but the Quaternion Constructor is Scalar-Vector
const Eigen::Quaterniond q1(m_AvgQuats[(feature1 * 4) + 3], m_AvgQuats[feature1 * 4], m_AvgQuats[(feature1 * 4) + 1], m_AvgQuats[(feature1 * 4) + 2]); // W X Y Z
const Eigen::Quaterniond q2(m_AvgQuats[(feature2 * 4) + 3], m_AvgQuats[feature2 * 4], m_AvgQuats[(feature2 * 4) + 1], m_AvgQuats[(feature2 * 4) + 2]); // W X Y Z

Matrix3x3 orientationMatrix = Matrix3x3{OrientationTransformation::qu2om<Eigen::Vector4d, std::vector<float64>>(q1.coeffs(), QuatD::Order::VectorScalar).data()};
Eigen::Vector3d xstl_norm = Eigen::Vector3d{m_FaceNormals[3 * i], m_FaceNormals[(3 * i) + 1], m_FaceNormals[(3 * i) + 2]}.transpose() * orientationMatrix;
const Matrix3x3 orientationMatrix = Matrix3x3{OrientationTransformation::qu2om<Eigen::Vector4d, std::vector<float64>>(q1.coeffs(), QuatD::Order::VectorScalar).data()};
const Eigen::Vector3d xstl_norm = Eigen::Vector3d{m_FaceNormals[3 * i], m_FaceNormals[(3 * i) + 1], m_FaceNormals[(3 * i) + 2]}.transpose() * orientationMatrix;

std::optional<float64> minIncoherence = FindTwinBoundaryIncoherence(xstl_norm, q1, q2, m_OrientationOps, phase1, m_AngTol, m_AxisTol);
std::optional<float64> minIncoherence = FindTwinBoundaryIncoherence(xstl_norm, q1, q2, m_OrientationOps, crystalStructure, m_AngTol, m_AxisTol);

if(minIncoherence.has_value())
{
m_TwinBoundaries->setValue(i, true);
m_TwinBoundaryIncoherence[i] = static_cast<float32>(minIncoherence.value());
}
if(minIncoherence.has_value())
{
m_TwinBoundaries->setValue(i, true);
m_TwinBoundaryIncoherence[i] = static_cast<float32>(minIncoherence.value());
}
}
}
Expand Down Expand Up @@ -257,20 +255,17 @@ class CalculateTwinBoundaryImpl
return;
}

int32 feature1 = m_FaceLabels[2 * i];
int32 feature2 = m_FaceLabels[(2 * i) + 1];

if(feature1 > 0 && feature2 > 0 && m_FeaturePhases[feature1] == m_FeaturePhases[feature2])
const int32 feature1 = m_FaceLabels[2 * i];
const int32 feature2 = m_FaceLabels[(2 * i) + 1];
const int32 phase = m_FeaturePhases[feature1]; // Feature1 was arbitrarily selected the feature phase index is identical
if(feature1 > 0 && feature2 > 0 && phase == m_FeaturePhases[feature2])
{
uint32 phase1 = m_CrystalStructures[m_FeaturePhases[feature1]];
uint32 phase2 = m_CrystalStructures[m_FeaturePhases[feature2]];
if(phase1 == phase2)
{
// Avg Quats is stored Vector Scalar but the Quaternion Constructor is Scalar-Vector
const Eigen::Quaterniond q1(m_AvgQuats[(feature1 * 4) + 3], m_AvgQuats[feature1 * 4], m_AvgQuats[(feature1 * 4) + 1], m_AvgQuats[(feature1 * 4) + 2]); // W X Y Z
const Eigen::Quaterniond q2(m_AvgQuats[(feature2 * 4) + 3], m_AvgQuats[feature2 * 4], m_AvgQuats[(feature2 * 4) + 1], m_AvgQuats[(feature2 * 4) + 2]); // W X Y Z
m_TwinBoundaries->setValue(i, IsTwinBoundary(q1, q2, m_OrientationOps, phase1, m_AngTol, m_AxisTol));
}
const uint32 crystalStructure = m_CrystalStructures[phase];

// Avg Quats is stored Vector Scalar but the Quaternion Constructor is Scalar-Vector
const Eigen::Quaterniond q1(m_AvgQuats[(feature1 * 4) + 3], m_AvgQuats[feature1 * 4], m_AvgQuats[(feature1 * 4) + 1], m_AvgQuats[(feature1 * 4) + 2]); // W X Y Z
const Eigen::Quaterniond q2(m_AvgQuats[(feature2 * 4) + 3], m_AvgQuats[feature2 * 4], m_AvgQuats[(feature2 * 4) + 1], m_AvgQuats[(feature2 * 4) + 2]); // W X Y Z
m_TwinBoundaries->setValue(i, IsTwinBoundary(q1, q2, m_OrientationOps, crystalStructure, m_AngTol, m_AxisTol));
}
}
}
Expand Down

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