// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void subtractVector3d(DataArray<double>::Pointer data, double* v)
{
size_t count = data->GetNumberOfTuples();
for(size_t i = 0; i < count; ++i)
{
double* ptr = data->GetPointer(i*3);
ptr[0] = ptr[0] - v[0];
ptr[1] = ptr[1] - v[1];
ptr[2] = ptr[2] - v[2];
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
std::vector<int32_t> TriangleOps::findAdjacentTriangles(SurfaceMeshDataContainer* sm,
int32_t triangleIndex,
int32_t label)
{
std::vector<int32_t> adjacentTris;
// Get the master list of triangles for the mesh
DREAM3D::SurfaceMesh::FaceList_t::Pointer facesPtr = sm->getFaces();
// DREAM3D::SurfaceMesh::Face_t* faces = facesPtr->GetPointer(0);
IDataArray::Pointer flPtr = sm->getFaceData(DREAM3D::FaceData::SurfaceMeshFaceLabels);
DataArray<int32_t>* faceLabelsPtr = DataArray<int32_t>::SafePointerDownCast(flPtr.get());
int32_t* faceLabels = faceLabelsPtr->GetPointer(0);
// Get the Triangle Neighbor Structure
MeshFaceNeighbors::Pointer triNeighbors = sm->getMeshFaceNeighborLists();
// For the specific triangle that was passed, get its neighbor list
uint16_t count = triNeighbors->getNumberOfFaces(triangleIndex);
int32_t* nList = triNeighbors->getNeighborListPointer(triangleIndex);
if (count < 3)
{
std::cout << "Triangle Neighbor List had only " << count << " neighbors. Must be at least 3." << std::endl;
BOOST_ASSERT(false);
}
else if (count == 3) // This triangle only has 3 neighbors so we are assuming all three have the same label set.
{
for (uint16_t n = 0; n < count; ++n)
{
adjacentTris.push_back(nList[n]);
}
}
else
{
// Iterate over the indices to find triangles that match the label and are NOT the current triangle index
for (uint16_t n = 0; n < count; ++n)
{
int32_t fl_0 = faceLabels[nList[n]*2];
int32_t fl_1 = faceLabels[nList[n]*2 + 1];
if ( (fl_0 == label || fl_1 == label) && (nList[n] != triangleIndex) )
{
// std::cout << " Found Adjacent Triangle: " << t->tIndex << std::endl;
adjacentTris.push_back(nList[n]);
// ++index;
}
}
}
return adjacentTris;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void LinkFieldMapToCellArray::dataCheck(bool preflight, size_t voxels, size_t fields, size_t ensembles)
{
setErrorCondition(0);
std::stringstream ss;
VoxelDataContainer* m = getVoxelDataContainer();
IDataArray::Pointer data = m->getCellData(m_SelectedCellDataArrayName);
if (NULL == data.get())
{
ss.str("");
ss << "Selected array '" << m_SelectedCellDataArrayName << "' does not exist in the Voxel Data Container. Was it spelled correctly?";
setErrorCondition(-11001);
addErrorMessage(getHumanLabel(),ss.str(),getErrorCondition());
return;
}
std::string dType = data->getTypeAsString();
IDataArray::Pointer p = IDataArray::NullPointer();
if (dType.compare("int32_t") == 0)
{
DataArray<int32_t>* field = DataArray<int32_t>::SafePointerDownCast(data.get());
m_SelectedCellData = field->GetPointer(0);
}
else
{
ss.str("");
ss << "Selected array '" << m_SelectedCellDataArrayName << "' is not an Integer array. Is this the array you want to use?";
setErrorCondition(-11001);
addErrorMessage(getHumanLabel(),ss.str(),getErrorCondition());
return;
}
m->clearFieldData();
BoolArrayType::Pointer active = BoolArrayType::CreateArray(fields, 1, DREAM3D::FieldData::Active);
// bool* mActive = m_Active->GetPointer(0);
m->addFieldData(DREAM3D::FieldData::Active, active);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void CalculateTriangleGroupCurvatures::operator()() const
{
// Get the Triangles Array
// DREAM3D::SurfaceMesh::FaceList_t::Pointer trianglesPtr = m_SurfaceMeshDataContainer->getFaces();
// DREAM3D::SurfaceMesh::Face_t* triangles = trianglesPtr->GetPointer(0);
IDataArray::Pointer flPtr = m_SurfaceMeshDataContainer->getFaceData(DREAM3D::FaceData::SurfaceMeshFaceLabels);
DataArray<int32_t>* faceLabelsPtr = DataArray<int32_t>::SafePointerDownCast(flPtr.get());
int32_t* faceLabels = faceLabelsPtr->GetPointer(0);
// Instantiate a FindNRingNeighbors class to use during the loop
FindNRingNeighbors::Pointer nRingNeighborAlg = FindNRingNeighbors::New();
// Make Sure we have triangle centroids calculated
IDataArray::Pointer centroidPtr = m_SurfaceMeshDataContainer->getFaceData(DREAM3D::FaceData::SurfaceMeshFaceCentroids);
if (NULL == centroidPtr.get())
{
std::cout << "Triangle Centroids are required for this algorithm" << std::endl;
return;
}
DataArray<double>* centroids = DataArray<double>::SafePointerDownCast(centroidPtr.get());
// Make sure we have triangle normals calculated
IDataArray::Pointer normalPtr = m_SurfaceMeshDataContainer->getFaceData(DREAM3D::FaceData::SurfaceMeshFaceNormals);
if (NULL == normalPtr.get())
{
std::cout << "Triangle Normals are required for this algorithm" << std::endl;
return;
}
DataArray<double>* normals = DataArray<double>::SafePointerDownCast(normalPtr.get());
int32_t* fl = faceLabels + m_TriangleIds[0] * 2;
int grain0 = 0;
int grain1 = 0;
if (fl[0] < fl[1])
{
grain0 = fl[0];
grain1 = fl[1];
}
else
{
grain0 = fl[1];
grain1 = fl[0];
}
bool computeGaussian = (m_GaussianCurvature.get() != NULL);
bool computeMean = (m_MeanCurvature.get() != NULL);
bool computeDirection = (m_PrincipleDirection1.get() != NULL);
std::stringstream ss;
std::vector<int>::size_type tCount = m_TriangleIds.size();
// For each triangle in the group
for(std::vector<int>::size_type i = 0; i < tCount; ++i)
{
if (m_ParentFilter->getCancel() == true) { return; }
int triId = m_TriangleIds[i];
nRingNeighborAlg->setTriangleId(triId);
nRingNeighborAlg->setRegionId0(grain0);
nRingNeighborAlg->setRegionId1(grain1);
nRingNeighborAlg->setRing(m_NRing);
nRingNeighborAlg->setSurfaceMeshDataContainer(m_SurfaceMeshDataContainer);
nRingNeighborAlg->generate();
DREAM3D::SurfaceMesh::UniqueFaceIds_t triPatch = nRingNeighborAlg->getNRingTriangles();
BOOST_ASSERT(triPatch.size() > 1);
DataArray<double>::Pointer patchCentroids = extractPatchData(triId, triPatch, centroids->GetPointer(0), std::string("Patch_Centroids"));
DataArray<double>::Pointer patchNormals = extractPatchData(triId, triPatch, normals->GetPointer(0), std::string("Patch_Normals"));
// Translate the patch to the 0,0,0 origin
double sub[3] = {patchCentroids->GetComponent(0,0),patchCentroids->GetComponent(0,1), patchCentroids->GetComponent(0,2)};
subtractVector3d(patchCentroids, sub);
double np[3] = {patchNormals->GetComponent(0,0), patchNormals->GetComponent(0,1), patchNormals->GetComponent(0, 2) };
double seedCentroid[3] = {patchCentroids->GetComponent(0,0), patchCentroids->GetComponent(0,1), patchCentroids->GetComponent(0,2) };
double firstCentroid[3] = {patchCentroids->GetComponent(1,0), patchCentroids->GetComponent(1,1), patchCentroids->GetComponent(1,2) };
double temp[3] = {firstCentroid[0] - seedCentroid[0], firstCentroid[1] - seedCentroid[1], firstCentroid[2] - seedCentroid[2]};
double vp[3] = {0.0, 0.0, 0.0};
// Cross Product of np and temp
MatrixMath::NormalizeVector(np);
MatrixMath::CrossProduct(np, temp, vp);
MatrixMath::NormalizeVector(vp);
// get the third orthogonal vector
double up[3] = {0.0, 0.0, 0.0};
MatrixMath::CrossProduct(vp, np, up);
// this constitutes a rotation matrix to a local coordinate system
double rot[3][3] = {{up[0], up[1], up[2]},
{vp[0], vp[1], vp[2]},
{np[0], np[1], np[2]} };
double out[3];
// Transform all centroids and normals to new coordinate system
for(size_t m = 0; m < patchCentroids->GetNumberOfTuples(); ++m)
{
::memcpy(out, patchCentroids->GetPointer(m*3), 3*sizeof(double));
MatrixMath::Multiply3x3with3x1(rot, patchCentroids->GetPointer(m*3), out);
::memcpy(patchCentroids->GetPointer(m*3), out, 3*sizeof(double));
::memcpy(out, patchNormals->GetPointer(m*3), 3*sizeof(double));
MatrixMath::Multiply3x3with3x1(rot, patchNormals->GetPointer(m*3), out);
::memcpy(patchNormals->GetPointer(m*3), out, 3*sizeof(double));
// We rotate the normals now but we dont use them yet. If we start using part 3 of Goldfeathers paper then we
// will need the normals.
}
{
// Solve the Least Squares fit
static const unsigned int NO_NORMALS = 3;
static const unsigned int USE_NORMALS = 7;
int cols = NO_NORMALS;
if (m_UseNormalsForCurveFitting == true)
{ cols = USE_NORMALS; }
int rows = patchCentroids->GetNumberOfTuples();
Eigen::MatrixXd A(rows, cols);
Eigen::VectorXd b(rows);
double x, y, z;
for(int m = 0; m < rows; ++m)
{
x = patchCentroids->GetComponent(m, 0);
y = patchCentroids->GetComponent(m, 1);
z = patchCentroids->GetComponent(m, 2);
A(m) = 0.5 * x * x; // 1/2 x^2
A(m + rows) = x * y; // x*y
A(m + rows*2) = 0.5 * y * y; // 1/2 y^2
if (m_UseNormalsForCurveFitting == true)
{
A(m + rows*3) = x*x*x;
A(m + rows*4) = x*x*y;
A(m + rows*5) = x*y*y;
A(m + rows*6) = y*y*y;
}
b[m] = z; // The Z Values
}
Eigen::Matrix2d M;
if (false == m_UseNormalsForCurveFitting)
{
typedef Eigen::Matrix<double, NO_NORMALS, 1> Vector3d;
Vector3d sln1 = A.colPivHouseholderQr().solve(b);
// Now that we have the A, B, C constants we can solve the Eigen value/vector problem
// to get the principal curvatures and pricipal directions.
M << sln1(0), sln1(1), sln1(1), sln1(2);
}
else
{
typedef Eigen::Matrix<double, USE_NORMALS, 1> Vector7d;
Vector7d sln1 = A.colPivHouseholderQr().solve(b);
// Now that we have the A, B, C, D, E, F & G constants we can solve the Eigen value/vector problem
// to get the principal curvatures and pricipal directions.
M << sln1(0), sln1(1), sln1(1), sln1(2);
}
Eigen::SelfAdjointEigenSolver<Eigen::Matrix2d> eig(M);
Eigen::SelfAdjointEigenSolver<Eigen::Matrix2d>::RealVectorType eValues = eig.eigenvalues();
Eigen::SelfAdjointEigenSolver<Eigen::Matrix2d>::MatrixType eVectors = eig.eigenvectors();
// Kappa1 >= Kappa2
double kappa1 = eValues(0) * -1;// Kappa 1
double kappa2 = eValues(1) * -1; //kappa 2
BOOST_ASSERT(kappa1 >= kappa2);
m_PrincipleCurvature1->SetValue(triId, kappa1);
m_PrincipleCurvature2->SetValue(triId, kappa2);
if (computeGaussian == true)
{
m_GaussianCurvature->SetValue(triId, kappa1*kappa2);
}
if (computeMean == true)
{
m_MeanCurvature->SetValue(triId, (kappa1+kappa2)/2.0);
}
if (computeDirection == true)
{
Eigen::Matrix3d e_rot_T;
e_rot_T.row(0) = Eigen::Vector3d(up[0], vp[0], np[0]);
e_rot_T.row(1) = Eigen::Vector3d(up[1], vp[1], np[1]);
e_rot_T.row(2) = Eigen::Vector3d(up[2], vp[2], np[2]);
// Rotate our principal directions back into the original coordinate system
Eigen::Vector3d dir1 ( eVectors.col(0)(0), eVectors.col(0)(1), 0.0 );
dir1 = e_rot_T * dir1;
::memcpy(m_PrincipleDirection1->GetPointer(triId * 3), dir1.data(), 3*sizeof(double) );
Eigen::Vector3d dir2 ( eVectors.col(1)(0), eVectors.col(1)(1), 0.0 );
dir2 = e_rot_T * dir2;
::memcpy(m_PrincipleDirection2->GetPointer(triId * 3), dir2.data(), 3*sizeof(double) );
}
}
} // End Loop over this triangle
m_ParentFilter->tbbTaskProgress();
}