// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int H5PrimaryStatsDataDelegate::readPrimaryStatsData(PrimaryStatsData* data, hid_t groupId)
{
int err = 0;
//Read the NumFields
err = readBoundaryArea(data, groupId);
//Read the PhaseFraction
err = readPhaseFraction(data, groupId);
// Read the Grain Diameter Info
err = readGrainDiameterInfo(data, groupId);
// Read the Grain Size Distribution
uint32_t dType = readDistributionType(groupId, DREAM3D::HDF5::Grain_Size_Distribution);
data->setGrainSize_DistType(dType);
data->setGrainSizeDistribution(createDistributionVector(data->getGrainSize_DistType()));
err = readDistributionData(groupId,
DREAM3D::HDF5::Grain_Size_Distribution,
data->getGrainSizeDistribution());
// Read the Bin Numbers
err = readBinNumbers(data, groupId);
// Read the B Over A
dType = readDistributionType(groupId, DREAM3D::HDF5::Grain_SizeVBoverA_Distributions);
data->setBOverA_DistType(dType);
data->setGrainSize_BOverA( createDistributionVector(data->getBOverA_DistType()));
err = readDistributionData(groupId,
DREAM3D::HDF5::Grain_SizeVBoverA_Distributions,
data->getGrainSize_BOverA());
// Read the C Over A
dType = readDistributionType(groupId, DREAM3D::HDF5::Grain_SizeVCoverA_Distributions);
data->setCOverA_DistType(dType);
data->setGrainSize_COverA( createDistributionVector(data->getCOverA_DistType()));
err = readDistributionData(groupId,
DREAM3D::HDF5::Grain_SizeVCoverA_Distributions,
data->getGrainSize_COverA());
// Read the Neighbors
dType = readDistributionType(groupId, DREAM3D::HDF5::Grain_SizeVNeighbors_Distributions);
data->setNeighbors_DistType(dType);
data->setGrainSize_Neighbors( createDistributionVector(data->getNeighbors_DistType()));
err = readDistributionData(groupId,
DREAM3D::HDF5::Grain_SizeVNeighbors_Distributions,
data->getGrainSize_Neighbors());
// Read the Omegas
dType = readDistributionType(groupId, DREAM3D::HDF5::Grain_SizeVOmega3_Distributions);
data->setOmegas_DistType(dType);
data->setGrainSize_Omegas( createDistributionVector(data->getOmegas_DistType()));
err = readDistributionData(groupId,
DREAM3D::HDF5::Grain_SizeVOmega3_Distributions,
data->getGrainSize_Omegas());
// Read the Misorientation Bins
FloatArrayType::Pointer misoBins = FloatArrayType::CreateArray(0, DREAM3D::HDF5::MisorientationBins);
err = misoBins->readH5Data(groupId);
if (err < 0)
{
misoBins = FloatArrayType::NullPointer();
}
data->setMisorientationBins(misoBins);
err = readMDFWeights(groupId, data);
// Read the ODF Data
FloatArrayType::Pointer odfBins = FloatArrayType::CreateArray(0, DREAM3D::HDF5::ODF);
err = odfBins->readH5Data(groupId);
if (err < 0)
{
odfBins = FloatArrayType::NullPointer();
}
data->setODF(odfBins);
err = readODFWeights(groupId, data);
// Read the Axis ODF Data
FloatArrayType::Pointer axisOdfBins = FloatArrayType::CreateArray(0, DREAM3D::HDF5::AxisOrientation);
err = axisOdfBins->readH5Data(groupId);
if (err < 0)
{
axisOdfBins = FloatArrayType::NullPointer();
}
data->setAxisOrientation(axisOdfBins);
err = readAxisODFWeights(groupId, data);
return err;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void InsertAtoms::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
// Validate that the selected AvgQuats array has tuples equal to the largest
// Feature Id; the filter would not crash otherwise, but the user should
// be notified of unanticipated behavior ; this cannot be done in the dataCheck since
// we don't have acces to the data yet
int32_t numFeaturesIn = static_cast<int32_t>(m_AvgQuatsPtr.lock()->getNumberOfTuples());
bool mismatchedFeatures = true;
int32_t largestFeature = 0;
size_t numTuples = m_SurfaceMeshFaceLabelsPtr.lock()->getNumberOfTuples();
for (size_t i = 0; i < numTuples; i++)
{
if (m_SurfaceMeshFaceLabels[2 * i] > largestFeature)
{
largestFeature = m_SurfaceMeshFaceLabels[2 * i];
if (largestFeature >= numFeaturesIn)
{
mismatchedFeatures = true;
break;
}
}
else if (m_SurfaceMeshFaceLabels[2 * i + 1] > largestFeature)
{
largestFeature = m_SurfaceMeshFaceLabels[2 * i + 1];
if (largestFeature >= numFeaturesIn)
{
mismatchedFeatures = true;
break;
}
}
}
if (mismatchedFeatures == true)
{
QString ss = QObject::tr("The number of Features in the AvgQuats array (%1) is larger than the largest Feature Id in the SurfaceMeshFaceLabels array").arg(numFeaturesIn);
setErrorCondition(-5555);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
if (largestFeature != (numFeaturesIn - 1))
{
QString ss = QObject::tr("The number of Features in the AvgQuats array (%1) does not match the largest Feature Id in the SurfaceMeshFaceLabels array").arg(numFeaturesIn);
setErrorCondition(-5555);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
FloatVec3_t latticeConstants;
latticeConstants.x = m_LatticeConstants.x / 10000.0;
latticeConstants.y = m_LatticeConstants.y / 10000.0;
latticeConstants.z = m_LatticeConstants.z / 10000.0;
DataContainer::Pointer sm = getDataContainerArray()->getDataContainer(getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
SIMPL_RANDOMNG_NEW()
#ifdef SIMPLib_USE_PARALLEL_ALGORITHMS
tbb::task_scheduler_init init;
bool doParallel = true;
#endif
// pull down faces
TriangleGeom::Pointer triangleGeom = sm->getGeometryAs<TriangleGeom>();
int64_t numFaces = m_SurfaceMeshFaceLabelsPtr.lock()->getNumberOfTuples();
// create array to hold bounding vertices for each face
FloatArrayType::Pointer llPtr = FloatArrayType::CreateArray(3, "Lower_Left_Internal_Use_Only");
FloatArrayType::Pointer urPtr = FloatArrayType::CreateArray(3, "Upper_Right_Internal_Use_Only");
float* ll = llPtr->getPointer(0);
float* ur = urPtr->getPointer(0);
VertexGeom::Pointer faceBBs = VertexGeom::CreateGeometry(2 * numFaces, "faceBBs");
// walk through faces to see how many features there are
int32_t g1 = 0, g2 = 0;
int32_t maxFeatureId = 0;
for (int64_t i = 0; i < numFaces; i++)
{
g1 = m_SurfaceMeshFaceLabels[2 * i];
g2 = m_SurfaceMeshFaceLabels[2 * i + 1];
if (g1 > maxFeatureId) { maxFeatureId = g1; }
if (g2 > maxFeatureId) { maxFeatureId = g2; }
}
// add one to account for feature 0
int32_t numFeatures = maxFeatureId + 1;
// create a dynamic list array to hold face lists
Int32Int32DynamicListArray::Pointer faceLists = Int32Int32DynamicListArray::New();
QVector<int32_t> linkCount(numFeatures, 0);
// fill out lists with number of references to cells
typedef boost::shared_array<int32_t> SharedInt32Array_t;
SharedInt32Array_t linkLocPtr(new int32_t[numFaces]);
int32_t* linkLoc = linkLocPtr.get();
::memset(linkLoc, 0, numFaces * sizeof(int32_t));
// traverse data to determine number of faces belonging to each feature
for (int64_t i = 0; i < numFaces; i++)
{
g1 = m_SurfaceMeshFaceLabels[2 * i];
g2 = m_SurfaceMeshFaceLabels[2 * i + 1];
if (g1 > 0) { linkCount[g1]++; }
if (g2 > 0) { linkCount[g2]++; }
}
// now allocate storage for the faces
faceLists->allocateLists(linkCount);
// traverse data again to get the faces belonging to each feature
for (int64_t i = 0; i < numFaces; i++)
{
g1 = m_SurfaceMeshFaceLabels[2 * i];
g2 = m_SurfaceMeshFaceLabels[2 * i + 1];
if (g1 > 0) { faceLists->insertCellReference(g1, (linkLoc[g1])++, i); }
if (g2 > 0) { faceLists->insertCellReference(g2, (linkLoc[g2])++, i); }
// find bounding box for each face
GeometryMath::FindBoundingBoxOfFace(triangleGeom, i, ll, ur);
faceBBs->setCoords(2 * i, ll);
faceBBs->setCoords(2 * i + 1, ur);
}
// generate the list of sampling points fom subclass
QVector<VertexGeom::Pointer> points(numFeatures);
QVector<BoolArrayType::Pointer> inFeature(numFeatures);
for (int32_t i = 0; i < numFeatures; i++)
{
points[i] = VertexGeom::CreateGeometry(0, "_INTERNAL_USE_ONLY_points");
inFeature[i] = BoolArrayType::CreateArray(0, "_INTERNAL_USE_ONLY_inside");
}
QuatF* avgQuats = reinterpret_cast<QuatF*>(m_AvgQuats);
#ifdef SIMPLib_USE_PARALLEL_ALGORITHMS
if (doParallel == true)
{
tbb::parallel_for(tbb::blocked_range<size_t>(0, numFeatures),
InsertAtomsImpl(triangleGeom, faceLists, faceBBs, avgQuats, latticeConstants, m_Basis, points, inFeature), tbb::auto_partitioner());
}
else
#endif
{
InsertAtomsImpl serial(triangleGeom, faceLists, faceBBs, avgQuats, latticeConstants, m_Basis, points, inFeature);
serial.checkPoints(0, numFeatures);
}
assign_points(points, inFeature);
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
FloatArrayType::Pointer AngleFileLoader::loadData()
{
FloatArrayType::Pointer angles = FloatArrayType::NullPointer();
// Make sure the input file variable is not empty
if (m_InputFile.size() == 0)
{
setErrorMessage("Input File Path is empty");
setErrorCode(-1);
return angles;
}
QFileInfo fi(getInputFile());
// Make sure the file exists on disk
if (fi.exists() == false)
{
setErrorMessage("Input File does not exist at path");
setErrorCode(-2);
return angles;
}
// Make sure we have a valid angle representation
if(m_AngleRepresentation != EulerAngles
&& m_AngleRepresentation != QuaternionAngles
&& m_AngleRepresentation != RodriguezAngles)
{
setErrorMessage("The Angle representation was not set to anything known to this code");
setErrorCode(-3);
return angles;
}
// The format of the file is quite simple. Comment lines start with a "#" symbol
// The only Key-Value pair we are looking for is 'Angle Count' which will have
// the total number of angles that will be read
int numOrients = 0;
QByteArray buf;
// Open the file and read the first line
QFile reader(getInputFile());
if (!reader.open(QIODevice::ReadOnly | QIODevice::Text))
{
QString msg = QObject::tr("Angle file could not be opened: %1").arg(getInputFile());
setErrorCode(-100);
setErrorMessage(msg);
return angles;
}
bool ok = false;
buf = reader.readLine();
while(buf[0] == '#')
{
buf = reader.readLine();
}
buf = buf.trimmed();
//Split the next line into a pair of tokens delimited by the ":" character
QList<QByteArray> tokens = buf.split(':');
if(tokens.count() != 2)
{
QString msg = QObject::tr("Proper Header was not detected. The file should have a single header line of 'Angle Count:XXXX'");
setErrorCode(-101);
setErrorMessage(msg);
return angles;
}
if(tokens[0].toStdString().compare("Angle Count") != 0)
{
QString msg = QObject::tr("Proper Header was not detected. The file should have a single header line of 'Angle Count:XXXX'");
setErrorCode(-102);
setErrorMessage(msg);
return angles;
}
numOrients = tokens[1].toInt(&ok, 10);
// Allocate enough for the angles
QVector<size_t> dims(1, 5);
angles = FloatArrayType::CreateArray(numOrients, dims, "EulerAngles_From_File");
for(int i = 0; i < numOrients; i++)
{
float weight = 0.0f;
float sigma = 1.0f;
buf = reader.readLine();
// Skip any lines that start with a '#' character
if(buf[0] == '#') { continue; }
buf = buf.trimmed();
// Remove multiple Delimiters if wanted by the user.
if (m_IgnoreMultipleDelimiters == true)
{
buf = buf.simplified();
}
tokens = buf.split( *(getDelimiter().toLatin1().data()));
FOrientArrayType euler(3);
if (m_AngleRepresentation == EulerAngles)
{
euler[0] = tokens[0].toFloat(&ok);
euler[1] = tokens[1].toFloat(&ok);
euler[2] = tokens[2].toFloat(&ok);
weight = tokens[3].toFloat(&ok);
sigma = tokens[4].toFloat(&ok);
}
else if (m_AngleRepresentation == QuaternionAngles)
{
FOrientArrayType quat(4);
quat[0] = tokens[0].toFloat(&ok);
quat[1] = tokens[1].toFloat(&ok);
quat[2] = tokens[2].toFloat(&ok);
quat[3] = tokens[3].toFloat(&ok);
FOrientTransformsType::qu2eu(quat, euler);
weight = tokens[4].toFloat(&ok);
sigma = tokens[5].toFloat(&ok);
}
else if (m_AngleRepresentation == RodriguezAngles)
{
FOrientArrayType rod(4, 0.0);
rod[0] = tokens[0].toFloat(&ok);
rod[1] = tokens[1].toFloat(&ok);
rod[2] = tokens[2].toFloat(&ok);
FOrientTransformsType::ro2eu(rod, euler);
weight = tokens[3].toFloat(&ok);
sigma = tokens[4].toFloat(&ok);
}
// Values in File are in Radians and the user wants them in Degrees
if (m_FileAnglesInDegrees == false && m_OutputAnglesInDegrees == true)
{
euler[0] = euler[0] * SIMPLib::Constants::k_RadToDeg;
euler[1] = euler[1] * SIMPLib::Constants::k_RadToDeg;
euler[2] = euler[2] * SIMPLib::Constants::k_RadToDeg;
}
// Values are in Degrees but user wants them in Radians
else if (m_FileAnglesInDegrees == true && m_OutputAnglesInDegrees == false)
{
euler[0] = euler[0] * SIMPLib::Constants::k_DegToRad;
euler[1] = euler[1] * SIMPLib::Constants::k_DegToRad;
euler[2] = euler[2] * SIMPLib::Constants::k_DegToRad;
}
// Store the values into our array
angles->setComponent(i, 0, euler[0]);
angles->setComponent(i, 1, euler[1]);
angles->setComponent(i, 2, euler[2]);
angles->setComponent(i, 3, weight);
angles->setComponent(i, 4, sigma);
// qDebug() << "reading line: " << i ;
}
return angles;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void VisualizeGBCDGMT::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer sm = getDataContainerArray()->getDataContainer(getGBCDArrayPath().getDataContainerName());
// Make sure any directory path is also available as the user may have just typed
// in a path without actually creating the full path
QFileInfo fi(getOutputFile());
QDir dir(fi.path());
if (!dir.mkpath("."))
{
QString ss;
ss = QObject::tr("Error creating parent path '%1'").arg(dir.path());
setErrorCondition(-1);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
QFile file(getOutputFile());
if (!file.open(QIODevice::WriteOnly | QIODevice::Text))
{
QString ss = QObject::tr("Error opening output file '%1'").arg(getOutputFile());
setErrorCondition(-100);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
FloatArrayType::Pointer gbcdDeltasArray = FloatArrayType::CreateArray(5, "GBCDDeltas");
gbcdDeltasArray->initializeWithZeros();
FloatArrayType::Pointer gbcdLimitsArray = FloatArrayType::CreateArray(10, "GBCDLimits");
gbcdLimitsArray->initializeWithZeros();
Int32ArrayType::Pointer gbcdSizesArray = Int32ArrayType::CreateArray(5, "GBCDSizes");
gbcdSizesArray->initializeWithZeros();
float* gbcdDeltas = gbcdDeltasArray->getPointer(0);
int32_t* gbcdSizes = gbcdSizesArray->getPointer(0);
float* gbcdLimits = gbcdLimitsArray->getPointer(0);
// Original Ranges from Dave R.
//m_GBCDlimits[0] = 0.0f;
//m_GBCDlimits[1] = cosf(1.0f*m_pi);
//m_GBCDlimits[2] = 0.0f;
//m_GBCDlimits[3] = 0.0f;
//m_GBCDlimits[4] = cosf(1.0f*m_pi);
//m_GBCDlimits[5] = 2.0f*m_pi;
//m_GBCDlimits[6] = cosf(0.0f);
//m_GBCDlimits[7] = 2.0f*m_pi;
//m_GBCDlimits[8] = 2.0f*m_pi;
//m_GBCDlimits[9] = cosf(0.0f);
// Greg R. Ranges
gbcdLimits[0] = 0.0f;
gbcdLimits[1] = 0.0f;
gbcdLimits[2] = 0.0f;
gbcdLimits[3] = -sqrtf(SIMPLib::Constants::k_Pi / 2.0f);
gbcdLimits[4] = -sqrtf(SIMPLib::Constants::k_Pi / 2.0f);
gbcdLimits[5] = SIMPLib::Constants::k_Pi / 2.0f;
gbcdLimits[6] = 1.0f;
gbcdLimits[7] = SIMPLib::Constants::k_Pi / 2.0f;
gbcdLimits[8] = sqrtf(SIMPLib::Constants::k_Pi / 2.0f);
gbcdLimits[9] = sqrtf(SIMPLib::Constants::k_Pi / 2.0f);
// get num components of GBCD
QVector<size_t> cDims = m_GBCDPtr.lock()->getComponentDimensions();
gbcdSizes[0] = cDims[0];
gbcdSizes[1] = cDims[1];
gbcdSizes[2] = cDims[2];
gbcdSizes[3] = cDims[3];
gbcdSizes[4] = cDims[4];
gbcdDeltas[0] = (gbcdLimits[5] - gbcdLimits[0]) / float(gbcdSizes[0]);
gbcdDeltas[1] = (gbcdLimits[6] - gbcdLimits[1]) / float(gbcdSizes[1]);
gbcdDeltas[2] = (gbcdLimits[7] - gbcdLimits[2]) / float(gbcdSizes[2]);
gbcdDeltas[3] = (gbcdLimits[8] - gbcdLimits[3]) / float(gbcdSizes[3]);
gbcdDeltas[4] = (gbcdLimits[9] - gbcdLimits[4]) / float(gbcdSizes[4]);
float vec[3] = { 0.0f, 0.0f, 0.0f };
float vec2[3] = { 0.0f, 0.0f, 0.0f };
float rotNormal[3] = { 0.0f, 0.0f, 0.0f };
float rotNormal2[3] = { 0.0f, 0.0f, 0.0f };
float sqCoord[2] = { 0.0f, 0.0f };
float dg[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float dgt[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float dg1[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float dg2[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float sym1[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float sym2[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float sym2t[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float mis_euler1[3] = { 0.0f, 0.0f, 0.0f };
float misAngle = m_MisorientationRotation.angle * SIMPLib::Constants::k_PiOver180;
float normAxis[3] = { m_MisorientationRotation.h, m_MisorientationRotation.k, m_MisorientationRotation.l };
MatrixMath::Normalize3x1(normAxis);
// convert axis angle to matrix representation of misorientation
FOrientArrayType om(9, 0.0f);
FOrientTransformsType::ax2om(FOrientArrayType(normAxis[0], normAxis[1], normAxis[2], misAngle), om);
om.toGMatrix(dg);
// take inverse of misorientation variable to use for switching symmetry
MatrixMath::Transpose3x3(dg, dgt);
// Get our SpaceGroupOps pointer for the selected crystal structure
SpaceGroupOps::Pointer orientOps = m_OrientationOps[m_CrystalStructures[m_PhaseOfInterest]];
// get number of symmetry operators
int32_t n_sym = orientOps->getNumSymOps();
int32_t thetaPoints = 120;
int32_t phiPoints = 30;
float thetaRes = 360.0f / float(thetaPoints);
float phiRes = 90.0f / float(phiPoints);
float theta = 0.0f, phi = 0.0f;
float thetaRad = 0.0f, phiRad = 0.0f;
float degToRad = SIMPLib::Constants::k_PiOver180;
float sum = 0.0f;
int32_t count = 0;
bool nhCheck = false;
int32_t hemisphere = 0;
int32_t shift1 = gbcdSizes[0];
int32_t shift2 = gbcdSizes[0] * gbcdSizes[1];
int32_t shift3 = gbcdSizes[0] * gbcdSizes[1] * gbcdSizes[2];
int32_t shift4 = gbcdSizes[0] * gbcdSizes[1] * gbcdSizes[2] * gbcdSizes[3];
int64_t totalGBCDBins = gbcdSizes[0] * gbcdSizes[1] * gbcdSizes[2] * gbcdSizes[3] * gbcdSizes[4] * 2;
std::vector<float> gmtValues;
for (int32_t k = 0; k < phiPoints + 1; k++)
{
for (int32_t l = 0; l < thetaPoints + 1; l++)
{
// get (x,y) for stereographic projection pixel
theta = float(l) * thetaRes;
phi = float(k) * phiRes;
thetaRad = theta * degToRad;
phiRad = phi * degToRad;
sum = 0.0f;
count = 0;
vec[0] = sinf(phiRad) * cosf(thetaRad);
vec[1] = sinf(phiRad) * sinf(thetaRad);
vec[2] = cosf(phiRad);
MatrixMath::Multiply3x3with3x1(dgt, vec, vec2);
// Loop over all the symetry operators in the given cystal symmetry
for (int32_t i = 0; i < n_sym; i++)
{
// get symmetry operator1
orientOps->getMatSymOp(i, sym1);
for (int32_t j = 0; j < n_sym; j++)
{
// get symmetry operator2
orientOps->getMatSymOp(j, sym2);
MatrixMath::Transpose3x3(sym2, sym2t);
// calculate symmetric misorientation
MatrixMath::Multiply3x3with3x3(dg, sym2t, dg1);
MatrixMath::Multiply3x3with3x3(sym1, dg1, dg2);
// convert to euler angle
FOrientArrayType mEuler(mis_euler1, 3);
FOrientTransformsType::om2eu(FOrientArrayType(dg2), mEuler);
if (mis_euler1[0] < SIMPLib::Constants::k_PiOver2 && mis_euler1[1] < SIMPLib::Constants::k_PiOver2 && mis_euler1[2] < SIMPLib::Constants::k_PiOver2)
{
mis_euler1[1] = cosf(mis_euler1[1]);
// find bins in GBCD
int32_t location1 = int32_t((mis_euler1[0] - gbcdLimits[0]) / gbcdDeltas[0]);
int32_t location2 = int32_t((mis_euler1[1] - gbcdLimits[1]) / gbcdDeltas[1]);
int32_t location3 = int32_t((mis_euler1[2] - gbcdLimits[2]) / gbcdDeltas[2]);
// find symmetric poles using the first symmetry operator
MatrixMath::Multiply3x3with3x1(sym1, vec, rotNormal);
// get coordinates in square projection of crystal normal parallel to boundary normal
nhCheck = getSquareCoord(rotNormal, sqCoord);
// Note the switch to have theta in the 4 slot and cos(Phi) int he 3 slot
int32_t location4 = int32_t((sqCoord[0] - gbcdLimits[3]) / gbcdDeltas[3]);
int32_t location5 = int32_t((sqCoord[1] - gbcdLimits[4]) / gbcdDeltas[4]);
if (location1 >= 0 && location2 >= 0 && location3 >= 0 && location4 >= 0 && location5 >= 0 &&
location1 < gbcdSizes[0] && location2 < gbcdSizes[1] && location3 < gbcdSizes[2] && location4 < gbcdSizes[3] && location5 < gbcdSizes[4])
{
hemisphere = 0;
if (nhCheck == false) { hemisphere = 1; }
sum += m_GBCD[(m_PhaseOfInterest * totalGBCDBins) + 2 * ((location5 * shift4) + (location4 * shift3) + (location3 * shift2) + (location2 * shift1) + location1) + hemisphere];
count++;
}
}
// again in second crystal reference frame
// calculate symmetric misorientation
MatrixMath::Multiply3x3with3x3(dgt, sym2, dg1);
MatrixMath::Multiply3x3with3x3(sym1, dg1, dg2);
// convert to euler angle
FOrientTransformsType::om2eu(FOrientArrayType(dg2), mEuler);
if (mis_euler1[0] < SIMPLib::Constants::k_PiOver2 && mis_euler1[1] < SIMPLib::Constants::k_PiOver2 && mis_euler1[2] < SIMPLib::Constants::k_PiOver2)
{
mis_euler1[1] = cosf(mis_euler1[1]);
// find bins in GBCD
int32_t location1 = int32_t((mis_euler1[0] - gbcdLimits[0]) / gbcdDeltas[0]);
int32_t location2 = int32_t((mis_euler1[1] - gbcdLimits[1]) / gbcdDeltas[1]);
int32_t location3 = int32_t((mis_euler1[2] - gbcdLimits[2]) / gbcdDeltas[2]);
// find symmetric poles using the first symmetry operator
MatrixMath::Multiply3x3with3x1(sym1, vec2, rotNormal2);
// get coordinates in square projection of crystal normal parallel to boundary normal
nhCheck = getSquareCoord(rotNormal2, sqCoord);
// Note the switch to have theta in the 4 slot and cos(Phi) int he 3 slot
int32_t location4 = int32_t((sqCoord[0] - gbcdLimits[3]) / gbcdDeltas[3]);
int32_t location5 = int32_t((sqCoord[1] - gbcdLimits[4]) / gbcdDeltas[4]);
if (location1 >= 0 && location2 >= 0 && location3 >= 0 && location4 >= 0 && location5 >= 0 &&
location1 < gbcdSizes[0] && location2 < gbcdSizes[1] && location3 < gbcdSizes[2] && location4 < gbcdSizes[3] && location5 < gbcdSizes[4])
{
hemisphere = 0;
if (nhCheck == false) { hemisphere = 1; }
sum += m_GBCD[(m_PhaseOfInterest * totalGBCDBins) + 2 * ((location5 * shift4) + (location4 * shift3) + (location3 * shift2) + (location2 * shift1) + location1) + hemisphere];
count++;
}
}
}
}
gmtValues.push_back(theta);
gmtValues.push_back((90.0f - phi));
gmtValues.push_back(sum / float(count));
}
}
FILE* f = NULL;
f = fopen(m_OutputFile.toLatin1().data(), "wb");
if (NULL == f)
{
QString ss = QObject::tr("Error opening output file '%1'").arg(m_OutputFile);
setErrorCondition(-1);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
// Remember to use the original Angle in Degrees!!!!
fprintf(f, "%.1f %.1f %.1f %.1f\n", m_MisorientationRotation.h, m_MisorientationRotation.k, m_MisorientationRotation.l, m_MisorientationRotation.angle);
size_t size = gmtValues.size() / 3;
for (size_t i = 0; i < size; i++)
{
fprintf(f, "%f %f %f\n", gmtValues[3 * i], gmtValues[3 * i + 1], gmtValues[3 * i + 2]);
}
fclose(f);
/* Let the GUI know we are done with this filter */
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void StatsGenODFWidget::on_m_CalculateODFBtn_clicked()
{
int err = 0;
QwtArray<float> e1s;
QwtArray<float> e2s;
QwtArray<float> e3s;
QwtArray<float> weights;
QwtArray<float> sigmas;
QwtArray<float> odf;
SGODFTableModel* tableModel = NULL;
if(weightSpreadGroupBox->isChecked() )
{
tableModel = m_ODFTableModel;
}
else
{
tableModel = m_OdfBulkTableModel;
}
e1s = tableModel->getData(SGODFTableModel::Euler1);
e2s = tableModel->getData(SGODFTableModel::Euler2);
e3s = tableModel->getData(SGODFTableModel::Euler3);
weights = tableModel->getData(SGODFTableModel::Weight);
sigmas = tableModel->getData(SGODFTableModel::Sigma);
// Convert from Degrees to Radians
for(int i = 0; i < e1s.size(); i++)
{
e1s[i] = e1s[i] * M_PI / 180.0;
e2s[i] = e2s[i] * M_PI / 180.0;
e3s[i] = e3s[i] * M_PI / 180.0;
}
size_t numEntries = e1s.size();
int imageSize = pfImageSize->value();
int lamberSize = pfLambertSize->value();
int numColors = 16;
int npoints = pfSamplePoints->value();
QVector<size_t> dims(1, 3);
FloatArrayType::Pointer eulers = FloatArrayType::CreateArray(npoints, dims, "Eulers");
PoleFigureConfiguration_t config;
QVector<UInt8ArrayType::Pointer> figures;
if ( Ebsd::CrystalStructure::Cubic_High == m_CrystalStructure)
{
// We now need to resize all the arrays here to make sure they are all allocated
odf.resize(CubicOps::k_OdfSize);
Texture::CalculateCubicODFData(e1s.data(), e2s.data(), e3s.data(),
weights.data(), sigmas.data(), true,
odf.data(), numEntries);
err = StatsGen::GenCubicODFPlotData(odf.data(), eulers->getPointer(0), npoints);
CubicOps ops;
config.eulers = eulers.get();
config.imageDim = imageSize;
config.lambertDim = lamberSize;
config.numColors = numColors;
figures = ops.generatePoleFigure(config);
}
else if ( Ebsd::CrystalStructure::Hexagonal_High == m_CrystalStructure)
{
// We now need to resize all the arrays here to make sure they are all allocated
odf.resize(HexagonalOps::k_OdfSize);
Texture::CalculateHexODFData(e1s.data(), e2s.data(), e3s.data(),
weights.data(), sigmas.data(), true,
odf.data(), numEntries);
err = StatsGen::GenHexODFPlotData(odf.data(), eulers->getPointer(0), npoints);
HexagonalOps ops;
config.eulers = eulers.get();
config.imageDim = imageSize;
config.lambertDim = lamberSize;
config.numColors = numColors;
figures = ops.generatePoleFigure(config);
}
else if ( Ebsd::CrystalStructure::OrthoRhombic == m_CrystalStructure)
{
// // We now need to resize all the arrays here to make sure they are all allocated
odf.resize(OrthoRhombicOps::k_OdfSize);
Texture::CalculateOrthoRhombicODFData(e1s.data(), e2s.data(), e3s.data(),
weights.data(), sigmas.data(), true,
odf.data(), numEntries);
err = StatsGen::GenOrthoRhombicODFPlotData(odf.data(), eulers->getPointer(0), npoints);
OrthoRhombicOps ops;
config.eulers = eulers.get();
config.imageDim = imageSize;
config.lambertDim = lamberSize;
config.numColors = numColors;
figures = ops.generatePoleFigure(config);
}
if (err == 1)
{
//TODO: Present Error Message
return;
}
QImage image = PoleFigureImageUtilities::Create3ImagePoleFigure(figures[0].get(), figures[1].get(), figures[2].get(), config, imageLayout->currentIndex());
m_PoleFigureLabel->setPixmap(QPixmap::fromImage(image));
// Enable the MDF tab
if (m_MDFWidget != NULL)
{
m_MDFWidget->setEnabled(true);
m_MDFWidget->updateMDFPlot(odf);
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void StatsGenODFWidget::on_loadODFTextureBtn_clicked()
{
QString file = angleFilePath->text();
if(true == file.isEmpty())
{
return;
}
QFileInfo fi(angleFilePath->text());
if(fi.exists() == false)
{
return;
}
size_t count = 0;
QVector<float> e1s(count);
QVector<float> e2s(count);
QVector<float> e3s(count);
QVector<float> weights(count);
QVector<float> sigmas(count);
QProgressDialog progress("Loading Data ....", "Cancel", 0, 3, this);
progress.setWindowModality(Qt::WindowModal);
progress.setMinimumDuration(2000);
if (fi.suffix().compare(Ebsd::Ang::FileExt) == 0)
{
progress.setValue(1);
progress.setLabelText("[1/3] Reading File ...");
AngReader loader;
loader.setFileName(angleFilePath->text());
int err = loader.readFile();
if(err < 0)
{
QMessageBox::critical(this, "Error loading the ANG file", loader.getErrorMessage(), QMessageBox::Ok);
return;
}
float* phi1 = loader.getPhi1Pointer();
float* phi = loader.getPhiPointer();
float* phi2 = loader.getPhi2Pointer();
int xDim = loader.getXDimension();
int yDim = loader.getYDimension();
count = xDim * yDim;
e1s.resize(count);
e2s.resize(count);
e3s.resize(count);
weights.resize(count);
sigmas.resize(count);
for(size_t i = 0; i < count; ++i)
{
e1s[i] = phi1[i];
e2s[i] = phi[i];
e3s[i] = phi2[i];
weights[i] = 1.0;
sigmas[i] = 0.0;
}
}
else if (fi.suffix().compare(Ebsd::Ctf::FileExt) == 0)
{
progress.setValue(1);
progress.setLabelText("[1/3] Reading File ...");
CtfReader loader;
loader.setFileName(angleFilePath->text());
int err = loader.readFile();
if(err < 0)
{
QMessageBox::critical(this, "Error loading the CTF file", loader.getErrorMessage(), QMessageBox::Ok);
return;
}
float* phi1 = loader.getEuler1Pointer();
float* phi = loader.getEuler2Pointer();
float* phi2 = loader.getEuler3Pointer();
int xDim = loader.getXDimension();
int yDim = loader.getYDimension();
count = xDim * yDim;
e1s.resize(count);
e2s.resize(count);
e3s.resize(count);
weights.resize(count);
sigmas.resize(count);
for(size_t i = 0; i < count; ++i)
{
e1s[i] = phi1[i];
e2s[i] = phi[i];
e3s[i] = phi2[i];
weights[i] = 1.0;
sigmas[i] = 0.0;
}
}
else
{
progress.setValue(1);
progress.setLabelText("[1/3] Reading File ...");
AngleFileLoader::Pointer loader = AngleFileLoader::New();
loader->setInputFile(angleFilePath->text());
loader->setAngleRepresentation(angleRepresentation->currentIndex());
loader->setFileAnglesInDegrees(anglesInDegrees->isChecked());
loader->setOutputAnglesInDegrees(true);
QString delim;
int index = delimiter->currentIndex();
switch(index)
{
case 0:
delim = " ";
break;
case 1:
delim = "\t";
break;
case 2:
delim = ",";
break;
case 3:
delim = ";";
break;
default:
delim = " ";
}
loader->setDelimiter(delim);
FloatArrayType::Pointer data = loader->loadData();
if (loader->getErrorCode() < 0)
{
QMessageBox::critical(this, "Error Loading Angle data", loader->getErrorMessage(), QMessageBox::Ok);
return;
}
count = data->getNumberOfTuples();
e1s.resize(count);
e2s.resize(count);
e3s.resize(count);
weights.resize(count);
sigmas.resize(count);
for(size_t i = 0; i < count; ++i)
{
e1s[i] = data->getComponent(i, 0);
e2s[i] = data->getComponent(i, 1);
e3s[i] = data->getComponent(i, 2);
weights[i] = data->getComponent(i, 3);
sigmas[i] = data->getComponent(i, 4);
}
}
progress.setValue(2);
progress.setLabelText("[2/3] Rendering Pole Figure ...");
m_OdfBulkTableModel->removeRows(0, m_OdfBulkTableModel->rowCount());
#if 1
m_OdfBulkTableModel->blockSignals(true);
m_OdfBulkTableModel->setColumnData(SGODFTableModel::Euler1, e1s);
m_OdfBulkTableModel->setColumnData(SGODFTableModel::Euler2, e2s);
m_OdfBulkTableModel->setColumnData(SGODFTableModel::Euler3, e3s);
m_OdfBulkTableModel->setColumnData(SGODFTableModel::Weight, weights);
m_OdfBulkTableModel->setColumnData(SGODFTableModel::Sigma, sigmas);
m_OdfBulkTableModel->blockSignals(false);
#endif
on_m_CalculateODFBtn_clicked();
progress.setValue(3);
}
void generate(size_t start, size_t end) const
{
// We want to work with the raw pointers for speed so get those pointers.
float* m_GBCDdeltas = m_GbcdDeltasArray->getPointer(0);
float* m_GBCDlimits = m_GbcdLimitsArray->getPointer(0);
int* m_GBCDsizes = m_GbcdSizesArray->getPointer(0);
int32_t* m_Bins = m_GbcdBinsArray->getPointer(0);
bool* m_HemiCheck = m_GbcdHemiCheckArray->getPointer(0);
int32_t* m_Labels = m_LabelsArray->getPointer(0);
double* m_Normals = m_NormalsArray->getPointer(0);
int32_t* m_Phases = m_PhasesArray->getPointer(0);
float* m_Eulers = m_EulersArray->getPointer(0);
uint32_t* m_CrystalStructures = m_CrystalStructuresArray->getPointer(0);
int32_t j = 0;//, j4;
int32_t k = 0;//, k4;
int32_t m = 0;
int32_t temp = 0;
//bool gbcd_indices_good;
int32_t feature1 = 0, feature2 = 0;
int32_t inversion = 1;
float g1ea[3] = { 0.0f, 0.0f, 0.0f }, g2ea[3] = { 0.0f, 0.0f, 0.0f };
float g1[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } }, g2[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float g1s[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } }, g2s[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float sym1[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } }, sym2[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float g2t[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } }, dg[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float euler_mis[3] = { 0.0f, 0.0f, 0.0f };
float normal[3] = { 0.0f, 0.0f, 0.0f };
float xstl1_norm1[3] = { 0.0f, 0.0f, 0.0f };
int32_t gbcd_index = 0;
float sqCoord[2] = { 0.0f, 0.0f }, sqCoordInv[2] = { 0.0f, 0.0f };
bool nhCheck = false, nhCheckInv = true;
int32_t SYMcounter = 0;
int64_t TRIcounter = static_cast<int64_t>(start - startOffset);
int64_t TRIcounterShift = 0;
for (size_t i = start; i < end; i++)
{
SYMcounter = 0;
feature1 = m_Labels[2 * i];
feature2 = m_Labels[2 * i + 1];
normal[0] = m_Normals[3 * i];
normal[1] = m_Normals[3 * i + 1];
normal[2] = m_Normals[3 * i + 2];
if (feature1 < 0 || feature2 < 0) { continue; }
if (m_Phases[feature1] == m_Phases[feature2] && m_Phases[feature1] > 0)
{
TRIcounterShift = (TRIcounter * numEntriesPerTri);
uint32_t cryst = m_CrystalStructures[m_Phases[feature1]];
for (int32_t q = 0; q < 2; q++)
{
if (q == 1)
{
temp = feature1;
feature1 = feature2;
feature2 = temp;
normal[0] = -normal[0];
normal[1] = -normal[1];
normal[2] = -normal[2];
}
for (m = 0; m < 3; m++)
{
g1ea[m] = m_Eulers[3 * feature1 + m];
g2ea[m] = m_Eulers[3 * feature2 + m];
}
FOrientArrayType om(9, 0.0f);
FOrientTransformsType::eu2om(FOrientArrayType(g1ea, 3), om);
om.toGMatrix(g1);
FOrientTransformsType::eu2om(FOrientArrayType(g2ea, 3), om);
om.toGMatrix(g2);
int32_t nsym = m_OrientationOps[cryst]->getNumSymOps();
for (j = 0; j < nsym; j++)
{
// rotate g1 by symOp
m_OrientationOps[cryst]->getMatSymOp(j, sym1);
MatrixMath::Multiply3x3with3x3(sym1, g1, g1s);
// get the crystal directions along the triangle normals
MatrixMath::Multiply3x3with3x1(g1s, normal, xstl1_norm1);
// get coordinates in square projection of crystal normal parallel to boundary normal
nhCheck = getSquareCoord(xstl1_norm1, sqCoord);
if (inversion == 1)
{
sqCoordInv[0] = -sqCoord[0];
sqCoordInv[1] = -sqCoord[1];
if (nhCheck == false) { nhCheckInv = true; }
else { nhCheckInv = false; }
}
for (k = 0; k < nsym; k++)
{
// calculate the symmetric misorienation
m_OrientationOps[cryst]->getMatSymOp(k, sym2);
// rotate g2 by symOp
MatrixMath::Multiply3x3with3x3(sym2, g2, g2s);
// transpose rotated g2
MatrixMath::Transpose3x3(g2s, g2t);
// calculate delta g
MatrixMath::Multiply3x3with3x3(g1s, g2t, dg);
// translate matrix to euler angles
FOrientArrayType om(dg);
FOrientArrayType eu(euler_mis, 3);
FOrientTransformsType::om2eu(om, eu);
if (euler_mis[0] < SIMPLib::Constants::k_PiOver2 && euler_mis[1] < SIMPLib::Constants::k_PiOver2 && euler_mis[2] < SIMPLib::Constants::k_PiOver2)
{
// PHI euler angle is stored in GBCD as cos(PHI)
euler_mis[1] = cosf(euler_mis[1]);
//get the indexes that this point would be in the GBCD histogram
gbcd_index = GBCDIndex(m_GBCDdeltas, m_GBCDsizes, m_GBCDlimits, euler_mis, sqCoord);
if (gbcd_index != -1)
{
m_HemiCheck[TRIcounterShift + SYMcounter] = nhCheck;
m_Bins[TRIcounterShift + SYMcounter] = gbcd_index;
}
SYMcounter++;
if (inversion == 1)
{
gbcd_index = GBCDIndex(m_GBCDdeltas, m_GBCDsizes, m_GBCDlimits, euler_mis, sqCoordInv);
if (gbcd_index != -1)
{
m_HemiCheck[TRIcounterShift + SYMcounter] = nhCheckInv;
m_Bins[TRIcounterShift + SYMcounter] = gbcd_index;
}
SYMcounter++;
}
}
else { SYMcounter += 2; }
}
}
}
}
TRIcounter++;
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void VisualizeGBCDPoleFigure::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
// Make sure any directory path is also available as the user may have just typed
// in a path without actually creating the full path
QFileInfo fi(getOutputFile());
QDir dir(fi.path());
if(!dir.mkpath("."))
{
QString ss;
ss = QObject::tr("Error creating parent path '%1'").arg(dir.path());
setErrorCondition(-1);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
QFile file(getOutputFile());
if (!file.open(QIODevice::WriteOnly | QIODevice::Text))
{
QString ss = QObject::tr("Error opening output file '%1'").arg(getOutputFile());
setErrorCondition(-100);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
FloatArrayType::Pointer gbcdDeltasArray = FloatArrayType::CreateArray(5, "GBCDDeltas");
gbcdDeltasArray->initializeWithZeros();
FloatArrayType::Pointer gbcdLimitsArray = FloatArrayType::CreateArray(10, "GBCDLimits");
gbcdLimitsArray->initializeWithZeros();
Int32ArrayType::Pointer gbcdSizesArray = Int32ArrayType::CreateArray(5, "GBCDSizes");
gbcdSizesArray->initializeWithZeros();
float* gbcdDeltas = gbcdDeltasArray->getPointer(0);
int* gbcdSizes = gbcdSizesArray->getPointer(0);
float* gbcdLimits = gbcdLimitsArray->getPointer(0);
// Original Ranges from Dave R.
//m_GBCDlimits[0] = 0.0f;
//m_GBCDlimits[1] = cosf(1.0f*m_pi);
//m_GBCDlimits[2] = 0.0f;
//m_GBCDlimits[3] = 0.0f;
//m_GBCDlimits[4] = cosf(1.0f*m_pi);
//m_GBCDlimits[5] = 2.0f*m_pi;
//m_GBCDlimits[6] = cosf(0.0f);
//m_GBCDlimits[7] = 2.0f*m_pi;
//m_GBCDlimits[8] = 2.0f*m_pi;
//m_GBCDlimits[9] = cosf(0.0f);
// Greg R. Ranges
gbcdLimits[0] = 0.0f;
gbcdLimits[1] = 0.0f;
gbcdLimits[2] = 0.0f;
gbcdLimits[3] = 0.0f;
gbcdLimits[4] = 0.0f;
gbcdLimits[5] = SIMPLib::Constants::k_PiOver2;
gbcdLimits[6] = 1.0f;
gbcdLimits[7] = SIMPLib::Constants::k_PiOver2;
gbcdLimits[8] = 1.0f;
gbcdLimits[9] = SIMPLib::Constants::k_2Pi;
// reset the 3rd and 4th dimensions using the square grid approach
gbcdLimits[3] = -sqrtf(SIMPLib::Constants::k_PiOver2);
gbcdLimits[4] = -sqrtf(SIMPLib::Constants::k_PiOver2);
gbcdLimits[8] = sqrtf(SIMPLib::Constants::k_PiOver2);
gbcdLimits[9] = sqrtf(SIMPLib::Constants::k_PiOver2);
// get num components of GBCD
QVector<size_t> cDims = m_GBCDPtr.lock()->getComponentDimensions();
gbcdSizes[0] = cDims[0];
gbcdSizes[1] = cDims[1];
gbcdSizes[2] = cDims[2];
gbcdSizes[3] = cDims[3];
gbcdSizes[4] = cDims[4];
gbcdDeltas[0] = (gbcdLimits[5] - gbcdLimits[0]) / float(gbcdSizes[0]);
gbcdDeltas[1] = (gbcdLimits[6] - gbcdLimits[1]) / float(gbcdSizes[1]);
gbcdDeltas[2] = (gbcdLimits[7] - gbcdLimits[2]) / float(gbcdSizes[2]);
gbcdDeltas[3] = (gbcdLimits[8] - gbcdLimits[3]) / float(gbcdSizes[3]);
gbcdDeltas[4] = (gbcdLimits[9] - gbcdLimits[4]) / float(gbcdSizes[4]);
float vec[3] = { 0.0f, 0.0f, 0.0f };
float vec2[3] = { 0.0f, 0.0f, 0.0f };
float rotNormal[3] = { 0.0f, 0.0f, 0.0f };
float rotNormal2[3] = { 0.0f, 0.0f, 0.0f };
float sqCoord[2] = { 0.0f, 0.0f };
float dg[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float dgt[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float dg1[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float dg2[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float sym1[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float sym2[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float sym2t[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float mis_euler1[3] = { 0.0f, 0.0f, 0.0f };
float misAngle = m_MisorientationRotation.angle * SIMPLib::Constants::k_PiOver180;
float normAxis[3] = { m_MisorientationRotation.h, m_MisorientationRotation.k, m_MisorientationRotation.l };
MatrixMath::Normalize3x1(normAxis);
// convert axis angle to matrix representation of misorientation
FOrientArrayType om(9, 0.0f);
FOrientTransformsType::ax2om(FOrientArrayType(normAxis[0], normAxis[1], normAxis[2], misAngle), om);
om.toGMatrix(dg);
// take inverse of misorientation variable to use for switching symmetry
MatrixMath::Transpose3x3(dg, dgt);
// Get our SpaceGroupOps pointer for the selected crystal structure
SpaceGroupOps::Pointer orientOps = m_OrientationOps[m_CrystalStructures[m_PhaseOfInterest]];
// get number of symmetry operators
int32_t n_sym = orientOps->getNumSymOps();
int32_t xpoints = 100;
int32_t ypoints = 100;
int32_t zpoints = 1;
int32_t xpointshalf = xpoints / 2;
int32_t ypointshalf = ypoints / 2;
float xres = 2.0f / float(xpoints);
float yres = 2.0f / float(ypoints);
float zres = (xres + yres) / 2.0;
float x = 0.0f, y = 0.0f;
float sum = 0;
int32_t count = 0;
bool nhCheck = false;
int32_t hemisphere = 0;
int32_t shift1 = gbcdSizes[0];
int32_t shift2 = gbcdSizes[0] * gbcdSizes[1];
int32_t shift3 = gbcdSizes[0] * gbcdSizes[1] * gbcdSizes[2];
int32_t shift4 = gbcdSizes[0] * gbcdSizes[1] * gbcdSizes[2] * gbcdSizes[3];
int64_t totalGBCDBins = gbcdSizes[0] * gbcdSizes[1] * gbcdSizes[2] * gbcdSizes[3] * gbcdSizes[4] * 2;
QVector<size_t> dims(1, 1);
DoubleArrayType::Pointer poleFigureArray = DoubleArrayType::NullPointer();
poleFigureArray = DoubleArrayType::CreateArray(xpoints * ypoints, dims, "PoleFigure");
poleFigureArray->initializeWithZeros();
double* poleFigure = poleFigureArray->getPointer(0);
for (int32_t k = 0; k < ypoints; k++)
{
for (int32_t l = 0; l < xpoints; l++)
{
// get (x,y) for stereographic projection pixel
x = float(l - xpointshalf) * xres + (xres / 2.0);
y = float(k - ypointshalf) * yres + (yres / 2.0);
if ((x * x + y * y) <= 1.0)
{
sum = 0.0f;
count = 0;
vec[2] = -((x * x + y * y) - 1) / ((x * x + y * y) + 1);
vec[0] = x * (1 + vec[2]);
vec[1] = y * (1 + vec[2]);
MatrixMath::Multiply3x3with3x1(dgt, vec, vec2);
// Loop over all the symetry operators in the given cystal symmetry
for (int32_t i = 0; i < n_sym; i++)
{
//get symmetry operator1
orientOps->getMatSymOp(i, sym1);
for (int32_t j = 0; j < n_sym; j++)
{
// get symmetry operator2
orientOps->getMatSymOp(j, sym2);
MatrixMath::Transpose3x3(sym2, sym2t);
// calculate symmetric misorientation
MatrixMath::Multiply3x3with3x3(dg, sym2t, dg1);
MatrixMath::Multiply3x3with3x3(sym1, dg1, dg2);
// convert to euler angle
FOrientArrayType eu(mis_euler1, 3);
FOrientTransformsType::om2eu(FOrientArrayType(dg2), eu);
if (mis_euler1[0] < SIMPLib::Constants::k_PiOver2 && mis_euler1[1] < SIMPLib::Constants::k_PiOver2 && mis_euler1[2] < SIMPLib::Constants::k_PiOver2)
{
mis_euler1[1] = cosf(mis_euler1[1]);
// find bins in GBCD
int32_t location1 = int32_t((mis_euler1[0] - gbcdLimits[0]) / gbcdDeltas[0]);
int32_t location2 = int32_t((mis_euler1[1] - gbcdLimits[1]) / gbcdDeltas[1]);
int32_t location3 = int32_t((mis_euler1[2] - gbcdLimits[2]) / gbcdDeltas[2]);
//find symmetric poles using the first symmetry operator
MatrixMath::Multiply3x3with3x1(sym1, vec, rotNormal);
//get coordinates in square projection of crystal normal parallel to boundary normal
nhCheck = getSquareCoord(rotNormal, sqCoord);
// Note the switch to have theta in the 4 slot and cos(Phi) int he 3 slot
int32_t location4 = int32_t((sqCoord[0] - gbcdLimits[3]) / gbcdDeltas[3]);
int32_t location5 = int32_t((sqCoord[1] - gbcdLimits[4]) / gbcdDeltas[4]);
if (location1 >= 0 && location2 >= 0 && location3 >= 0 && location4 >= 0 && location5 >= 0 &&
location1 < gbcdSizes[0] && location2 < gbcdSizes[1] && location3 < gbcdSizes[2] && location4 < gbcdSizes[3] && location5 < gbcdSizes[4])
{
hemisphere = 0;
if (nhCheck == false) { hemisphere = 1; }
sum += m_GBCD[(m_PhaseOfInterest * totalGBCDBins) + 2 * ((location5 * shift4) + (location4 * shift3) + (location3 * shift2) + (location2 * shift1) + location1) + hemisphere];
count++;
}
}
// again in second crystal reference frame
// calculate symmetric misorientation
MatrixMath::Multiply3x3with3x3(dgt, sym2, dg1);
MatrixMath::Multiply3x3with3x3(sym1, dg1, dg2);
// convert to euler angle
FOrientTransformsType::om2eu(FOrientArrayType(dg2), eu);
if (mis_euler1[0] < SIMPLib::Constants::k_PiOver2 && mis_euler1[1] < SIMPLib::Constants::k_PiOver2 && mis_euler1[2] < SIMPLib::Constants::k_PiOver2)
{
mis_euler1[1] = cosf(mis_euler1[1]);
// find bins in GBCD
int32_t location1 = int32_t((mis_euler1[0] - gbcdLimits[0]) / gbcdDeltas[0]);
int32_t location2 = int32_t((mis_euler1[1] - gbcdLimits[1]) / gbcdDeltas[1]);
int32_t location3 = int32_t((mis_euler1[2] - gbcdLimits[2]) / gbcdDeltas[2]);
// find symmetric poles using the first symmetry operator
MatrixMath::Multiply3x3with3x1(sym1, vec2, rotNormal2);
// get coordinates in square projection of crystal normal parallel to boundary normal
nhCheck = getSquareCoord(rotNormal2, sqCoord);
// Note the switch to have theta in the 4 slot and cos(Phi) int he 3 slot
int32_t location4 = int32_t((sqCoord[0] - gbcdLimits[3]) / gbcdDeltas[3]);
int32_t location5 = int32_t((sqCoord[1] - gbcdLimits[4]) / gbcdDeltas[4]);
if (location1 >= 0 && location2 >= 0 && location3 >= 0 && location4 >= 0 && location5 >= 0 &&
location1 < gbcdSizes[0] && location2 < gbcdSizes[1] && location3 < gbcdSizes[2] && location4 < gbcdSizes[3] && location5 < gbcdSizes[4])
{
hemisphere = 0;
if (nhCheck == false) { hemisphere = 1; }
sum += m_GBCD[(m_PhaseOfInterest * totalGBCDBins) + 2 * ((location5 * shift4) + (location4 * shift3) + (location3 * shift2) + (location2 * shift1) + location1) + hemisphere];
count++;
}
}
}
}
if (count > 0)
{
poleFigure[(k * xpoints) + l] = sum / float(count);
}
}
}
}
FILE* f = NULL;
f = fopen(m_OutputFile.toLatin1().data(), "wb");
if (NULL == f)
{
QString ss = QObject::tr("Error opening output file '%1'").arg(m_OutputFile);
setErrorCondition(-1);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
// Write the correct header
fprintf(f, "# vtk DataFile Version 2.0\n");
fprintf(f, "data set from DREAM3D\n");
fprintf(f, "BINARY");
fprintf(f, "\n");
fprintf(f, "DATASET RECTILINEAR_GRID\n");
fprintf(f, "DIMENSIONS %d %d %d\n", xpoints + 1, ypoints + 1, zpoints + 1);
// Write the Coords
writeCoords(f, "X_COORDINATES", "float", xpoints + 1, (-float(xpoints)*xres / 2.0f), xres);
writeCoords(f, "Y_COORDINATES", "float", ypoints + 1, (-float(ypoints)*yres / 2.0f), yres);
writeCoords(f, "Z_COORDINATES", "float", zpoints + 1, (-float(zpoints)*zres / 2.0f), zres);
int32_t total = xpoints * ypoints * zpoints;
fprintf(f, "CELL_DATA %d\n", total);
fprintf(f, "SCALARS %s %s 1\n", "Intensity", "float");
fprintf(f, "LOOKUP_TABLE default\n");
{
float* gn = new float[total];
float t;
count = 0;
for (int32_t j = 0; j < ypoints; j++)
{
for (int32_t i = 0; i < xpoints; i++)
{
t = float(poleFigure[(j * xpoints) + i]);
SIMPLib::Endian::FromSystemToBig::convert(t);
gn[count] = t;
count++;
}
}
size_t totalWritten = fwrite(gn, sizeof(float), (total), f);
delete[] gn;
if (totalWritten != (total))
{
QString ss = QObject::tr("Error writing binary VTK data to file '%1'").arg(m_OutputFile);
setErrorCondition(-1);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
fclose(f);
return;
}
}
fclose(f);
/* Let the GUI know we are done with this filter */
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ReadH5Ebsd::copyTSLArrays(H5EbsdVolumeReader* ebsdReader)
{
float* f1 = NULL;
float* f2 = NULL;
float* f3 = NULL;
int* phasePtr = NULL;
FloatArrayType::Pointer fArray = FloatArrayType::NullPointer();
Int32ArrayType::Pointer iArray = Int32ArrayType::NullPointer();
VoxelDataContainer* m = getVoxelDataContainer();
int64_t totalPoints = m->getTotalPoints();
if (m_SelectedVoxelCellArrays.find(m_CellPhasesArrayName) != m_SelectedVoxelCellArrays.end() )
{
phasePtr = reinterpret_cast<int*>(ebsdReader->getPointerByName(Ebsd::Ang::PhaseData));
iArray = Int32ArrayType::CreateArray(totalPoints, DREAM3D::CellData::Phases);
iArray->SetNumberOfComponents(1);
::memcpy(iArray->GetPointer(0), phasePtr, sizeof(int32_t) * totalPoints);
m->addCellData(DREAM3D::CellData::Phases, iArray);
}
if (m_SelectedVoxelCellArrays.find(m_CellEulerAnglesArrayName) != m_SelectedVoxelCellArrays.end() )
{
f1 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Ang::Phi1));
f2 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Ang::Phi));
f3 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Ang::Phi2));
fArray = FloatArrayType::CreateArray(totalPoints, 3, DREAM3D::CellData::EulerAngles);
float* cellEulerAngles = fArray->GetPointer(0);
for (int64_t i = 0; i < totalPoints; i++)
{
cellEulerAngles[3 * i] = f1[i];
cellEulerAngles[3 * i + 1] = f2[i];
cellEulerAngles[3 * i + 2] = f3[i];
}
m->addCellData(DREAM3D::CellData::EulerAngles, fArray);
}
if (m_SelectedVoxelCellArrays.find(Ebsd::Ang::ImageQuality) != m_SelectedVoxelCellArrays.end() )
{
f1 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Ang::ImageQuality));
fArray = FloatArrayType::CreateArray(totalPoints, Ebsd::Ang::ImageQuality);
::memcpy(fArray->GetPointer(0), f1, sizeof(float) * totalPoints);
m->addCellData(Ebsd::Ang::ImageQuality, fArray);
}
if (m_SelectedVoxelCellArrays.find(Ebsd::Ang::ConfidenceIndex) != m_SelectedVoxelCellArrays.end() )
{
f1 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Ang::ConfidenceIndex));
fArray = FloatArrayType::CreateArray(totalPoints, Ebsd::Ang::ConfidenceIndex);
::memcpy(fArray->GetPointer(0), f1, sizeof(float) * totalPoints);
m->addCellData(Ebsd::Ang::ConfidenceIndex, fArray);
}
if (m_SelectedVoxelCellArrays.find(Ebsd::Ang::SEMSignal) != m_SelectedVoxelCellArrays.end() )
{
f1 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Ang::SEMSignal));
fArray = FloatArrayType::CreateArray(totalPoints, Ebsd::Ang::SEMSignal);
::memcpy(fArray->GetPointer(0), f1, sizeof(float) * totalPoints);
m->addCellData(Ebsd::Ang::SEMSignal, fArray);
}
if (m_SelectedVoxelCellArrays.find(Ebsd::Ang::Fit) != m_SelectedVoxelCellArrays.end() )
{
f1 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Ang::Fit));
fArray = FloatArrayType::CreateArray(totalPoints, Ebsd::Ang::Fit);
::memcpy(fArray->GetPointer(0), f1, sizeof(float) * totalPoints);
m->addCellData(Ebsd::Ang::Fit, fArray);
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ReadH5Ebsd::copyHKLArrays(H5EbsdVolumeReader* ebsdReader)
{
float* f1 = NULL;
float* f2 = NULL;
float* f3 = NULL;
int* phasePtr = NULL;
FloatArrayType::Pointer fArray = FloatArrayType::NullPointer();
Int32ArrayType::Pointer iArray = Int32ArrayType::NullPointer();
VoxelDataContainer* m = getVoxelDataContainer();
int64_t totalPoints = m->getTotalPoints();
phasePtr = reinterpret_cast<int*>(ebsdReader->getPointerByName(Ebsd::Ctf::Phase));
iArray = Int32ArrayType::CreateArray(totalPoints, DREAM3D::CellData::Phases);
iArray->SetNumberOfComponents(1);
::memcpy(iArray->GetPointer(0), phasePtr, sizeof(int32_t) * totalPoints);
m->addCellData(DREAM3D::CellData::Phases, iArray);
if (m_SelectedVoxelCellArrays.find(m_CellEulerAnglesArrayName) != m_SelectedVoxelCellArrays.end() )
{
// radianconversion = M_PI / 180.0;
f1 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Ctf::Euler1));
f2 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Ctf::Euler2));
f3 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Ctf::Euler3));
fArray = FloatArrayType::CreateArray(totalPoints * 3, DREAM3D::CellData::EulerAngles);
fArray->SetNumberOfComponents(3);
float* cellEulerAngles = fArray->GetPointer(0);
int* cellPhases = iArray->GetPointer(0);
for (int64_t i = 0; i < totalPoints; i++)
{
cellEulerAngles[3 * i] = f1[i];
cellEulerAngles[3 * i + 1] = f2[i];
cellEulerAngles[3 * i + 2] = f3[i];
if(m_CrystalStructures[cellPhases[i]] == Ebsd::CrystalStructure::Hexagonal_High)
{cellEulerAngles[3 * i + 2] = cellEulerAngles[3 * i + 2] + (30.0);}
}
m->addCellData(DREAM3D::CellData::EulerAngles, fArray);
}
if (m_SelectedVoxelCellArrays.find(Ebsd::Ctf::Bands) != m_SelectedVoxelCellArrays.end() )
{
phasePtr = reinterpret_cast<int*>(ebsdReader->getPointerByName(Ebsd::Ctf::Bands));
iArray = Int32ArrayType::CreateArray(totalPoints, Ebsd::Ctf::Bands);
iArray->SetNumberOfComponents(1);
::memcpy(iArray->GetPointer(0), phasePtr, sizeof(int32_t) * totalPoints);
m->addCellData(Ebsd::Ctf::Bands, iArray);
}
if (m_SelectedVoxelCellArrays.find(Ebsd::Ctf::Error) != m_SelectedVoxelCellArrays.end() )
{
phasePtr = reinterpret_cast<int*>(ebsdReader->getPointerByName(Ebsd::Ctf::Error));
iArray = Int32ArrayType::CreateArray(totalPoints, Ebsd::Ctf::Error);
iArray->SetNumberOfComponents(1);
::memcpy(iArray->GetPointer(0), phasePtr, sizeof(int32_t) * totalPoints);
m->addCellData(Ebsd::Ctf::Error, iArray);
}
if (m_SelectedVoxelCellArrays.find(Ebsd::Ctf::MAD) != m_SelectedVoxelCellArrays.end() )
{
f1 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Ctf::MAD));
fArray = FloatArrayType::CreateArray(totalPoints, Ebsd::Ctf::MAD);
fArray->SetNumberOfComponents(1);
::memcpy(fArray->GetPointer(0), f1, sizeof(float) * totalPoints);
m->addCellData(Ebsd::Ctf::MAD, fArray);
}
if (m_SelectedVoxelCellArrays.find(Ebsd::Ctf::BC) != m_SelectedVoxelCellArrays.end() )
{
phasePtr = reinterpret_cast<int*>(ebsdReader->getPointerByName(Ebsd::Ctf::BC));
iArray = Int32ArrayType::CreateArray(totalPoints, Ebsd::Ctf::BC);
iArray->SetNumberOfComponents(1);
::memcpy(iArray->GetPointer(0), phasePtr, sizeof(int32_t) * totalPoints);
m->addCellData(Ebsd::Ctf::BC, iArray);
}
if (m_SelectedVoxelCellArrays.find(Ebsd::Ctf::BS) != m_SelectedVoxelCellArrays.end() )
{
phasePtr = reinterpret_cast<int*>(ebsdReader->getPointerByName(Ebsd::Ctf::BS));
iArray = Int32ArrayType::CreateArray(totalPoints, Ebsd::Ctf::BS);
iArray->SetNumberOfComponents(1);
::memcpy(iArray->GetPointer(0), phasePtr, sizeof(int32_t) * totalPoints);
m->addCellData(Ebsd::Ctf::BS, iArray);
}
}
/**
* @brief ConvertData Templated function that converts an IDataArray to a given primitive type
* @param ptr IDataArray instance pointer
* @param dims Component dimensions
* @param m DataContainer instance pointer
* @param scalarType Primitive type to convert to
* @param attributeMatrixName Name of target AttributeMatrix
* @param name Name of converted array
*/
void ConvertData(T* ptr, QVector<size_t> dims, DataContainer::Pointer m, int32_t scalarType, const QString attributeMatrixName, const QString& name)
{
int voxels = ptr->getNumberOfTuples();
size_t size = ptr->getSize();
if (scalarType == Detail::Int8)
{
Int8ArrayType::Pointer p = Int8ArrayType::CreateArray(voxels, dims, name);
m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
for(size_t v = 0; v < size; ++v)
{
p->setValue(v, ptr->getValue(v) );
}
}
else if (scalarType == Detail::UInt8)
{
UInt8ArrayType::Pointer p = UInt8ArrayType::CreateArray(voxels, dims, name);
m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
for(size_t v = 0; v < size; ++v)
{
p->setValue(v, ptr->getValue(v) );
}
}
else if (scalarType == Detail::Int16)
{
Int16ArrayType::Pointer p = Int16ArrayType::CreateArray(voxels, dims, name);
m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
for(size_t v = 0; v < size; ++v)
{
p->setValue(v, ptr->getValue(v) );
}
}
else if (scalarType == Detail::UInt16)
{
UInt16ArrayType::Pointer p = UInt16ArrayType::CreateArray(voxels, dims, name);
m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
for(size_t v = 0; v < size; ++v)
{
p->setValue(v, ptr->getValue(v) );
}
}
else if (scalarType == Detail::Int32)
{
Int32ArrayType::Pointer p = Int32ArrayType::CreateArray(voxels, dims, name);
m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
for(size_t v = 0; v < size; ++v)
{
p->setValue(v, ptr->getValue(v) );
}
}
else if (scalarType == Detail::UInt32)
{
UInt32ArrayType::Pointer p = UInt32ArrayType::CreateArray(voxels, dims, name);
m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
for(size_t v = 0; v < size; ++v)
{
p->setValue(v, ptr->getValue(v) );
}
}
else if (scalarType == Detail::Int64)
{
Int64ArrayType::Pointer p = Int64ArrayType::CreateArray(voxels, dims, name);
m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
for(size_t v = 0; v < size; ++v)
{
p->setValue(v, ptr->getValue(v) );
}
}
else if (scalarType == Detail::UInt64)
{
UInt64ArrayType::Pointer p = UInt64ArrayType::CreateArray(voxels, dims, name);
m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
for(size_t v = 0; v < size; ++v)
{
p->setValue(v, ptr->getValue(v) );
}
}
else if (scalarType == Detail::Float)
{
FloatArrayType::Pointer p = FloatArrayType::CreateArray(voxels, dims, name);
m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
for(size_t v = 0; v < size; ++v)
{
p->setValue(v, ptr->getValue(v) );
}
}
else if (scalarType == Detail::Double)
{
DoubleArrayType::Pointer p = DoubleArrayType::CreateArray(voxels, dims, name);
m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
for(size_t v = 0; v < size; ++v)
{
p->setValue(v, ptr->getValue(v) );
}
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void WritePoleFigure::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(m_CellPhasesArrayPath.getDataContainerName());
size_t dims[3] = { 0, 0, 0 };
m->getGeometryAs<ImageGeom>()->getDimensions(dims);
// Make sure any directory path is also available as the user may have just typed
// in a path without actually creating the full path
QDir path(getOutputPath());
if (!path.mkpath(".") )
{
QString ss = QObject::tr("Error creating parent path '%1'").arg(path.absolutePath());
setErrorCondition(-1);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
bool missingGoodVoxels = true;
if (NULL != m_GoodVoxels)
{
missingGoodVoxels = false;
}
// Find how many phases we have by getting the number of Crystal Structures
size_t numPoints = m->getGeometryAs<ImageGeom>()->getNumberOfElements();
size_t numPhases = m_CrystalStructuresPtr.lock()->getNumberOfTuples();
// Loop over all the voxels gathering the Eulers for a specific phase into an array
for (size_t phase = 1; phase < numPhases; ++phase)
{
size_t count = 0;
// First find out how many voxels we are going to have. This is probably faster to loop twice than to
// keep allocating memory everytime we find one.
for (size_t i = 0; i < numPoints; ++i)
{
if (m_CellPhases[i] == phase)
{
if (missingGoodVoxels == true || m_GoodVoxels[i] == true)
{
count++;
}
}
}
QVector<size_t> eulerCompDim(1, 3);
FloatArrayType::Pointer subEulers = FloatArrayType::CreateArray(count, eulerCompDim, "Eulers_Per_Phase");
subEulers->initializeWithValue(std::numeric_limits<float>::signaling_NaN());
float* eu = subEulers->getPointer(0);
// Now loop through the eulers again and this time add them to the subEulers Array
count = 0;
for (size_t i = 0; i < numPoints; ++i)
{
if (m_CellPhases[i] == phase)
{
if (missingGoodVoxels == true || m_GoodVoxels[i] == true)
{
eu[count * 3] = m_CellEulerAngles[i * 3];
eu[count * 3 + 1] = m_CellEulerAngles[i * 3 + 1];
eu[count * 3 + 2] = m_CellEulerAngles[i * 3 + 2];
count++;
}
}
}
if (subEulers->getNumberOfTuples() == 0) { continue; } // Skip because we have no Pole Figure data
QVector<UInt8ArrayType::Pointer> figures;
PoleFigureConfiguration_t config;
config.eulers = subEulers.get();
config.imageDim = getImageSize();
config.lambertDim = getLambertSize();
config.numColors = getNumColors();
QString label("Phase_");
label.append(QString::number(phase));
QString ss = QObject::tr("Generating Pole Figures for Phase %1").arg(phase);
notifyStatusMessage(getMessagePrefix(), getHumanLabel(), ss);
switch(m_CrystalStructures[phase])
{
case Ebsd::CrystalStructure::Cubic_High:
figures = makePoleFigures<CubicOps>(config);
break;
case Ebsd::CrystalStructure::Cubic_Low:
figures = makePoleFigures<CubicLowOps>(config);
break;
case Ebsd::CrystalStructure::Hexagonal_High:
figures = makePoleFigures<HexagonalOps>(config);
break;
case Ebsd::CrystalStructure::Hexagonal_Low:
figures = makePoleFigures<HexagonalLowOps>(config);
break;
case Ebsd::CrystalStructure::Trigonal_High:
// figures = makePoleFigures<TrigonalOps>(config);
notifyWarningMessage(getHumanLabel(), "Trigonal High Symmetry is not supported for Pole figures. This phase will be omitted from results", -1010);
break;
case Ebsd::CrystalStructure::Trigonal_Low:
// figures = makePoleFigures<TrigonalLowOps>(config);
notifyWarningMessage(getHumanLabel(), "Trigonal Low Symmetry is not supported for Pole figures. This phase will be omitted from results", -1010);
break;
case Ebsd::CrystalStructure::Tetragonal_High:
// figures = makePoleFigures<TetragonalOps>(config);
notifyWarningMessage(getHumanLabel(), "Tetragonal High Symmetry is not supported for Pole figures. This phase will be omitted from results", -1010);
break;
case Ebsd::CrystalStructure::Tetragonal_Low:
// figures = makePoleFigures<TetragonalLowOps>(config);
notifyWarningMessage(getHumanLabel(), "Tetragonal Low Symmetry is not supported for Pole figures. This phase will be omitted from results", -1010);
break;
case Ebsd::CrystalStructure::OrthoRhombic:
figures = makePoleFigures<OrthoRhombicOps>(config);
break;
case Ebsd::CrystalStructure::Monoclinic:
figures = makePoleFigures<MonoclinicOps>(config);
break;
case Ebsd::CrystalStructure::Triclinic:
figures = makePoleFigures<TriclinicOps>(config);
break;
default:
break;
}
if (figures.size() == 3)
{
QImage combinedImage = PoleFigureImageUtilities::Create3ImagePoleFigure(figures[0].get(), figures[1].get(), figures[2].get(), config, getImageLayout());
writeImage(combinedImage, label);
}
}
/* Let the GUI know we are done with this filter */
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SampleSurfaceMesh::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer sm = getDataContainerArray()->getDataContainer(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName());
SIMPL_RANDOMNG_NEW()
#ifdef SIMPLib_USE_PARALLEL_ALGORITHMS
tbb::task_scheduler_init init;
bool doParallel = true;
#endif
TriangleGeom::Pointer triangleGeom = sm->getGeometryAs<TriangleGeom>();
// pull down faces
int64_t numFaces = m_SurfaceMeshFaceLabelsPtr.lock()->getNumberOfTuples();
// create array to hold bounding vertices for each face
FloatArrayType::Pointer llPtr = FloatArrayType::CreateArray(3, "_INTERNAL_USE_ONLY_Lower_Left");
FloatArrayType::Pointer urPtr = FloatArrayType::CreateArray(3, "_INTERNAL_USE_ONLY_Upper_Right");
float* ll = llPtr->getPointer(0);
float* ur = urPtr->getPointer(0);
VertexGeom::Pointer faceBBs = VertexGeom::CreateGeometry(2 * numFaces, "_INTERNAL_USE_ONLY_faceBBs");
// walk through faces to see how many features there are
int32_t g1 = 0, g2 = 0;
int32_t maxFeatureId = 0;
for (int64_t i = 0; i < numFaces; i++)
{
g1 = m_SurfaceMeshFaceLabels[2 * i];
g2 = m_SurfaceMeshFaceLabels[2 * i + 1];
if (g1 > maxFeatureId) { maxFeatureId = g1; }
if (g2 > maxFeatureId) { maxFeatureId = g2; }
}
// add one to account for feature 0
int32_t numFeatures = maxFeatureId + 1;
// create a dynamic list array to hold face lists
Int32Int32DynamicListArray::Pointer faceLists = Int32Int32DynamicListArray::New();
std::vector<int32_t> linkCount(numFeatures, 0);
// fill out lists with number of references to cells
typedef boost::shared_array<int32_t> SharedInt32Array_t;
SharedInt32Array_t linkLocPtr(new int32_t[numFaces]);
int32_t* linkLoc = linkLocPtr.get();
::memset(linkLoc, 0, numFaces * sizeof(int32_t));
// traverse data to determine number of faces belonging to each feature
for (int64_t i = 0; i < numFaces; i++)
{
g1 = m_SurfaceMeshFaceLabels[2 * i];
g2 = m_SurfaceMeshFaceLabels[2 * i + 1];
if (g1 > 0) { linkCount[g1]++; }
if (g2 > 0) { linkCount[g2]++; }
}
// now allocate storage for the faces
faceLists->allocateLists(linkCount);
// traverse data again to get the faces belonging to each feature
for (int64_t i = 0; i < numFaces; i++)
{
g1 = m_SurfaceMeshFaceLabels[2 * i];
g2 = m_SurfaceMeshFaceLabels[2 * i + 1];
if (g1 > 0) { faceLists->insertCellReference(g1, (linkLoc[g1])++, i); }
if (g2 > 0) { faceLists->insertCellReference(g2, (linkLoc[g2])++, i); }
// find bounding box for each face
GeometryMath::FindBoundingBoxOfFace(triangleGeom, i, ll, ur);
faceBBs->setCoords(2 * i, ll);
faceBBs->setCoords(2 * i + 1, ur);
}
// generate the list of sampling points from subclass
VertexGeom::Pointer points = generate_points();
if(getErrorCondition() < 0 || NULL == points.get()) { return; }
int64_t numPoints = points->getNumberOfVertices();
// create array to hold which polyhedron (feature) each point falls in
Int32ArrayType::Pointer iArray = Int32ArrayType::NullPointer();
iArray = Int32ArrayType::CreateArray(numPoints, "_INTERNAL_USE_ONLY_polyhedronIds");
iArray->initializeWithZeros();
int32_t* polyIds = iArray->getPointer(0);
#ifdef SIMPLib_USE_PARALLEL_ALGORITHMS
if (doParallel == true)
{
tbb::parallel_for(tbb::blocked_range<size_t>(0, numFeatures),
SampleSurfaceMeshImpl(triangleGeom, faceLists, faceBBs, points, polyIds), tbb::auto_partitioner());
}
else
#endif
{
SampleSurfaceMeshImpl serial(triangleGeom, faceLists, faceBBs, points, polyIds);
serial.checkPoints(0, numFeatures);
}
assign_points(iArray);
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void FindFeatureReferenceCAxisMisorientations::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(m_FeatureIdsArrayPath.getDataContainerName());
size_t totalPoints = m_FeatureIdsPtr.lock()->getNumberOfTuples();
size_t totalFeatures = m_AvgCAxesPtr.lock()->getNumberOfTuples();
int32_t avgMisoComps = 3;
QVector<size_t> dims(1, avgMisoComps);
FloatArrayType::Pointer avgmisoPtr = FloatArrayType::CreateArray(totalFeatures, dims, "_INTERNAL_USE_ONLY_AvgMiso_Temp");
avgmisoPtr->initializeWithZeros();
float* avgmiso = avgmisoPtr->getPointer(0);
QuatF q1 = QuaternionMathF::New();
QuatF* quats = reinterpret_cast<QuatF*>(m_Quats);
float w = 0.0f;
size_t udims[3] = { 0, 0, 0 };
m->getGeometryAs<ImageGeom>()->getDimensions(udims);
#if (CMP_SIZEOF_SIZE_T == 4)
typedef uint32_t DimType;
uint32_t maxUInt32 = std::numeric_limits<uint32_t>::max();
// We have more points than can be allocated on a 32 bit machine. Assert Now.
if(totalPoints > maxUInt32)
{
QString ss = QObject::tr("The volume is too large for a 32 bit machine. Try reducing the input volume size. Total Voxels: %1").arg(totalPoints);
notifyStatusMessage(getMessagePrefix(), getHumanLabel(), ss);
return;
}
#else
typedef int64_t DimType;
#endif
DimType xPoints = static_cast<DimType>(udims[0]);
DimType yPoints = static_cast<DimType>(udims[1]);
DimType zPoints = static_cast<DimType>(udims[2]);
DimType point = 0;
float g1[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float g1t[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
float caxis[3] = {0.0f, 0.0f, 1.0f};
float c1[3] = {0.0f, 0.0f, 0.0f};
float AvgCAxis[3] = {0.0f, 0.0f, 0.0f};
size_t index = 0;
for (DimType col = 0; col < xPoints; col++)
{
for (DimType row = 0; row < yPoints; row++)
{
for (DimType plane = 0; plane < zPoints; plane++)
{
point = (plane * xPoints * yPoints) + (row * xPoints) + col;
if (m_FeatureIds[point] > 0 && m_CellPhases[point] > 0)
{
QuaternionMathF::Copy(quats[point], q1);
FOrientArrayType om(9);
FOrientTransformsType::qu2om(FOrientArrayType(q1), om);
om.toGMatrix(g1);
// transpose the g matricies so when caxis is multiplied by it
// it will give the sample direction that the caxis is along
MatrixMath::Transpose3x3(g1, g1t);
MatrixMath::Multiply3x3with3x1(g1t, caxis, c1);
// normalize so that the magnitude is 1
MatrixMath::Normalize3x1(c1);
AvgCAxis[0] = m_AvgCAxes[3 * m_FeatureIds[point]];
AvgCAxis[1] = m_AvgCAxes[3 * m_FeatureIds[point] + 1];
AvgCAxis[2] = m_AvgCAxes[3 * m_FeatureIds[point] + 2];
// normalize so that the magnitude is 1
MatrixMath::Normalize3x1(AvgCAxis);
w = GeometryMath::CosThetaBetweenVectors(c1, AvgCAxis);
DREAM3DMath::boundF(w, -1, 1);
w = acosf(w);
w = w * DREAM3D::Constants::k_180OverPi;
if (w > 90.0) { w = 180.0 - w; }
m_FeatureReferenceCAxisMisorientations[point] = w;
index = m_FeatureIds[point] * avgMisoComps;
avgmiso[index]++;
avgmiso[index + 1] += w;
}
if (m_FeatureIds[point] == 0 || m_CellPhases[point] == 0)
{
m_FeatureReferenceCAxisMisorientations[point] = 0;
}
}
}
}
for (size_t i = 1; i < totalFeatures; i++)
{
if (i % 1000 == 0)
{
QString ss = QObject::tr("Working On Feature %1 of %2").arg(i).arg(totalFeatures);
notifyStatusMessage(getMessagePrefix(), getHumanLabel(), ss);
}
index = i * avgMisoComps;
m_FeatureAvgCAxisMisorientations[i] = avgmiso[index + 1] / avgmiso[index];
if (avgmiso[index] == 0) { m_FeatureAvgCAxisMisorientations[i] = 0.0; }
}
int32_t gNum = 0;
for (size_t j = 0; j < totalPoints; j++)
{
gNum = m_FeatureIds[j];
avgmiso[(gNum * avgMisoComps) + 2] += ((m_FeatureReferenceCAxisMisorientations[j] - m_FeatureAvgCAxisMisorientations[gNum]) * (m_FeatureReferenceCAxisMisorientations[j] - m_FeatureAvgCAxisMisorientations[gNum]));
}
for (size_t i = 1; i < totalFeatures; i++)
{
index = i * avgMisoComps;
m_FeatureStdevCAxisMisorientations[i] = sqrtf((1 / avgmiso[index]) * avgmiso[index + 2]);
}
notifyStatusMessage(getHumanLabel(), "Complete");
}
void ConvertData(T* ptr, VoxelDataContainer* m, int32_t scalarType, const std::string &name)
{
int numberOfComponents = ptr->GetNumberOfComponents();
int voxels = ptr->GetNumberOfTuples();
size_t size = ptr->GetSize();
if (scalarType == Detail::Int8)
{
Int8ArrayType::Pointer p = Int8ArrayType::CreateArray(voxels, numberOfComponents, name);
m->addCellData(p->GetName(), p);
for(size_t v = 0; v < size; ++v)
{
p->SetValue(v, ptr->GetValue(v) );
}
}
else if (scalarType == Detail::UInt8)
{
UInt8ArrayType::Pointer p = UInt8ArrayType::CreateArray(voxels, numberOfComponents, name);
m->addCellData(p->GetName(), p);
for(size_t v = 0; v < size; ++v)
{
p->SetValue(v, ptr->GetValue(v) );
}
}
else if (scalarType == Detail::Int16)
{
Int16ArrayType::Pointer p = Int16ArrayType::CreateArray(voxels, numberOfComponents, name);
m->addCellData(p->GetName(), p);
for(size_t v = 0; v < size; ++v)
{
p->SetValue(v, ptr->GetValue(v) );
}
}
else if (scalarType == Detail::UInt16)
{
UInt16ArrayType::Pointer p = UInt16ArrayType::CreateArray(voxels, numberOfComponents, name);
m->addCellData(p->GetName(), p);
for(size_t v = 0; v < size; ++v)
{
p->SetValue(v, ptr->GetValue(v) );
}
}
else if (scalarType == Detail::Int32)
{
Int32ArrayType::Pointer p = Int32ArrayType::CreateArray(voxels, numberOfComponents, name);
m->addCellData(p->GetName(), p);
for(size_t v = 0; v < size; ++v)
{
p->SetValue(v, ptr->GetValue(v) );
}
}
else if (scalarType == Detail::UInt32)
{
UInt32ArrayType::Pointer p = UInt32ArrayType::CreateArray(voxels, numberOfComponents, name);
m->addCellData(p->GetName(), p);
for(size_t v = 0; v < size; ++v)
{
p->SetValue(v, ptr->GetValue(v) );
}
}
else if (scalarType == Detail::Int64)
{
Int64ArrayType::Pointer p = Int64ArrayType::CreateArray(voxels, numberOfComponents, name);
m->addCellData(p->GetName(), p);
for(size_t v = 0; v < size; ++v)
{
p->SetValue(v, ptr->GetValue(v) );
}
}
else if (scalarType == Detail::UInt64)
{
UInt64ArrayType::Pointer p = UInt64ArrayType::CreateArray(voxels, numberOfComponents, name);
m->addCellData(p->GetName(), p);
for(size_t v = 0; v < size; ++v)
{
p->SetValue(v, ptr->GetValue(v) );
}
}
else if (scalarType == Detail::Float)
{
FloatArrayType::Pointer p = FloatArrayType::CreateArray(voxels, numberOfComponents, name);
m->addCellData(p->GetName(), p);
}
else if (scalarType == Detail::Double)
{
DoubleArrayType::Pointer p = DoubleArrayType::CreateArray(voxels, numberOfComponents, name);
m->addCellData(p->GetName(), p);
for(size_t v = 0; v < size; ++v)
{
p->SetValue(v, ptr->GetValue(v) );
}
}
}
