// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ModifiedLambertProjection::initializeSquares(int dims, float sphereRadius)
{
m_Dimension = dims;
m_SphereRadius = sphereRadius;
// We want half the sphere area for each square because each square represents a hemisphere.
float halfSphereArea = 4 * M_PI * sphereRadius * sphereRadius / 2.0;
// The length of a side of the square is the square root of the area
float squareEdge = sqrt(halfSphereArea);
m_StepSize = squareEdge / static_cast<float>(m_Dimension);
m_MaxCoord = squareEdge / 2.0;
m_MinCoord = -squareEdge / 2.0;
m_HalfDimension = static_cast<float>(m_Dimension) / 2.0;
m_HalfDimensionTimesStepSize = m_HalfDimension * m_StepSize;
QVector<size_t> tDims(2, m_Dimension);
QVector<size_t> cDims(1, 1);
m_NorthSquare = DoubleArrayType::CreateArray(tDims, cDims, "ModifiedLambert_NorthSquare");
m_NorthSquare->initializeWithZeros();
m_SouthSquare = DoubleArrayType::CreateArray(tDims, cDims, "ModifiedLambert_SouthSquare");
m_SouthSquare->initializeWithZeros();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ReadStlFile::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
if (m_StlFilePath.isEmpty() == true)
{
setErrorCondition(-1003);
notifyErrorMessage(getHumanLabel(), "The input file must be set", -1003);
}
// Create a SufaceMesh Data Container with Faces, Vertices, Feature Labels and optionally Phase labels
DataContainer::Pointer sm = getDataContainerArray()->createNonPrereqDataContainer<AbstractFilter>(this, getSurfaceMeshDataContainerName());
if(getErrorCondition() < 0) { return; }
SharedVertexList::Pointer sharedVertList = TriangleGeom::CreateSharedVertexList(0);
TriangleGeom::Pointer triangleGeom = TriangleGeom::CreateGeometry(0, sharedVertList, DREAM3D::Geometry::TriangleGeometry);
sm->setGeometry(triangleGeom);
QVector<size_t> tDims(1, 0);
sm->createNonPrereqAttributeMatrix<AbstractFilter>(this, getFaceAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::Face);
QVector<size_t> cDims(1, 3);
tempPath.update(getSurfaceMeshDataContainerName(), getFaceAttributeMatrixName(), getFaceNormalsArrayName() );
m_FaceNormalsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<double>, AbstractFilter, double>(this, tempPath, 0, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_FaceNormalsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_FaceNormals = m_FaceNormalsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int H5PrimaryStatsDataDelegate::writeVectorOfArrays(hid_t pid,
VectorOfFloatArray colData)
{
herr_t err = 0;
herr_t retErr = 0;
// Loop through all the column data and write each one to the HDF5 file
size_t numColumns = colData.size();
for (size_t c = 0; c < numColumns; ++c)
{
//qDebug() << "Writing Dataset:" << hdf5GroupName << "/" << columnHeaders[c] ;
err = -1;
if(NULL != colData[c].get() && colData[c]->getSize() > 0)
{
QVector<size_t> tDims(1, colData[c]->getNumberOfTuples());
err = colData[c]->writeH5Data(pid, tDims);
if(err < 0)
{
retErr = err;
break;
}
}
else
{
qDebug() << ":Null Data Column had no data. Did you create the data?" ;
qDebug() << " File: " << __FILE__ ;
qDebug() << " Line: " << __LINE__ ;
break;
}
}
return retErr;
}
void _TestNeighborListDeepCopy()
{
QVector<size_t> tDims(10);
AttributeMatrix::Pointer am = AttributeMatrix::New(tDims, "AttributeMatrix", DREAM3D::AttributeMatrixType::Cell);
typename NeighborList<T>::Pointer neiList = NeighborList<T>::CreateArray(10, "NeighborList");
for(int i = 0; i < 10; ++i)
{
for(T j = 0; j < (T)(i + 4); ++j)
{
neiList->addEntry(i, static_cast<T>(i + 3) );
}
}
typename NeighborList<T>::Pointer copy = std::dynamic_pointer_cast<NeighborList<T> >(neiList->deepCopy());
for(int i = 0; i < 10; ++i)
{
unsigned char value = 255;
typename NeighborList<T>::SharedVectorType nEntry = neiList->getList(i);
typename NeighborList<T>::SharedVectorType cEntry = copy->getList(i);
DREAM3D_REQUIRED(nEntry.get(), !=, cEntry.get());
(*nEntry)[0] = static_cast<T>(value);
DREAM3D_REQUIRED( (*cEntry)[0], !=, 10000000);
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int32_t MergeColonies::getSeed(int32_t newFid)
{
setErrorCondition(0);
int32_t numfeatures = static_cast<int32_t>(m_FeaturePhasesPtr.lock()->getNumberOfTuples());
SIMPL_RANDOMNG_NEW()
int32_t seed = -1;
int32_t randfeature = 0;
// Precalculate some constants
int32_t totalFMinus1 = numfeatures - 1;
size_t counter = 0;
randfeature = int32_t(float(rg.genrand_res53()) * float(totalFMinus1));
while (seed == -1 && counter < numfeatures)
{
if (randfeature > totalFMinus1) { randfeature = randfeature - numfeatures; }
if (m_FeatureParentIds[randfeature] == -1) { seed = randfeature; }
randfeature++;
counter++;
}
if (seed >= 0)
{
m_FeatureParentIds[seed] = newFid;
QVector<size_t> tDims(1, newFid + 1);
getDataContainerArray()->getDataContainer(m_FeatureIdsArrayPath.getDataContainerName())->getAttributeMatrix(getNewCellFeatureAttributeMatrixName())->resizeAttributeArrays(tDims);
updateFeatureInstancePointers();
}
return seed;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int64_t EBSDSegmentFeatures::getSeed(int32_t gnum, int64_t nextSeed)
{
setErrorCondition(0);
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getDataContainerName());
size_t totalPoints = m_FeatureIdsPtr.lock()->getNumberOfTuples();
int64_t seed = -1;
// start with the next voxel after the last seed
size_t randpoint = static_cast<size_t>(nextSeed);
while (seed == -1 && randpoint < totalPoints)
{
if (m_FeatureIds[randpoint] == 0) // If the GrainId of the voxel is ZERO then we can use this as a seed point
{
if ((m_UseGoodVoxels == false || m_GoodVoxels[randpoint] == true) && m_CellPhases[randpoint] > 0)
{
seed = randpoint;
}
else { randpoint += 1; }
}
else { randpoint += 1; }
}
if (seed >= 0)
{
m_FeatureIds[seed] = gnum;
QVector<size_t> tDims(1, gnum + 1);
m->getAttributeMatrix(getCellFeatureAttributeMatrixName())->resizeAttributeArrays(tDims);
updateFeatureInstancePointers();
}
return seed;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RegularGridSampleSurfaceMesh::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
DataContainer::Pointer m = getDataContainerArray()->createNonPrereqDataContainer<AbstractFilter>(this, getDataContainerName());
if (getErrorCondition() < 0) { return; }
ImageGeom::Pointer image = ImageGeom::CreateGeometry(DREAM3D::Geometry::ImageGeometry);
m->setGeometry(image);
// Set the Dimensions, Resolution and Origin of the output data container
m->getGeometryAs<ImageGeom>()->setDimensions(m_XPoints, m_YPoints, m_ZPoints);
m->getGeometryAs<ImageGeom>()->setResolution(m_Resolution.x, m_Resolution.y, m_Resolution.z);
m->getGeometryAs<ImageGeom>()->setOrigin(m_Origin.x, m_Origin.y, m_Origin.z);
QVector<size_t> tDims(3, 0);
tDims[0] = m_XPoints;
tDims[1] = m_YPoints;
tDims[2] = m_ZPoints;
AttributeMatrix::Pointer cellAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::Cell);
if (getErrorCondition() < 0 || NULL == cellAttrMat.get()) { return; }
QVector<size_t> cDims(1, 1);
tempPath.update(getDataContainerName(), getCellAttributeMatrixName(), getFeatureIdsArrayName() );
m_FeatureIdsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, 0, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_FeatureIdsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_FeatureIds = m_FeatureIdsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int64_t EBSDSegmentFeatures::getSeed(int32_t gnum)
{
setErrorCondition(0);
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getDataContainerName());
size_t totalPoints = m_FeatureIdsPtr.lock()->getNumberOfTuples();
int64_t seed = -1;
Generator& numberGenerator = *m_NumberGenerator;
while (seed == -1 && m_TotalRandomNumbersGenerated < totalPoints)
{
// Get the next voxel index in the precomputed list of voxel seeds
int64_t randpoint = numberGenerator();
m_TotalRandomNumbersGenerated++; // Increment this counter
if (m_FeatureIds[randpoint] == 0) // If the GrainId of the voxel is ZERO then we can use this as a seed point
{
if ((m_UseGoodVoxels == false || m_GoodVoxels[randpoint] == true) && m_CellPhases[randpoint] > 0)
{
seed = randpoint;
}
}
}
if (seed >= 0)
{
m_FeatureIds[seed] = gnum;
QVector<size_t> tDims(1, gnum + 1);
m->getAttributeMatrix(getCellFeatureAttributeMatrixName())->resizeAttributeArrays(tDims);
updateFeatureInstancePointers();
}
return seed;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int VertexGeom::writeGeometryToHDF5(hid_t parentId, bool writeXdmf)
{
herr_t err = 0;
QVector<size_t> tDims(1, 0);
if (m_VertexList.get() != NULL)
{
err = GeometryHelpers::GeomIO::WriteListToHDF5(parentId, m_VertexList);
if (err < 0)
{
return err;
}
if(writeXdmf == true)
{
QVector<size_t> cDims(1, 1);
DataArray<int64_t>::Pointer vertsPtr = DataArray<int64_t>::CreateArray(getNumberOfVertices(), cDims, DREAM3D::StringConstants::VertsName);
int64_t* verts = vertsPtr->getPointer(0);
for(size_t i = 0; i < vertsPtr->getNumberOfTuples(); i++)
{
verts[i] = i;
}
tDims[0] = vertsPtr->getNumberOfTuples();
err = vertsPtr->writeH5Data(parentId, tDims);
}
}
return err;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void LinkFeatureMapToElementArray::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getSelectedCellArrayPath().getDataContainerName());
size_t totalPoints = m_SelectedCellDataPtr.lock()->getNumberOfTuples();
int32_t maxIndex = 0;
std::vector<bool> active;
for (size_t i = 0; i < totalPoints; i++)
{
int32_t index = m_SelectedCellData[i];
if ((index + 1) > maxIndex)
{
active.resize(index + 1);
active[index] = true;
maxIndex = index + 1;
}
}
QVector<size_t> tDims(1, maxIndex);
m->getAttributeMatrix(getCellFeatureAttributeMatrixName())->resizeAttributeArrays(tDims);
updateFeatureInstancePointers();
for (int32_t i = 0; i < maxIndex; i++)
{
m_Active[i] = active[i];
}
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void MergeTwins::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
GroupFeatures::dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, m_FeatureIdsArrayPath.getDataContainerName(), false);
if(getErrorCondition() < 0 || NULL == m.get()) { return; }
QVector<size_t> tDims(1, 0);
m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getNewCellFeatureAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::CellFeature);
QVector<size_t> cDims(1, 1);
QVector<DataArrayPath> dataArrayPaths;
// Cell Data
m_FeatureIdsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getFeatureIdsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_FeatureIdsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_FeatureIds = m_FeatureIdsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
tempPath.update(m_FeatureIdsArrayPath.getDataContainerName(), m_FeatureIdsArrayPath.getAttributeMatrixName(), getCellParentIdsArrayName() );
m_CellParentIdsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, -1, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_CellParentIdsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_CellParentIds = m_CellParentIdsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
// Feature Data
m_FeaturePhasesPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getFeaturePhasesArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_FeaturePhasesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_FeaturePhases = m_FeaturePhasesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() >= 0) { dataArrayPaths.push_back(getFeaturePhasesArrayPath()); }
tempPath.update(m_FeaturePhasesArrayPath.getDataContainerName(), m_FeaturePhasesArrayPath.getAttributeMatrixName(), getFeatureParentIdsArrayName() );
m_FeatureParentIdsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, -1, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_FeatureParentIdsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_FeatureParentIds = m_FeatureParentIdsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
cDims[0] = 4;
m_AvgQuatsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<float>, AbstractFilter>(this, getAvgQuatsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_AvgQuatsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_AvgQuats = m_AvgQuatsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() >= 0) { dataArrayPaths.push_back(getAvgQuatsArrayPath()); }
// New Feature Data
cDims[0] = 1;
tempPath.update(m_FeatureIdsArrayPath.getDataContainerName(), getNewCellFeatureAttributeMatrixName(), getActiveArrayName() );
m_ActivePtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<bool>, AbstractFilter, bool>(this, tempPath, true, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_ActivePtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_Active = m_ActivePtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
// Ensemble Data
m_CrystalStructuresPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<unsigned int>, AbstractFilter>(this, getCrystalStructuresArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_CrystalStructuresPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_CrystalStructures = m_CrystalStructuresPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
getDataContainerArray()->validateNumberOfTuples<AbstractFilter>(this, dataArrayPaths);
}
void __TestArrayCreation()
{
int err = 0;
size_t numTuples = NUM_TUPLES;
int rank = RANK;
size_t dims[RANK] = { DIM0, DIM1, DIM2};
int numComp = 1;
{
typename DataArray<T>::Pointer array = DataArray<T>::CreateArray(numTuples, "TEST");
err = __ValidateArray<T>(array, numTuples, numComp);
DREAM3D_REQUIRED(err, >=, 0)
}
{
numComp = DIM0 * DIM1 * DIM2;
typename DataArray<T>::Pointer array = DataArray<T>::CreateArray(numTuples, rank, dims, "TEST");
err = __ValidateArray<T>(array, numTuples, numComp);
DREAM3D_REQUIRED(err, >=, 0)
}
{
numComp = DIM0 * DIM1 * DIM2;
std::vector<size_t> vDims(3, 0);
vDims[0] = DIM0;
vDims[1] = DIM1;
vDims[2] = DIM2;
typename DataArray<T>::Pointer array = DataArray<T>::CreateArray(numTuples, vDims, "TEST");
err = __ValidateArray<T>(array, numTuples, numComp);
DREAM3D_REQUIRED(err, >=, 0)
}
{
numComp = DIM0 * DIM1 * DIM2;
QVector<size_t> vDims(3, 0);
vDims[0] = DIM0;
vDims[1] = DIM1;
vDims[2] = DIM2;
typename DataArray<T>::Pointer array = DataArray<T>::CreateArray(numTuples, vDims, "TEST");
err = __ValidateArray<T>(array, numTuples, numComp);
DREAM3D_REQUIRED(err, >=, 0)
}
{
QVector<size_t> tDims(2, 4);
QVector<size_t> vDims(3, 0);
vDims[0] = DIM0;
vDims[1] = DIM1;
vDims[2] = DIM2;
typename DataArray<T>::Pointer array = DataArray<T>::CreateArray(tDims, vDims, "TEST");
err = __ValidateArray<T>(array, tDims[0] * tDims[1], numComp);
DREAM3D_REQUIRED(err, >=, 0)
}
////FromQVector(QVector<T>& vec, const QString& name)
///FromStdVector(std::vector<T>& vec, const QString& name)
/// FromPointer(T* data, size_t size, const QString& name)
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int32_t GroupMicroTextureRegions::getSeed(int32_t newFid)
{
setErrorCondition(0);
int32_t numfeatures = static_cast<int32_t>(m_FeaturePhasesPtr.lock()->getNumberOfTuples());
float c1[3] = { 0.0f, 0.0f, 0.0f };
uint32_t phase1 = 0;
QuatF* avgQuats = reinterpret_cast<QuatF*>(m_AvgQuats);
float caxis[3] = { 0.0f, 0.0f, 1.0f };
QuatF q1 = QuaternionMathF::New();
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 } };
SIMPL_RANDOMNG_NEW()
int32_t seed = -1;
int32_t randfeature = 0;
// Precalculate some constants
int32_t totalFMinus1 = numfeatures - 1;
size_t counter = 0;
randfeature = int32_t(float(rg.genrand_res53()) * float(totalFMinus1));
while (seed == -1 && counter < numfeatures)
{
if (randfeature > totalFMinus1) { randfeature = randfeature - numfeatures; }
if (m_FeatureParentIds[randfeature] == -1) { seed = randfeature; }
randfeature++;
counter++;
}
if (seed >= 0)
{
m_FeatureParentIds[seed] = newFid;
QVector<size_t> tDims(1, newFid + 1);
getDataContainerArray()->getDataContainer(m_FeatureIdsArrayPath.getDataContainerName())->getAttributeMatrix(getNewCellFeatureAttributeMatrixName())->resizeAttributeArrays(tDims);
updateFeatureInstancePointers();
if (m_UseRunningAverage == true)
{
QuaternionMathF::Copy(avgQuats[seed], q1);
phase1 = m_CrystalStructures[m_FeaturePhases[seed]];
FOrientArrayType om(9);
FOrientTransformsType::qu2om(FOrientArrayType(q1), om);
om.toGMatrix(g1);
// transpose the g matrix 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 dot product can be taken below without
// dividing by the magnitudes (they would be 1)
MatrixMath::Normalize3x1(c1);
MatrixMath::Copy3x1(c1, avgCaxes);
MatrixMath::Multiply3x1withConstant(avgCaxes, m_Volumes[seed]);
}
}
return seed;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
DoubleArrayType::Pointer ModifiedLambertProjection::createStereographicProjection(int dim)
{
QVector<size_t> tDims(2, dim);
QVector<size_t> cDims(1, 1);
DoubleArrayType::Pointer stereoIntensity = DoubleArrayType::CreateArray(tDims, cDims, "ModifiedLambertProjection_StereographicProjection");
stereoIntensity->initializeWithZeros();
createStereographicProjection(dim, stereoIntensity.get());
return stereoIntensity;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int H5PrimaryStatsDataDelegate::writeBinNumbers(PrimaryStatsData* data, hid_t groupId)
{
// Ensure we have valid bin numbers
if(NULL == data->getBinNumbers().get())
{
data->generateBinNumbers();
}
QVector<size_t> tDims(1, data->getBinNumbers()->getNumberOfTuples());
return data->getBinNumbers()->writeH5Data(groupId, tDims);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ChangeResolution::preflight()
{
setInPreflight(true);
emit preflightAboutToExecute();
emit updateFilterParameters(this);
dataCheck();
if (getErrorCondition() < 0)
{
emit preflightExecuted();
setInPreflight(false);
return;
}
DataContainer::Pointer m;
if (m_SaveAsNewDataContainer == false)
{
m = getDataContainerArray()->getDataContainer(getCellAttributeMatrixPath().getDataContainerName());
}
else
{
m = getDataContainerArray()->getDataContainer(getNewDataContainerName());
}
size_t dims[3] = { 0, 0, 0 };
m->getGeometryAs<ImageGeom>()->getDimensions(dims);
float sizex = (dims[0]) * m->getGeometryAs<ImageGeom>()->getXRes();
float sizey = (dims[1]) * m->getGeometryAs<ImageGeom>()->getYRes();
float sizez = (dims[2]) * m->getGeometryAs<ImageGeom>()->getZRes();
size_t m_XP = size_t(sizex / m_Resolution.x);
size_t m_YP = size_t(sizey / m_Resolution.y);
size_t m_ZP = size_t(sizez / m_Resolution.z);
if (m_XP == 0) { m_XP = 1; }
if (m_YP == 0) { m_YP = 1; }
if (m_ZP == 0) { m_ZP = 1; }
m->getGeometryAs<ImageGeom>()->setDimensions(m_XP, m_YP, m_ZP);
m->getGeometryAs<ImageGeom>()->setResolution(m_Resolution.x, m_Resolution.y, m_Resolution.z);
QVector<size_t> tDims(3, 0);
tDims[0] = m_XP;
tDims[1] = m_YP;
tDims[2] = m_ZP;
m->getAttributeMatrix(getCellAttributeMatrixPath().getAttributeMatrixName())->setTupleDimensions(tDims);
if (m_RenumberFeatures == true)
{
AttributeMatrix::Pointer cellFeatureAttrMat = m->getAttributeMatrix(getCellFeatureAttributeMatrixPath().getAttributeMatrixName());
QVector<bool> activeObjects(cellFeatureAttrMat->getNumTuples(), true);
cellFeatureAttrMat->removeInactiveObjects(activeObjects, m_FeatureIdsPtr.lock());
}
emit preflightExecuted();
setInPreflight(false);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void EBSDSegmentFeatures::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
SegmentFeatures::dataCheck();
if(getErrorCondition() < 0) { return; }
// Set the DataContainerName for the Parent Class (SegmentFeatures) to Use
setDataContainerName(m_QuatsArrayPath.getDataContainerName());
DataContainer::Pointer m = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getDataContainerName(), false);
if(getErrorCondition() < 0 || NULL == m.get()) { return; }
QVector<size_t> tDims(1, 0);
m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellFeatureAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::CellFeature);
QVector<DataArrayPath> dataArrayPaths;
QVector<size_t> cDims(1, 1);
if(m_UseGoodVoxels == true)
{
m_GoodVoxelsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<bool>, AbstractFilter>(this, getGoodVoxelsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_GoodVoxelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_GoodVoxels = m_GoodVoxelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() >= 0) { dataArrayPaths.push_back(getGoodVoxelsArrayPath()); }
}
m_CellPhasesPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getCellPhasesArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_CellPhasesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_CellPhases = m_CellPhasesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() >= 0) { dataArrayPaths.push_back(getCellPhasesArrayPath()); }
tempPath.update(getDataContainerName(), m_QuatsArrayPath.getAttributeMatrixName(), getFeatureIdsArrayName() );
m_FeatureIdsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, 0, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_FeatureIdsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_FeatureIds = m_FeatureIdsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
tempPath.update(getDataContainerName(), getCellFeatureAttributeMatrixName(), getActiveArrayName() );
m_ActivePtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<bool>, AbstractFilter, bool>(this, tempPath, true, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_ActivePtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_Active = m_ActivePtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
m_CrystalStructuresPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<uint32_t>, AbstractFilter>(this, getCrystalStructuresArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_CrystalStructuresPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_CrystalStructures = m_CrystalStructuresPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
cDims[0] = 4;
m_QuatsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<float>, AbstractFilter>(this, getQuatsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_QuatsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_Quats = m_QuatsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() >= 0) { dataArrayPaths.push_back(getQuatsArrayPath()); }
getDataContainerArray()->validateNumberOfTuples<AbstractFilter>(this, dataArrayPaths);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RegularizeZSpacing::dataCheck()
{
setErrorCondition(0);
if (getNewZRes() <= 0)
{
QString ss = QObject::tr("The new Z resolution Y (%1) must be positive").arg(getNewZRes());
setErrorCondition(-5555);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
std::ifstream inFile;
inFile.open(m_InputFile.toLatin1().data());
if (!inFile.good())
{
QString ss = QObject::tr("Unable to open input file with name '%1'").arg(getInputFile());
setErrorCondition(-5556);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
ImageGeom::Pointer image = getDataContainerArray()->getPrereqGeometryFromDataContainer<ImageGeom, AbstractFilter>(this, getCellAttributeMatrixPath().getDataContainerName());
AttributeMatrix::Pointer cellAttrMat = getDataContainerArray()->getPrereqAttributeMatrixFromPath<AbstractFilter>(this, getCellAttributeMatrixPath(), -301);
if(getErrorCondition() < 0) {
return;
}
float zval = 0.0f;
for (size_t iter = 0; iter < image->getZPoints() + 1; iter++)
{
inFile >> zval;
}
size_t zP = static_cast<size_t>(zval / getNewZRes());
if(zP == 0) {
zP = 1;
}
if (getInPreflight())
{
image->setDimensions(image->getXPoints(), image->getYPoints(), zP);
QVector<size_t> tDims(3, 0);
tDims[0] = image->getXPoints();
tDims[1] = image->getYPoints();
tDims[2] = zP;
cellAttrMat->resizeAttributeArrays(tDims);
}
inFile.close();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SineParamsSegmentFeatures::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getDataContainerName());
QVector<size_t> tDims(1, 1);
m->getAttributeMatrix(getCellFeatureAttributeMatrixName())->resizeAttributeArrays(tDims);
// This runs a subfilter
int64_t totalPoints = m_FeatureIdsPtr.lock()->getNumberOfTuples();
// Tell the user we are starting the filter
notifyStatusMessage(getMessagePrefix(), getHumanLabel(), "Starting");
//Convert user defined tolerance to radians.
//angleTolerance = m_AngleTolerance * SIMPLib::Constants::k_Pi / 180.0f;
for(int64_t i = 0; i < totalPoints; i++)
{
m_FeatureIds[i] = 0;
}
// Generate the random voxel indices that will be used for the seed points to start a new grain growth/agglomeration
const size_t rangeMin = 0;
const size_t rangeMax = totalPoints - 1;
initializeVoxelSeedGenerator(rangeMin, rangeMax);
SegmentFeatures::execute();
size_t totalFeatures = m->getAttributeMatrix(getCellFeatureAttributeMatrixName())->getNumTuples();
if (totalFeatures < 2)
{
setErrorCondition(-87000);
notifyErrorMessage(getHumanLabel(), "The number of Features was 0 or 1 which means no features were detected. Is a threshold value set to high?", getErrorCondition());
return;
}
// By default we randomize grains
if (true == m_RandomizeFeatureIds)
{
randomizeFeatureIds(totalPoints, totalFeatures);
}
// If there is an error set this to something negative and also set a message
notifyStatusMessage(getHumanLabel(), "Completed");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void MakeDataContainer::dataCheck()
{
DataArrayPath tempPath;
setErrorCondition(0);
DataContainer::Pointer m = getDataContainerArray()->createNonPrereqDataContainer<AbstractFilter>(this, getDataContainerName());
if (getErrorCondition() < 0)
{
return;
}
QVector<size_t> tDims(3, 64);
AttributeMatrix::Pointer cellAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::Cell);
if (getErrorCondition() < 0)
{
return;
}
// tDims.resize(1);
// tDims[0] = 0;
// AttributeMatrix::Pointer cellEnsembleAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellEnsembleAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::CellEnsemble);
// if(getErrorCondition() < 0)
// {
// return;
// }
QVector<size_t> dims(1, 1);
m_FeatureIdsPtr = cellAttrMat->createNonPrereqArray<DataArray<int32_t>, AbstractFilter, int32_t>(this, m_FeatureIdsArrayName, 0, dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_FeatureIdsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{
m_FeatureIds = m_FeatureIdsPtr.lock()->getPointer(0); /* Now assign the raw pointer to data from the DataArray<T> object */
}
//ImageGeom::Pointer image = ImageGeom::CreateGeometry("TestImageGeom");
//image->setResolution(0.1f, 0.2f, 0.3f);
//image->setOrigin(100.3f, 987.234f, 0.0f);
//image->setDimensions(64, 64, 64);
//m->setGeometry(image);
VertexGeom::Pointer vertices = VertexGeom::CreateGeometry(100, "TestVertexGeom");
SharedVertexList::Pointer test = vertices->getVertices();
float* verts = test->getPointer(0);
for (int64_t i = 0; i < vertices->getNumberOfVertices(); i++)
{
verts[3 * i] = float(0.1 + i);
verts[3 * i + 1] = float(0.2 + i);
verts[3 * i + 2] = float(0.3 + i);
}
m->setGeometry(vertices);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void FindGBCD::dataCheckSurfaceMesh()
{
setErrorCondition(0);
initialize();
DataArrayPath tempPath;
getDataContainerArray()->getPrereqGeometryFromDataContainer<TriangleGeom, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
DataContainer::Pointer sm = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName(), false);
if(getErrorCondition() < 0 || NULL == sm.get()) { return; }
QVector<size_t> tDims(1, m_CrystalStructuresPtr.lock()->getNumberOfTuples());
sm->createNonPrereqAttributeMatrix<AbstractFilter>(this, getFaceEnsembleAttributeMatrixName(), tDims, SIMPL::AttributeMatrixType::FaceEnsemble);
QVector<size_t> cDims(1, 2);
m_SurfaceMeshFaceLabelsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFaceLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFaceLabels = m_SurfaceMeshFaceLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
cDims[0] = 3;
m_SurfaceMeshFaceNormalsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<double>, AbstractFilter>(this, getSurfaceMeshFaceNormalsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFaceNormalsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFaceNormals = m_SurfaceMeshFaceNormalsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
cDims[0] = 1;
m_SurfaceMeshFaceAreasPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<double>, AbstractFilter>(this, getSurfaceMeshFaceAreasArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFaceAreasPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFaceAreas = m_SurfaceMeshFaceAreasPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
// call the sizeGBCD function to get the GBCD ranges, dimensions, etc. Note that the input parameters do not affect the size and can be dummy values here;
sizeGBCD(0, 0);
cDims.resize(6);
cDims[0] = m_GbcdSizes[0];
cDims[1] = m_GbcdSizes[1];
cDims[2] = m_GbcdSizes[2];
cDims[3] = m_GbcdSizes[3];
cDims[4] = m_GbcdSizes[4];
cDims[5] = 2;
tempPath.update(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName(), getFaceEnsembleAttributeMatrixName(), getGBCDArrayName() );
m_GBCDPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<double>, AbstractFilter, double>(this, tempPath, 0, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_GBCDPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_GBCD = m_GBCDPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void InitializeSyntheticVolume::dataCheck()
{
setErrorCondition(0);
// Create the output Data Container
DataContainer::Pointer m = getDataContainerArray()->createNonPrereqDataContainer<AbstractFilter>(this, getDataContainerName());
if(getErrorCondition() < 0) { return; }
ImageGeom::Pointer image = ImageGeom::CreateGeometry(DREAM3D::Geometry::ImageGeometry);
m->setGeometry(image);
// Sanity Check the Dimensions and Resolution
INIT_SYNTH_VOLUME_CHECK(Dimensions.x, -5000);
INIT_SYNTH_VOLUME_CHECK(Dimensions.y, -5001);
INIT_SYNTH_VOLUME_CHECK(Dimensions.z, -5002);
INIT_SYNTH_VOLUME_CHECK(Resolution.x, -5003);
INIT_SYNTH_VOLUME_CHECK(Resolution.y, -5004);
INIT_SYNTH_VOLUME_CHECK(Resolution.z, -5005);
// Set the Dimensions, Resolution and Origin of the output data container
m->getGeometryAs<ImageGeom>()->setDimensions(m_Dimensions.x, m_Dimensions.y, m_Dimensions.z);
m->getGeometryAs<ImageGeom>()->setResolution(m_Resolution.x, m_Resolution.y, m_Resolution.z);
m->getGeometryAs<ImageGeom>()->setOrigin(m_Origin.x, m_Origin.y, m_Origin.z);
// Create our output Cell and Ensemble Attribute Matrix objects
QVector<size_t> tDims(3, 0);
tDims[0] = m_Dimensions.x;
tDims[1] = m_Dimensions.y;
tDims[2] = m_Dimensions.z;
AttributeMatrix::Pointer cellAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::Cell);
if(getErrorCondition() < 0 && cellAttrMat.get() == NULL) { return; }
QVector<size_t> cDims(1, 1); // This states that we are looking for an array with a single component
UInt32ArrayType::Pointer phaseType = getDataContainerArray()->getPrereqArrayFromPath<UInt32ArrayType, AbstractFilter>(this, getInputPhaseTypesArrayPath(), cDims);
if(getErrorCondition() < 0 && phaseType.get() == NULL) { return; }
QVector<size_t> statsDims(1, 1);
StatsDataArray::Pointer statsPtr = getDataContainerArray()->getPrereqArrayFromPath<StatsDataArray, AbstractFilter>(this, getInputStatsArrayPath(), statsDims);
if(getErrorCondition() < 0 && statsPtr.get() == NULL) { return; }
if(m_EstimateNumberOfFeatures)
{
m_EstimatedPrimaryFeatures = estimateNumFeatures(m_Dimensions, m_Resolution);
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void VectorSegmentFeatures::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getDataContainerName());
QVector<size_t> tDims(1, 1);
m->getAttributeMatrix(getCellFeatureAttributeMatrixName())->resizeAttributeArrays(tDims);
updateFeatureInstancePointers();
int64_t totalPoints = static_cast<int64_t>(m_FeatureIdsPtr.lock()->getNumberOfTuples());
m_BeenPickedPtr = BoolArrayType::CreateArray(totalPoints, "BeenPicked INTERNAL ARRAY ONLY");
m_BeenPickedPtr->initializeWithValue(0);
m_BeenPicked = m_BeenPickedPtr->getPointer(0);
// Convert user defined tolerance to radians.
angleTolerance = m_AngleTolerance * SIMPLib::Constants::k_Pi / 180.0f;
// Generate the random voxel indices that will be used for the seed points to start a new grain growth/agglomeration
const int64_t rangeMin = 0;
const int64_t rangeMax = totalPoints - 1;
initializeVoxelSeedGenerator(rangeMin, rangeMax);
SegmentFeatures::execute();
int32_t totalFeatures = static_cast<int32_t>(m->getAttributeMatrix(getCellFeatureAttributeMatrixName())->getNumTuples());
if (totalFeatures < 2)
{
setErrorCondition(-87000);
notifyErrorMessage(getHumanLabel(), "The number of Features was 0 or 1 which means no Features were detected. A threshold value may be set too high", getErrorCondition());
return;
}
// By default we randomize grains
if (true == m_RandomizeFeatureIds)
{
randomizeFeatureIds(totalPoints, totalFeatures);
}
// If there is an error set this to something negative and also set a message
notifyStatusMessage(getHumanLabel(), "Completed");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void InitializeSyntheticVolume::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getDataContainerName());
AttributeMatrix::Pointer cellAttrMat = m->getAttributeMatrix(getCellAttributeMatrixName());
// Resize the Cell AttributeMatrix to have the correct Tuple Dimensions.
QVector<size_t> tDims(3, 0);
tDims[0] = m->getGeometryAs<ImageGeom>()->getXPoints();
tDims[1] = m->getGeometryAs<ImageGeom>()->getYPoints();
tDims[2] = m->getGeometryAs<ImageGeom>()->getZPoints();
cellAttrMat->resizeAttributeArrays(tDims);
// If there is an error set this to something negative and also set a message
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void InsertAtoms::assign_points(QVector<VertexGeom::Pointer> points, QVector<BoolArrayType::Pointer> inFeature)
{
size_t count = 0;
int32_t numFeatures = points.size();
for (int32_t i = 0; i < numFeatures; i++)
{
int64_t numPoints = points[i]->getNumberOfVertices();
bool* inside = inFeature[i]->getPointer(0);
for (int64_t j = 0; j < numPoints; j++)
{
if (inside[j] == true) { count++; }
}
}
DataContainer::Pointer v = getDataContainerArray()->getDataContainer(getVertexDataContainerName());
VertexGeom::Pointer vertices = VertexGeom::CreateGeometry(count, DREAM3D::VertexData::SurfaceMeshNodes);
AttributeMatrix::Pointer vertexAttrMat = v->getAttributeMatrix(getVertexAttributeMatrixName());
QVector<size_t> tDims(1, count);
vertexAttrMat->resizeAttributeArrays(tDims);
updateVertexInstancePointers();
count = 0;
float coords[3] = { 0.0f, 0.0f, 0.0f };
for (int32_t i = 0; i < numFeatures; i++)
{
int64_t numPoints = points[i]->getNumberOfVertices();
bool* inside = inFeature[i]->getPointer(0);
for (int64_t j = 0; j < numPoints; j++)
{
if (inside[j] == true)
{
coords[0] = points[i]->getVertexPointer(j)[0];
coords[1] = points[i]->getVertexPointer(j)[1];
coords[2] = points[i]->getVertexPointer(j)[2];
vertices->setCoords(count, coords);
m_AtomFeatureLabels[count] = i;
count++;
}
}
}
v->setGeometry(vertices);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void EBSDSegmentFeatures::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getDataContainerName());
int64_t totalPoints = static_cast<int64_t>(m_FeatureIdsPtr.lock()->getNumberOfTuples());
QVector<size_t> tDims(1, 1);
m->getAttributeMatrix(getCellFeatureAttributeMatrixName())->resizeAttributeArrays(tDims);
updateFeatureInstancePointers();
// Convert user defined tolerance to radians.
misoTolerance = m_MisorientationTolerance * DREAM3D::Constants::k_Pi / 180.0f;
// Generate the random voxel indices that will be used for the seed points to start a new grain growth/agglomeration
const int64_t rangeMin = 0;
const int64_t rangeMax = totalPoints - 1;
initializeVoxelSeedGenerator(rangeMin, rangeMax);
SegmentFeatures::execute();
int64_t totalFeatures = static_cast<int64_t>(m_ActivePtr.lock()->getNumberOfTuples());
if (totalFeatures < 2)
{
setErrorCondition(-87000);
notifyErrorMessage(getHumanLabel(), "The number of Features was 0 or 1 which means no Features were detected. A threshold value may be set too high", getErrorCondition());
return;
}
// By default we randomize grains
if (true == getRandomizeFeatureIds())
{
totalPoints = static_cast<int64_t>(m->getGeometryAs<ImageGeom>()->getNumberOfElements());
randomizeFeatureIds(totalPoints, totalFeatures);
}
// If there is an error set this to something negative and also set a message
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SineParamsSegmentFeatures::dataCheck()
{
DataArrayPath tempPath;
setErrorCondition(0);
//Set the DataContainerName for the Parent Class (SegmentFeatures) to Use
setDataContainerName(m_SineParamsArrayPath.getDataContainerName());
SegmentFeatures::dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getDataContainerName(), false);
if(getErrorCondition() < 0 || NULL == m) { return; }
QVector<size_t> tDims(1, 0);
AttributeMatrix::Pointer cellFeatureAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellFeatureAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::CellFeature);
if(getErrorCondition() < 0 || NULL == cellFeatureAttrMat.get()) { return; }
ImageGeom::Pointer image = m->getPrereqGeometry<ImageGeom, AbstractFilter>(this);
if(getErrorCondition() < 0 || NULL == image.get()) { return; }
QVector<size_t> dims(1, 3);
m_SineParamsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<float>, AbstractFilter>(this, getSineParamsArrayPath(), dims);
if( NULL != m_SineParamsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SineParams = m_SineParamsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
dims[0] = 1;
tempPath.update(getDataContainerName(), m_SineParamsArrayPath.getAttributeMatrixName(), getFeatureIdsArrayName() );
m_FeatureIdsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, 0, dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_FeatureIdsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_FeatureIds = m_FeatureIdsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(m_UseGoodVoxels == true)
{
m_GoodVoxelsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<bool>, AbstractFilter>(this, getGoodVoxelsArrayPath(), dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_GoodVoxelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_GoodVoxels = m_GoodVoxelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
tempPath.update(getDataContainerName(), getCellFeatureAttributeMatrixName(), getActiveArrayName() );
m_ActivePtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<bool>, AbstractFilter, bool>(this, tempPath, true, dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_ActivePtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_Active = m_ActivePtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void InsertAtoms::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
TriangleGeom::Pointer triangles = getDataContainerArray()->getPrereqGeometryFromDataContainer<TriangleGeom, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
QVector<IDataArray::Pointer> dataArrays;
if(getErrorCondition() >= 0) { dataArrays.push_back(triangles->getTriangles()); }
DataContainer::Pointer v = getDataContainerArray()->createNonPrereqDataContainer<AbstractFilter>(this, getVertexDataContainerName());
if(getErrorCondition() < 0) { return; }
VertexGeom::Pointer vertices = VertexGeom::CreateGeometry(0, DREAM3D::Geometry::VertexGeometry);
v->setGeometry(vertices);
QVector<size_t> tDims(1, 0);
AttributeMatrix::Pointer vertexAttrMat = v->createNonPrereqAttributeMatrix<AbstractFilter>(this, getVertexAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::Vertex);
if(getErrorCondition() < 0 || NULL == vertexAttrMat.get()) { return; }
QVector<size_t> cDims(1, 2);
m_SurfaceMeshFaceLabelsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFaceLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFaceLabels = m_SurfaceMeshFaceLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() >= 0) { dataArrays.push_back(m_SurfaceMeshFaceLabelsPtr.lock()); }
cDims[0] = 4;
m_AvgQuatsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<float>, AbstractFilter>(this, getAvgQuatsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_AvgQuatsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_AvgQuats = m_AvgQuatsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
cDims[0] = 1;
tempPath.update(getVertexDataContainerName(), getVertexAttributeMatrixName(), getAtomFeatureLabelsArrayName() );
m_AtomFeatureLabelsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, -301, cDims); /* Assigns the shared_ptr<>(this, tempPath, -301, dims); Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_AtomFeatureLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_AtomFeatureLabels = m_AtomFeatureLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
getDataContainerArray()->validateNumberOfTuples<AbstractFilter>(this, dataArrays);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void LinkFeatureMapToElementArray::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
DataContainer::Pointer m = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getSelectedCellArrayPath().getDataContainerName(), false);
if(getErrorCondition() < 0 || NULL == m.get()) { return; }
QVector<size_t> tDims(1, 0);
m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellFeatureAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::CellFeature);
QVector<size_t> cDims(1, 1);
m_SelectedCellDataPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getSelectedCellArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SelectedCellDataPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SelectedCellData = m_SelectedCellDataPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() < 0) { return; }
tempPath.update(getSelectedCellArrayPath().getDataContainerName(), getCellFeatureAttributeMatrixName(), getActiveArrayName() );
m_ActivePtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<bool>, AbstractFilter, bool>(this, tempPath, 0, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_ActivePtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_Active = m_ActivePtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SharedFeatureFaceFilter::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
getDataContainerArray()->getPrereqGeometryFromDataContainer<TriangleGeom, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
DataContainer::Pointer sm = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName(), false);
if(getErrorCondition() < 0) { return; }
QVector<size_t> tDims(1, 0);
AttributeMatrix::Pointer facefeatureAttrMat = sm->createNonPrereqAttributeMatrix<AbstractFilter>(this, getFaceFeatureAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::FaceFeature);
if(getErrorCondition() < 0 || NULL == facefeatureAttrMat.get()) { return; }
QVector<size_t> cDims(1, 2);
m_SurfaceMeshFaceLabelsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFaceLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFaceLabels = m_SurfaceMeshFaceLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
cDims[0] = 1;
tempPath.update(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName(), m_SurfaceMeshFaceLabelsArrayPath.getAttributeMatrixName(), getSurfaceMeshFeatureFaceIdsArrayName() );
m_SurfaceMeshFeatureFaceIdsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, 0, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFeatureFaceIdsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFeatureFaceIds = m_SurfaceMeshFeatureFaceIdsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
tempPath.update(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName(), getFaceFeatureAttributeMatrixName(), getSurfaceMeshFeatureFaceNumTrianglesArrayName() );
m_SurfaceMeshFeatureFaceNumTrianglesPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, 0, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFeatureFaceNumTrianglesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFeatureFaceNumTriangles = m_SurfaceMeshFeatureFaceNumTrianglesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
cDims[0] = 2;
tempPath.update(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName(), getFaceFeatureAttributeMatrixName(), getSurfaceMeshFeatureFaceLabelsArrayName() );
m_SurfaceMeshFeatureFaceLabelsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, 0, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFeatureFaceLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFeatureFaceLabels = m_SurfaceMeshFeatureFaceLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
