// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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;
}
/**
*
* @param FileName
* @param data
* @param nx X Dimension
* @param ny Y Dimension
* @param nz Z Dimension
*/
int ReadPHFile(QString FileName, QVector<int>& data, int& nx, int& ny, int& nz)
{
DataContainerArray::Pointer dca = DataContainerArray::New();
DataContainer::Pointer m = DataContainer::New(); /* FIXME: What Geometry do we need? */
dca->pushBack(m);
FilterManager::Pointer fm = FilterManager::Instance();
AbstractFilter::Pointer reader = fm->getFactoryForFilter("PhReader")->create();
reader->setDataContainerArray(dca);
bool propWasSet = reader->setProperty("InputFile", FileName);
if(propWasSet == false)
{
}
reader->execute();
if (reader->getErrorCondition() < 0)
{
qDebug() << "Error Reading the Ph File '" << FileName << "' Error Code:" << reader->getErrorCondition();
return -1;
}
Int32ArrayType* featureIds = Int32ArrayType::SafePointerDownCast(m->getAttributeMatrix(DREAM3D::Defaults::CellAttributeMatrixName)->getAttributeArray(DREAM3D::CellData::FeatureIds).get());
size_t count = featureIds->getNumberOfTuples();
data.resize(count);
for(size_t i = 0; i < count; ++i)
{
data[i] = featureIds->getValue(i);
}
return 0;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AvizoUniformCoordinateWriter::dataCheck()
{
setErrorCondition(0);
DataContainer::Pointer dc = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getFeatureIdsArrayPath().getDataContainerName(), false);
if (getErrorCondition() < 0 || NULL == dc.get()) {
return;
}
ImageGeom::Pointer image = dc->getPrereqGeometry<ImageGeom, AbstractFilter>(this);
if (getErrorCondition() < 0 || NULL == image.get()) {
return;
}
if(m_OutputFile.isEmpty() == true)
{
QString ss = QObject::tr("The output file must be set before executing this filter.");
setErrorCondition(-1);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
if(m_WriteFeatureIds == true)
{
QVector<size_t> dims(1, 1);
m_FeatureIdsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getFeatureIdsArrayPath(), 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 */
}
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
IntVec3_t CropImageGeometry::getCurrentVolumeDataContainerDimensions()
{
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getCellAttributeMatrixPath().getDataContainerName());
IntVec3_t data;
if (NULL != m.get() )
{
ImageGeom::Pointer image = m->getGeometryAs<ImageGeom>();
if (image.get() != NULL)
{
data.x = image->getXPoints();
data.y = image->getYPoints();
data.z = image->getZPoints();
}
else
{
data.x = 0;
data.y = 0;
data.z = 0;
}
}
else
{
data.x = 0;
data.y = 0;
data.z = 0;
}
return data;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ConvertData::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(m_SelectedCellArrayPath.getDataContainerName());
IDataArray::Pointer iArray = m->getAttributeMatrix(m_SelectedCellArrayPath.getAttributeMatrixName())->getAttributeArray(m_SelectedCellArrayPath.getDataArrayName());
bool completed = false;
CHECK_AND_CONVERT(UInt8ArrayType, m, m_ScalarType, iArray, m_SelectedCellArrayPath.getAttributeMatrixName(), m_OutputArrayName)
CHECK_AND_CONVERT(Int8ArrayType, m, m_ScalarType, iArray, m_SelectedCellArrayPath.getAttributeMatrixName(), m_OutputArrayName)
CHECK_AND_CONVERT(UInt16ArrayType, m, m_ScalarType, iArray, m_SelectedCellArrayPath.getAttributeMatrixName(), m_OutputArrayName)
CHECK_AND_CONVERT(Int16ArrayType, m, m_ScalarType, iArray, m_SelectedCellArrayPath.getAttributeMatrixName(), m_OutputArrayName)
CHECK_AND_CONVERT(UInt32ArrayType, m, m_ScalarType, iArray, m_SelectedCellArrayPath.getAttributeMatrixName(), m_OutputArrayName)
CHECK_AND_CONVERT(Int32ArrayType, m, m_ScalarType, iArray, m_SelectedCellArrayPath.getAttributeMatrixName(), m_OutputArrayName)
CHECK_AND_CONVERT(UInt64ArrayType, m, m_ScalarType, iArray, m_SelectedCellArrayPath.getAttributeMatrixName(), m_OutputArrayName)
CHECK_AND_CONVERT(Int64ArrayType, m, m_ScalarType, iArray, m_SelectedCellArrayPath.getAttributeMatrixName(), m_OutputArrayName)
CHECK_AND_CONVERT(FloatArrayType, m, m_ScalarType, iArray, m_SelectedCellArrayPath.getAttributeMatrixName(), m_OutputArrayName)
CHECK_AND_CONVERT(DoubleArrayType, m, m_ScalarType, iArray, m_SelectedCellArrayPath.getAttributeMatrixName(), m_OutputArrayName)
CHECK_AND_CONVERT(BoolArrayType, m, m_ScalarType, iArray, m_SelectedCellArrayPath.getAttributeMatrixName(), m_OutputArrayName)
/* Let the GUI know we are done with this filter */
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RenameAttributeMatrix::dataCheck()
{
setErrorCondition(0);
if (m_NewAttributeMatrix.isEmpty() == true)
{
setErrorCondition(-11004);
QString ss = QObject::tr("The new Attribute Matrix name must be set");
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
QString amName = getSelectedAttributeMatrixPath().getAttributeMatrixName();
DataContainer::Pointer dc = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getSelectedAttributeMatrixPath().getDataContainerName());
getDataContainerArray()->getPrereqAttributeMatrixFromPath<AbstractFilter>(this, getSelectedAttributeMatrixPath(), -301);
if(getErrorCondition() < 0) { return; }
bool check = dc->renameAttributeMatrix(amName, getNewAttributeMatrix() );
if (check == false)
{
setErrorCondition(-11006);
QString ss = QObject::tr("Attempt to rename Attribute Matrix '%1' to '%2' failed").arg(amName).arg(getNewAttributeMatrix());
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
QVector<DataArrayPath> DataContainerBundle::findCommonDataArrayPaths(bool filterMetaData)
{
QVector<DataArrayPath> commonPaths;
if(m_DataContainers.count() == 0)
{
return commonPaths;
}
// Get the first DataContainer
DataContainer::Pointer dc0 = m_DataContainers[0];
if(NULL == dc0.get())
{
return commonPaths;
}
QVector<DataArrayPath> dc0Paths = dc0->getAllDataArrayPaths();
if(m_DataContainers.count() == 1)
{
return commonPaths;
}
int count = m_DataContainers.count();
// We already have the first DataContainer, so start at the 2nd
for (int dcIdx = 1; dcIdx < count; ++dcIdx)
{
DataContainer::Pointer dcX = m_DataContainers[dcIdx];
QVector<DataArrayPath> paths = dcX->getAllDataArrayPaths();
int numPaths = dc0Paths.count();
// Loop over the paths from the first data container from back to front,
// removing the path if it does not exist.
for(int i = numPaths - 1; i >= 0; i--)
{
DataArrayPath dc0Path = dc0Paths[i];
bool match = false;
foreach(DataArrayPath path, paths)
{
//qDebug() << "Comparing " << dc0Path.serialize() << " TO " << path.serialize();
if(path.hasSameAttributeMatrix(dc0Path) && path.hasSameDataArray(dc0Path) )
{
match = true;
}
if(filterMetaData == true && (path.getAttributeMatrixName() == DREAM3D::StringConstants::MetaData) )
{
match = false;
}
}
if(!match)
{
dc0Paths.remove(i);
}
}
}
commonPaths = dc0Paths;
return commonPaths;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 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 CombineAttributeMatrices::execute()
{
setErrorCondition(0);
dataCheck();
if (getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getFirstAttributeMatrixPath().getDataContainerName());
AttributeMatrix::Pointer firstAttrMat = m->getAttributeMatrix(getFirstAttributeMatrixPath().getAttributeMatrixName());
AttributeMatrix::Pointer secondAttrMat = m->getAttributeMatrix(getSecondAttributeMatrixPath().getAttributeMatrixName());
AttributeMatrix::Pointer combinedAttrMat = m->getAttributeMatrix(getCombinedAttributeMatrixName());
size_t firstAttrMatNumTuples = firstAttrMat->getNumTuples();
size_t totalTuples1 = m_SecondIndexPtr.lock()->getNumberOfTuples();
size_t totalTuples2 = m_SecondIndexPtr.lock()->getNumberOfTuples();
for (size_t i = 0; i < totalTuples1; i++)
{
if (m_FirstIndex > 0) { m_NewIndex[i] = m_FirstIndex[i]; }
}
for (size_t i = 0; i < totalTuples2; i++)
{
//subtract 1 from the index plus numTuples because the second index should be shifted to account for the zeroth tuple (all AMs above element start at tuple 1)
if (m_SecondIndex[i] > 0 && m_NewIndex[i] == 0) m_NewIndex[i] = m_SecondIndex[i] + firstAttrMatNumTuples - 1;
else if (m_SecondIndex[i] > 0 && m_NewIndex[i] != 0)
{
QString ss = QObject::tr("When copying the indices, the indices of the two attribute matrices overlapped. The index of the first attribute matrix was kept.");
notifyWarningMessage(getHumanLabel(), ss, -111);
}
}
QList<QString> arrayNames = firstAttrMat->getAttributeArrayNames();
size_t location = 0;
for (QList<QString>::iterator iter = arrayNames.begin(); iter != arrayNames.end(); ++iter)
{
IDataArray::Pointer fromDataArray = firstAttrMat->getAttributeArray(*iter);
IDataArray::Pointer toDataArray = combinedAttrMat->getAttributeArray(*iter);
EXECUTE_FUNCTION_TEMPLATE(this, copyData, fromDataArray, fromDataArray, toDataArray, location);
}
arrayNames.clear();
arrayNames = secondAttrMat->getAttributeArrayNames();
location = firstAttrMatNumTuples;
for (QList<QString>::iterator iter = arrayNames.begin(); iter != arrayNames.end(); ++iter)
{
IDataArray::Pointer fromDataArray = secondAttrMat->getAttributeArray(*iter);
IDataArray::Pointer toDataArray = combinedAttrMat->getAttributeArray(*iter);
EXECUTE_FUNCTION_TEMPLATE(this, copyData, fromDataArray, fromDataArray, toDataArray, location);
}
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 writePointScalarData(DataContainer::Pointer dc, const QString& vertexAttributeMatrixName, const QString& dataName, const QString& dataType,
bool writeBinaryData, FILE* vtkFile, int nT)
{
IDataArray::Pointer data = dc->getAttributeMatrix(vertexAttributeMatrixName)->getAttributeArray(dataName);
QString ss;
if (NULL != data.get())
{
T* m = reinterpret_cast<T*>(data->getVoidPointer(0));
fprintf(vtkFile, "\n");
fprintf(vtkFile, "SCALARS %s %s\n", dataName.toLatin1().data(), dataType.toLatin1().data());
fprintf(vtkFile, "LOOKUP_TABLE default\n");
for(int i = 0; i < nT; ++i)
{
T swapped = 0x00;
if(writeBinaryData == true)
{
swapped = static_cast<T>(m[i]);
SIMPLib::Endian::FromSystemToBig::convert(swapped);
fwrite(&swapped, sizeof(T), 1, vtkFile);
}
else
{
ss = QString::number(m[i]) + " ";
fprintf(vtkFile, "%s ", ss.toLatin1().data());
//if (i%50 == 0)
{ fprintf(vtkFile, "\n"); }
}
}
}
}
void writeCellScalarData(DataContainer::Pointer dc, const QString& faceAttributeMatrixName, const QString& dataName, const QString& dataType,
bool writeBinaryData, FILE* vtkFile, QMap<int32_t, int32_t>& featureIds, int32_t* m_SurfaceMeshFaceLabels)
{
TriangleGeom::Pointer triangleGeom = dc->getGeometryAs<TriangleGeom>();
int64_t numTriangles = triangleGeom->getNumberOfTris();
IDataArray::Pointer data = dc->getAttributeMatrix(faceAttributeMatrixName)->getAttributeArray(dataName);
QString ss;
if (NULL != data.get())
{
int32_t totalCellsWritten = 0;
T* m = reinterpret_cast<T*>(data->getVoidPointer(0));
fprintf(vtkFile, "\n");
fprintf(vtkFile, "SCALARS %s %s 1\n", dataName.toLatin1().data(), dataType.toLatin1().data());
fprintf(vtkFile, "LOOKUP_TABLE default\n");
// Loop over all the features
for(QMap<int32_t, int32_t>::iterator featureIter = featureIds.begin(); featureIter != featureIds.end(); ++featureIter)
{
int32_t gid = featureIter.key(); // The current Feature Id
size_t size = featureIter.value(); // The number of triangles for this feature id
std::vector<T> buffer(size, 0);
totalCellsWritten += size;
size_t index = 0;
for (int j = 0; j < numTriangles; j++)
{
if (m_SurfaceMeshFaceLabels[j * 2] != gid && m_SurfaceMeshFaceLabels[j * 2 + 1] != gid) { continue; }
// Get the data
T s0 = static_cast<T>(m[j]);
if (m_SurfaceMeshFaceLabels[j * 2 + 1] == gid)
{ s0 = s0 * -1; }
// Write the values to the buffer after an Endian swap.
if(writeBinaryData == true)
{
SIMPLib::Endian::FromSystemToBig::convert(s0);
buffer[index] = s0;
++index;
}
else
{
ss = QString::number(s0);
fprintf(vtkFile, "%s\n", ss.toLatin1().data());
}
}
// Write the Buffer
if(writeBinaryData == true)
{
fwrite(&(buffer.front()), sizeof(T), size, vtkFile);
}
}
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 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 FindModulusMismatch::dataCheckSurfaceMesh()
{
DataArrayPath tempPath;
setErrorCondition(0);
DataContainer::Pointer sm = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
if(getErrorCondition() < 0 || NULL == sm.get()) { return; }
QVector<size_t> dims(1, 2);
m_SurfaceMeshFaceLabelsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath(), dims); /* 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 */
dims[0] = 1;
tempPath.update(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName(), m_SurfaceMeshFaceLabelsArrayPath.getAttributeMatrixName(), getSurfaceMeshDeltaModulusArrayName() );
m_SurfaceMeshDeltaModulusPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<float>, AbstractFilter, float>(this, tempPath, 180.0, dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshDeltaModulusPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshDeltaModulus = m_SurfaceMeshDeltaModulusPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void MinNeighbors::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
// If running on a single phase, validate that the user has not entered a phase number
// that is not in the system ; 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
if (m_ApplyToSinglePhase == true)
{
AttributeMatrix::Pointer featAttrMat = getDataContainerArray()->getDataContainer(getFeaturePhasesArrayPath().getDataContainerName())->getAttributeMatrix(getFeaturePhasesArrayPath().getAttributeMatrixName());
size_t numFeatures = featAttrMat->getNumTuples();
bool unavailablePhase = true;
for (size_t i = 0; i < numFeatures; i++)
{
if (m_FeaturePhases[i] == m_PhaseNumber)
{
unavailablePhase = false;
break;
}
}
if (unavailablePhase == true)
{
QString ss = QObject::tr("The phase number (%1) is not available in the supplied Feature phases array with path (%2)").arg(m_PhaseNumber).arg(m_FeaturePhasesArrayPath.serialize());
setErrorCondition(-5555);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
}
QVector<bool> activeObjects = merge_containedfeatures();
if(getErrorCondition() < 0) { return; }
assign_badpoints();
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(m_NumNeighborsArrayPath.getDataContainerName());
AttributeMatrix::Pointer cellFeatureAttrMat = m->getAttributeMatrix(m_NumNeighborsArrayPath.getAttributeMatrixName());
cellFeatureAttrMat->removeInactiveObjects(activeObjects, m_FeatureIdsPtr.lock());
// If there is an error set this to something negative and also set a message
notifyStatusMessage(getHumanLabel(), "Complete");
}
void writeCellNormalData(DataContainer::Pointer dc, const QString& faceAttributeMatrixName, const QString& dataName, const QString& dataType,
bool writeBinaryData, bool writeConformalMesh,
FILE* vtkFile, int nT)
{
IDataArray::Pointer data = dc->getAttributeMatrix(faceAttributeMatrixName)->getAttributeArray(dataName);
QString buf;
QTextStream ss(&buf);
if (NULL != data.get())
{
T* m = reinterpret_cast<T*>(data->getVoidPointer(0));
fprintf(vtkFile, "\n");
fprintf(vtkFile, "NORMALS %s %s\n", dataName.toLatin1().data(), dataType.toLatin1().data());
for(int i = 0; i < nT; ++i)
{
T s0 = 0x00;
T s1 = 0x00;
T s2 = 0x00;
if(writeBinaryData == true)
{
s0 = static_cast<T>(m[i * 3 + 0]);
s1 = static_cast<T>(m[i * 3 + 1]);
s2 = static_cast<T>(m[i * 3 + 2]);
SIMPLib::Endian::FromSystemToBig::convert(s0);
SIMPLib::Endian::FromSystemToBig::convert(s1);
SIMPLib::Endian::FromSystemToBig::convert(s2);
fwrite(&s0, sizeof(T), 1, vtkFile);
fwrite(&s1, sizeof(T), 1, vtkFile);
fwrite(&s2, sizeof(T), 1, vtkFile);
if(false == writeConformalMesh)
{
s0 = static_cast<T>(m[i * 3 + 0]) * -1.0;
s1 = static_cast<T>(m[i * 3 + 1]) * -1.0;
s2 = static_cast<T>(m[i * 3 + 2]) * -1.0;
SIMPLib::Endian::FromSystemToBig::convert(s0);
SIMPLib::Endian::FromSystemToBig::convert(s1);
SIMPLib::Endian::FromSystemToBig::convert(s2);
fwrite(&s0, sizeof(T), 1, vtkFile);
fwrite(&s1, sizeof(T), 1, vtkFile);
fwrite(&s2, sizeof(T), 1, vtkFile);
}
}
else
{
ss << m[i * 3 + 0] << " " << m[i * 3 + 1] << " " << m[i * 3 + 2] << " ";
if(false == writeConformalMesh)
{
ss << -1.0 * m[i * 3 + 0] << " " << -1.0 * m[i * 3 + 1] << " " << -1.0 * m[i * 3 + 2] << " ";
}
fprintf(vtkFile, "%s ", buf.toLatin1().data());
buf.clear();
if (i % 50 == 0) { fprintf(vtkFile, "\n"); }
}
}
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 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");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
DataContainer::Pointer DataContainer::deepCopy()
{
DataContainer::Pointer dcCopy = DataContainer::New(getName());
dcCopy->setName(getName());
if (m_Geometry.get() != NULL)
{
IGeometry::Pointer geomCopy = m_Geometry->deepCopy();
dcCopy->setGeometry(geomCopy);
}
for (AttributeMatrixMap_t::iterator iter = getAttributeMatrices().begin(); iter != getAttributeMatrices().end(); ++iter)
{
AttributeMatrix::Pointer attrMat = (*iter)->deepCopy();
dcCopy->addAttributeMatrix(attrMat->getName(), attrMat);
}
return dcCopy;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void DataContainerBundle::removeDataContainer(DataContainer::Pointer dc)
{
for(qint32 i = 0; i < m_DataContainers.size(); i++)
{
if(m_DataContainers[i].get() == dc.get())
{
m_DataContainers.remove(i);
return;
}
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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");
}