// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 ScaleVolume::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
if (m_ApplyToVoxelVolume == true)
{
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getDataContainerName());
ImageGeom::Pointer image = m->getGeometryAs<ImageGeom>();
float resolution[3] = { 0.0f, 0.0f, 0.0f };
image->getResolution(resolution);
resolution[0] *= m_ScaleFactor.x;
resolution[1] *= m_ScaleFactor.y;
resolution[2] *= m_ScaleFactor.z;
image->setResolution(resolution);
}
if (m_ApplyToSurfaceMesh == true)
{
updateSurfaceMesh();
}
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AlignSectionsList::find_shifts(std::vector<int64_t>& xshifts, std::vector<int64_t>& yshifts)
{
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getDataContainerName());
std::ifstream inFile;
inFile.open(m_InputFile.toLatin1().data());
size_t udims[3] = { 0, 0, 0 };
m->getGeometryAs<ImageGeom>()->getDimensions(udims);
#if (CMP_SIZEOF_SIZE_T == 4)
typedef int32_t DimType;
#else
typedef int64_t DimType;
#endif
DimType dims[3] =
{
static_cast<DimType>(udims[0]),
static_cast<DimType>(udims[1]),
static_cast<DimType>(udims[2]),
};
int64_t slice = 0;
int64_t newxshift = 0, newyshift = 0;
for (DimType iter = 1; iter < dims[2]; iter++)
{
inFile >> slice >> newxshift >> newyshift;
xshifts[iter] = xshifts[iter - 1] + newxshift;
yshifts[iter] = yshifts[iter - 1] + newyshift;
}
inFile.close();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 AlignSections::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
ImageGeom::Pointer image = getDataContainerArray()->getPrereqGeometryFromDataContainer<ImageGeom, AbstractFilter>(this, getDataContainerName());
if(getErrorCondition() < 0) { return; }
if (image->getXPoints() <= 1 || image->getYPoints() <= 1 || image->getZPoints() <= 1)
{
QString ss = QObject::tr("The Image Geometry is not 3D and cannot be run through this filter. The dimensions are (%1,%2,%3)").arg(image->getXPoints()).arg(image->getYPoints()).arg(image->getZPoints());
setErrorCondition(-3010);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
tempPath.update(getDataContainerName(), getCellAttributeMatrixName(), "");
getDataContainerArray()->getPrereqAttributeMatrixFromPath<AbstractFilter>(this, tempPath, -301);
if (true == m_WriteAlignmentShifts && m_AlignmentShiftFileName.isEmpty() == true)
{
QString ss = QObject::tr("The alignment shift file name is empty");
setErrorCondition(-1);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ReadImage::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setInputFileName( reader->readString( "InputFileName", getInputFileName() ) );
setDataContainerName( reader->readString( "DataContainerName", getDataContainerName() ) );
setCellAttributeMatrixName( reader->readString( "CellAttributeMatrixName", getCellAttributeMatrixName() ) );
setImageDataArrayName( reader->readString( "ImageDataArrayName", getImageDataArrayName() ) );
reader->closeFilterGroup();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SetOriginResolutionImageGeom::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setChangeOrigin( reader->readValue("ChangeOrigin", getChangeOrigin()) );
setChangeResolution( reader->readValue("ChangeResolution", getChangeResolution()) );
setOrigin( reader->readFloatVec3("Origin", getOrigin() ) );
setResolution(reader->readFloatVec3("Resolution", getResolution() ) );
setDataContainerName(reader->readString("DataContainerName", getDataContainerName()));
reader->closeFilterGroup();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void EnsembleInfoReader::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setDataContainerName(reader->readString("DataContainerName", getDataContainerName() ) );
setCellEnsembleAttributeMatrixName(reader->readString("CellEnsembleAttributeMatrixName", getCellEnsembleAttributeMatrixName() ) );
setPhaseTypesArrayName(reader->readString("PhaseTypesArrayName", getPhaseTypesArrayName() ) );
setCrystalStructuresArrayName(reader->readString("CrystalStructuresArrayName", getCrystalStructuresArrayName() ) );
setInputFile( reader->readString( "InputFile", getInputFile() ) );
reader->closeFilterGroup();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ScaleVolume::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setApplyToVoxelVolume( reader->readValue("ApplyToVoxelVolume", getApplyToVoxelVolume()) );
setApplyToSurfaceMesh( reader->readValue("ApplyToSurfaceMesh", getApplyToSurfaceMesh()) );
setScaleFactor( reader->readFloatVec3("ScaleFactor", getScaleFactor() ) );
setDataContainerName(reader->readString("DataContainerName", getDataContainerName()));
setSurfaceDataContainerName(reader->readString("SurfaceDataContainerName", getSurfaceDataContainerName()));
reader->closeFilterGroup();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 RegularGridSampleSurfaceMesh::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
SampleSurfaceMesh::readFilterParameters(reader, index);
reader->openFilterGroup(this, index);
setXPoints(reader->readValue("XPoints", getXPoints()));
setYPoints(reader->readValue("YPoints", getYPoints()));
setZPoints(reader->readValue("ZPoints", getZPoints()));
setResolution(reader->readFloatVec3("Resolution", getResolution()));
setOrigin(reader->readFloatVec3("Origin", getOrigin()));
setDataContainerName(reader->readString("DataContainerName", getDataContainerName()));
setCellAttributeMatrixName(reader->readString("CellAttributeMatrixName", getCellAttributeMatrixName() ) );
setFeatureIdsArrayName(reader->readString("FeatureIdsArrayName", getFeatureIdsArrayName() ) );
reader->closeFilterGroup();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void InitializeSyntheticVolume::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setDataContainerName(reader->readString("DataContainerName", getDataContainerName() ) );
setCellAttributeMatrixName(reader->readString("CellAttributeMatrixName", getCellAttributeMatrixName() ) );
setDimensions( reader->readIntVec3("Dimensions", getDimensions() ) );
setResolution( reader->readFloatVec3("Resolution", getResolution() ) );
setOrigin( reader->readFloatVec3("Origin", getOrigin() ) );
setInputStatsArrayPath(reader->readDataArrayPath("InputStatsArrayPath", getInputStatsArrayPath() ) );
setInputPhaseTypesArrayPath(reader->readDataArrayPath("InputPhaseTypesArrayPath", getInputPhaseTypesArrayPath() ) );
setInputStatsFile(reader->readString("InputStatsFile", getInputStatsFile() ) );
setEstimateNumberOfFeatures(reader->readValue("EstimateNumberOfFeatures", getEstimateNumberOfFeatures() ) );
reader->closeFilterGroup();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 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 RegularGridSampleSurfaceMesh::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
SIMPL_RANDOMNG_NEW()
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getDataContainerName());
m->getGeometryAs<ImageGeom>()->setDimensions(m_XPoints, m_YPoints, m_ZPoints);
m->getGeometryAs<ImageGeom>()->setOrigin(m_Origin.x, m_Origin.y, m_Origin.z);
m->getGeometryAs<ImageGeom>()->setResolution(m_Resolution.x, m_Resolution.y, m_Resolution.z);
SampleSurfaceMesh::execute();
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void YSChoiAbaqusReader::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setDataContainerName(reader->readString("DataContainerName", getDataContainerName() ) );
setCellAttributeMatrixName(reader->readString("CellAttributeMatrixName", getCellAttributeMatrixName() ) );
setCellFeatureAttributeMatrixName(reader->readString("CellFeatureAttributeMatrixName", getCellFeatureAttributeMatrixName() ) );
setCellEnsembleAttributeMatrixName(reader->readString("CellEnsembleAttributeMatrixName", getCellEnsembleAttributeMatrixName() ) );
setCrystalStructuresArrayName(reader->readString("CrystalStructuresArrayName", getCrystalStructuresArrayName() ) );
setFeatureIdsArrayName(reader->readString("FeatureIdsArrayName", getFeatureIdsArrayName() ) );
setSurfaceFeaturesArrayName(reader->readString("SurfaceFeaturesArrayName", getSurfaceFeaturesArrayName() ) );
setCellPhasesArrayName(reader->readString("CellPhasesArrayName", getCellPhasesArrayName() ) );
setAvgQuatsArrayName(reader->readString("AvgQuatsArrayName", getAvgQuatsArrayName() ) );
setQuatsArrayName(reader->readString("QuatsArrayName", getQuatsArrayName() ) );
setCellEulerAnglesArrayName(reader->readString("CellEulerAnglesArrayName", getCellEulerAnglesArrayName() ) );
setInputFile( reader->readString( "InputFile", getInputFile() ) );
setInputFeatureInfoFile( reader->readString( "InputFeatureInfoFile", getInputFeatureInfoFile() ) );
reader->closeFilterGroup();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 MakeDataContainer::execute()
{
int err = 0;
setErrorCondition(err);
// Run the data check to get references to all of our data arrays initialized to the values stored in memory
dataCheck();
if (getErrorCondition() < 0)
{
return;
}
//ImageGeom::Pointer image = getDataContainerArray()->getDataContainer(getDataContainerName())->getGeometryAs<ImageGeom>();
//size_t index;
//size_t iDims[3] = {0, 0, 0};
//image->getDimensions(iDims);
//for (size_t z=0;z<image->getZPoints();z++)
//{
// for (size_t y=0;y<image->getYPoints();y++)
// {
// for (size_t x=0;x<image->getXPoints();x++)
// {
// index = (z * iDims[0] * iDims[1]) + (y * iDims[0]) + x;
// m_FeatureIds[index] = z + x + y;
// }
// }
//}
VertexGeom::Pointer verts = getDataContainerArray()->getDataContainer(getDataContainerName())->getGeometryAs<VertexGeom>();
for (int64_t i = 0; i < verts->getNumberOfVertices(); i++)
{
m_FeatureIds[i] = i;
}
/* Let the GUI know we are done with this filter */
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 EnsembleInfoReader::setupFilterParameters()
{
FilterParameterVector parameters;
parameters.push_back(InputFileFilterParameter::New("Input Ensemble Info File", "InputFile", getInputFile(), FilterParameter::Parameter, "*.ini *.txt"));
{
DataContainerSelectionFilterParameter::RequirementType req;
parameters.push_back(DataContainerSelectionFilterParameter::New("Data Container", "DataContainerName", getDataContainerName(), FilterParameter::RequiredArray, req));
}
parameters.push_back(SeparatorFilterParameter::New("Ensemble Data", FilterParameter::CreatedArray));
parameters.push_back(StringFilterParameter::New("Ensemble Attribute Matrix", "CellEnsembleAttributeMatrixName", getCellEnsembleAttributeMatrixName(), FilterParameter::CreatedArray));
parameters.push_back(StringFilterParameter::New("Crystal Structures", "CrystalStructuresArrayName", getCrystalStructuresArrayName(), FilterParameter::CreatedArray));
parameters.push_back(StringFilterParameter::New("Phase Types", "PhaseTypesArrayName", getPhaseTypesArrayName(), FilterParameter::CreatedArray));
setFilterParameters(parameters);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int32_t EnsembleInfoReader::readFile()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return getErrorCondition(); }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getDataContainerName());
AttributeMatrix::Pointer cellensembleAttrMat = m->getAttributeMatrix(getCellEnsembleAttributeMatrixName());
int32_t numphases = 0;
QSettings settings(getInputFile(), QSettings::IniFormat); // The .ini or .txt input file
settings.beginGroup("EnsembleInfo");
numphases = settings.value("Number_Phases").toInt(); // read number of phases from input file
settings.endGroup();
if (0 == numphases) // Either the group name "EnsembleInfo" is incorrect or 0 was entered as the Number_Phases
{
QString ss = QObject::tr("Check the group name EnsembleInfo and that Number_Phases > 0");
setErrorCondition(-10003);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return -1;
}
// Figure out if we are reading contiguous groups
std::vector<bool> visited(numphases + 1, false);
visited[0] = true; //this is DREAM3D's internal, which is always visited.
QVector<size_t> tDims(1, numphases + 1);
cellensembleAttrMat->resizeAttributeArrays(tDims);
updateEnsembleInstancePointers();
for (int32_t index = 1; index < numphases + 1; index++)
{
QString group = QString::number(index);
settings.beginGroup(group);
QString xtalString = settings.value(DREAM3D::StringConstants::CrystalStructure, "MissingCrystalStructure").toString();
QString phaseTypeString = settings.value(DREAM3D::StringConstants::PhaseType, "MissingPhaseType").toString();
// Check to make sure the user has something for each of the Crystal Structure and Phase Type
if (xtalString.compare("MissingCrystalStructure") == 0)
{
QString ss = QObject::tr("Missing crystal structure for phase '%1'").arg(group);
setErrorCondition(-10008);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return -1;
}
if (phaseTypeString.compare("MissingPhaseType") == 0)
{
QString ss = QObject::tr("Missing phase type for phase '%1'").arg(group);
setErrorCondition(-10009);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return -1;
}
// Past that sanity check, so we have values, lets parse them
QStringList values;
values << xtalString << phaseTypeString;
ensembleLookup(values); // Lookup number for the crystal number string and the phase type string read from the file
// Check to see if the Crystal Structure string was valid
if (m_crystruct == Ebsd::CrystalStructure::UnknownCrystalStructure) // The crystal structure name read from the file was not found in the lookup table
{
QString ss = QObject::tr("Incorrect crystal structure name '%1'").arg(xtalString);
setErrorCondition(-10006);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return -1;
}
else
{
m_CrystalStructures[index] = m_crystruct;
}
// now check to see if the Phase type string was valid.
if (m_ptype == DREAM3D::PhaseType::UnknownPhaseType)
{
QString ss = QObject::tr("Incorrect phase type name '%1'").arg(phaseTypeString); // The phase type name read from the file was not found in the lookup table
setErrorCondition(-10007);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return -1;
}
else
{
m_PhaseTypes[index] = m_ptype;
}
visited[index] = true;
// Close up this group
settings.endGroup();
}
//Make sure we visited all the groups.
for(std::vector<bool>::size_type i = 0; i < visited.size(); i++)
{
if(visited[i] == false)
{
QString ss = QObject::tr("Phase '%1' did not have entries in the file. Phase numbering must start at 1 and no phases may be skipped").arg(i); // The phase type name read from the file was not found in the lookup table
setErrorCondition(-10005);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return -1;
}
}
notifyStatusMessage(getHumanLabel(), "Complete");
return 0;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void EnsembleInfoReader::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
QFileInfo fi(getInputFile());
if (getInputFile().isEmpty() == true)
{
QString ss = QObject::tr("The input file must be set");
setErrorCondition(-387);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
else if (fi.exists() == false)
{
QString ss = QObject::tr("The input file does not exist");
setErrorCondition(-388);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
QString ext = fi.suffix();
if (ext != "ini" && ext != "txt")
{
QString ss = QObject::tr("Incorrect file extension in '%1'. The file extension must be .ini or .txt").arg(getInputFile());
setErrorCondition(-10018);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
if (m_CellEnsembleAttributeMatrixName.isEmpty() == true)
{
QString ss = QObject::tr("Ensemble Attribute Matrix name must be set");
setErrorCondition(-1);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
DataContainer::Pointer m = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getDataContainerName());
if(getErrorCondition() < 0) { return; }
int32_t numphases = 0;
QSettings settings(getInputFile(), QSettings::IniFormat); // The .ini or .txt input file
settings.beginGroup("EnsembleInfo");
numphases = settings.value("Number_Phases").toInt(); // read number of phases from input file
settings.endGroup();
if (0 == numphases) // Either the group name "EnsembleInfo" is incorrect or 0 was entered as the Number_Phases
{
QString ss = QObject::tr("Check the group name EnsembleInfo and that Number_Phases > 0");
setErrorCondition(-10003);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
QVector<size_t> tDims(1, numphases + 1);
m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellEnsembleAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::CellEnsemble);
if(getErrorCondition() < 0) { return; }
QVector<size_t> cDims(1, 1);
tempPath.update(getDataContainerName(), getCellEnsembleAttributeMatrixName(), getCrystalStructuresArrayName() );
m_CrystalStructuresPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<uint32_t>, AbstractFilter, uint32_t>(this, tempPath, Ebsd::CrystalStructure::UnknownCrystalStructure, 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 */
tempPath.update(getDataContainerName(), getCellEnsembleAttributeMatrixName(), getPhaseTypesArrayName() );
m_PhaseTypesPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<uint32_t>, AbstractFilter, uint32_t>(this, tempPath, DREAM3D::PhaseType::UnknownPhaseType, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_PhaseTypesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_PhaseTypes = m_PhaseTypesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void YSChoiAbaqusReader::dataCheck()
{
DataArrayPath tempPath;
setErrorCondition(0);
DataContainer::Pointer m = getDataContainerArray()->createNonPrereqDataContainer<AbstractFilter>(this, getDataContainerName());
if(getErrorCondition() < 0) { return; }
ImageGeom::Pointer image = ImageGeom::CreateGeometry(DREAM3D::Geometry::ImageGeometry);
m->setGeometry(image);
QVector<size_t> tDims(3, 0);
AttributeMatrix::Pointer cellAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::Cell);
if(getErrorCondition() < 0 || NULL == cellAttrMat.get()) { return; }
tDims.resize(1);
tDims[0] = 0;
AttributeMatrix::Pointer cellFeatureAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellFeatureAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::CellFeature);
if(getErrorCondition() < 0 || NULL == cellFeatureAttrMat.get()) { return; }
AttributeMatrix::Pointer cellEnsembleAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellEnsembleAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::CellEnsemble);
if(getErrorCondition() < 0 || NULL == cellEnsembleAttrMat.get()) { return; }
QFileInfo fi(getInputFile());
if (getInputFile().isEmpty() == true)
{
QString ss = QObject::tr("%1 needs the Input File Set and it was not.").arg(ClassName());
setErrorCondition(-387);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
else if (fi.exists() == false)
{
QString ss = QObject::tr("The input file does not exist");
setErrorCondition(-388);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
else
{
bool ok = false;
//const unsigned int size(1024);
// Read header from data file to figure out how many points there are
QFile in(getInputFile());
if (!in.open(QIODevice::ReadOnly | QIODevice::Text))
{
QString msg = QObject::tr("Abaqus file could not be opened: %1").arg(getInputFile());
setErrorCondition(-100);
notifyErrorMessage(getHumanLabel(), "", getErrorCondition());
return;
}
QString word;
bool headerdone = false;
int xpoints, ypoints, zpoints;
float resx, resy, resz;
while (headerdone == false)
{
QByteArray buf = in.readLine();
if (buf.startsWith(DIMS))
{
QList<QByteArray> tokens = buf.split(' ');
xpoints = tokens[1].toInt(&ok, 10);
ypoints = tokens[2].toInt(&ok, 10);
zpoints = tokens[3].toInt(&ok, 10);
size_t dims[3] = { static_cast<size_t>(xpoints), static_cast<size_t>(ypoints), static_cast<size_t>(zpoints) };
m->getGeometryAs<ImageGeom>()->setDimensions(dims);
m->getGeometryAs<ImageGeom>()->setOrigin(0, 0, 0);
}
if (RES == word)
{
QList<QByteArray> tokens = buf.split(' ');
resx = tokens[1].toInt(&ok, 10);
resy = tokens[2].toInt(&ok, 10);
resz = tokens[3].toInt(&ok, 10);
float res[3] = {resx, resy, resz};
m->getGeometryAs<ImageGeom>()->setResolution(res);
}
}
}
QVector<size_t> dims(1, 3);
tempPath.update(getDataContainerName(), getCellAttributeMatrixName(), getCellEulerAnglesArrayName() );
m_CellEulerAnglesPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<float>, AbstractFilter, float>(this, tempPath, 0, dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_CellEulerAnglesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_CellEulerAngles = m_CellEulerAnglesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
dims[0] = 4;
tempPath.update(getDataContainerName(), getCellAttributeMatrixName(), getQuatsArrayName() );
m_QuatsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<float>, AbstractFilter, float>(this, tempPath, 0, dims); /* 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 */
tempPath.update(getDataContainerName(), getCellFeatureAttributeMatrixName(), getAvgQuatsArrayName() );
m_AvgQuatsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<float>, AbstractFilter, float>(this, tempPath, 0, dims); /* 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 */
dims[0] = 1;
tempPath.update(getDataContainerName(), getCellAttributeMatrixName(), getCellPhasesArrayName() );
m_CellPhasesPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, 1, dims); /* 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 */
tempPath.update(getDataContainerName(), getCellFeatureAttributeMatrixName(), getSurfaceFeaturesArrayName() );
m_SurfaceFeaturesPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<bool>, AbstractFilter, bool>(this, tempPath, false, dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceFeaturesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceFeatures = m_SurfaceFeaturesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
tempPath.update(getDataContainerName(), getCellAttributeMatrixName(), 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 */
//typedef DataArray<unsigned int> XTalStructArrayType;
tempPath.update(getDataContainerName(), getCellEnsembleAttributeMatrixName(), getCrystalStructuresArrayName() );
m_CrystalStructuresPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<uint32_t>, AbstractFilter, uint32_t>(this, tempPath, Ebsd::CrystalStructure::Cubic_High, dims); /* 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 */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AlignSections::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getDataContainerName());
size_t dims[3] = { 0, 0, 0 };
m->getGeometryAs<ImageGeom>()->getDimensions(dims);
int64_t xspot = 0, yspot = 0;
int64_t newPosition = 0;
int64_t currentPosition = 0;
std::vector<int64_t> xshifts(dims[2], 0);
std::vector<int64_t> yshifts(dims[2], 0);
find_shifts(xshifts, yshifts);
QList<QString> voxelArrayNames = m->getAttributeMatrix(getCellAttributeMatrixName())->getAttributeArrayNames();
size_t progIncrement = dims[2] / 100;
size_t prog = 1;
size_t progressInt = 0;
size_t slice = 0;
for (size_t i = 1; i < dims[2]; i++)
{
if (i > prog)
{
progressInt = ((float)i / dims[2]) * 100.0f;
QString ss = QObject::tr("Transferring Cell Data || %1% Complete").arg(progressInt);
notifyStatusMessage(getMessagePrefix(), getHumanLabel(), ss);
prog = prog + progIncrement;
}
if (getCancel() == true)
{
return;
}
slice = (dims[2] - 1) - i;
for (size_t l = 0; l < dims[1]; l++)
{
for (size_t n = 0; n < dims[0]; n++)
{
if (yshifts[i] >= 0) { yspot = l; }
else if (yshifts[i] < 0) { yspot = dims[1] - 1 - l; }
if (xshifts[i] >= 0) { xspot = n; }
else if (xshifts[i] < 0) { xspot = dims[0] - 1 - n; }
newPosition = (slice * dims[0] * dims[1]) + (yspot * dims[0]) + xspot;
currentPosition = (slice * dims[0] * dims[1]) + ((yspot + yshifts[i]) * dims[0]) + (xspot + xshifts[i]);
if ((yspot + yshifts[i]) >= 0 && (yspot + yshifts[i]) <= static_cast<int64_t>(dims[1]) - 1 && (xspot + xshifts[i]) >= 0
&& (xspot + xshifts[i]) <= static_cast<int64_t>(dims[0]) - 1)
{
for (QList<QString>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
IDataArray::Pointer p = m->getAttributeMatrix(getCellAttributeMatrixName())->getAttributeArray(*iter);
p->copyTuple( static_cast<size_t>(currentPosition), static_cast<size_t>(newPosition));
}
}
if ((yspot + yshifts[i]) < 0 || (yspot + yshifts[i]) > static_cast<int64_t>(dims[1] - 1) || (xspot + xshifts[i]) < 0
|| (xspot + xshifts[i]) > static_cast<int64_t>(dims[0]) - 1)
{
for (QList<QString>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
IDataArray::Pointer p = m->getAttributeMatrix(getCellAttributeMatrixName())->getAttributeArray(*iter);
EXECUTE_FUNCTION_TEMPLATE(this, initializeArrayValues, p, p, newPosition)
}
}
}
}
}
// If there is an error set this to something negative and also set a message
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void InitializeSyntheticVolume::setupFilterParameters()
{
FilterParameterVector parameters;
QStringList linkedProps("EstimatedPrimaryFeatures");
linkedProps << "InputStatsFile";
parameters.push_back(LinkedBooleanFilterParameter::New("Estimate Number of Features", "EstimateNumberOfFeatures", getEstimateNumberOfFeatures(), linkedProps, FilterParameter::Parameter));
parameters.push_back(InputFileFilterParameter::New("Input Statistics File", "InputStatsFile", getInputStatsFile(), FilterParameter::Parameter, "*.dream3d"));
PreflightUpdatedValueFilterParameter::Pointer param = PreflightUpdatedValueFilterParameter::New("Estimated Primary Features", "EstimatedPrimaryFeatures", getEstimatedPrimaryFeatures(), FilterParameter::Parameter);
param->setReadOnly(true);
parameters.push_back(param);
parameters.push_back(SeparatorFilterParameter::New("Cell Ensemble Data", FilterParameter::RequiredArray));
{
DataArraySelectionFilterParameter::RequirementType req = DataArraySelectionFilterParameter::CreateRequirement(DREAM3D::TypeNames::StatsDataArray, 1, DREAM3D::AttributeMatrixType::CellEnsemble, DREAM3D::Defaults::AnyGeometry);
QVector<uint32_t> geomTypes;
geomTypes.push_back(DREAM3D::GeometryType::ImageGeometry);
geomTypes.push_back(DREAM3D::GeometryType::UnknownGeometry);
req.dcGeometryTypes = geomTypes;
parameters.push_back(DataArraySelectionFilterParameter::New("Statistics", "InputStatsArrayPath", getInputStatsArrayPath(), FilterParameter::RequiredArray, req));
}
{
DataArraySelectionFilterParameter::RequirementType req = DataArraySelectionFilterParameter::CreateRequirement(DREAM3D::TypeNames::UInt32, 1, DREAM3D::AttributeMatrixType::CellEnsemble, DREAM3D::Defaults::AnyGeometry);
QVector<uint32_t> geomTypes;
geomTypes.push_back(DREAM3D::GeometryType::ImageGeometry);
geomTypes.push_back(DREAM3D::GeometryType::UnknownGeometry);
req.dcGeometryTypes = geomTypes;
parameters.push_back(DataArraySelectionFilterParameter::New("Phase Types", "InputPhaseTypesArrayPath", getInputPhaseTypesArrayPath(), FilterParameter::RequiredArray, req));
}
parameters.push_back(StringFilterParameter::New("Synthetic Volume Data Container", "DataContainerName", getDataContainerName(), FilterParameter::CreatedArray));
parameters.push_back(SeparatorFilterParameter::New("Cell Data", FilterParameter::CreatedArray));
parameters.push_back(StringFilterParameter::New("Cell Attribute Matrix", "CellAttributeMatrixName", getCellAttributeMatrixName(), FilterParameter::CreatedArray));
parameters.push_back(IntVec3FilterParameter::New("Dimensions", "Dimensions", getDimensions(), FilterParameter::Parameter));
parameters.push_back(FloatVec3FilterParameter::New("Resolution", "Resolution", getResolution(), FilterParameter::Parameter));
parameters.push_back(FloatVec3FilterParameter::New("Origin", "Origin", getOrigin(), FilterParameter::Parameter));
setFilterParameters(parameters);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 YSChoiAbaqusReader::execute()
{
dataCheck();
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getDataContainerName());
int xpoints, ypoints, zpoints, totalpoints = 0;
float resx, resy, resz;
float** *mat = NULL;
//const unsigned int size(1024);
// Read header from data file to figure out how many points there are
QFile in(getInputFile());
if (!in.open(QIODevice::ReadOnly | QIODevice::Text))
{
QString msg = QObject::tr("Abaqus file could not be opened: %1").arg(getInputFile());
setErrorCondition(-100);
notifyErrorMessage(getHumanLabel(), "", getErrorCondition());
return;
}
QString word;
bool ok = false;
bool headerdone = false;
while (headerdone == false)
{
QByteArray buf = in.readLine();
if (buf.startsWith(DIMS))
{
QList<QByteArray> tokens = buf.split(' ');
xpoints = tokens[1].toInt(&ok, 10);
ypoints = tokens[2].toInt(&ok, 10);
zpoints = tokens[3].toInt(&ok, 10);
totalpoints = xpoints * ypoints * zpoints;
size_t dims[3] = { static_cast<size_t>(xpoints), static_cast<size_t>(ypoints), static_cast<size_t>(zpoints) };
m->getGeometryAs<ImageGeom>()->setDimensions(dims);
m->getGeometryAs<ImageGeom>()->setOrigin(0, 0, 0);
}
if (buf.startsWith(RES))
{
QList<QByteArray> tokens = buf.split(' ');
resx = tokens[1].toInt(&ok, 10);
resy = tokens[2].toInt(&ok, 10);
resz = tokens[3].toInt(&ok, 10);
float res[3] = {resx, resy, resz};
m->getGeometryAs<ImageGeom>()->setResolution(res);
}
if (buf.startsWith(LOOKUP))
{
headerdone = true;
word = QString(buf);
}
}
// Read header from grain info file to figure out how many features there are
QFile in2(getInputFeatureInfoFile());
if (!in2.open(QIODevice::ReadOnly | QIODevice::Text))
{
QString msg = QObject::tr("Abaqus Feature Info file could not be opened: %1").arg(getInputFeatureInfoFile());
setErrorCondition(-100);
notifyErrorMessage(getHumanLabel(), "", getErrorCondition());
return;
}
int numfeatures;
QByteArray buf = in2.readLine();
numfeatures = buf.toInt(&ok, 10);
buf = in2.readLine();
QList<QByteArray> tokens = buf.split(' ');
// in2 >> word >> word >> word >> word >> word >> word;
QVector<size_t> tDims(3, 0);
tDims[0] = xpoints;
tDims[1] = ypoints;
tDims[2] = zpoints;
m->getAttributeMatrix(getCellAttributeMatrixName())->resizeAttributeArrays(tDims);
tDims.resize(1);
tDims[0] = numfeatures + 1;
m->getAttributeMatrix(getCellFeatureAttributeMatrixName())->resizeAttributeArrays(tDims);
tDims[0] = 2;
m->getAttributeMatrix(getCellEnsembleAttributeMatrixName())->resizeAttributeArrays(tDims);
updateCellInstancePointers();
updateFeatureInstancePointers();
updateEnsembleInstancePointers();
//Read data file
int gnum = 0;
bool onedge = false;
int col, row, plane;
float value;
for (int i = 0; i < totalpoints; i++)
{
mat[i] = new float *[3];
for(int j = 0; j < 3; j++)
{
mat[i][j] = new float [3];
}
onedge = false;
gnum = tokens[6].toInt(&ok, 10);
col = i % xpoints;
row = (i / xpoints) % ypoints;
plane = i / (xpoints * ypoints);
if (col == 0 || col == (xpoints - 1) || row == 0 || row == (ypoints - 1) || plane == 0 || plane == (zpoints - 1)) { onedge = true; }
m_FeatureIds[i] = gnum;
m_SurfaceFeatures[gnum] = onedge;
}
for (int iter1 = 0; iter1 < 3; iter1++)
{
for (int iter2 = 0; iter2 < 3; iter2++)
{
headerdone = false;
while (headerdone == false)
{
buf = in2.readLine();
if (buf.startsWith(LOOKUP))
{
headerdone = true;
//in >> word;
}
}
for (int i = 0; i < totalpoints; i++)
{
onedge = 0;
value = buf.toInt(&ok, 10);
mat[i][iter1][iter2] = value;
}
}
}
//Read feature info
QuatF* avgQuats = reinterpret_cast<QuatF*>(m_AvgQuats);
avgQuats[0].x = 0.0;
avgQuats[0].y = 0.0;
avgQuats[0].z = 0.0;
avgQuats[0].w = 0.0;
for (int i = 1; i < numfeatures + 1; i++)
{
buf = in2.readLine();
tokens = buf.split(' ');
gnum = tokens[0].toInt(&ok, 10);
avgQuats[i].x = tokens[2].toFloat(&ok);
avgQuats[i].y = tokens[3].toFloat(&ok);
avgQuats[i].z = tokens[4].toFloat(&ok);
avgQuats[i].w = tokens[5].toFloat(&ok);
}
QuatF q;
QuatF* quats = reinterpret_cast<QuatF*>(m_Quats);
float g[3][3];
for(int i = 0; i < (xpoints * ypoints * zpoints); i++)
{
for(int j = 0; j < 3; j++)
{
for(int k = 0; k < 3; k++)
{
g[j][k] = mat[i][j][k];
}
}
MatrixMath::Normalize3x3(g);
q.w = static_cast<float>( sqrt((1.0 + g[0][0] + g[1][1] + g[2][2])) / 2.0 );
q.x = static_cast<float>( (g[1][2] - g[2][1]) / (4.0 * q.w) );
q.y = static_cast<float>( (g[2][0] - g[0][2]) / (4.0 * q.w) );
q.z = static_cast<float>( (g[0][1] - g[1][0]) / (4.0 * q.w) );
QuaternionMathF::Copy(q, quats[i]);
FOrientArrayType eu(m_CellEulerAngles + (3 * i), 3);
FOrientTransformsType::qu2eu(FOrientArrayType(q), eu);
delete[] mat[i];
}
delete[] mat;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AlignSectionsMutualInformation::form_features_sections()
{
DREAM3D_RANDOMNG_NEW()
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getDataContainerName());
size_t udims[3] = { 0, 0, 0 };
m->getGeometryAs<ImageGeom>()->getDimensions(udims);
#if (CMP_SIZEOF_SIZE_T == 4)
typedef int32_t DimType;
#else
typedef int64_t DimType;
#endif
DimType dims[3] =
{
static_cast<DimType>(udims[0]),
static_cast<DimType>(udims[1]),
static_cast<DimType>(udims[2]),
};
DimType point = 0;
DimType seed = 0;
bool noseeds = false;
int32_t featurecount = 1;
DimType neighbor = 0;
QuatF q1 = QuaternionMathF::New();
QuatF q2 = QuaternionMathF::New();
QuatF* quats = reinterpret_cast<QuatF*>(m_Quats);
float w = 0.0f;
float n1 = 0.0f;
float n2 = 0.0f;
float n3 = 0.0f;
DimType randx = 0;
DimType randy = 0;
bool good = false;
DimType x = 0, y = 0, z = 0;
DimType col = 0, row = 0;
size_t size = 0;
size_t initialVoxelsListSize = 1000;
m_FeatureCounts->resize(dims[2]);
featurecounts = m_FeatureCounts->getPointer(0);
std::vector<DimType> voxelslist(initialVoxelsListSize, -1);
DimType neighpoints[4] = { 0, 0, 0, 0 };
neighpoints[0] = -dims[0];
neighpoints[1] = -1;
neighpoints[2] = 1;
neighpoints[3] = dims[0];
uint32_t phase1 = 0, phase2 = 0;
for (DimType slice = 0; slice < dims[2]; slice++)
{
QString ss = QObject::tr("Aligning Sections || Identifying Features on Sections || %1% Complete").arg(((float)slice / dims[2]) * 100);
notifyStatusMessage(getMessagePrefix(), getHumanLabel(), ss);
featurecount = 1;
noseeds = false;
while (noseeds == false)
{
seed = -1;
randx = DimType(float(rg.genrand_res53()) * float(dims[0]));
randy = DimType(float(rg.genrand_res53()) * float(dims[1]));
for (DimType j = 0; j < dims[1]; ++j)
{
for (DimType i = 0; i < dims[0]; ++i)
{
x = randx + i;
y = randy + j;
z = slice;
if (x > dims[0] - 1) { x = x - dims[0]; }
if (y > dims[1] - 1) { y = y - dims[1]; }
point = (z * dims[0] * dims[1]) + (y * dims[0]) + x;
if ((m_UseGoodVoxels == false || m_GoodVoxels[point] == true) && m_FeatureIds[point] == 0 && m_CellPhases[point] > 0)
{
seed = point;
}
if (seed > -1) { break; }
}
if( seed > -1) { break; }
}
if (seed == -1) { noseeds = true; }
if (seed >= 0)
{
size = 0;
m_FeatureIds[seed] = featurecount;
voxelslist[size] = seed;
size++;
for (size_t j = 0; j < size; ++j)
{
DimType currentpoint = voxelslist[j];
col = currentpoint % dims[0];
row = (currentpoint / dims[0]) % dims[1];
QuaternionMathF::Copy(quats[currentpoint], q1);
phase1 = m_CrystalStructures[m_CellPhases[currentpoint]];
for (int32_t i = 0; i < 4; i++)
{
good = true;
neighbor = currentpoint + neighpoints[i];
if ((i == 0) && row == 0) { good = false; }
if ((i == 3) && row == (dims[1] - 1)) { good = false; }
if ((i == 1) && col == 0) { good = false; }
if ((i == 2) && col == (dims[0] - 1)) { good = false; }
if (good == true && m_FeatureIds[neighbor] <= 0 && m_CellPhases[neighbor] > 0)
{
w = std::numeric_limits<float>::max();
QuaternionMathF::Copy(quats[neighbor], q2);
phase2 = m_CrystalStructures[m_CellPhases[neighbor]];
if (phase1 == phase2)
{
w = m_OrientationOps[phase1]->getMisoQuat(q1, q2, n1, n2, n3);
}
if (w < m_MisorientationTolerance)
{
m_FeatureIds[neighbor] = featurecount;
voxelslist[size] = neighbor;
size++;
if (std::vector<DimType>::size_type(size) >= voxelslist.size())
{
size = voxelslist.size();
voxelslist.resize(size + initialVoxelsListSize);
for (std::vector<DimType>::size_type v = size; v < voxelslist.size(); ++v) { voxelslist[v] = -1; }
}
}
}
}
}
voxelslist.erase(std::remove(voxelslist.begin(), voxelslist.end(), -1), voxelslist.end());
featurecount++;
voxelslist.assign(initialVoxelsListSize, -1);
}
}
featurecounts[slice] = featurecount;
}
}