// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void MoveData::dataCheck()
{
setErrorCondition(0);
DataArrayPath amSrcPath = getAttributeMatrixSource();
DataArrayPath amDestPath = getAttributeMatrixDestination();
DataArrayPath daSrcPath = getDataArraySource();
if (getWhatToMove() == k_MoveAttributeMatrix)
{
DataContainer::Pointer amDestDataContainer = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getDataContainerDestination());
DataContainer::Pointer amSrcDataContainer = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, amSrcPath.getDataContainerName());
AttributeMatrix::Pointer amSrcAttributeMatrix = getDataContainerArray()->getPrereqAttributeMatrixFromPath<AbstractFilter>(this, amSrcPath, -301);
if(getErrorCondition() < 0) { return; }
if (amSrcDataContainer->getName() == amDestDataContainer->getName())
{
QString ss = QObject::tr("The source and destination Data Container are the same. Is this what you meant to do?");
notifyWarningMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
amDestDataContainer->addAttributeMatrix(amSrcAttributeMatrix->getName(), amSrcAttributeMatrix);
amSrcDataContainer->removeAttributeMatrix(amSrcAttributeMatrix->getName());
}
else if (getWhatToMove() == k_MoveDataArray )
{
AttributeMatrix::Pointer daSrcAttributeMatrix = getDataContainerArray()->getPrereqAttributeMatrixFromPath<AbstractFilter>(this, daSrcPath, -301);
AttributeMatrix::Pointer daDestAttributeMatrix = getDataContainerArray()->getPrereqAttributeMatrixFromPath<AbstractFilter>(this, amDestPath, -301);
IDataArray::Pointer daSrcDataArray = getDataContainerArray()->getPrereqIDataArrayFromPath<IDataArray, AbstractFilter>(this, daSrcPath);
if(getErrorCondition() < 0) { return; }
if (daDestAttributeMatrix->getNumTuples() != daSrcDataArray->getNumberOfTuples())
{
setErrorCondition(-11019);
QString ss = QObject::tr("The number of tuples of source Attribute Array (%1) and destination Attribute Matrix (%2) do not match").arg(daSrcDataArray->getNumberOfTuples()).arg(daDestAttributeMatrix->getNumTuples());
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
else if (amSrcPath == amDestPath)
{
QString ss = QObject::tr("The source and destination Attribute Matrix are the same. Is this what you meant to do?");
notifyWarningMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
daDestAttributeMatrix->addAttributeArray(daSrcPath.getDataArrayName(), daSrcDataArray);
daSrcAttributeMatrix->removeAttributeArray(daSrcPath.getDataArrayName());
}
else
{
setErrorCondition(-11020);
QString ss = QObject::tr("Neither an Attribute Matrix nor an Attribute Array was selected to be moved");
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void GenerateMisorientationColors::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
size_t totalPoints = m_CellPhasesPtr.lock()->getNumberOfTuples();
// Make sure we are dealing with a unit 1 vector.
FloatVec3_t normRefDir = m_ReferenceAxis; // Make a copy of the reference Direction
MatrixMath::Normalize3x1(normRefDir.x, normRefDir.y, normRefDir.z);
// Create 1 of every type of Ops class. This condenses the code below
UInt8ArrayType::Pointer notSupported = UInt8ArrayType::CreateArray(13, "_INTERNAL_USE_ONLY_NotSupportedArray");
notSupported->initializeWithZeros();
#ifdef DREAM3D_USE_PARALLEL_ALGORITHMS
tbb::task_scheduler_init init;
bool doParallel = true;
#endif
#ifdef DREAM3D_USE_PARALLEL_ALGORITHMS
if (doParallel == true)
{
tbb::parallel_for(tbb::blocked_range<size_t>(0, totalPoints),
GenerateMisorientationColorsImpl( normRefDir, m_ReferenceAngle, reinterpret_cast<QuatF*>(m_Quats), m_CellPhases, m_CrystalStructures, m_GoodVoxels, notSupported->getPointer(0), m_MisorientationColor), tbb::auto_partitioner());
}
else
#endif
{
GenerateMisorientationColorsImpl serial( normRefDir, m_ReferenceAngle, reinterpret_cast<QuatF*>(m_Quats), m_CellPhases, m_CrystalStructures, m_GoodVoxels, notSupported->getPointer(0), m_MisorientationColor);
serial.convert(0, totalPoints);
}
QVector<SpaceGroupOps::Pointer> ops = SpaceGroupOps::getOrientationOpsQVector();
// Check and warn about unsupported crystal symmetries in the computation which will show as black
for (size_t i = 0; i < notSupported->getNumberOfTuples() - 1; i++)
{
if (notSupported->getValue(i) == 1)
{
QString msg("The symmetry of ");
msg.append(ops[i]->getSymmetryName()).append(" is not currently supported for misorientation coloring. Elements with this symmetry have been set to black");
notifyWarningMessage(getHumanLabel(), msg, -5000);
}
}
// Check for bad voxels which will show up as black also.
if (notSupported->getValue(12) == 1)
{
QString msg("There were elements with an unknown crystal symmetry due most likely being marked as 'a 'bad'. These elements have been colored black BUT black is a valid color for misorientation coloring. Please understand this when visualizing your data");
notifyWarningMessage(getHumanLabel(), msg, -5001);
}
/* Let the GUI know we are done with this filter */
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AbaqusSurfaceMeshWriter::dataCheck()
{
setErrorCondition(0);
if (m_OutputFile.isEmpty() == true)
{
setErrorCondition(-1003);
notifyErrorMessage(getHumanLabel(), "The output file must be set", getErrorCondition());
}
QFileInfo fi(m_OutputFile);
QDir parentPath = fi.path();
if (parentPath.exists() == false)
{
QString ss = QObject::tr( "The directory path for the output file does not exist. DREAM.3D will attempt to create this path during execution of the filter");
notifyWarningMessage(getHumanLabel(), ss, -1);
}
QVector<IDataArray::Pointer> dataArrays;
TriangleGeom::Pointer triangles = getDataContainerArray()->getPrereqGeometryFromDataContainer<TriangleGeom, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
if(getErrorCondition() >= 0) { dataArrays.push_back(triangles->getTriangles()); }
QVector<size_t> cDims(1, 2);
m_SurfaceMeshFaceLabelsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFaceLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFaceLabels = m_SurfaceMeshFaceLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() >= 0) { dataArrays.push_back(m_SurfaceMeshFaceLabelsPtr.lock()); }
getDataContainerArray()->validateNumberOfTuples<AbstractFilter>(this, dataArrays);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void INLWriter::dataCheck()
{
setErrorCondition(0);
getDataContainerArray()->getPrereqGeometryFromDataContainer<ImageGeom, AbstractFilter>(this, getFeatureIdsArrayPath().getDataContainerName());
if (getOutputFile().isEmpty() == true)
{
QString ss = QObject::tr("The output file must be set");
setErrorCondition(-1);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
QFileInfo fi(getOutputFile());
QDir parentPath = fi.path();
if (parentPath.exists() == false)
{
QString ss = QObject::tr("The directory path for the output file does not exist. DREAM.3D will attempt to create this path during execution of the filter");
notifyWarningMessage(getHumanLabel(), ss, -1);
}
QVector<DataArrayPath> cellDataArrayPaths;
QVector<DataArrayPath> ensembleDataArrayPaths;
QVector<size_t> cDims(1, 1);
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 */
if(getErrorCondition() >= 0) { cellDataArrayPaths.push_back(getFeatureIdsArrayPath()); }
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) { cellDataArrayPaths.push_back(getCellPhasesArrayPath()); }
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 */
if(getErrorCondition() >= 0) { ensembleDataArrayPaths.push_back(getCrystalStructuresArrayPath()); }
m_NumFeaturesPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getNumFeaturesArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_NumFeaturesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_NumFeatures = m_NumFeaturesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() >= 0) { ensembleDataArrayPaths.push_back(getNumFeaturesArrayPath()); }
m_MaterialNamePtr = getDataContainerArray()->getPrereqArrayFromPath<StringDataArray, AbstractFilter>(this, getMaterialNameArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if(getErrorCondition() >= 0) { ensembleDataArrayPaths.push_back(getMaterialNameArrayPath()); }
cDims[0] = 3;
m_CellEulerAnglesPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<float>, AbstractFilter>(this, getCellEulerAnglesArrayPath(), cDims); /* 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 */
if(getErrorCondition() >= 0) { cellDataArrayPaths.push_back(getCellEulerAnglesArrayPath()); }
getDataContainerArray()->validateNumberOfTuples<AbstractFilter>(this, cellDataArrayPaths);
getDataContainerArray()->validateNumberOfTuples<AbstractFilter>(this, ensembleDataArrayPaths);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void WritePoleFigure::dataCheck()
{
setErrorCondition(0);
QDir path(getOutputPath());
getDataContainerArray()->getPrereqGeometryFromDataContainer<ImageGeom, AbstractFilter>(this, getCellPhasesArrayPath().getDataContainerName());
if (m_OutputPath.isEmpty() == true)
{
setErrorCondition(-1003);
notifyErrorMessage(getHumanLabel(), "The output directory must be set", getErrorCondition());
}
else if (path.exists() == false)
{
QString ss = QObject::tr("The directory path for the output file does not exist. DREAM.3D will attempt to create this path during execution of the filter");
notifyWarningMessage(getHumanLabel(), ss, -1);
}
QVector<DataArrayPath> dataArrayPaths;
QVector<size_t> cDims(1, 3);
m_CellEulerAnglesPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<float>, AbstractFilter>(this, getCellEulerAnglesArrayPath(), cDims); /* 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 */
if(getErrorCondition() >= 0) { dataArrayPaths.push_back(getCellEulerAnglesArrayPath()); }
cDims[0] = 1;
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()); }
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 */
// The good voxels array is optional, If it is available we are going to use it, otherwise we are going to create it
cDims[0] = 1;
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())
{
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()); }
}
else
{
m_GoodVoxels = NULL;
}
getDataContainerArray()->validateNumberOfTuples<AbstractFilter>(this, dataArrayPaths);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void WriteStatsGenOdfAngleFile::dataCheck()
{
setErrorCondition(0);
QString ss;
if (getOutputFile().isEmpty() == true)
{
ss = QObject::tr( "The output file must be set");
setErrorCondition(-1);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
QFileInfo fi(getOutputFile());
QDir parentPath = fi.path();
if (parentPath.exists() == false)
{
ss = QObject::tr( "The directory path for the output file does not exist");
notifyWarningMessage(getHumanLabel(), ss, -1);
}
QVector<size_t> cDims(1, 1);
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 */
}
cDims[0] = 3;
m_CellEulerAnglesPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<float>, AbstractFilter>(this, getCellEulerAnglesArrayPath(), cDims); /* 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 */
}
if (getUseGoodVoxels() == true)
{
// The good voxels array is optional, If it is available we are going to use it, otherwise we are going to create it
cDims[0] = 1;
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 */
}
}
else
{
m_GoodVoxels = NULL;
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void VisualizeGBCDPoleFigure::dataCheck()
{
setErrorCondition(0);
getDataContainerArray()->getPrereqGeometryFromDataContainer<TriangleGeom, AbstractFilter>(this, getGBCDArrayPath().getDataContainerName());
if (getOutputFile().isEmpty() == true)
{
QString ss = QObject::tr( "The output file must be set");
setErrorCondition(-1000);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
QFileInfo fi(getOutputFile());
QDir parentPath = fi.path();
if (parentPath.exists() == false && getInPreflight())
{
QString ss = QObject::tr( "The directory path for the output file does not exist. DREAM.3D will attempt to create this path during execution of the filter");
notifyWarningMessage(getHumanLabel(), ss, -1);
}
if (fi.suffix().compare("") == 0)
{
setOutputFile(getOutputFile().append(".vtk"));
}
QVector<size_t> cDims(1, 1);
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 */
IDataArray::Pointer tmpGBCDPtr = getDataContainerArray()->getPrereqIDataArrayFromPath<IDataArray, AbstractFilter>(this, getGBCDArrayPath());
if(getErrorCondition() < 0) { return; }
if (NULL != tmpGBCDPtr.get())
{
QVector<size_t> cDims = tmpGBCDPtr->getComponentDimensions();
m_GBCDPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<double>, AbstractFilter>(this, getGBCDArrayPath(), 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 */
}
if (NULL != m_GBCDPtr.lock().get() && getPhaseOfInterest() >= m_GBCDPtr.lock()->getNumberOfTuples())
{
QString ss = QObject::tr("The phase index is larger than the number of Ensembles").arg(ClassName());
setErrorCondition(-1);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 WriteImages::dataCheck()
{
setErrorCondition(0);
getDataContainerArray()->getPrereqGeometryFromDataContainer<ImageGeom, AbstractFilter>(this, getColorsArrayPath().getDataContainerName());
QDir dir(getOutputPath());
if (getOutputPath().isEmpty() == true)
{
setErrorCondition(-1003);
notifyErrorMessage(getHumanLabel(), "The output directory must be set", getErrorCondition());
}
else if (dir.exists() == false)
{
QString ss = QObject::tr("The output directory path does not exist. DREAM.3D will attempt to create this path during execution");
notifyWarningMessage(getHumanLabel(), ss, -1);
}
IDataArray::Pointer iDa = getDataContainerArray()->getPrereqIDataArrayFromPath<IDataArray, AbstractFilter>(this, getColorsArrayPath());
if (getErrorCondition() < 0) { return; }
QVector<size_t> cDims = iDa->getComponentDimensions();
if (cDims[0] == 1)
{
m_ColorsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<uint8_t>, AbstractFilter>(this, getColorsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if (NULL != m_ColorsPtr.lock().get()) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_Colors = m_ColorsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
else if (cDims[0] == 3)
{
m_ColorsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<uint8_t>, AbstractFilter>(this, getColorsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if (NULL != m_ColorsPtr.lock().get()) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_Colors = m_ColorsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
else if (cDims[0] == 4)
{
m_ColorsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<uint8_t>, AbstractFilter>(this, getColorsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if (NULL != m_ColorsPtr.lock().get()) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_Colors = m_ColorsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
else
{
setErrorCondition(-1006);
notifyErrorMessage(getHumanLabel(), "Number of components must be 1 (grayscale), 3 (RGB) or 4 (ARGB) arrays", getErrorCondition());
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void FindFeaturePhases::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
size_t totalPoints = m_FeatureIdsPtr.lock()->getNumberOfTuples();
int32_t gnum = 0;
QMap<int32_t, int32_t> featureMap;
QMap<int32_t, int32_t> warningMap;
for (size_t i = 0; i < totalPoints; i++)
{
gnum = m_FeatureIds[i];
if (!featureMap.contains(gnum)) { featureMap.insert(gnum, m_CellPhases[i]); }
int32_t curPhaseVal = featureMap.value(gnum);
if (curPhaseVal != m_CellPhases[i])
{
if(!warningMap.contains(gnum)) { warningMap[gnum] = 1; }
else {
warningMap[gnum]++;
}
}
m_FeaturePhases[gnum] = m_CellPhases[i];
}
if(warningMap.size() > 0)
{
QStringList warnings;
QString header = QString("Elements from some features did not all have the same phase Id. The last phase Id copied into each feature will be used");
warnings.append(header);
QMapIterator<int32_t, int32_t> i(warningMap);
while (i.hasNext()) {
i.next();
QString str;
QTextStream ss(&str);
ss << " Phase Feature " << i.key() << " created " << i.value() << " warnings.";
warnings.append(str);
}
notifyWarningMessage(getHumanLabel(), warnings.join("\n"), getErrorCondition());
}
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RequiredZThickness::dataCheck()
{
setErrorCondition(0);
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer dataContainer = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getDataContainerSelection());
if (getErrorCondition() < 0) { return; }
ImageGeom::Pointer image = dataContainer->getGeometryAs<ImageGeom>();
if( NULL == image.get() )
{
setErrorCondition(-7789);
notifyErrorMessage(getHumanLabel(), "Missing Image Geometry in the selected DataContainer", getErrorCondition());
return;
}
size_t dims[3] = { 0, 0, 0 };
image->getDimensions(dims);
if (dims[2] < getNumZVoxels() && m_PreflightCheck)
{
setErrorCondition(-7787);
QString str;
QTextStream ss(&str);
ss << "Number of Z Voxels does not meet required value during preflight of the filter. \n";
ss << " Required Z Voxels: " << m_NumZVoxels << "\n";
ss << " Current Z Voxels: " << dims[2];
notifyErrorMessage(getHumanLabel(), str, getErrorCondition());
}
else if (dims[2] < getNumZVoxels() && !m_PreflightCheck)
{
QString str;
QTextStream ss(&str);
ss << "Number of Z Voxels does not meet required value during preflight but will be checked during pipeline execution.\n";
ss << " Required Z Voxels: " << m_NumZVoxels << "\n";
ss << " Current Z Voxels: " << dims[2];
notifyWarningMessage(getHumanLabel(), str, getErrorCondition());
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
QString InitializeSyntheticVolume::estimateNumFeatures(IntVec3_t dims, FloatVec3_t res)
{
float totalvol = 0.0f;
int32_t phase = 0;
totalvol = (dims.x * res.x) * (dims.y * res.y) * (dims.z * res.z);
if (totalvol == 0.0)
{
return "-1";
}
DataContainerArray::Pointer dca = getDataContainerArray();
// Get the PhaseTypes - Remember there is a Dummy PhaseType in the first slot of the array
QVector<size_t> cDims(1, 1); // This states that we are looking for an array with a single component
UInt32ArrayType::Pointer phaseType = dca->getPrereqArrayFromPath<UInt32ArrayType, AbstractFilter>(NULL, getInputPhaseTypesArrayPath(), cDims);
if (phaseType.get() == NULL)
{
QString ss = QObject::tr("Phase types array could not be downcast using std::dynamic_pointer_cast<T> when estimating the number of grains. The path is %1").arg(getInputPhaseTypesArrayPath().serialize());
setErrorCondition(-11002);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return "0";
}
QVector<size_t> statsDims(1, 1);
StatsDataArray::Pointer statsPtr = dca->getPrereqArrayFromPath<StatsDataArray, AbstractFilter>(this, getInputStatsArrayPath(), statsDims);
if (statsPtr.get() == NULL)
{
QString ss = QObject::tr("Statistics array could not be downcast using std::dynamic_pointer_cast<T> when estimating the number of grains. The path is %1").arg(getInputStatsArrayPath().serialize());
notifyErrorMessage(getHumanLabel(), ss, -11001);
return "0";
}
if (!phaseType->isAllocated())
{
if (getInputStatsFile().isEmpty())
{
QString ss = QObject::tr("Phase types array has not been allocated and the input statistics file is empty");
setErrorCondition(-1000);
notifyWarningMessage(getHumanLabel(), ss, getErrorCondition());
return "-1";
}
QFileInfo fi(getInputStatsFile());
if (fi.exists() == false)
{
QString ss = QObject::tr("Phase types array has not been allocated and the input statistics file does not exist at '%1'").arg(fi.absoluteFilePath());
setErrorCondition(-1001);
notifyWarningMessage(getHumanLabel(), ss, getErrorCondition());
return "-1";
}
hid_t fileId = -1;
herr_t err = 0;
// open the file
fileId = H5Utilities::openFile(getInputStatsFile().toLatin1().constData(), true);
// This will make sure if we return early from this method that the HDF5 File is properly closed.
HDF5ScopedFileSentinel scopedFileSentinel(&fileId, true);
DataArrayPath dap = getInputPhaseTypesArrayPath();
// Generate the path to the AttributeMatrix
QString hPath = DREAM3D::StringConstants::DataContainerGroupName + "/" + dap.getDataContainerName() + "/" + dap.getAttributeMatrixName();
// Open the AttributeMatrix Group
hid_t amGid = H5Gopen(fileId, hPath.toLatin1().data(), H5P_DEFAULT );
scopedFileSentinel.addGroupId(&amGid);
err = phaseType->readH5Data(amGid);
if (err < 0)
{
QString ss = QObject::tr("Error reading phase type data");
setErrorCondition(-1003);
notifyWarningMessage(getHumanLabel(), ss, getErrorCondition());
return "-1";
}
if (!phaseType->isAllocated())
{
QString ss = QObject::tr("Phase types Array was not allocated due to an error reading the data from the statistics file %1").arg(fi.absoluteFilePath());
setErrorCondition(-1002);
notifyWarningMessage(getHumanLabel(), ss, getErrorCondition());
return "-1";
}
}
// Create a Reference Variable so we can use the [] syntax
StatsDataArray& statsDataArray = *(statsPtr.get());
std::vector<int32_t> primaryphases;
std::vector<double> primaryphasefractions;
double totalprimaryfractions = 0.0;
// find which phases are primary phases
for (size_t i = 1; i < phaseType->getNumberOfTuples(); ++i)
{
if (phaseType->getValue(i) == DREAM3D::PhaseType::PrimaryPhase)
{
PrimaryStatsData* pp = PrimaryStatsData::SafePointerDownCast(statsDataArray[i].get());
primaryphases.push_back(i);
primaryphasefractions.push_back(pp->getPhaseFraction());
totalprimaryfractions = totalprimaryfractions + pp->getPhaseFraction();
}
}
// scale the primary phase fractions to total to 1
for (int32_t i = 0; i < primaryphasefractions.size(); i++)
{
primaryphasefractions[i] = primaryphasefractions[i] / totalprimaryfractions;
}
SIMPL_RANDOMNG_NEW()
// generate the Features
int32_t gid = 1;
float currentvol = 0.0f;
float vol = 0.0f;
float diam = 0.0f;
bool volgood = false;
for (int32_t j = 0; j < primaryphases.size(); ++j)
{
float curphasetotalvol = totalvol * primaryphasefractions[j];
while (currentvol < curphasetotalvol)
{
volgood = false;
phase = primaryphases[j];
PrimaryStatsData* pp = PrimaryStatsData::SafePointerDownCast(statsDataArray[phase].get());
if (NULL == pp)
{
QString ss = QObject::tr("Tried to cast a statsDataArray[%1].get() to a PrimaryStatsData* "
"pointer but this resulted in a NULL pointer.\n")
.arg(phase).arg(phase);
setErrorCondition(-666);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return "-1";
}
while (volgood == false)
{
volgood = true;
if (pp->getFeatureSize_DistType() == DREAM3D::DistributionType::LogNormal)
{
float avgdiam = pp->getFeatureSizeDistribution().at(0)->getValue(0);
float sddiam = pp->getFeatureSizeDistribution().at(1)->getValue(0);
diam = rg.genrand_norm(avgdiam, sddiam);
diam = expf(diam);
if (diam >= pp->getMaxFeatureDiameter()) { volgood = false; }
if (diam < pp->getMinFeatureDiameter()) { volgood = false; }
vol = (4.0f / 3.0f) * (M_PI) * ((diam * 0.5f) * (diam * 0.5f) * (diam * 0.5f));
}
}
currentvol = currentvol + vol;
gid++;
}
}
return QString::number(gid);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void Hex2SqrConverter::execute()
{
std::stringstream ss;
herr_t err = 0;
std::vector<int> indices;
// Loop on Each EBSD File
float total = static_cast<float>( m_ZEndIndex - m_ZStartIndex );
int progress = 0;
int64_t z = m_ZStartIndex;
/* There is a frailness about the z index and the file list. The programmer
* using this code MUST ensure that the list of files that is sent into this
* class is in the appropriate order to match up with the z index (slice index)
* otherwise the import will have subtle errors. The programmer is urged NOT to
* simply gather a list from the file system as those lists are sorted in such
* a way that if the number of digits appearing in the filename are NOT the same
* then the list will be wrong, ie, this example:
*
* slice_1.ang
* slice_2.ang
* ....
* slice_10.ang
*
* Most, if not ALL C++ libraries when asked for that list will return the list
* sorted like the following:
*
* slice_1.ang
* slice_10.ang
* slice_2.ang
*
* which is going to cause problems because the data is going to be placed
* into the HDF5 file at the wrong index. YOU HAVE BEEN WARNED.
*/
// int totalSlicesImported = 0;
for (std::vector<std::string>::iterator filepath = m_EbsdFileList.begin(); filepath != m_EbsdFileList.end(); ++filepath)
{
std::string ebsdFName = *filepath;
progress = static_cast<int>( z - m_ZStartIndex );
progress = (int)(100.0f * (float)(progress) / total);
std::string msg = "Converting File: " + ebsdFName;
ss.str("");
notifyStatusMessage(msg.c_str());
// Write the Manufacturer of the OIM file here
// This list will grow to be the number of EBSD file formats we support
std::string ext = MXAFileInfo::extension(ebsdFName);
std::string base = MXAFileInfo::fileNameWithOutExtension(ebsdFName);
std::string path = MXAFileInfo::parentPath(ebsdFName);
if(ext.compare(Ebsd::Ang::FileExt) == 0)
{
AngReader reader;
reader.setFileName(ebsdFName);
reader.setReadHexGrid(true);
int err = reader.readFile();
if(err < 0 && err != -600)
{
addErrorMessage(getHumanLabel(), reader.getErrorMessage(), reader.getErrorCode());
setErrorCondition(reader.getErrorCode());
return;
}
else if(reader.getGrid().find(Ebsd::Ang::SquareGrid) == 0)
{
ss.str("");
ss << "Ang File is already a square grid: " << ebsdFName;
setErrorCondition(-55000);
addErrorMessage(getHumanLabel(), ss.str(), getErrorCondition());
return;
}
else
{
if (err == -600)
{
notifyWarningMessage( reader.getErrorMessage(), reader.getErrorCode() );
}
std::string origHeader = reader.getOriginalHeader();
if (origHeader.empty() == true)
{
ss.str();
ss << "Header could not be retrieved: " << ebsdFName;
setErrorCondition(-55001);
addErrorMessage(getHumanLabel(), ss.str(), getErrorCondition());
}
char buf[kBufferSize];
std::stringstream in(origHeader);
std::string newEbsdFName = path + "/Sqr_" + base + "." + ext;
std::ofstream outFile;
outFile.open(newEbsdFName.c_str());
m_HeaderIsComplete = false;
float HexXStep = reader.getXStep();
float HexYStep = reader.getYStep();
int HexNumColsOdd = reader.getNumOddCols();
int HexNumColsEven = reader.getNumEvenCols();
int HexNumRows = reader.getNumRows();
m_NumCols = (HexNumColsOdd*HexXStep)/m_XResolution;
m_NumRows = (HexNumRows*HexYStep)/m_YResolution;
float xSqr, ySqr, xHex1, yHex1, xHex2, yHex2;
int point, point1, point2;
int row1, row2, col1, col2;
float dist1, dist2;
float* phi1 = reader.getPhi1Pointer();
float* PHI = reader.getPhiPointer();
float* phi2 = reader.getPhi2Pointer();
float* ci = reader.getConfidenceIndexPointer();
float* iq = reader.getImageQualityPointer();
float* semsig = reader.getSEMSignalPointer();
float* fit = reader.getFitPointer();
int* phase = reader.getPhaseDataPointer();
while (!in.eof())
{
std::string line;
::memset(buf, 0, kBufferSize);
in.getline(buf, kBufferSize);
line = modifyAngHeaderLine(buf, kBufferSize);
if(m_HeaderIsComplete == false) outFile << line << std::endl;
}
for(int j = 0; j < m_NumRows; j++)
{
for(int i = 0; i < m_NumCols; i++)
{
xSqr = float(i)*m_XResolution;
ySqr = float(j)*m_YResolution;
row1 = ySqr/(HexYStep);
yHex1 = row1*HexYStep;
row2 = row1 + 1;
yHex2 = row2*HexYStep;
if(row1%2 == 0)
{
col1 = xSqr/(HexXStep);
xHex1 = col1*HexXStep;
point1 = ((row1/2)*HexNumColsEven) + ((row1/2)*HexNumColsOdd) + col1;
col2 = (xSqr-(HexXStep/2.0))/(HexXStep);
xHex2 = col2*HexXStep + (HexXStep/2.0);
point2 = ((row1/2)*HexNumColsEven) + (((row1/2)+1)*HexNumColsOdd) + col2;
}
else
{
col1 = (xSqr-(HexXStep/2.0))/(HexXStep);
xHex1 = col1*HexXStep + (HexXStep/2.0);
point1 = ((row1/2)*HexNumColsEven) + (((row1/2)+1)*HexNumColsOdd) + col1;
col2 = xSqr/(HexXStep);
xHex2 = col2*HexXStep;
point2 = (((row1/2)+1)*HexNumColsEven) + (((row1/2)+1)*HexNumColsOdd) + col2;
}
dist1 = ((xSqr-xHex1)*(xSqr-xHex1)) + ((ySqr-yHex1)*(ySqr-yHex1));
dist2 = ((xSqr-xHex2)*(xSqr-xHex2)) + ((ySqr-yHex2)*(ySqr-yHex2));
if(dist1 <= dist2 || row1 == (HexNumRows-1)) {point = point1;}
else {point = point2;}
outFile << " " << phi1[point] << " " << PHI[point] << " " << phi2[point] << " " << xSqr << " " << ySqr << " " << iq[point] << " " << ci[point] << " " << phase[point] << " " << semsig[point] << " " << fit[point] << " " << std::endl;
}
}
}
}
else if(ext.compare(Ebsd::Ctf::FileExt) == 0)
{
std::cout << "Ctf files are not on a hexagonal grid and do not need to be converted." << std::endl;
}
else
{
err = -1;
ss.str("");
ss << "The File extension was not detected correctly";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
return;
}
}
notifyStatusMessage("Import Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void EbsdToH5Ebsd::execute()
{
std::stringstream ss;
herr_t err = 0;
hid_t fileId = -1;
if(m_OutputFile.empty() == true)
{
std::string s("EbsdToH5Ebsd Error: The output file was not set correctly or is empty. The current value is '");
s.append("'. Please set the output file before running the importer. ");
ss << "EbsdToH5Ebsd input filename was empty";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
return;
}
// Make sure any directory path is also available as the user may have just typed
// in a path without actually creating the full path
std::string parentPath = MXAFileInfo::parentPath(m_OutputFile);
if(!MXADir::mkdir(parentPath, true))
{
std::stringstream ss;
PipelineMessage em (getHumanLabel(), ss.str(), -1);
addErrorMessage(em);
setErrorCondition(-1);
return;
}
// Create File
fileId = H5Utilities::createFile(m_OutputFile);
if(fileId < 0)
{
err = -1;
ss.str("");
ss << "The Output HDF5 file could not be created. Check Permissions, if the File is in use by another program.";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
return;
}
HDF5ScopedFileSentinel sentinel(&fileId, true);
err = H5Lite::writeScalarDataset(fileId, Ebsd::H5::ZResolution, m_ZResolution);
if(err < 0)
{
ss.str("");
ss << "Could not write the Z Resolution Scalar to the HDF5 File";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
}
unsigned int ui = static_cast<unsigned int>(m_RefFrameZDir);
err = H5Lite::writeScalarDataset(fileId, Ebsd::H5::StackingOrder, ui);
if(err < 0)
{
ss.str("");
ss << "Could not write the Stacking Order Scalar to the HDF5 File";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
}
std::string s = Ebsd::StackingOrder::Utils::getStringForEnum(m_RefFrameZDir);
err = H5Lite::writeStringAttribute(fileId, Ebsd::H5::StackingOrder, "Name", s);
if(err < 0)
{
ss.str("");
ss << "Could not write the Stacking Order Name Attribute to the HDF5 File";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
}
err = H5Lite::writeScalarDataset(fileId, Ebsd::H5::SampleTransformationAngle, m_SampleTransformationAngle);
if(err < 0)
{
ss.str("");
ss << "Could not write the Sample Transformation Angle to the HDF5 File";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
}
std::vector<hsize_t> dims(1,3);
err = H5Lite::writeVectorDataset(fileId, Ebsd::H5::SampleTransformationAxis, dims, m_SampleTransformationAxis);
if(err < 0)
{
ss.str("");
ss << "Could not write the Sample Transformation Axis to the HDF5 File";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
}
err = H5Lite::writeScalarDataset(fileId, Ebsd::H5::EulerTransformationAngle, m_EulerTransformationAngle);
if(err < 0)
{
ss.str("");
ss << "Could not write the Euler Transformation Angle to the HDF5 File";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
}
err = H5Lite::writeVectorDataset(fileId, Ebsd::H5::EulerTransformationAxis, dims, m_EulerTransformationAxis);
if(err < 0)
{
ss.str("");
ss << "Could not write the Euler Transformation Axis to the HDF5 File";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
}
EbsdImporter::Pointer fileImporter;
// Write the Manufacturer of the OIM file here
// This list will grow to be the number of EBSD file formats we support
std::string ext = MXAFileInfo::extension(m_EbsdFileList.front());
if(ext.compare(Ebsd::Ang::FileExt) == 0)
{
err = H5Lite::writeStringDataset(fileId, Ebsd::H5::Manufacturer, Ebsd::Ang::Manufacturer);
if(err < 0)
{
ss.str("");
ss << "Could not write the Manufacturer Data to the HDF5 File";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
}
fileImporter = H5AngImporter::New();
}
else if(ext.compare(Ebsd::Ctf::FileExt) == 0)
{
err = H5Lite::writeStringDataset(fileId, Ebsd::H5::Manufacturer, Ebsd::Ctf::Manufacturer);
if(err < 0)
{
ss.str("");
ss << "Could not write the Manufacturer Data to the HDF5 File";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
}
fileImporter = H5CtfImporter::New();
}
else if(ext.compare(Ebsd::Mic::FileExt) == 0)
{
err = H5Lite::writeStringDataset(fileId, Ebsd::H5::Manufacturer, Ebsd::Mic::Manufacturer);
if(err < 0)
{
ss.str("");
ss << "Could not write the Manufacturer Data to the HDF5 File";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
}
fileImporter = H5MicImporter::New();
}
else
{
err = -1;
ss.str("");
ss << "The File extension was not detected correctly";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
return;
}
std::vector<int> indices;
// Loop on Each EBSD File
float total = static_cast<float>( m_ZEndIndex - m_ZStartIndex );
int progress = 0;
int64_t z = m_ZStartIndex;
int64_t xDim = 0, yDim = 0;
float xRes = 0.0f, yRes = 0.0f;
/* There is a frailness about the z index and the file list. The programmer
* using this code MUST ensure that the list of files that is sent into this
* class is in the appropriate order to match up with the z index (slice index)
* otherwise the import will have subtle errors. The programmer is urged NOT to
* simply gather a list from the file system as those lists are sorted in such
* a way that if the number of digits appearing in the filename are NOT the same
* then the list will be wrong, ie, this example:
*
* slice_1.ang
* slice_2.ang
* ....
* slice_10.ang
*
* Most, if not ALL C++ libraries when asked for that list will return the list
* sorted like the following:
*
* slice_1.ang
* slice_10.ang
* slice_2.ang
*
* which is going to cause problems because the data is going to be placed
* into the HDF5 file at the wrong index. YOU HAVE BEEN WARNED.
*/
int64_t biggestxDim = 0;
int64_t biggestyDim = 0;
int totalSlicesImported = 0;
for (std::vector<std::string>::iterator filepath = m_EbsdFileList.begin(); filepath != m_EbsdFileList.end(); ++filepath)
{
std::string ebsdFName = *filepath;
progress = static_cast<int>( z - m_ZStartIndex );
progress = (int)(100.0f * (float)(progress) / total);
std::string msg = "Converting File: " + ebsdFName;
ss.str("");
notifyStatusMessage(msg.c_str());
err = fileImporter->importFile(fileId, z, ebsdFName);
if (err < 0)
{
if (err != -600)
{
setErrorCondition(fileImporter->getErrorCondition());
notifyErrorMessage(fileImporter->getPipelineMessage(), getErrorCondition());
return;
}
else
{
notifyWarningMessage(fileImporter->getPipelineMessage(), fileImporter->getErrorCondition() );
//setErrorCondition(fileImporter->getErrorCondition() );
err = 0;
}
}
totalSlicesImported = totalSlicesImported + fileImporter->numberOfSlicesImported();
fileImporter->getDims(xDim, yDim);
fileImporter->getResolution(xRes, yRes);
if(xDim > biggestxDim) biggestxDim = xDim;
if(yDim > biggestyDim) biggestyDim = yDim;
indices.push_back( static_cast<int>(z) );
++z;
if(getCancel() == true)
{
notifyStatusMessage("Conversion was Canceled");
return;
}
}
// Write Z index start, Z index end and Z Resolution to the HDF5 file
err = H5Lite::writeScalarDataset(fileId, Ebsd::H5::ZStartIndex, m_ZStartIndex);
if(err < 0)
{
ss.str("");
ss << "Could not write the Z Start Index Scalar to the HDF5 File";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
}
m_ZEndIndex = m_ZStartIndex + totalSlicesImported - 1;
err = H5Lite::writeScalarDataset(fileId, Ebsd::H5::ZEndIndex, m_ZEndIndex);
if(err < 0)
{
ss.str("");
ss << "Could not write the Z End Index Scalar to the HDF5 File";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
}
err = H5Lite::writeScalarDataset(fileId, Ebsd::H5::XPoints, biggestxDim);
if(err < 0)
{
ss.str("");
ss << "Could not write the XPoints Scalar to HDF5 file";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
}
err = H5Lite::writeScalarDataset(fileId, Ebsd::H5::YPoints, biggestyDim);
if(err < 0)
{
ss.str("");
ss << "Could not write the YPoints Scalar to HDF5 file";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
}
err = H5Lite::writeScalarDataset(fileId, Ebsd::H5::XResolution, xRes);
if(err < 0)
{
ss.str("");
ss << "Could not write the XResolution Scalar to HDF5 file";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
}
err = H5Lite::writeScalarDataset(fileId, Ebsd::H5::YResolution, yRes);
if(err < 0)
{
ss.str("");
ss << "Could not write the YResolution Scalar to HDF5 file";
addErrorMessage(getHumanLabel(), ss.str(), err);
setErrorCondition(-1);
}
if(false == getCancel())
{
// Write an Index data set which contains all the z index values which
// should help speed up the reading side of this file
std::vector<hsize_t> dims(1, indices.size());
err = H5Lite::writeVectorDataset(fileId, Ebsd::H5::Index, dims, indices);
}
err = H5Utilities::closeFile(fileId);
fileId = -1;
notifyStatusMessage("Import Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RawBinaryReader::execute()
{
int err = 0;
std::stringstream ss;
setErrorCondition(err);
VoxelDataContainer* m = getVoxelDataContainer();
if(NULL == m)
{
setErrorCondition(-999);
notifyErrorMessage("The Voxel DataContainer Object was NULL", -999);
return;
}
setErrorCondition(0);
// Get the total size of the array from the options
size_t voxels = m_Dimensions.x * m_Dimensions.y * m_Dimensions.z;
if (m_OverRideOriginResolution == true)
{
m->setOrigin(m_Origin.x, m_Origin.y, m_Origin.z);
m->setResolution(m_Resolution.x, m_Resolution.y, m_Resolution.z);
}
m->setDimensions(m_Dimensions.x, m_Dimensions.y, m_Dimensions.z);
array = IDataArray::NullPointer();
if (m_ScalarType == Detail::Int8)
{
Int8ArrayType::Pointer p = Int8ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<int8_t>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
else if (m_ScalarType == Detail::UInt8)
{
UInt8ArrayType::Pointer p = UInt8ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<uint8_t>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
else if (m_ScalarType == Detail::Int16)
{
Int16ArrayType::Pointer p = Int16ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<int16_t>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
else if (m_ScalarType == Detail::UInt16)
{
UInt16ArrayType::Pointer p = UInt16ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<uint16_t>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
else if (m_ScalarType == Detail::Int32)
{
Int32ArrayType::Pointer p = Int32ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<int32_t>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
else if (m_ScalarType == Detail::UInt32)
{
UInt32ArrayType::Pointer p = UInt32ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<uint32_t>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
else if (m_ScalarType == Detail::Int64)
{
Int64ArrayType::Pointer p = Int64ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<int64_t>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
else if (m_ScalarType == Detail::UInt64)
{
UInt64ArrayType::Pointer p = UInt64ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<uint64_t>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
else if (m_ScalarType == Detail::Float)
{
FloatArrayType::Pointer p = FloatArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<float>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
else if (m_ScalarType == Detail::Double)
{
DoubleArrayType::Pointer p = DoubleArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<double>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
if (NULL != array.get())
{
m->addCellData(array->GetName(), array);
}
else if(err == RBR_FILE_NOT_OPEN )
{
setErrorCondition(RBR_FILE_NOT_OPEN);
notifyErrorMessage("RawBinaryReader was unable to open the specified file.", getErrorCondition());
}
else if (err == RBR_FILE_TOO_SMALL)
{
setErrorCondition(RBR_FILE_TOO_SMALL);
notifyErrorMessage("The file size is smaller than the allocated size.", getErrorCondition());
}
else if (err == RBR_FILE_TOO_BIG)
{
notifyWarningMessage("The file size is larger than the allocated size.", RBR_FILE_TOO_BIG);
}
else if(err == RBR_READ_EOF)
{
setErrorCondition(RBR_READ_EOF);
notifyErrorMessage("RawBinaryReader read past the end of the specified file.", getErrorCondition());
}
/* Let the GUI know we are done with this filter */
notifyStatusMessage("Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void WritePoleFigure::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(m_CellPhasesArrayPath.getDataContainerName());
size_t dims[3] = { 0, 0, 0 };
m->getGeometryAs<ImageGeom>()->getDimensions(dims);
// Make sure any directory path is also available as the user may have just typed
// in a path without actually creating the full path
QDir path(getOutputPath());
if (!path.mkpath(".") )
{
QString ss = QObject::tr("Error creating parent path '%1'").arg(path.absolutePath());
setErrorCondition(-1);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
bool missingGoodVoxels = true;
if (NULL != m_GoodVoxels)
{
missingGoodVoxels = false;
}
// Find how many phases we have by getting the number of Crystal Structures
size_t numPoints = m->getGeometryAs<ImageGeom>()->getNumberOfElements();
size_t numPhases = m_CrystalStructuresPtr.lock()->getNumberOfTuples();
// Loop over all the voxels gathering the Eulers for a specific phase into an array
for (size_t phase = 1; phase < numPhases; ++phase)
{
size_t count = 0;
// First find out how many voxels we are going to have. This is probably faster to loop twice than to
// keep allocating memory everytime we find one.
for (size_t i = 0; i < numPoints; ++i)
{
if (m_CellPhases[i] == phase)
{
if (missingGoodVoxels == true || m_GoodVoxels[i] == true)
{
count++;
}
}
}
QVector<size_t> eulerCompDim(1, 3);
FloatArrayType::Pointer subEulers = FloatArrayType::CreateArray(count, eulerCompDim, "Eulers_Per_Phase");
subEulers->initializeWithValue(std::numeric_limits<float>::signaling_NaN());
float* eu = subEulers->getPointer(0);
// Now loop through the eulers again and this time add them to the subEulers Array
count = 0;
for (size_t i = 0; i < numPoints; ++i)
{
if (m_CellPhases[i] == phase)
{
if (missingGoodVoxels == true || m_GoodVoxels[i] == true)
{
eu[count * 3] = m_CellEulerAngles[i * 3];
eu[count * 3 + 1] = m_CellEulerAngles[i * 3 + 1];
eu[count * 3 + 2] = m_CellEulerAngles[i * 3 + 2];
count++;
}
}
}
if (subEulers->getNumberOfTuples() == 0) { continue; } // Skip because we have no Pole Figure data
QVector<UInt8ArrayType::Pointer> figures;
PoleFigureConfiguration_t config;
config.eulers = subEulers.get();
config.imageDim = getImageSize();
config.lambertDim = getLambertSize();
config.numColors = getNumColors();
QString label("Phase_");
label.append(QString::number(phase));
QString ss = QObject::tr("Generating Pole Figures for Phase %1").arg(phase);
notifyStatusMessage(getMessagePrefix(), getHumanLabel(), ss);
switch(m_CrystalStructures[phase])
{
case Ebsd::CrystalStructure::Cubic_High:
figures = makePoleFigures<CubicOps>(config);
break;
case Ebsd::CrystalStructure::Cubic_Low:
figures = makePoleFigures<CubicLowOps>(config);
break;
case Ebsd::CrystalStructure::Hexagonal_High:
figures = makePoleFigures<HexagonalOps>(config);
break;
case Ebsd::CrystalStructure::Hexagonal_Low:
figures = makePoleFigures<HexagonalLowOps>(config);
break;
case Ebsd::CrystalStructure::Trigonal_High:
// figures = makePoleFigures<TrigonalOps>(config);
notifyWarningMessage(getHumanLabel(), "Trigonal High Symmetry is not supported for Pole figures. This phase will be omitted from results", -1010);
break;
case Ebsd::CrystalStructure::Trigonal_Low:
// figures = makePoleFigures<TrigonalLowOps>(config);
notifyWarningMessage(getHumanLabel(), "Trigonal Low Symmetry is not supported for Pole figures. This phase will be omitted from results", -1010);
break;
case Ebsd::CrystalStructure::Tetragonal_High:
// figures = makePoleFigures<TetragonalOps>(config);
notifyWarningMessage(getHumanLabel(), "Tetragonal High Symmetry is not supported for Pole figures. This phase will be omitted from results", -1010);
break;
case Ebsd::CrystalStructure::Tetragonal_Low:
// figures = makePoleFigures<TetragonalLowOps>(config);
notifyWarningMessage(getHumanLabel(), "Tetragonal Low Symmetry is not supported for Pole figures. This phase will be omitted from results", -1010);
break;
case Ebsd::CrystalStructure::OrthoRhombic:
figures = makePoleFigures<OrthoRhombicOps>(config);
break;
case Ebsd::CrystalStructure::Monoclinic:
figures = makePoleFigures<MonoclinicOps>(config);
break;
case Ebsd::CrystalStructure::Triclinic:
figures = makePoleFigures<TriclinicOps>(config);
break;
default:
break;
}
if (figures.size() == 3)
{
QImage combinedImage = PoleFigureImageUtilities::Create3ImagePoleFigure(figures[0].get(), figures[1].get(), figures[2].get(), config, getImageLayout());
writeImage(combinedImage, label);
}
}
/* Let the GUI know we are done with this filter */
notifyStatusMessage(getHumanLabel(), "Complete");
}
