// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 FileWriter::execute()
{
setErrorCondition(0);
// Make sure any directory path is also available as the user may have just typed
// in a path without actually creating the full path
QFileInfo fi(m_OutputFile);
QString parentPath = fi.path();
QDir dir;
if (!dir.mkpath(parentPath))
{
setErrorCondition(-200);
QString ss = QObject::tr("Error creating parent path '%1'").arg(parentPath);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
int32_t err = writeHeader();
if (err < 0)
{
QString ss = QObject::tr("Error writing the header portion of the file");
setErrorCondition(err);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
err = writeFile();
if (err < 0)
{
QString ss = QObject::tr("Error writing the data to the file");
setErrorCondition(err);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void CopyAttributeArray::dataCheck()
{
setErrorCondition(0);
if(m_NewArrayName.isEmpty() == true)
{
setErrorCondition(-11009);
QString ss = QObject::tr("The new Attribute Array name must be set");
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
QString daName = getSelectedArrayPath().getDataArrayName();
IDataArray::Pointer dataArray = getDataContainerArray()->getPrereqIDataArrayFromPath<IDataArray, AbstractFilter>(this, getSelectedArrayPath());
if(getErrorCondition() < 0) { return; }
DataArrayPath path(getSelectedArrayPath().getDataContainerName(), getSelectedArrayPath().getAttributeMatrixName(), "");
AttributeMatrix::Pointer attrMat = getDataContainerArray()->getAttributeMatrix(path);
IDataArray::Pointer pNew = dataArray->deepCopy();
pNew->setName(m_NewArrayName); // Set the name of the array
int32_t err = attrMat->addAttributeArray(m_NewArrayName, pNew);
if (0 != err)
{
setErrorCondition(err);
QString ss = QObject::tr("Attempt to copy Attribute Array '%1' to '%2' failed").arg(daName).arg(m_NewArrayName);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RenameAttributeMatrix::dataCheck()
{
setErrorCondition(0);
if (m_NewAttributeMatrix.isEmpty() == true)
{
setErrorCondition(-11004);
QString ss = QObject::tr("The new Attribute Matrix name must be set");
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
QString amName = getSelectedAttributeMatrixPath().getAttributeMatrixName();
DataContainer::Pointer dc = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getSelectedAttributeMatrixPath().getDataContainerName());
getDataContainerArray()->getPrereqAttributeMatrixFromPath<AbstractFilter>(this, getSelectedAttributeMatrixPath(), -301);
if(getErrorCondition() < 0) { return; }
bool check = dc->renameAttributeMatrix(amName, getNewAttributeMatrix() );
if (check == false)
{
setErrorCondition(-11006);
QString ss = QObject::tr("Attempt to rename Attribute Matrix '%1' to '%2' failed").arg(amName).arg(getNewAttributeMatrix());
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void 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 ConvertOrientations::dataCheck()
{
setErrorCondition(0);
if(getInputType() == getOutputType())
{
QString ss = QObject::tr("Input and output orientation representation types must be different");
setErrorCondition(-1000);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
if( getInputType() < OrientationConverter<float>::GetMinIndex() || getInputType() > OrientationConverter<float>::GetMaxIndex() )
{
QString ss = QObject::tr("There was an error with teh selection of the input orientation type. The valid values range from 0 to %1").arg(OrientationConverter<float>::GetMaxIndex());
setErrorCondition(-1001);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
if( getOutputType() < OrientationConverter<float>::GetMinIndex() || getOutputType() > OrientationConverter<float>::GetMaxIndex() )
{
QString ss = QObject::tr("There was an error with the selection of the output orientation type. The valid values range from 0 to %1").arg(OrientationConverter<float>::GetMaxIndex());
setErrorCondition(-1002);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
// We need to return NOW because the next lines assume we have and index that is within
// the valid bounds
if(getErrorCondition() < 0) { return; }
// Figure out what kind of Array the user selected
// Get the input data and create the output Data appropriately
IDataArray::Pointer iDataArrayPtr = getDataContainerArray()->getPrereqIDataArrayFromPath<IDataArray, AbstractFilter>(this, getInputOrientationArrayPath());
DataArrayPath outputArrayPath = getInputOrientationArrayPath();
outputArrayPath.setDataArrayName(getOutputOrientationArrayName());
FloatArrayType::Pointer fArray = std::dynamic_pointer_cast<FloatArrayType>(iDataArrayPtr);
if(NULL != fArray.get())
{
QVector<int32_t> componentCounts = OrientationConverter<float>::GetComponentCounts();
QVector<size_t> outputCDims(1, componentCounts[getOutputType()]);
getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<float>, AbstractFilter, float>(this, outputArrayPath, 0, outputCDims);
}
DoubleArrayType::Pointer dArray = std::dynamic_pointer_cast<DoubleArrayType>(iDataArrayPtr);
if(NULL != dArray.get())
{
QVector<int32_t> componentCounts = OrientationConverter<double>::GetComponentCounts();
QVector<size_t> outputCDims(1, componentCounts[getOutputType()]);
getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<double>, AbstractFilter, double>(this, outputArrayPath, 0, outputCDims);
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ConditionalSetValue::dataCheck()
{
setErrorCondition(0);
QVector<DataArrayPath> dataArrayPaths;
m_ArrayPtr = getDataContainerArray()->getPrereqIDataArrayFromPath<IDataArray, AbstractFilter>(this, getSelectedArrayPath());
if (getErrorCondition() < 0) { return; }
if (getErrorCondition() >= 0) { dataArrayPaths.push_back(getSelectedArrayPath()); }
if (m_ArrayPtr.lock()->getNumberOfComponents() > 1)
{
QString ss = QObject::tr("Selected array '%1' must be a scalar array (1 component). The number of components is %2").arg(getSelectedArrayPath().getDataArrayName()).arg(m_ArrayPtr.lock()->getNumberOfComponents());
setErrorCondition(-11002);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
QVector<size_t> cDims(1, 1);
m_ConditionalArrayPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<bool>, AbstractFilter>(this, getConditionalArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if (NULL != m_ConditionalArrayPtr.lock().get()) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{
m_ConditionalArray = m_ConditionalArrayPtr.lock()->getPointer(0);
} /* Now assign the raw pointer to data from the DataArray<T> object */
if (getErrorCondition() >= 0) { dataArrayPaths.push_back(getConditionalArrayPath()); }
getDataContainerArray()->validateNumberOfTuples<AbstractFilter>(this, dataArrayPaths);
QString dType = m_ArrayPtr.lock()->getTypeAsString();
if (dType.compare(DREAM3D::TypeNames::Int8) == 0) { checkValuesInt<int8_t>(this, m_ReplaceValue, DREAM3D::TypeNames::Int8); }
else if (dType.compare(DREAM3D::TypeNames::UInt8) == 0) { checkValuesInt<uint8_t>(this, m_ReplaceValue, DREAM3D::TypeNames::UInt8); }
else if (dType.compare(DREAM3D::TypeNames::Int16) == 0) { checkValuesInt<int16_t>(this, m_ReplaceValue, DREAM3D::TypeNames::Int16); }
else if (dType.compare(DREAM3D::TypeNames::UInt16) == 0) { checkValuesInt<uint16_t>(this, m_ReplaceValue, DREAM3D::TypeNames::UInt16); }
else if (dType.compare(DREAM3D::TypeNames::Int32) == 0) { checkValuesInt<int32_t>(this, m_ReplaceValue, DREAM3D::TypeNames::Int32); }
else if (dType.compare(DREAM3D::TypeNames::UInt32) == 0) { checkValuesInt<uint32_t>(this, m_ReplaceValue, DREAM3D::TypeNames::UInt32); }
else if (dType.compare(DREAM3D::TypeNames::Int64) == 0) { checkValuesInt<int64_t>(this, m_ReplaceValue, DREAM3D::TypeNames::Int64); }
else if (dType.compare(DREAM3D::TypeNames::UInt64) == 0) { checkValuesInt<uint64_t>(this, m_ReplaceValue, DREAM3D::TypeNames::UInt64); }
else if (dType.compare(DREAM3D::TypeNames::Float) == 0) { checkValuesFloatDouble<float>(this, m_ReplaceValue, DREAM3D::TypeNames::Float); }
else if (dType.compare(DREAM3D::TypeNames::Double) == 0) { checkValuesFloatDouble<double>(this, m_ReplaceValue, DREAM3D::TypeNames::Double); }
else if (dType.compare(DREAM3D::TypeNames::Bool) == 0)
{
if (m_ReplaceValue != 0.0)
{
m_ReplaceValue = 1.0; // anything that is not a zero is a one
}
}
else
{
setErrorCondition(-4060);
QString ss = QObject::tr("Incorrect data scalar type");
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RemoveComponentFromArray::dataCheck()
{
setErrorCondition(0);
m_InArrayPtr = getDataContainerArray()->getPrereqIDataArrayFromPath<IDataArray, AbstractFilter>(this, getSelectedArrayPath());
if (m_SaveRemovedComponent == true)
{
if (m_NewArrayArrayName.isEmpty() == true)
{
setErrorCondition(-11001);
notifyErrorMessage(getHumanLabel(), "Removed Component array name must be set.", getErrorCondition());
return;
}
}
if (m_ReducedArrayArrayName.isEmpty() == true)
{
setErrorCondition(-11002);
notifyErrorMessage(getHumanLabel(), "Reduced array name must be set.", getErrorCondition());
return;
}
if(getErrorCondition() < 0) { return; }
if (m_InArrayPtr.lock()->getNumberOfComponents() < 2)
{
setErrorCondition(-11003);
QString ss = QObject::tr("Selected array '%1' must have more than 1 component. The number of components is %2").arg(getSelectedArrayPath().getDataArrayName()).arg(m_InArrayPtr.lock()->getNumberOfComponents());
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
if(m_CompNumber >= m_InArrayPtr.lock()->getNumberOfComponents())
{
setErrorCondition(-11004);
QString ss = QObject::tr("Component to extract (%1) is larger than the number of components (%2) for array selected: '%1'").arg(m_CompNumber).arg(m_InArrayPtr.lock()->getNumberOfComponents()).arg(getSelectedArrayPath().getDataArrayName());
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
QVector<size_t> cDims(1, 1);
if (m_SaveRemovedComponent == true)
{
DataArrayPath tempPath(getSelectedArrayPath().getDataContainerName(), getSelectedArrayPath().getAttributeMatrixName(), getNewArrayArrayName());
m_NewArrayPtr = TemplateHelpers::CreateNonPrereqArrayFromArrayType()(this, tempPath, cDims, m_InArrayPtr.lock());
}
cDims[0] = m_InArrayPtr.lock()->getNumberOfComponents() - 1;
DataArrayPath tempPath2(getSelectedArrayPath().getDataContainerName(), getSelectedArrayPath().getAttributeMatrixName(), getReducedArrayArrayName());
m_ReducedArrayPtr = TemplateHelpers::CreateNonPrereqArrayFromArrayType()(this, tempPath2, cDims, m_InArrayPtr.lock());
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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());
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int VoxelDataContainerWriter::writeEnsembleData(hid_t dcGid)
{
std::stringstream ss;
int err = 0;
VoxelDataContainer* m = getVoxelDataContainer();
// Write the Ensemble data
err = H5Utilities::createGroupsFromPath(H5_ENSEMBLE_DATA_GROUP_NAME, dcGid);
if(err < 0)
{
ss.str("");
ss << "Error creating HDF Group " << H5_ENSEMBLE_DATA_GROUP_NAME << std::endl;
setErrorCondition(-66);
notifyErrorMessage( ss.str(), err);
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
err = H5Lite::writeStringAttribute(dcGid, H5_ENSEMBLE_DATA_GROUP_NAME, H5_NAME, H5_ENSEMBLE_DATA_DEFAULT);
hid_t ensembleGid = H5Gopen(dcGid, H5_ENSEMBLE_DATA_GROUP_NAME, H5P_DEFAULT);
if(err < 0)
{
ss.str("");
ss << "Error opening ensemble Group " << H5_ENSEMBLE_DATA_GROUP_NAME << std::endl;
setErrorCondition(-67);
notifyErrorMessage( ss.str(), err);
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
NameListType names = m->getEnsembleArrayNameList();
for (NameListType::iterator iter = names.begin(); iter != names.end(); ++iter)
{
IDataArray::Pointer array = m->getEnsembleData(*iter);
err = array->writeH5Data(ensembleGid);
if(err < 0)
{
ss.str("");
ss << "Error writing Ensemble array '" << *iter << "' to the HDF5 File";
notifyErrorMessage( ss.str(), err);
setErrorCondition(err);
H5Gclose(ensembleGid); // Close the Cell Group
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
}
H5Gclose(ensembleGid);
return err;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RegularizeZSpacing::dataCheck()
{
setErrorCondition(0);
if (getNewZRes() <= 0)
{
QString ss = QObject::tr("The new Z resolution Y (%1) must be positive").arg(getNewZRes());
setErrorCondition(-5555);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
std::ifstream inFile;
inFile.open(m_InputFile.toLatin1().data());
if (!inFile.good())
{
QString ss = QObject::tr("Unable to open input file with name '%1'").arg(getInputFile());
setErrorCondition(-5556);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
ImageGeom::Pointer image = getDataContainerArray()->getPrereqGeometryFromDataContainer<ImageGeom, AbstractFilter>(this, getCellAttributeMatrixPath().getDataContainerName());
AttributeMatrix::Pointer cellAttrMat = getDataContainerArray()->getPrereqAttributeMatrixFromPath<AbstractFilter>(this, getCellAttributeMatrixPath(), -301);
if(getErrorCondition() < 0) {
return;
}
float zval = 0.0f;
for (size_t iter = 0; iter < image->getZPoints() + 1; iter++)
{
inFile >> zval;
}
size_t zP = static_cast<size_t>(zval / getNewZRes());
if(zP == 0) {
zP = 1;
}
if (getInPreflight())
{
image->setDimensions(image->getXPoints(), image->getYPoints(), zP);
QVector<size_t> tDims(3, 0);
tDims[0] = image->getXPoints();
tDims[1] = image->getYPoints();
tDims[2] = zP;
cellAttrMat->resizeAttributeArrays(tDims);
}
inFile.close();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AvizoRectilinearCoordinateWriter::execute()
{
int err = 0;
setErrorCondition(err);
VoxelDataContainer* m = getVoxelDataContainer();
if(NULL == m)
{
setErrorCondition(-999);
notifyErrorMessage("The DataContainer Object was NULL", -999);
return;
}
setErrorCondition(0);
// 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;
ss << "Error creating parent path '" << parentPath << "'";
notifyErrorMessage(ss.str(), -1);
setErrorCondition(-1);
return;
}
int64_t totalPoints = m->getTotalPoints();
size_t totalFields = m->getNumFieldTuples();
size_t totalEnsembleTuples = m->getNumEnsembleTuples();
dataCheck(false, totalPoints, totalFields, totalEnsembleTuples);
MXAFileWriter64 writer(m_OutputFile);
if(false == writer.initWriter())
{
std::stringstream ss;
ss << "Error opening file '" << parentPath << "'";
notifyErrorMessage(ss.str(), -1);
setErrorCondition(-1);
return;
}
std::string header = generateHeader();
writer.writeString(header);
err = writeData(writer);
/* Let the GUI know we are done with this filter */
notifyStatusMessage("Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int VoxelDataContainerWriter::writeFaceData(hid_t dcGid)
{
std::stringstream ss;
int err = 0;
VoxelDataContainer* m = getVoxelDataContainer();
// Write the Voxel Data
err = H5Utilities::createGroupsFromPath(H5_FACE_DATA_GROUP_NAME, dcGid);
if(err < 0)
{
ss.str("");
ss << "Error creating HDF Group " << H5_FACE_DATA_GROUP_NAME << std::endl;
setErrorCondition(-63);
notifyErrorMessage( ss.str(), err);
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
hid_t FaceGroupId = H5Gopen(dcGid, H5_FACE_DATA_GROUP_NAME, H5P_DEFAULT);
if(err < 0)
{
ss.str("");
ss << "Error writing string attribute to HDF Group " << H5_FACE_DATA_GROUP_NAME << std::endl;
setErrorCondition(-64);
notifyErrorMessage( ss.str(), err);
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
NameListType names = m->getFaceArrayNameList();
for (NameListType::iterator iter = names.begin(); iter != names.end(); ++iter)
{
ss.str("");
ss << "Writing Face Data '" << *iter << "' to HDF5 File" << std::endl;
notifyStatusMessage(ss.str());
IDataArray::Pointer array = m->getFaceData(*iter);
err = array->writeH5Data(FaceGroupId);
if(err < 0)
{
ss.str("");
ss << "Error writing array '" << *iter << "' to the HDF5 File";
notifyErrorMessage( ss.str(), err);
setErrorCondition(err);
H5Gclose(FaceGroupId); // Close the Face Group
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
}
H5Gclose(FaceGroupId); // Close the Face Group
return err;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ImportR3DStack::readXYSize(int &x, int &y)
{
if (m_R3DFileList.size() == 0)
{
x = -1; y = -1;
return;
}
QString r3dFName = QString::fromStdString(m_R3DFileList[0]);
QByteArray buf;
QFile in(r3dFName);
if (!in.open(QIODevice::ReadOnly | QIODevice::Text))
{
QString msg = QString("R3D file could not be opened: ") + r3dFName;
setErrorCondition(-14000);
notifyErrorMessage(msg.toStdString(), getErrorCondition());
}
buf = in.readLine(); // Read first line which is the x and y sizes
QList<QByteArray> tokens = buf.split(',');
if(tokens.size() < 2)
{
setErrorCondition(-2002);
notifyErrorMessage("Header line is an incorrect length", getErrorCondition());
x = -1;
y = -1;
return;
}
bool ok = false;
x = tokens.at(0).toInt(&ok, 10);
if (!ok)
{
setErrorCondition(-2000);
notifyErrorMessage("Width dimension entry was not an integer", getErrorCondition());
return;
}
y = tokens.at(1).toInt(&ok, 10);
if(!ok)
{
setErrorCondition(-2001);
notifyErrorMessage("Height dimension entry was not an integer", getErrorCondition());
return;
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 AvizoUniformCoordinateWriter::dataCheck()
{
setErrorCondition(0);
DataContainer::Pointer dc = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getFeatureIdsArrayPath().getDataContainerName(), false);
if (getErrorCondition() < 0 || NULL == dc.get()) {
return;
}
ImageGeom::Pointer image = dc->getPrereqGeometry<ImageGeom, AbstractFilter>(this);
if (getErrorCondition() < 0 || NULL == image.get()) {
return;
}
if(m_OutputFile.isEmpty() == true)
{
QString ss = QObject::tr("The output file must be set before executing this filter.");
setErrorCondition(-1);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
if(m_WriteFeatureIds == true)
{
QVector<size_t> dims(1, 1);
m_FeatureIdsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getFeatureIdsArrayPath(), dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_FeatureIdsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{
m_FeatureIds = m_FeatureIdsPtr.lock()->getPointer(0); /* Now assign the raw pointer to data from the DataArray<T> object */
}
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void CopyFeatureArrayToElementArray::dataCheck()
{
setErrorCondition(0);
if (getCreatedArrayName().isEmpty() == true)
{
setErrorCondition(-11002);
notifyErrorMessage(getHumanLabel(), "The new Element array name must be set", getErrorCondition());
return;
}
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 */
m_InArrayPtr = getDataContainerArray()->getPrereqIDataArrayFromPath<IDataArray, AbstractFilter>(this, getSelectedFeatureArrayPath()); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
DataArrayPath tempPath(getFeatureIdsArrayPath().getDataContainerName(), getFeatureIdsArrayPath().getAttributeMatrixName(), "");
getDataContainerArray()->getPrereqAttributeMatrixFromPath<AbstractFilter>(this, tempPath, -301);
if(getErrorCondition() < 0 ) { return; }
tempPath.update(getFeatureIdsArrayPath().getDataContainerName(), getFeatureIdsArrayPath().getAttributeMatrixName(), getCreatedArrayName());
TemplateHelpers::CreateNonPrereqArrayFromArrayType()(this, tempPath, m_InArrayPtr.lock()->getComponentDimensions(), m_InArrayPtr.lock());
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void WriteStlFile::dataCheck()
{
setErrorCondition(0);
TriangleGeom::Pointer triangles = getDataContainerArray()->getPrereqGeometryFromDataContainer<TriangleGeom, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
QVector<IDataArray::Pointer> dataArrays;
if(getErrorCondition() >= 0) { dataArrays.push_back(triangles->getTriangles()); }
if (m_OutputStlDirectory.isEmpty() == true)
{
setErrorCondition(-1003);
notifyErrorMessage(getHumanLabel(), "The output directory must be set", -1003);
}
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()); }
if (m_GroupByPhase == true)
{
m_SurfaceMeshFacePhasesPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getSurfaceMeshFacePhasesArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFacePhasesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFacePhases = m_SurfaceMeshFacePhasesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() >= 0) { dataArrays.push_back(m_SurfaceMeshFacePhasesPtr.lock()); }
}
getDataContainerArray()->validateNumberOfTuples<AbstractFilter>(this, dataArrays);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 ReadStlFile::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
if (m_StlFilePath.isEmpty() == true)
{
setErrorCondition(-1003);
notifyErrorMessage(getHumanLabel(), "The input file must be set", -1003);
}
// Create a SufaceMesh Data Container with Faces, Vertices, Feature Labels and optionally Phase labels
DataContainer::Pointer sm = getDataContainerArray()->createNonPrereqDataContainer<AbstractFilter>(this, getSurfaceMeshDataContainerName());
if(getErrorCondition() < 0) { return; }
SharedVertexList::Pointer sharedVertList = TriangleGeom::CreateSharedVertexList(0);
TriangleGeom::Pointer triangleGeom = TriangleGeom::CreateGeometry(0, sharedVertList, DREAM3D::Geometry::TriangleGeometry);
sm->setGeometry(triangleGeom);
QVector<size_t> tDims(1, 0);
sm->createNonPrereqAttributeMatrix<AbstractFilter>(this, getFaceAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::Face);
QVector<size_t> cDims(1, 3);
tempPath.update(getSurfaceMeshDataContainerName(), getFaceAttributeMatrixName(), getFaceNormalsArrayName() );
m_FaceNormalsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<double>, AbstractFilter, double>(this, tempPath, 0, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_FaceNormalsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_FaceNormals = m_FaceNormalsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void GenerateNodeTriangleConnectivity::execute()
{
int err = 0;
std::stringstream ss;
setErrorCondition(err);
SurfaceMeshDataContainer* m = getSurfaceMeshDataContainer();
if(NULL == m)
{
setErrorCondition(-999);
notifyErrorMessage("The SurfaceMesh DataContainer Object was NULL", -999);
return;
}
setErrorCondition(0);
// Just to double check we have everything.
dataCheck(false, 0,0,0);
if (getErrorCondition() < 0)
{
return;
}
notifyStatusMessage("Starting");
// Generate the connectivity data
generateConnectivity();
/* Let the GUI know we are done with this filter */
notifyStatusMessage("Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RequiredZThickness::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer dataContainer = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getDataContainerSelection());
if (getErrorCondition() < 0) { return; }
ImageGeom::Pointer image = dataContainer->getGeometryAs<ImageGeom>();
size_t dims[3] = { 0, 0, 0 };
image->getDimensions(dims);
if (dims[2] < getNumZVoxels())
{
QString str;
QTextStream ss(&str);
ss << "Number of Z Voxels does not meet required value during execution of the filter. \n";
ss << " Required Z Voxels: " << m_NumZVoxels << "\n";
ss << " Current Z Voxels: " << dims[2];
setErrorCondition(-7788);
notifyErrorMessage(getHumanLabel(), str, getErrorCondition());
bool needMoreData = true;
emit decisionMade(needMoreData);
}
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AlignSectionsFeatureCentroid::dataCheck()
{
setErrorCondition(0);
// Set the DataContainerName and AttributematrixName for the Parent Class (AlignSections) to Use.
// These are checked for validity in the Parent Class dataCheck
setDataContainerName(m_GoodVoxelsArrayPath.getDataContainerName());
setCellAttributeMatrixName(m_GoodVoxelsArrayPath.getAttributeMatrixName());
AlignSections::dataCheck();
if(getErrorCondition() < 0) { return; }
ImageGeom::Pointer image = getDataContainerArray()->getPrereqGeometryFromDataContainer<ImageGeom, AbstractFilter>(this, m_GoodVoxelsArrayPath.getDataContainerName());
if(getErrorCondition() < 0) { return; }
if (m_ReferenceSlice > image->getZPoints())
{
QString ss = QObject::tr("The Image Geometry extent (%1) is smaller than the supplied reference slice (%2)").arg(image->getZPoints()).arg(m_ReferenceSlice);
setErrorCondition(-5556);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
QVector<size_t> cDims(1, 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 */
if(getErrorCondition() < 0) { return; }
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void PerPhaseMinSize::preflight()
{
dataCheck(true, 1, 1, 1);
VoxelDataContainer* m = getVoxelDataContainer();
if(NULL == m)
{
setErrorCondition(-999);
notifyErrorMessage("The DataContainer Object was NULL", -999);
return;
}
RenumberGrains::Pointer renumber_grains = RenumberGrains::New();
renumber_grains->setObservers(this->getObservers());
renumber_grains->setVoxelDataContainer(m);
renumber_grains->setMessagePrefix(getMessagePrefix());
renumber_grains->preflight();
int err = renumber_grains->getErrorCondition();
if (err < 0)
{
setErrorCondition(renumber_grains->getErrorCondition());
addErrorMessages(renumber_grains->getPipelineMessages());
return;
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AdjustVolumeOrigin::execute()
{
VoxelDataContainer* m = getVoxelDataContainer();
if(NULL == m)
{
setErrorCondition(-999);
notifyErrorMessage("The DataContainer Object was NULL", -999);
return;
}
setErrorCondition(0);
std::stringstream ss;
// Set the Voxel Volume First, since this is easy
if (m_ApplyToVoxelVolume ==true)
{
m->setOrigin(m_Origin.x, m_Origin.y, m_Origin.z);
}
if (m_ApplyToSurfaceMesh == true)
{
updateSurfaceMesh();
}
if (m_ApplyToSolidMesh == true)
{
updatesSolidMesh();
}
notifyStatusMessage("Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int32_t VisualizeGBCDPoleFigure::writeCoords(FILE* f, const char* axis, const char* type,
int64_t npoints, float min, float step)
{
int32_t err = 0;
fprintf(f, "%s %lld %s\n", axis, (long long int)(npoints), type);
float* data = new float[npoints];
float d;
for (int64_t idx = 0; idx < npoints; ++idx)
{
d = idx * step + min;
SIMPLib::Endian::FromSystemToBig::convert(d);
data[idx] = d;
}
size_t totalWritten = fwrite(static_cast<void*>(data), sizeof(float), static_cast<size_t>(npoints), f);
delete[] data;
if (totalWritten != static_cast<size_t>(npoints) )
{
QString ss = QObject::tr("Error writing binary VTK data to file '%1'").arg(m_OutputFile);
setErrorCondition(-1);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
fclose(f);
return getErrorCondition();
}
return err;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void MinNeighbors::dataCheck()
{
setErrorCondition(0);
QVector<DataArrayPath> dataArrayPaths;
if (getMinNumNeighbors() < 0)
{
QString ss = QObject::tr("The minimum number of neighbors (%1) must be 0 or positive").arg(getMinNumNeighbors());
setErrorCondition(-5555);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
getDataContainerArray()->getPrereqGeometryFromDataContainer<ImageGeom, AbstractFilter>(this, getFeatureIdsArrayPath().getDataContainerName());
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 */
m_NumNeighborsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getNumNeighborsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_NumNeighborsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_NumNeighbors = m_NumNeighborsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() >= 0) { dataArrayPaths.push_back(getNumNeighborsArrayPath()); }
if (getApplyToSinglePhase() == true)
{
m_FeaturePhasesPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getFeaturePhasesArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_FeaturePhasesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_FeaturePhases = m_FeaturePhasesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() >= 0) { dataArrayPaths.push_back(getFeaturePhasesArrayPath()); }
}
getDataContainerArray()->validateNumberOfTuples(this, dataArrayPaths);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AlignSectionsFeature::execute()
{
setErrorCondition(0);
VoxelDataContainer* m = getVoxelDataContainer();
if(NULL == m)
{
setErrorCondition(-999);
notifyErrorMessage("The DataContainer Object was NULL", -999);
return;
}
int64_t totalPoints = m->getTotalPoints();
size_t numgrains = m->getNumFieldTuples();
size_t numensembles = m->getNumEnsembleTuples();
dataCheck(false, totalPoints, numgrains, numensembles);
if (getErrorCondition() < 0)
{
return;
}
AlignSections::execute();
// If there is an error set this to something negative and also set a message
notifyStatusMessage("Aligning Sections Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
QVector<bool> RemoveFlaggedFeatures::remove_flaggedfeatures()
{
size_t totalPoints = m_FeatureIdsPtr.lock()->getNumberOfTuples();
bool good = false;
int32_t gnum;
size_t totalFeatures = m_FlaggedFeaturesPtr.lock()->getNumberOfTuples();
QVector<bool> activeObjects(totalFeatures, true);
for (size_t i = 1; i < totalFeatures; i++)
{
if (m_FlaggedFeatures[i] == false) { good = true; }
else { activeObjects[i] = false; }
}
if (good == false)
{
setErrorCondition(-1);
notifyErrorMessage(getHumanLabel(), "All Features were flagged and would all be removed. The filter has quit.", -1);
return activeObjects;
}
for (size_t i = 0; i < totalPoints; i++)
{
gnum = m_FeatureIds[i];
if (activeObjects[gnum] == false)
{
if (m_FillRemovedFeatures == false) { m_FeatureIds[i] = 0; }
else { m_FeatureIds[i] = -1; }
}
}
return activeObjects;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AddOrientationNoise::execute()
{
int err = 0;
setErrorCondition(err);
DREAM3D_RANDOMNG_NEW()
VoxelDataContainer* m = getVoxelDataContainer();
if(NULL == m)
{
setErrorCondition(-999);
notifyErrorMessage("The DataContainer Object was NULL", -999);
return;
}
int64_t totalPoints = m->getTotalPoints();
size_t totalFields = m->getNumFieldTuples();
dataCheck(false, totalPoints, totalFields, m->getNumEnsembleTuples());
if (getErrorCondition() < 0)
{
return;
}
m_Magnitude = m_Magnitude*m_pi/180.0;
add_orientation_noise();
// If there is an error set this to something negative and also set a message
notifyStatusMessage("AddOrientationNoises Completed");
}
