// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void FindMaxima::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
//check for required arrays
QVector<size_t> compDims(1, 1);
m_SelectedCellArrayPtr = TemplateHelpers::GetPrereqArrayFromPath<AbstractFilter>()(this, getSelectedCellArrayPath(), compDims);
if(NULL != m_SelectedCellArrayPtr.lock().get())
{
m_SelectedCellArray = m_SelectedCellArrayPtr.lock().get();
}
if(getErrorCondition() < 0) { return; }
ImageGeom::Pointer image = getDataContainerArray()->getDataContainer(getSelectedCellArrayPath().getDataContainerName())->getPrereqGeometry<ImageGeom, AbstractFilter>(this);
if(getErrorCondition() < 0 || NULL == image.get()) { return; }
//configured created name / location
tempPath.update(getSelectedCellArrayPath().getDataContainerName(), getSelectedCellArrayPath().getAttributeMatrixName(), getNewCellArrayName() );
DataContainer::Pointer dataContiner = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getSelectedCellArrayPath().getDataContainerName() );
AttributeMatrix::Pointer attrMatrix = dataContiner->getPrereqAttributeMatrix<AbstractFilter>(this, getSelectedCellArrayPath().getAttributeMatrixName(), 80000);
IDataArray::Pointer redArrayptr = attrMatrix->getPrereqIDataArray<IDataArray, AbstractFilter>(this, getSelectedCellArrayPath().getDataArrayName(), 80000);
//create new boolean array
tempPath.update(getSelectedCellArrayPath().getDataContainerName(), getSelectedCellArrayPath().getAttributeMatrixName(), getNewCellArrayName() );
m_NewCellArrayPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<bool>, AbstractFilter, bool>(this, tempPath, 0, compDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_NewCellArrayPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_NewCellArray = m_NewCellArrayPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void Watershed::execute()
{
//int err = 0;
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getSelectedCellArrayPath().getDataContainerName());
QString attrMatName = getSelectedCellArrayPath().getAttributeMatrixName();
//wrap m_RawImageData as itk::image
ImageProcessing::DefaultImageType::Pointer inputImage = ITKUtilitiesType::CreateItkWrapperForDataPointer(m, attrMatName, m_SelectedCellArray);
//create gradient magnitude filter
notifyStatusMessage(getHumanLabel(), "Calculating Gradient Magnitude");
typedef itk::GradientMagnitudeImageFilter<ImageProcessing::DefaultImageType, ImageProcessing::DefaultImageType > GradientMagnitudeImageFilterType;
GradientMagnitudeImageFilterType::Pointer gradientMagnitudeImageFilter = GradientMagnitudeImageFilterType::New();
gradientMagnitudeImageFilter->SetInput(inputImage);
gradientMagnitudeImageFilter->Update();
//watershed image
notifyStatusMessage(getHumanLabel(), "Watershedding");
typedef itk::WatershedImageFilter<ImageProcessing::DefaultImageType> WatershedFilterType;
WatershedFilterType::Pointer watershed = WatershedFilterType::New();
watershed->SetThreshold(m_Threshold);
watershed->SetLevel(m_Level);
watershed->SetInput(gradientMagnitudeImageFilter->GetOutput());
//execute filter
try
{
watershed->Update();
}
catch( itk::ExceptionObject& err )
{
setErrorCondition(-5);
QString ss = QObject::tr("Failed to execute itk::GradientMagnitudeImageFilter filter. Error Message returned from ITK:\n %1").arg(err.GetDescription());
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
//get output and copy to grainids
typedef itk::Image<unsigned long, ImageProcessing::ImageDimension> WatershedImageType;
WatershedImageType::Pointer output = watershed->GetOutput();
WatershedImageType::RegionType filterRegion = output->GetLargestPossibleRegion();
typedef itk::ImageRegionConstIterator<itk::Image<unsigned long, ImageProcessing::ImageDimension> > WatershedIteratorType;
WatershedIteratorType it(output, filterRegion);
it.GoToBegin();
int index = 0;
while(!it.IsAtEnd())
{
m_FeatureIds[index] = it.Get();
++it;
++index;
}
/* Let the GUI know we are done with this filter */
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void LinkFeatureMapToElementArray::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getSelectedCellArrayPath().getDataContainerName());
size_t totalPoints = m_SelectedCellDataPtr.lock()->getNumberOfTuples();
int32_t maxIndex = 0;
std::vector<bool> active;
for (size_t i = 0; i < totalPoints; i++)
{
int32_t index = m_SelectedCellData[i];
if ((index + 1) > maxIndex)
{
active.resize(index + 1);
active[index] = true;
maxIndex = index + 1;
}
}
QVector<size_t> tDims(1, maxIndex);
m->getAttributeMatrix(getCellFeatureAttributeMatrixName())->resizeAttributeArrays(tDims);
updateFeatureInstancePointers();
for (int32_t i = 0; i < maxIndex; i++)
{
m_Active[i] = active[i];
}
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ConvertData::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setSelectedCellArrayPath( reader->readDataArrayPath( "SelectedCellArrayPath", getSelectedCellArrayPath() ) );
setScalarType( reader->readValue("ScalarType", getScalarType()) );
setOutputArrayName( reader->readString( "OutputArrayName", getOutputArrayName() ) );
reader->closeFilterGroup();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void FindMaxima::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setSelectedCellArrayPath( reader->readDataArrayPath( "SelectedCellArrayPath", getSelectedCellArrayPath() ) );
setMinValue( reader->readValue( "MinValue", getMinValue() ) );
setNewCellArrayName( reader->readString( "NewCellArrayName", getNewCellArrayName() ) );
reader->closeFilterGroup();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void LinkFeatureMapToElementArray::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setCellFeatureAttributeMatrixName(reader->readString("CellFeatureAttributeMatrixName", getCellFeatureAttributeMatrixName()));
setActiveArrayName(reader->readString("ActiveArrayName", getActiveArrayName()));
setSelectedCellArrayPath( reader->readDataArrayPath( "SelectedCellArrayPath", getSelectedCellArrayPath() ) );
reader->closeFilterGroup();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void Watershed::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setSelectedCellArrayPath( reader->readDataArrayPath( "SelectedCellArrayPath", getSelectedCellArrayPath() ) );
setFeatureIdsArrayName( reader->readString( "FeatureIdsArrayName", getFeatureIdsArrayName() ) );
setThreshold( reader->readValue( "Threshold", getThreshold() ) );
setLevel( reader->readValue( "Level", getLevel() ) );
reader->closeFilterGroup();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SobelEdge::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setSelectedCellArrayPath( reader->readDataArrayPath( "SelectedCellArrayPath", getSelectedCellArrayPath() ) );
setNewCellArrayName( reader->readString( "NewCellArrayName", getNewCellArrayName() ) );
setSaveAsNewArray( reader->readValue( "SaveAsNewArray", getSaveAsNewArray() ) );
setSlice( reader->readValue( "Slice", getSlice() ) );
reader->closeFilterGroup();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int Watershed::writeFilterParameters(AbstractFilterParametersWriter* writer, int index)
{
writer->openFilterGroup(this, index);
writer->writeValue( "SelectedCellArrayPath", getSelectedCellArrayPath() );
writer->writeValue( "FeatureIdsArrayName", getFeatureIdsArrayName() );
writer->writeValue( "Threshold", getThreshold() );
writer->writeValue( "Level", getLevel() );
writer->closeFilterGroup();
return ++index; // we want to return the next index that was just written to
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void Watershed::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
QVector<size_t> dims(1, 1);
m_SelectedCellArrayPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<ImageProcessing::DefaultPixelType>, AbstractFilter>(this, getSelectedCellArrayPath(), dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SelectedCellArrayPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SelectedCellArray = m_SelectedCellArrayPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() < 0) { return; }
ImageGeom::Pointer image = getDataContainerArray()->getDataContainer(getSelectedCellArrayPath().getDataContainerName())->getPrereqGeometry<ImageGeom, AbstractFilter>(this);
if(getErrorCondition() < 0 || NULL == image.get()) { return; }
tempPath.update(getSelectedCellArrayPath().getDataContainerName(), getSelectedCellArrayPath().getAttributeMatrixName(), getFeatureIdsArrayName() );
m_FeatureIdsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, 0, dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_FeatureIdsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_FeatureIds = m_FeatureIdsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ImageMath::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setSelectedCellArrayPath( reader->readDataArrayPath( "SelectedCellArrayPath", getSelectedCellArrayPath() ) );
setOperator( reader->readValue( "Operator", getOperator() ) );
setValue( reader->readValue( "Value", getValue() ) );
setSaveAsNewArray( reader->readValue( "SaveAsNewArray", getSaveAsNewArray() ) );
setNewCellArrayName( reader->readString( "NewCellArrayName", getNewCellArrayName() ) );
reader->closeFilterGroup();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void LinkFeatureMapToElementArray::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
DataContainer::Pointer m = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getSelectedCellArrayPath().getDataContainerName(), false);
if(getErrorCondition() < 0 || NULL == m.get()) { return; }
QVector<size_t> tDims(1, 0);
m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellFeatureAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::CellFeature);
QVector<size_t> cDims(1, 1);
m_SelectedCellDataPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getSelectedCellArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SelectedCellDataPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SelectedCellData = m_SelectedCellDataPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() < 0) { return; }
tempPath.update(getSelectedCellArrayPath().getDataContainerName(), getCellFeatureAttributeMatrixName(), getActiveArrayName() );
m_ActivePtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<bool>, AbstractFilter, bool>(this, tempPath, 0, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_ActivePtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_Active = m_ActivePtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void FindMaxima::execute()
{
QString ss;
dataCheck();
if(getErrorCondition() < 0)
{
setErrorCondition(-10000);
ss = QObject::tr("DataCheck did not pass during execute");
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
//get volume container
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getSelectedCellArrayPath().getDataContainerName());
QString attrMatName = getSelectedCellArrayPath().getAttributeMatrixName();
//get input data
IDataArray::Pointer inputData = m_SelectedCellArrayPtr.lock();
//execute type dependant portion using a Private Implementation that takes care of figuring out if
// we can work on the correct type and actually handling the algorithm execution. We pass in "this" so
// that the private implementation can get access to the current object to pass up status notifications,
// progress or handle "cancel" if needed.
if(FindMaximaPrivate<int8_t>()(inputData))
{
FindMaximaPrivate<int8_t>::Execute(this, inputData, m_MinValue, m_NewCellArray, m, attrMatName);
}
else if(FindMaximaPrivate<uint8_t>()(inputData) )
{
FindMaximaPrivate<uint8_t>::Execute(this, inputData, m_MinValue, m_NewCellArray, m, attrMatName);
}
else if(FindMaximaPrivate<int16_t>()(inputData) )
{
FindMaximaPrivate<int16_t>::Execute(this, inputData, m_MinValue, m_NewCellArray, m, attrMatName);
}
else if(FindMaximaPrivate<uint16_t>()(inputData) )
{
FindMaximaPrivate<uint16_t>::Execute(this, inputData, m_MinValue, m_NewCellArray, m, attrMatName);
}
else if(FindMaximaPrivate<int32_t>()(inputData) )
{
FindMaximaPrivate<int32_t>::Execute(this, inputData, m_MinValue, m_NewCellArray, m, attrMatName);
}
else if(FindMaximaPrivate<uint32_t>()(inputData) )
{
FindMaximaPrivate<uint32_t>::Execute(this, inputData, m_MinValue, m_NewCellArray, m, attrMatName);
}
else if(FindMaximaPrivate<int64_t>()(inputData) )
{
FindMaximaPrivate<int64_t>::Execute(this, inputData, m_MinValue, m_NewCellArray, m, attrMatName);
}
else if(FindMaximaPrivate<uint64_t>()(inputData) )
{
FindMaximaPrivate<uint64_t>::Execute(this, inputData, m_MinValue, m_NewCellArray, m, attrMatName);
}
else if(FindMaximaPrivate<float>()(inputData) )
{
FindMaximaPrivate<float>::Execute(this, inputData, m_MinValue, m_NewCellArray, m, attrMatName);
}
else if(FindMaximaPrivate<double>()(inputData) )
{
FindMaximaPrivate<double>::Execute(this, inputData, m_MinValue, m_NewCellArray, m, attrMatName);
}
else
{
setErrorCondition(-10001);
ss = QObject::tr("A Supported DataArray type was not used for an input array.");
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
/* Let the GUI know we are done with this filter */
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ImageMath::execute()
{
//int err = 0;
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getSelectedCellArrayPath().getDataContainerName());
QString attrMatName = getSelectedCellArrayPath().getAttributeMatrixName();
//wrap m_RawImageData as itk::image
ImageProcessing::DefaultImageType::Pointer inputImage = ITKUtilitiesType::CreateItkWrapperForDataPointer(m, attrMatName, m_SelectedCellArray);
//define filter types
typedef itk::AddImageFilter<ImageProcessing::DefaultImageType, ImageProcessing::FloatImageType, ImageProcessing::FloatImageType> AddType;
typedef itk::SubtractImageFilter<ImageProcessing::DefaultImageType, ImageProcessing::FloatImageType, ImageProcessing::FloatImageType> SubtractType;
typedef itk::MultiplyImageFilter<ImageProcessing::DefaultImageType, ImageProcessing::FloatImageType, ImageProcessing::FloatImageType> MultiplyType;
typedef itk::DivideImageFilter<ImageProcessing::DefaultImageType, ImageProcessing::FloatImageType, ImageProcessing::FloatImageType> DivideType;
typedef itk::MinimumImageFilter<ImageProcessing::DefaultImageType, ImageProcessing::FloatImageType, ImageProcessing::FloatImageType> MinType;
typedef itk::MaximumImageFilter<ImageProcessing::DefaultImageType, ImageProcessing::FloatImageType, ImageProcessing::FloatImageType> MaxType;
typedef itk::BinaryFunctorImageFilter< ImageProcessing::DefaultImageType, ImageProcessing::FloatImageType, ImageProcessing::FloatImageType, ImageProcessing::Functor::Gamma<ImageProcessing::FloatPixelType> > GammaType;
typedef itk::LogImageFilter<ImageProcessing::DefaultImageType, ImageProcessing::FloatImageType> LogType;
typedef itk::ExpImageFilter<ImageProcessing::DefaultImageType, ImageProcessing::FloatImageType> ExpType;
typedef itk::SquareImageFilter<ImageProcessing::DefaultImageType, ImageProcessing::FloatImageType> SquareType;
typedef itk::SqrtImageFilter<ImageProcessing::DefaultImageType, ImageProcessing::FloatImageType> SqrtType;
typedef itk::InvertIntensityImageFilter<ImageProcessing::DefaultImageType, ImageProcessing::DefaultImageType> InvertType;
//set up filter to cap image range + round
typedef itk::UnaryFunctorImageFilter< ImageProcessing::FloatImageType, ImageProcessing::DefaultImageType, ImageProcessing::Functor::LimitsRound<ImageProcessing::FloatPixelType, ImageProcessing::DefaultPixelType> > LimitsRoundType;
LimitsRoundType::Pointer limitsRound = LimitsRoundType::New();
//apply selected operation
switch(m_Operator)
{
case 0://add
{
AddType::Pointer add = AddType::New();
add->SetInput1(inputImage);
add->SetConstant2(m_Value);
limitsRound->SetInput(add->GetOutput());
ITKUtilitiesType::SetITKFilterOutput(limitsRound->GetOutput(), m_NewCellArrayPtr.lock());
limitsRound->Update();
}
break;
case 1://subtract
{
SubtractType::Pointer subtract = SubtractType::New();
subtract->SetInput1(inputImage);
subtract->SetConstant2(m_Value);
limitsRound->SetInput(subtract->GetOutput());
ITKUtilitiesType::SetITKFilterOutput(limitsRound->GetOutput(), m_NewCellArrayPtr.lock());
limitsRound->Update();
}
break;
case 2://multiply
{
MultiplyType::Pointer multiply = MultiplyType::New();
multiply->SetInput1(inputImage);
multiply->SetConstant2(m_Value);
limitsRound->SetInput(multiply->GetOutput());
ITKUtilitiesType::SetITKFilterOutput(limitsRound->GetOutput(), m_NewCellArrayPtr.lock());
limitsRound->Update();
}
break;
case 3://divide
{
DivideType::Pointer divide = DivideType::New();
divide->SetInput1(inputImage);
divide->SetConstant2(m_Value);
limitsRound->SetInput(divide->GetOutput());
ITKUtilitiesType::SetITKFilterOutput(limitsRound->GetOutput(), m_NewCellArrayPtr.lock());
limitsRound->Update();
}
break;
case 4://min
{
MinType::Pointer minimum = MinType::New();
minimum->SetInput1(inputImage);
minimum->SetConstant2(m_Value);
limitsRound->SetInput(minimum->GetOutput());
ITKUtilitiesType::SetITKFilterOutput(limitsRound->GetOutput(), m_NewCellArrayPtr.lock());
limitsRound->Update();
}
break;
case 5://max
{
MaxType::Pointer maximum = MaxType::New();
maximum->SetInput1(inputImage);
maximum->SetConstant2(m_Value);
limitsRound->SetInput(maximum->GetOutput());
ITKUtilitiesType::SetITKFilterOutput(limitsRound->GetOutput(), m_NewCellArrayPtr.lock());
limitsRound->Update();
}
break;
case 6://gamma
{
GammaType::Pointer gamma = GammaType::New();
gamma->SetInput1(inputImage);
gamma->SetConstant2(m_Value);
limitsRound->SetInput(gamma->GetOutput());
ITKUtilitiesType::SetITKFilterOutput(limitsRound->GetOutput(), m_NewCellArrayPtr.lock());
limitsRound->Update();
}
break;
case 7://log
{
LogType::Pointer logfilter = LogType::New();
logfilter->SetInput(inputImage);
limitsRound->SetInput(logfilter->GetOutput());
ITKUtilitiesType::SetITKFilterOutput(limitsRound->GetOutput(), m_NewCellArrayPtr.lock());
limitsRound->Update();
}
break;
case 8://exp
{
ExpType::Pointer expfilter = ExpType::New();
expfilter->SetInput(inputImage);
limitsRound->SetInput(expfilter->GetOutput());
ITKUtilitiesType::SetITKFilterOutput(limitsRound->GetOutput(), m_NewCellArrayPtr.lock());
limitsRound->Update();
}
break;
case 9://square
{
SquareType::Pointer square = SquareType::New();
square->SetInput(inputImage);
limitsRound->SetInput(square->GetOutput());
ITKUtilitiesType::SetITKFilterOutput(limitsRound->GetOutput(), m_NewCellArrayPtr.lock());
limitsRound->Update();
}
break;
case 10://squareroot
{
SqrtType::Pointer sqrtfilter = SqrtType::New();
sqrtfilter->SetInput(inputImage);
limitsRound->SetInput(sqrtfilter->GetOutput());
ITKUtilitiesType::SetITKFilterOutput(limitsRound->GetOutput(), m_NewCellArrayPtr.lock());
limitsRound->Update();
}
break;
case 11://invert
{
InvertType::Pointer invert = InvertType::New();
invert->SetInput(inputImage);
ITKUtilitiesType::SetITKFilterOutput(invert->GetOutput(), m_NewCellArrayPtr.lock());
invert->Update();
}
break;
}
//array name changing/cleanup
if(m_SaveAsNewArray == false)
{
AttributeMatrix::Pointer attrMat = m->getAttributeMatrix(m_SelectedCellArrayPath.getAttributeMatrixName());
attrMat->removeAttributeArray(m_SelectedCellArrayPath.getDataArrayName());
attrMat->renameAttributeArray(m_NewCellArrayName, m_SelectedCellArrayPath.getDataArrayName());
}
/* Let the GUI know we are done with this filter */
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void FindMaxima::setupFilterParameters()
{
FilterParameterVector parameters;
parameters.push_back(FilterParameter::New("Input Array", "SelectedCellArrayPath", FilterParameterWidgetType::DataArraySelectionWidget, getSelectedCellArrayPath(), false, ""));
parameters.push_back(FilterParameter::New("Minimum Peak Intensity", "MinValue", FilterParameterWidgetType::DoubleWidget, getMinValue(), false, ""));
parameters.push_back(FilterParameter::New("Created Array Name", "NewCellArrayName", FilterParameterWidgetType::StringWidget, getNewCellArrayName(), false, ""));
setFilterParameters(parameters);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void CreateFeatureArrayFromElementArray::dataCheck()
{
setErrorCondition(0);
if (getCreatedArrayName().isEmpty() == true)
{
setErrorCondition(-11002);
notifyErrorMessage(getHumanLabel(), "The new Feature 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, getSelectedCellArrayPath());
getDataContainerArray()->getPrereqAttributeMatrixFromPath<AbstractFilter>(this, getCellFeatureAttributeMatrixName(), -301);
if(getErrorCondition() < 0 ) { return; }
DataArrayPath tempPath(getCellFeatureAttributeMatrixName().getDataContainerName(), getCellFeatureAttributeMatrixName().getAttributeMatrixName(), getCreatedArrayName());
TemplateHelpers::CreateNonPrereqArrayFromArrayType()(this, tempPath, m_InArrayPtr.lock()->getComponentDimensions(), m_InArrayPtr.lock());
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void LinkFeatureMapToElementArray::setupFilterParameters()
{
FilterParameterVector parameters;
parameters.push_back(SeparatorFilterParameter::New("Element Data", FilterParameter::RequiredArray));
{
DataArraySelectionFilterParameter::RequirementType req = DataArraySelectionFilterParameter::CreateCategoryRequirement(DREAM3D::TypeNames::Int32, 1, DREAM3D::AttributeMatrixObjectType::Element);
parameters.push_back(DataArraySelectionFilterParameter::New("Element Attribute Array to Link", "SelectedCellArrayPath", getSelectedCellArrayPath(), FilterParameter::RequiredArray, req));
}
parameters.push_back(SeparatorFilterParameter::New("Feature Data", FilterParameter::CreatedArray));
parameters.push_back(StringFilterParameter::New("Feature Attribute Matrix", "CellFeatureAttributeMatrixName", getCellFeatureAttributeMatrixName(), FilterParameter::CreatedArray));
parameters.push_back(StringFilterParameter::New("Active", "ActiveArrayName", getActiveArrayName(), FilterParameter::CreatedArray));
setFilterParameters(parameters);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ImageMath::setupFilterParameters()
{
FilterParameterVector parameters;
parameters.push_back(FilterParameter::New("Array to Operate On", "SelectedCellArrayPath", FilterParameterWidgetType::DataArraySelectionWidget, getSelectedCellArrayPath(), false, ""));
{
ChoiceFilterParameter::Pointer parameter = ChoiceFilterParameter::New();
parameter->setHumanLabel("Operator");
parameter->setPropertyName("Operator");
parameter->setWidgetType(FilterParameterWidgetType::ChoiceWidget);
QVector<QString> choices;
choices.push_back("Add");
choices.push_back("Subtract");
choices.push_back("Multiply");
choices.push_back("Divide");
choices.push_back("Min");
choices.push_back("Max");
choices.push_back("Gamma");
choices.push_back("Log");
choices.push_back("Exp");
choices.push_back("Square");
choices.push_back("Square Root");
choices.push_back("Invert");
parameter->setChoices(choices);
parameters.push_back(parameter);
}
parameters.push_back(FilterParameter::New("Value", "Value", FilterParameterWidgetType::DoubleWidget, getValue(), false, ""));
QStringList linkedProps;
linkedProps << "NewCellArrayName";
parameters.push_back(LinkedBooleanFilterParameter::New("Save As New Array", "SaveAsNewArray", getSaveAsNewArray(), linkedProps, false));
parameters.push_back(FilterParameter::New("Created Array Name", "NewCellArrayName", FilterParameterWidgetType::StringWidget, getNewCellArrayName(), false, ""));
setFilterParameters(parameters);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void Watershed::setupFilterParameters()
{
FilterParameterVector parameters;
parameters.push_back(FilterParameter::New("Image Data Array", "SelectedCellArrayPath", FilterParameterWidgetType::DataArraySelectionWidget, getSelectedCellArrayPath(), false, ""));
parameters.push_back(FilterParameter::New("Feature Ids Array", "FeatureIdsArrayName", FilterParameterWidgetType::StringWidget, getFeatureIdsArrayName(), false, ""));
parameters.push_back(FilterParameter::New("Threshold", "Threshold", FilterParameterWidgetType::DoubleWidget, getThreshold(), false));
parameters.push_back(FilterParameter::New("Level", "Level", FilterParameterWidgetType::DoubleWidget, getLevel(), false));
setFilterParameters(parameters);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void MultiOtsuThreshold::execute()
{
//int err = 0;
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getSelectedCellArrayPath().getDataContainerName());
QString attrMatName = getSelectedCellArrayPath().getAttributeMatrixName();
//get dims
size_t udims[3] = {0, 0, 0};
m->getGeometryAs<ImageGeom>()->getDimensions(udims);
#if (CMP_SIZEOF_SIZE_T == 4)
typedef int32_t DimType;
#else
typedef int64_t DimType;
#endif
DimType dims[3] =
{
static_cast<DimType>(udims[0]),
static_cast<DimType>(udims[1]),
static_cast<DimType>(udims[2]),
};
//wrap input as itk image
ImageProcessing::DefaultImageType::Pointer inputImage = ITKUtilitiesType::CreateItkWrapperForDataPointer(m, attrMatName, m_SelectedCellArray);
if(m_Slice)
{
//define 2d histogram generator
typedef itk::OtsuMultipleThresholdsImageFilter< ImageProcessing::DefaultSliceType, ImageProcessing::DefaultSliceType > ThresholdType;
ThresholdType::Pointer otsuThresholder = ThresholdType::New();
//wrap output buffer as image
ImageProcessing::DefaultImageType::Pointer outputImage = ITKUtilitiesType::CreateItkWrapperForDataPointer(m, attrMatName, m_NewCellArray);
//loop over slices
for(int i = 0; i < dims[2]; i++)
{
//get slice
ImageProcessing::DefaultSliceType::Pointer slice = ITKUtilitiesType::ExtractSlice(inputImage, ImageProcessing::ZSlice, i);
//threshold
otsuThresholder->SetInput(slice);
otsuThresholder->SetNumberOfThresholds(m_Levels);
otsuThresholder->SetLabelOffset(1);
//execute filters
try
{
otsuThresholder->Update();
}
catch( itk::ExceptionObject& err )
{
setErrorCondition(-5);
QString ss = QObject::tr("Failed to execute itk::OtsuMultipleThresholdsImageFilter filter. Error Message returned from ITK:\n %1").arg(err.GetDescription());
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
//copy back into volume
ITKUtilitiesType::SetSlice(outputImage, otsuThresholder->GetOutput(), ImageProcessing::ZSlice, i);
}
}
else
{
typedef itk::OtsuMultipleThresholdsImageFilter< ImageProcessing::DefaultImageType, ImageProcessing::DefaultImageType > ThresholdType;
ThresholdType::Pointer otsuThresholder = ThresholdType::New();
otsuThresholder->SetInput(inputImage);
otsuThresholder->SetNumberOfThresholds(m_Levels);
otsuThresholder->SetLabelOffset(1);
ITKUtilitiesType::SetITKFilterOutput(otsuThresholder->GetOutput(), m_NewCellArrayPtr.lock());
//execute filters
try
{
otsuThresholder->Update();
}
catch( itk::ExceptionObject& err )
{
setErrorCondition(-5);
QString ss = QObject::tr("Failed to execute itk::OtsuMultipleThresholdsImageFilter filter. Error Message returned from ITK:\n %1").arg(err.GetDescription());
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
}
//array name changing/cleanup
if(m_SaveAsNewArray == false)
{
AttributeMatrix::Pointer attrMat = m->getAttributeMatrix(m_SelectedCellArrayPath.getAttributeMatrixName());
attrMat->removeAttributeArray(m_SelectedCellArrayPath.getDataArrayName());
attrMat->renameAttributeArray(m_NewCellArrayName, m_SelectedCellArrayPath.getDataArrayName());
}
/* Let the GUI know we are done with this filter */
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void CreateFeatureArrayFromElementArray::setupFilterParameters()
{
FilterParameterVector parameters;
parameters.push_back(SeparatorFilterParameter::New("Element Data", FilterParameter::RequiredArray));
{
DataArraySelectionFilterParameter::RequirementType req = DataArraySelectionFilterParameter::CreateCategoryRequirement(DREAM3D::Defaults::AnyPrimitive, DREAM3D::Defaults::AnyComponentSize, DREAM3D::AttributeMatrixObjectType::Element);
parameters.push_back(DataArraySelectionFilterParameter::New("Element Data to Copy to Feature Data", "SelectedCellArrayPath", getSelectedCellArrayPath(), FilterParameter::RequiredArray, req));
}
{
DataArraySelectionFilterParameter::RequirementType req = DataArraySelectionFilterParameter::CreateCategoryRequirement(DREAM3D::TypeNames::Int32, 1, DREAM3D::AttributeMatrixObjectType::Element);
parameters.push_back(DataArraySelectionFilterParameter::New("Feature Ids", "FeatureIdsArrayPath", getFeatureIdsArrayPath(), FilterParameter::RequiredArray, req));
}
parameters.push_back(SeparatorFilterParameter::New("Feature Data", FilterParameter::CreatedArray));
{
AttributeMatrixSelectionFilterParameter::RequirementType req = AttributeMatrixSelectionFilterParameter::CreateRequirement(DREAM3D::AttributeMatrixType::CellFeature, DREAM3D::Defaults::AnyGeometry);
parameters.push_back(AttributeMatrixSelectionFilterParameter::New("Feature Attribute Matrix", "CellFeatureAttributeMatrixName", getCellFeatureAttributeMatrixName(), FilterParameter::CreatedArray, req));
}
parameters.push_back(StringFilterParameter::New("Copied Attribute Array", "CreatedArrayName", getCreatedArrayName(), FilterParameter::CreatedArray));
setFilterParameters(parameters);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SobelEdge::execute()
{
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getSelectedCellArrayPath().getDataContainerName());
QString attrMatName = getSelectedCellArrayPath().getAttributeMatrixName();
//wrap m_RawImageData as itk::image
ImageProcessing::DefaultImageType::Pointer inputImage = ITKUtilitiesType::CreateItkWrapperForDataPointer(m, attrMatName, m_SelectedCellArray);
if(m_Slice)
{
//wrap output array
ImageProcessing::DefaultImageType::Pointer outputImage = ITKUtilitiesType::CreateItkWrapperForDataPointer(m, attrMatName, m_NewCellArray);
//get dimensions
size_t udims[3] = {0, 0, 0};
m->getGeometryAs<ImageGeom>()->getDimensions(udims);
#if (CMP_SIZEOF_SIZE_T == 4)
typedef int32_t DimType;
#else
typedef int64_t DimType;
#endif
DimType dims[3] =
{
static_cast<DimType>(udims[0]),
static_cast<DimType>(udims[1]),
static_cast<DimType>(udims[2]),
};
//create edge filter
typedef itk::SobelEdgeDetectionImageFilter<ImageProcessing::DefaultSliceType, ImageProcessing::FloatSliceType> SobelFilterType;
SobelFilterType::Pointer sobelFilter = SobelFilterType::New();
//convert result back to uint8
typedef itk::RescaleIntensityImageFilter<ImageProcessing::FloatSliceType, ImageProcessing::DefaultSliceType> RescaleImageType;
RescaleImageType::Pointer rescaleFilter = RescaleImageType::New();
rescaleFilter->SetOutputMinimum(0);
rescaleFilter->SetOutputMaximum(255);
//loop over slices applying filters
for(int i = 0; i < dims[2]; ++i)
{
QString ss = QObject::tr("Finding Edges On Slice: %1").arg(i + 1);
notifyStatusMessage(getMessagePrefix(), getHumanLabel(), ss);
//get slice
ImageProcessing::DefaultSliceType::Pointer inputSlice = ITKUtilitiesType::ExtractSlice(inputImage, ImageProcessing::ZSlice, i);
//run filters
sobelFilter->SetInput(inputSlice);
rescaleFilter->SetInput(sobelFilter->GetOutput());
//execute filters
try
{
sobelFilter->Update();
rescaleFilter->Update();
}
catch( itk::ExceptionObject& err )
{
setErrorCondition(-5);
QString ss = QObject::tr("Failed to execute itk::SobelEdgeDetectionImageFilter filter. Error Message returned from ITK:\n %1").arg(err.GetDescription());
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
//copy into volume
ITKUtilitiesType::SetSlice(outputImage, rescaleFilter->GetOutput(), ImageProcessing::ZSlice, i);
}
}
else
{
//create edge filter
typedef itk::SobelEdgeDetectionImageFilter<ImageProcessing::DefaultImageType, ImageProcessing::FloatImageType> SobelFilterType;
SobelFilterType::Pointer sobelFilter = SobelFilterType::New();
sobelFilter->SetInput(inputImage);
//convert result back to uint8
typedef itk::RescaleIntensityImageFilter<ImageProcessing::FloatImageType, ImageProcessing::DefaultImageType> RescaleImageType;
RescaleImageType::Pointer rescaleFilter = RescaleImageType::New();
rescaleFilter->SetInput(sobelFilter->GetOutput());
rescaleFilter->SetOutputMinimum(0);
rescaleFilter->SetOutputMaximum(255);
//have filter write to dream3d array instead of creating its own buffer
ITKUtilitiesType::SetITKFilterOutput(rescaleFilter->GetOutput(), m_NewCellArrayPtr.lock());
//execute filters
try
{
sobelFilter->Update();
rescaleFilter->Update();
}
catch( itk::ExceptionObject& err )
{
setErrorCondition(-5);
QString ss = QObject::tr("Failed to execute itk::SobelEdgeDetectionImageFilter filter. Error Message returned from ITK:\n %1").arg(err.GetDescription());
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
}
}
//array name changing/cleanup
if(m_SaveAsNewArray == false)
{
AttributeMatrix::Pointer attrMat = m->getAttributeMatrix(m_SelectedCellArrayPath.getAttributeMatrixName());
attrMat->removeAttributeArray(m_SelectedCellArrayPath.getDataArrayName());
attrMat->renameAttributeArray(m_NewCellArrayName, m_SelectedCellArrayPath.getDataArrayName());
}
/* Let the GUI know we are done with this filter */
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ConvertData::dataCheck()
{
setErrorCondition(0);
DataContainer::Pointer m = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getSelectedCellArrayPath().getDataContainerName(), false);
QString ss;
if (m_OutputArrayName.isEmpty() == true)
{
ss = QObject::tr("The output array name must be set");
setErrorCondition(-398);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
if (getInPreflight())
{
AttributeMatrix::Pointer cellAttrMat = getDataContainerArray()->getPrereqAttributeMatrixFromPath<AbstractFilter>(this, m_SelectedCellArrayPath, -301);
if(getErrorCondition() < 0) { return; }
IDataArray::Pointer p = getDataContainerArray()->getPrereqIDataArrayFromPath<IDataArray, AbstractFilter>(this, getSelectedCellArrayPath());
if(getErrorCondition() < 0) { return; }
QVector<size_t> dims = p->getComponentDimensions();
size_t voxels = cellAttrMat->getNumTuples();
if (m_ScalarType == Detail::Int8)
{
p = Int8ArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
else if (m_ScalarType == Detail::UInt8)
{
p = UInt8ArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
else if (m_ScalarType == Detail::Int16)
{
p = Int16ArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
else if (m_ScalarType == Detail::UInt16)
{
p = UInt16ArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
else if (m_ScalarType == Detail::Int32)
{
p = Int32ArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
else if (m_ScalarType == Detail::UInt32)
{
p = UInt32ArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
else if (m_ScalarType == Detail::Int64)
{
p = Int64ArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
else if (m_ScalarType == Detail::UInt64)
{
p = UInt64ArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
else if (m_ScalarType == Detail::Float)
{
p = FloatArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
else if (m_ScalarType == Detail::Double)
{
p = DoubleArrayType::CreateArray(voxels, dims, m_OutputArrayName);
}
cellAttrMat->addAttributeArray(p->getName(), p);
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SobelEdge::setupFilterParameters()
{
FilterParameterVector parameters;
parameters.push_back(FilterParameter::New("Array to Process", "SelectedCellArrayPath", FilterParameterWidgetType::DataArraySelectionWidget, getSelectedCellArrayPath(), false, ""));
QStringList linkedProps;
linkedProps << "NewCellArrayName";
parameters.push_back(LinkedBooleanFilterParameter::New("Save As New Array", "SaveAsNewArray", getSaveAsNewArray(), linkedProps, false));
parameters.push_back(FilterParameter::New("Created Array Name", "NewCellArrayName", FilterParameterWidgetType::StringWidget, getNewCellArrayName(), false, ""));
parameters.push_back(FilterParameter::New("Slice at a Time", "Slice", FilterParameterWidgetType::BooleanWidget, getSlice(), false));
setFilterParameters(parameters);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ConvertData::setupFilterParameters()
{
FilterParameterVector parameters;
{
ChoiceFilterParameter::Pointer parameter = ChoiceFilterParameter::New();
parameter->setHumanLabel("Scalar Type");
parameter->setPropertyName("ScalarType");
QVector<QString> choices;
choices.push_back("signed int 8 bit");
choices.push_back("unsigned int 8 bit");
choices.push_back("signed int 16 bit");
choices.push_back("unsigned int 16 bit");
choices.push_back("signed int 32 bit");
choices.push_back("unsigned int 32 bit");
choices.push_back("signed int 64 bit");
choices.push_back("unsigned int 64 bit");
choices.push_back(" Float 32 bit");
choices.push_back(" Double 64 bit");
parameter->setChoices(choices);
parameter->setCategory(FilterParameter::Parameter);
parameters.push_back(parameter);
}
parameters.push_back(DataArraySelectionFilterParameter::New("Attribute Array to Convert", "SelectedCellArrayPath", getSelectedCellArrayPath(), FilterParameter::RequiredArray));
parameters.push_back(StringFilterParameter::New("Converted Attribute Array", "OutputArrayName", getOutputArrayName(), FilterParameter::CreatedArray));
setFilterParameters(parameters);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void CreateFeatureArrayFromElementArray::setupFilterParameters()
{
FilterParameterVector parameters;
parameters.push_back(SeparatorFilterParameter::New("Element Data", FilterParameter::RequiredArray));
parameters.push_back(DataArraySelectionFilterParameter::New("Element Data to Copy to Feature Data", "SelectedCellArrayPath", getSelectedCellArrayPath(), FilterParameter::RequiredArray));
parameters.push_back(DataArraySelectionFilterParameter::New("Feature Ids", "FeatureIdsArrayPath", getFeatureIdsArrayPath(), FilterParameter::RequiredArray));
parameters.push_back(SeparatorFilterParameter::New("Feature Data", FilterParameter::CreatedArray));
parameters.push_back(AttributeMatrixSelectionFilterParameter::New("Feature Attribute Matrix", "CellFeatureAttributeMatrixName", getCellFeatureAttributeMatrixName(), FilterParameter::CreatedArray));
parameters.push_back(StringFilterParameter::New("Copied Attribute Array", "CreatedArrayName", getCreatedArrayName(), FilterParameter::CreatedArray));
setFilterParameters(parameters);
}