void DoubleThresholdImageFilterITK::doubleThresholdImageFilterITK() {
insideValue_.setVolume(inport1_.getData());
outsideValue_.setVolume(inport1_.getData());
threshold1_.setVolume(inport1_.getData());
threshold2_.setVolume(inport1_.getData());
threshold3_.setVolume(inport1_.getData());
threshold4_.setVolume(inport1_.getData());
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::DoubleThresholdImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetInsideValue(insideValue_.getValue<T>());
filter->SetOutsideValue(outsideValue_.getValue<T>());
filter->SetThreshold1(threshold1_.getValue<T>());
filter->SetThreshold2(threshold2_.getValue<T>());
filter->SetThreshold3(threshold3_.getValue<T>());
filter->SetThreshold4(threshold4_.getValue<T>());
filter->SetFullyConnected(fullyConnected_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void SignedDanielssonDistanceMapImageFilterITK::signedDanielssonDistanceMapImageFilterITK() {
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typedef itk::Image<T, 3> OutputImageType2;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::SignedDanielssonDistanceMapImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetInsideIsPositive(insideIsPositive_.get());
filter->SetSquaredDistance(squaredDistance_.get());
filter->SetUseImageSpacing(useImageSpacing_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetDistanceMap());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
Volume* outputVolume2 = 0;
outputVolume2 = ITKToVoreenCopy<T>(filter->GetVoronoiMap());
if (outputVolume2) {
transferRWM(inport1_.getData(), outputVolume2);
transferTransformation(inport1_.getData(), outputVolume2);
outport2_.setData(outputVolume2);
} else
outport2_.setData(0);
}
void DiscreteGaussianImageFilterITK::discreteGaussianImageFilterITK() {
maximumError_.setVolume(inport1_.getData());
maximumError_.setMinValue<T>(1.0f);
variance_.setVolume(inport1_.getData());
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<float, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::DiscreteGaussianImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetInternalNumberOfStreamDivisions(internalNumberOfStreamDivisions_.get());
filter->SetMaximumError(maximumError_.getValue<T>());
filter->SetVariance(variance_.getValue<T>());
filter->SetUseImageSpacing(useImageSpacing_.get());
filter->SetFilterDimensionality(filterDimensionality_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<float>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void BayesianClassifierImageFilterITK::bayesianClassifierImageFilterITK() {
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType;
typedef itk::Image<uint8_t, 3> OutputImageType;
typedef itk::VectorImage<float, 3> VectorImageType;
typename InputImageType::Pointer p1 = voreenToITK<T>(inport1_.getData());
typedef itk::BayesianClassifierInitializationImageFilter<InputImageType> InitFilterType;
typename InitFilterType::Pointer initializer = InitFilterType::New();
initializer->SetInput(p1);
initializer->SetNumberOfClasses(numberOfClasses_.get());
try
{
initializer->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
//Filter define
typedef itk::BayesianClassifierImageFilter<VectorImageType> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(0, initializer->GetOutput());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<uint8_t>(filter->GetOutput());
if (outputVolume1) {
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
}
else
outport1_.setData(0);
}
void IntensityWindowingImageFilterITK::intensityWindowingImageFilterITK() {
outputMinimum_.setVolume(inport1_.getData());
outputMaximum_.setVolume(inport1_.getData());
windowMinimum_.setVolume(inport1_.getData());
windowMaximum_.setVolume(inport1_.getData());
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::IntensityWindowingImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetOutputMinimum(outputMinimum_.getValue<T>());
filter->SetOutputMaximum(outputMaximum_.getValue<T>());
filter->SetWindowMinimum(windowMinimum_.getValue<T>());
filter->SetWindowMaximum(windowMaximum_.getValue<T>());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void OtsuThresholdImageFilterITK::otsuThresholdImageFilterITK() {
outsideValue_.setVolume(inport1_.getData());
outsideValue_.setMinValue<T>(0.0001f);
insideValue_.setVolume(inport1_.getData());
insideValue_.setMinValue<T>(0.0001f);
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::OtsuThresholdImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetNumberOfHistogramBins(numberOfHistogramBins_.get());
filter->SetOutsideValue(outsideValue_.getValue<T>());
filter->SetInsideValue(insideValue_.getValue<T>());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void NarrowBandThresholdSegmentationLevelSetImageFilterITK::narrowBandThresholdSegmentationLevelSetImageFilterITK() {
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<S, 3> InputImageType2;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
typename InputImageType2::Pointer p2 = voreenToITK<S>(inport2_.getData());
//Filter define
typedef itk::NarrowBandThresholdSegmentationLevelSetImageFilter<InputImageType1, InputImageType2> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetFeatureImage(p2);
filter->SetPropagationScaling(propagationScaling_.get());
filter->SetCurvatureScaling(curvatureScaling_.get());
filter->SetAdvectionScaling(advectionScaling_.get());
filter->SetMaximumRMSError(maximumRMSError_.get());
filter->SetNumberOfIterations(numberOfIterations_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void GradientAnisotropicDiffusionImageFilterITK::gradientAnisotropicDiffusionImageFilterITK() {
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::GradientAnisotropicDiffusionImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetNumberOfIterations(numberOfIterations_.get());
filter->SetTimeStep(timeStep_.get());
filter->SetConductanceParameter(conductanceParameter_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void ScalarConnectedComponentImageFilterITK::scalarConnectedComponentImageFilterITK() {
distanceThreshold_.setVolume(inport1_.getData());
distanceThreshold_.setMinValue<T>(0.001f);
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::ScalarConnectedComponentImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetDistanceThreshold(distanceThreshold_.getValue<T>());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void GradientRecursiveGaussianImageFilterITK::gradientRecursiveGaussianImageFilterITK() {
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<itk::CovariantVector<double,3>, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::GradientRecursiveGaussianImageFilter<InputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetNormalizeAcrossScale(normalizeAcrossScale_.get());
filter->SetUseImageDirection(useImageDirection_.get());
filter->SetSigma(sigma_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKVec3ToVoreenVec3Copy<double>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void RelabelComponentImageFilterITK::relabelComponentImageFilterITK() {
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::RelabelComponentImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetMinimumObjectSize(minimumObjectSize_.get());
observe(filter.GetPointer());
try
{
filter->Update();
numberOfObjects_.set(filter->GetNumberOfObjects());
originalNumberOfObjects_.set(filter->GetOriginalNumberOfObjects());
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void LabelOverlayImageFilterITK::labelOverlayImageFilterITK() {
backgroundValue_.setVolume(inport1_.getData());
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<S, 3> InputImageType2;
typedef itk::Image<itk::CovariantVector<uint8_t,3>, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
typename InputImageType2::Pointer p2 = voreenToITK<S>(inport2_.getData());
//Filter define
typedef itk::LabelOverlayImageFilter<InputImageType1, InputImageType2, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetLabelImage(p2);
filter->SetOpacity(opacity_.get());
filter->SetBackgroundValue(backgroundValue_.getValue<T>());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKVec3ToVoreenVec3Copy<uint8_t>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void MaskImageFilterITK::maskImageFilterITK() {
outsideValue_.setVolume(inport1_.getData());
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<S, 3> InputImageType2;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
typename InputImageType2::Pointer p2 = voreenToITK<S>(inport2_.getData());
//Filter define
typedef itk::MaskImageFilter<InputImageType1, InputImageType2, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetMaskImage(p2);
filter->SetOutsideValue(outsideValue_.getValue<T>());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void WatershedImageFilterITK::watershedImageFilterITK() {
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<VolumeRAM_UInt64, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::WatershedImageFilter<InputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetLevel(level_.get());
filter->SetThreshold(threshold_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<itk::IdentifierType>(filter->GetOutput());
if (outputVolume1) {
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
}
else
outport1_.setData(0);
}
void GrayscaleGrindPeakImageFilterITK::grayscaleGrindPeakImageFilterITK() {
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::GrayscaleGrindPeakImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetFullyConnected(fullyConnected_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void VotingBinaryIterativeHoleFillingImageFilterITK::votingBinaryIterativeHoleFillingImageFilterITK() {
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::VotingBinaryIterativeHoleFillingImageFilter<InputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetMaximumNumberOfIterations(maximumNumberOfIterations_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void MinMaxCurvatureFlowImageFilterITK::minMaxCurvatureFlowImageFilterITK() {
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<float, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::MinMaxCurvatureFlowImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetStencilRadius(stencilRadius_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<float>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
Volume* ValuedRegionalMaximaImageFilter::applyFilter(const VolumeBase* inputVolume) {
typedef itk::Image<T, 3> InputImageType;
typedef itk::Image<T, 3> OutputImageType;
typename InputImageType::Pointer p = voreenToITK<T>(inputVolume);
typedef itk::ValuedRegionalMaximaImageFilter<InputImageType, OutputImageType> FilterType;
// Create the filter
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p);
observe(filter.GetPointer());
// Run the filter
filter->Update();
return ITKToVoreenCopy<T>(filter->GetOutput());
}
void HausdorffDistanceImageFilterITK::hausdorffDistanceImageFilterITK() {
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<S, 3> InputImageType2;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
typename InputImageType2::Pointer p2 = voreenToITK<S>(inport2_.getData());
//Filter define
typedef itk::HausdorffDistanceImageFilter<InputImageType1, InputImageType2> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput1(p1);
filter->SetInput2(p2);
observe(filter.GetPointer());
try
{
filter->Update();
hausdorffDistance_.set(filter->GetHausdorffDistance());
averageHausdorffDistance_.set(filter->GetAverageHausdorffDistance());
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
}
void SimilarityIndexImageFilterITK::similarityIndexImageFilterITK() {
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<S, 3> InputImageType2;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
typename InputImageType2::Pointer p2 = voreenToITK<S>(inport2_.getData());
//Filter define
typedef itk::SimilarityIndexImageFilter<InputImageType1, InputImageType2> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput1(p1);
filter->SetInput2(p2);
observe(filter.GetPointer());
try
{
filter->Update();
similarityIndex_.set(filter->GetSimilarityIndex());
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
}
void DilateObjectMorphologyImageFilterITK::dilateObjectMorphologyImageFilterITK() {
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typedef T PixelType;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
if(structuringElement_.get() == "binaryBall"){
shape_.setVisible(false);
typedef itk::BinaryBallStructuringElement < PixelType, 3 > KernelType;
typedef itk::DilateObjectMorphologyImageFilter<InputImageType1, OutputImageType1, KernelType> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
KernelType structuringElement;
typename KernelType::SizeType radius;
radius[0] = radius_.get().x;
radius[1] = radius_.get().y;
radius[2] = radius_.get().z;
structuringElement.SetRadius(radius);
structuringElement.CreateStructuringElement();
filter->SetKernel(structuringElement);
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
else if(structuringElement_.get() == "binaryCross"){
shape_.setVisible(false);
typedef itk::BinaryCrossStructuringElement < PixelType, 3 > KernelType;
typedef itk::DilateObjectMorphologyImageFilter<InputImageType1, OutputImageType1, KernelType> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
KernelType structuringElement;
typename KernelType::SizeType radius;
radius[0] = radius_.get().x;
radius[1] = radius_.get().y;
radius[2] = radius_.get().z;
structuringElement.SetRadius(radius);
structuringElement.CreateStructuringElement();
filter->SetKernel(structuringElement);
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
else if(structuringElement_.get() == "flat"){
shape_.setVisible(true);
typedef itk::FlatStructuringElement < 3 > KernelType;
typename KernelType::SizeType radius;
radius[0] = radius_.get().x;
radius[1] = radius_.get().y;
radius[2] = radius_.get().z;
if(shape_.get() == "box"){
KernelType structuringElement = KernelType::Box(radius);
typedef itk::DilateObjectMorphologyImageFilter<InputImageType1, OutputImageType1, KernelType> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetKernel(structuringElement);
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
else if(shape_.get() == "ball"){
KernelType structuringElement = KernelType::Ball(radius);
typedef itk::DilateObjectMorphologyImageFilter<InputImageType1, OutputImageType1, KernelType> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetKernel(structuringElement);
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
else if(shape_.get() == "cross"){
KernelType structuringElement = KernelType::Cross(radius);
typedef itk::DilateObjectMorphologyImageFilter<InputImageType1, OutputImageType1, KernelType> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetKernel(structuringElement);
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
else if(shape_.get() == "annulus"){
KernelType structuringElement = KernelType::Annulus(radius);
typedef itk::DilateObjectMorphologyImageFilter<InputImageType1, OutputImageType1, KernelType> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetKernel(structuringElement);
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
}
}
void GrayscaleConnectedClosingImageFilterITK::grayscaleConnectedClosingImageFilterITK() {
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::GrayscaleConnectedClosingImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetFullyConnected(fullyConnected_.get());
if (seedPointPort_.hasChanged()) {
const PointListGeometry<tgt::vec3>* pointList = dynamic_cast< const PointListGeometry<tgt::vec3>* >(seedPointPort_.getData());
if (pointList) {
seedPoints = pointList->getData();
if (!seedPoints.empty()) {
numSeedPoint_.setMinValue(1);
numSeedPoint_.setMaxValue(seedPoints.size());
numSeedPoint_.set(seedPoints.size());
}
else {
numSeedPoint_.setMinValue(0);
numSeedPoint_.setMaxValue(0);
numSeedPoint_.set(0);
}
}
}
if(!seedPoints.empty()) {
seedPoint_.set(seedPoints[numSeedPoint_.get()-1]);
}
else {
seedPoint_.set(tgt::vec3 (1));
}
typename InputImageType1::IndexType seed;
seed[0] = seedPoint_.get().x;
seed[1] = seedPoint_.get().y;
seed[2] = seedPoint_.get().z;
filter->SetSeed(seed);
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void IsolatedWatershedImageFilterITK::isolatedWatershedImageFilterITK() {
replaceValue1_.setVolume(inport1_.getData());
replaceValue2_.setVolume(inport1_.getData());
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::IsolatedWatershedImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
if (seedPointPort1_.hasChanged()) {
const PointListGeometry<tgt::vec3>* pointList1 = dynamic_cast< const PointListGeometry<tgt::vec3>* >(seedPointPort1_.getData());
if (pointList1) {
seedPoints1 = pointList1->getData();
if (!seedPoints1.empty()) {
numSeedPoint1_.setMinValue(1);
numSeedPoint1_.setMaxValue(seedPoints1.size());
numSeedPoint1_.set(seedPoints1.size());
}
else {
numSeedPoint1_.setMinValue(0);
numSeedPoint1_.setMaxValue(0);
numSeedPoint1_.set(0);
}
}
}
if(!seedPoints1.empty()) {
seedPoint1_.set(seedPoints1[numSeedPoint1_.get()-1]);
}
else {
seedPoint1_.set(tgt::vec3 (1));
}
typename InputImageType1::IndexType seed1;
seed1[0] = seedPoint1_.get().x;
seed1[1] = seedPoint1_.get().y;
seed1[2] = seedPoint1_.get().z;
filter->SetSeed1(seed1);
if (seedPointPort2_.hasChanged()) {
const PointListGeometry<tgt::vec3>* pointList2 = dynamic_cast< const PointListGeometry<tgt::vec3>* >(seedPointPort2_.getData());
if (pointList2) {
seedPoints2 = pointList2->getData();
if (!seedPoints2.empty()) {
numSeedPoint2_.setMinValue(1);
numSeedPoint2_.setMaxValue(seedPoints2.size());
numSeedPoint2_.set(seedPoints2.size());
}
else {
numSeedPoint2_.setMinValue(0);
numSeedPoint2_.setMaxValue(0);
numSeedPoint2_.set(0);
}
}
}
if(!seedPoints2.empty()) {
seedPoint2_.set(seedPoints2[numSeedPoint2_.get()-1]);
}
else {
seedPoint2_.set(tgt::vec3 (1));
}
typename InputImageType1::IndexType seed2;
seed2[0] = seedPoint2_.get().x;
seed2[1] = seedPoint2_.get().y;
seed2[2] = seedPoint2_.get().z;
filter->SetSeed2(seed2);
filter->SetThreshold(threshold_.get());
filter->SetIsolatedValueTolerance(isolatedValueTolerance_.get());
filter->SetUpperValueLimit(upperValueLimit_.get());
filter->SetReplaceValue1(replaceValue1_.getValue<T>());
filter->SetReplaceValue2(replaceValue2_.getValue<T>());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void IsolatedConnectedImageFilterITK::isolatedConnectedImageFilterITK() {
replaceValue_.setVolume(inport1_.getData());
isolatedValueTolerance_.setVolume(inport1_.getData());
upper_.setVolume(inport1_.getData());
lower_.setVolume(inport1_.getData());
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::IsolatedConnectedImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
if (seedPointPort1_.hasChanged()) {
const PointListGeometry<tgt::vec3>* pointList1 = dynamic_cast< const PointListGeometry<tgt::vec3>* >(seedPointPort1_.getData());
if (pointList1) {
seedPoints1 = pointList1->getData();
}
}
filter->ClearSeeds1();
typename InputImageType1::IndexType seed1;
for (size_t i = 0; i < seedPoints1.size(); i++) {
seed1[0] = seedPoints1[i].x;
seed1[1] = seedPoints1[i].y;
seed1[2] = seedPoints1[i].z;
filter->AddSeed1(seed1);
}
if (seedPointPort2_.hasChanged()) {
const PointListGeometry<tgt::vec3>* pointList2 = dynamic_cast< const PointListGeometry<tgt::vec3>* >(seedPointPort2_.getData());
if (pointList2) {
seedPoints2 = pointList2->getData();
}
}
filter->ClearSeeds2();
typename InputImageType1::IndexType seed2;
for (size_t i = 0; i < seedPoints2.size(); i++) {
seed2[0] = seedPoints2[i].x;
seed2[1] = seedPoints2[i].y;
seed2[2] = seedPoints2[i].z;
filter->AddSeed2(seed2);
}
filter->SetReplaceValue(replaceValue_.getValue<T>());
filter->SetIsolatedValueTolerance(isolatedValueTolerance_.getValue<T>());
filter->SetUpper(upper_.getValue<T>());
filter->SetLower(lower_.getValue<T>());
filter->SetFindUpperThreshold(findUpperThreshold_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void ConfidenceConnectedImageFilterITK::confidenceConnectedImageFilterITK() {
replaceValue_.setVolume(inport1_.getData());
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::ConfidenceConnectedImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
if (seedPointPort_.hasChanged()) {
const PointListGeometry<tgt::vec3>* pointList = dynamic_cast< const PointListGeometry<tgt::vec3>* >(seedPointPort_.getData());
if (pointList) {
seedPoints = pointList->getData();
}
}
filter->ClearSeeds();
typename InputImageType1::IndexType seed;
for (size_t i = 0; i < seedPoints.size(); i++) {
seed[0] = seedPoints[i].x;
seed[1] = seedPoints[i].y;
seed[2] = seedPoints[i].z;
filter->AddSeed(seed);
}
filter->SetNumberOfIterations(numberOfIterations_.get());
filter->SetReplaceValue(replaceValue_.getValue<T>());
filter->SetMultiplier(multiplier_.get());
filter->SetInitialNeighborhoodRadius(initialNeighborhoodRadius_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
