bool mitk::NavigationDataLandmarkTransformFilter::FindCorrespondentLandmarks(LandmarkPointContainer& sources, const LandmarkPointContainer& targets) const
{
if (sources.size() < 6 || targets.size() < 6)
return false;
//throw std::invalid_argument("ICP correspondence finding needs at least 6 landmarks");
/* lots of type definitions */
typedef itk::PointSet<mitk::ScalarType, 3> PointSetType;
//typedef itk::BoundingBox<PointSetType::PointIdentifier, PointSetType::PointDimension> BoundingBoxType;
typedef itk::EuclideanDistancePointMetric< PointSetType, PointSetType> MetricType;
//typedef MetricType::TransformType TransformBaseType;
//typedef MetricType::TransformType::ParametersType ParametersType;
//typedef TransformBaseType::JacobianType JacobianType;
//typedef itk::Euler3DTransform< double > TransformType;
typedef itk::VersorRigid3DTransform< double > TransformType;
typedef TransformType ParametersType;
typedef itk::PointSetToPointSetRegistrationMethod< PointSetType, PointSetType > RegistrationType;
/* copy landmarks to itk pointsets for registration */
PointSetType::Pointer sourcePointSet = PointSetType::New();
unsigned int i = 0;
for (LandmarkPointContainer::const_iterator it = sources.begin(); it != sources.end(); ++it)
{
PointSetType::PointType doublePoint;
mitk::itk2vtk(*it, doublePoint); // copy mitk::ScalarType point into double point as workaround to ITK 3.10 bug
sourcePointSet->SetPoint(i++, doublePoint /**it*/);
}
i = 0;
PointSetType::Pointer targetPointSet = PointSetType::New();
for (LandmarkPointContainer::const_iterator it = targets.begin(); it != targets.end(); ++it)
{
PointSetType::PointType doublePoint;
mitk::itk2vtk(*it, doublePoint); // copy mitk::ScalarType point into double point as workaround to ITK 3.10 bug
targetPointSet->SetPoint(i++, doublePoint /**it*/);
}
/* get centroid and extends of our pointsets */
//BoundingBoxType::Pointer sourceBoundingBox = BoundingBoxType::New();
//sourceBoundingBox->SetPoints(sourcePointSet->GetPoints());
//sourceBoundingBox->ComputeBoundingBox();
//BoundingBoxType::Pointer targetBoundingBox = BoundingBoxType::New();
//targetBoundingBox->SetPoints(targetPointSet->GetPoints());
//targetBoundingBox->ComputeBoundingBox();
TransformType::Pointer transform = TransformType::New();
transform->SetIdentity();
//transform->SetTranslation(targetBoundingBox->GetCenter() - sourceBoundingBox->GetCenter());
itk::LevenbergMarquardtOptimizer::Pointer optimizer = itk::LevenbergMarquardtOptimizer::New();
optimizer->SetUseCostFunctionGradient(false);
RegistrationType::Pointer registration = RegistrationType::New();
// Scale the translation components of the Transform in the Optimizer
itk::LevenbergMarquardtOptimizer::ScalesType scales(transform->GetNumberOfParameters());
const double translationScale = 5000; //sqrtf(targetBoundingBox->GetDiagonalLength2()) * 1000; // dynamic range of translations
const double rotationScale = 1.0; // dynamic range of rotations
scales[0] = 1.0 / rotationScale;
scales[1] = 1.0 / rotationScale;
scales[2] = 1.0 / rotationScale;
scales[3] = 1.0 / translationScale;
scales[4] = 1.0 / translationScale;
scales[5] = 1.0 / translationScale;
//scales.Fill(0.01);
unsigned long numberOfIterations = 80000;
double gradientTolerance = 1e-10; // convergence criterion
double valueTolerance = 1e-10; // convergence criterion
double epsilonFunction = 1e-10; // convergence criterion
optimizer->SetScales( scales );
optimizer->SetNumberOfIterations( numberOfIterations );
optimizer->SetValueTolerance( valueTolerance );
optimizer->SetGradientTolerance( gradientTolerance );
optimizer->SetEpsilonFunction( epsilonFunction );
registration->SetInitialTransformParameters( transform->GetParameters() );
//------------------------------------------------------
// Connect all the components required for Registration
//------------------------------------------------------
MetricType::Pointer metric = MetricType::New();
registration->SetMetric( metric );
registration->SetOptimizer( optimizer );
registration->SetTransform( transform );
registration->SetFixedPointSet( targetPointSet );
registration->SetMovingPointSet( sourcePointSet );
try
{
//registration->StartRegistration();
registration->Update();
}
catch( itk::ExceptionObject & e )
{
MITK_INFO << "Exception caught during ICP optimization: " << e;
return false;
//throw e;
}
MITK_INFO << "ICP successful: Solution = " << transform->GetParameters() << std::endl;
MITK_INFO << "Metric value: " << metric->GetValue(transform->GetParameters());
/* find point correspondences */
//mitk::PointLocator::Pointer pointLocator = mitk::PointLocator::New(); // <<- use mitk::PointLocator instead of searching manually?
//pointLocator->SetPoints()
for (LandmarkPointContainer::const_iterator sourcesIt = sources.begin(); sourcesIt != sources.end(); ++sourcesIt)
{
}
//MetricType::MeasureType closestDistances = metric->GetValue(transform->GetParameters());
//unsigned int index = 0;
LandmarkPointContainer sortedSources;
for (LandmarkPointContainer::const_iterator targetsIt = targets.begin(); targetsIt != targets.end(); ++targetsIt)
{
double minDistance = itk::NumericTraits<double>::max();
LandmarkPointContainer::iterator minDistanceIterator = sources.end();
for (LandmarkPointContainer::iterator sourcesIt = sources.begin(); sourcesIt != sources.end(); ++sourcesIt)
{
TransformInitializerType::LandmarkPointType transformedSource = transform->TransformPoint(*sourcesIt);
double dist = targetsIt->EuclideanDistanceTo(transformedSource);
MITK_INFO << "target: " << *targetsIt << ", source: " << *sourcesIt << ", transformed source: " << transformedSource << ", dist: " << dist;
if (dist < minDistance )
{
minDistanceIterator = sourcesIt;
minDistance = dist;
}
}
if (minDistanceIterator == sources.end())
return false;
MITK_INFO << "minimum distance point is: " << *minDistanceIterator << " (dist: " << targetsIt->EuclideanDistanceTo(transform->TransformPoint(*minDistanceIterator)) << ", minDist: " << minDistance << ")";
sortedSources.push_back(*minDistanceIterator); // this point is assigned
sources.erase(minDistanceIterator); // erase it from sources to avoid duplicate assigns
}
//for (LandmarkPointContainer::const_iterator sortedSourcesIt = sortedSources.begin(); targetsIt != sortedSources.end(); ++targetsIt)
sources = sortedSources;
return true;
}
void MutualInformationRegistration::updateRegistration() {
if(!isReady())
return;
convertVolumes();
//typedef itk::RegularStepGradientDescentOptimizer OptimizerType;
typedef itk::VersorRigid3DTransformOptimizer OptimizerType;
typedef OptimizerType::ScalesType OptimizerScalesType;
typedef itk::LinearInterpolateImageFunction< InternalImageType, double > InterpolatorType;
typedef itk::MattesMutualInformationImageToImageMetric< InternalImageType, InternalImageType > MetricType;
typedef itk::MultiResolutionImageRegistrationMethod< InternalImageType, InternalImageType > RegistrationType;
typedef itk::MultiResolutionPyramidImageFilter< InternalImageType, InternalImageType > FixedImagePyramidType;
typedef itk::MultiResolutionPyramidImageFilter< InternalImageType, InternalImageType > MovingImagePyramidType;
OptimizerType::Pointer optimizer = OptimizerType::New();
InterpolatorType::Pointer interpolator = InterpolatorType::New();
RegistrationType::Pointer registration = RegistrationType::New();
MetricType::Pointer metric = MetricType::New();
FixedImagePyramidType::Pointer fixedImagePyramid = FixedImagePyramidType::New();
MovingImagePyramidType::Pointer movingImagePyramid = MovingImagePyramidType::New();
registration->SetOptimizer(optimizer);
registration->SetTransform(transform_);
registration->SetInterpolator(interpolator);
registration->SetMetric(metric);
registration->SetFixedImagePyramid(fixedImagePyramid);
registration->SetMovingImagePyramid(movingImagePyramid);
OptimizerScalesType optimizerScales( transform_->GetNumberOfParameters() );
float rotScale = 1.0 / 1000.0f;
optimizerScales[0] = 1.0f;
optimizerScales[1] = 1.0f;
optimizerScales[2] = 1.0f;
optimizerScales[3] = rotScale;
optimizerScales[4] = rotScale;
optimizerScales[5] = rotScale;
optimizer->SetScales( optimizerScales );
optimizer->SetMaximumStepLength(0.2);
optimizer->SetMinimumStepLength(0.0001);
InternalImageType::Pointer fixed = voreenToITK<float>(fixedVolumeFloat_);
InternalImageType::Pointer moving = voreenToITK<float>(movingVolumeFloat_);
registration->SetFixedImage(fixed);
registration->SetMovingImage(moving);
registration->SetFixedImageRegion( fixed->GetBufferedRegion() );
registration->SetInitialTransformParameters( transform_->GetParameters() );
metric->SetNumberOfHistogramBins(numHistogramBins_.get());
size_t numVoxels = hmul(fixedVolumeFloat_->getDimensions());
metric->SetNumberOfSpatialSamples(numVoxels * numSamples_.get());
metric->ReinitializeSeed( 76926294 );
//// Define whether to calculate the metric derivative by explicitly
//// computing the derivatives of the joint PDF with respect to the Transform
//// parameters, or doing it by progressively accumulating contributions from
//// each bin in the joint PDF.
metric->SetUseExplicitPDFDerivatives(explicitPDF_.get());
optimizer->SetNumberOfIterations(numIterations_.get());
optimizer->SetRelaxationFactor(relaxationFactor_.get());
// Create the Command observer and register it with the optimizer.
CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
optimizer->AddObserver( itk::IterationEvent(), observer );
typedef RegistrationInterfaceCommand<RegistrationType> CommandType;
CommandType::Pointer command = CommandType::New();
registration->AddObserver( itk::IterationEvent(), command );
registration->SetNumberOfLevels(numLevels_.get());
try
{
registration->StartRegistration();
std::cout << "Optimizer stop condition: " << registration->GetOptimizer()->GetStopConditionDescription() << std::endl;
}
catch( itk::ExceptionObject & err )
{
std::cout << "ExceptionObject caught !" << std::endl;
std::cout << err << std::endl;
//return EXIT_FAILURE;
}
ParametersType finalParameters = registration->GetLastTransformParameters();
transform_->SetParameters(finalParameters);
unsigned int numberOfIterations = optimizer->GetCurrentIteration();
double bestValue = optimizer->GetValue();
// Print out results
std::cout << "Result = " << std::endl;
std::cout << " Versor " << finalParameters[0] << " " << finalParameters[1] << " " << finalParameters[2] << std::endl;
std::cout << " Translation " << finalParameters[1] << " " << finalParameters[4] << " " << finalParameters[5] << std::endl;
std::cout << " Iterations = " << numberOfIterations << std::endl;
std::cout << " Metric value = " << bestValue << std::endl;
invalidate(INVALID_RESULT);
}
void
SoItkMeanSquaresImageToImageMetric::evaluate()
{
if( mOutput )
{
mOutput->unref();
mOutput = 0;
SO_ENGINE_OUTPUT( Output, SoItkSFDataImageMetric, setValue( 0 ) );
}
/*
if( mGradientImage )
{
mGradientImage->unref();
mGradientImage = 0;
SO_ENGINE_OUTPUT( GradientImage, SoItkSFDataImage, setValue( 0 ) );
}
*/
try
{
switch( PixelType.getValue() )
{
case FLOAT:
{
switch( Dimension.getValue() )
{
case 2:
{
typedef itk::Image< float, 2 > InputImageType;
typedef itk::Image< float, 2 > OutputImageType;
typedef itk::MeanSquaresImageToImageMetric< InputImageType, OutputImageType > MetricType;
typedef itk::Transform< double, 2, 2 > TransformType;
typedef itk::InterpolateImageFunction< InputImageType, double > InterpolatorType;
MetricType::Pointer metric = MetricType::New();
metric->Register();
// Fixed Image
/*
SoItkDataImage* FixedImage_ = FixedImage.getValue();
InputImageType* itkFixedImage =
static_cast< InputImageType* >( FixedImage_->getPointer() );
if( !itkFixedImage )
return ;
metric->SetFixedImage( itkFixedImage );
// Moving Image
SoItkDataImage* MovingImage_ = MovingImage.getValue();
InputImageType* itkMovingImage =
static_cast< InputImageType* >( MovingImage_->getPointer() );
if( !itkMovingImage )
return ;
metric->SetMovingImage( itkMovingImage );
// Transform
SoItkDataTransform* Transform_ = Transform.getValue();
TransformType* itkTransform =
static_cast< TransformType* >( Transform_->getPointer() );
if( !itkTransform )
return ;
metric->SetTransform( itkTransform );
// Interpolator
SoItkDataInterpolator* Interpolator_ = Interpolator.getValue();
InterpolatorType* itkInterpolator =
static_cast< InterpolatorType* >( Interpolator_->getPointer() );
if( !itkInterpolator )
return ;
metric->SetInterpolator( itkInterpolator );
// Fixed Image Region
typedef itk::ImageRegion< 2 > ImageRegionType;
typedef itk::Index< 2 > ImageRegionIndexType;
typedef itk::Size< 2 > ImageRegionSizeType;
ImageRegionIndexType fixedImageRegionIndex;
fixedImageRegionIndex[0] = FixedImageRegionOrigin.getValue()[0];
fixedImageRegionIndex[1] = FixedImageRegionOrigin.getValue()[1];
ImageRegionSizeType fixedImageRegionSize;
fixedImageRegionSize[0] = FixedImageRegionSize.getValue()[0];
fixedImageRegionSize[1] = FixedImageRegionSize.getValue()[1];
ImageRegionType fixedImageRegion;
fixedImageRegion.SetIndex( fixedImageRegionIndex );
fixedImageRegion.SetSize( fixedImageRegionSize );
metric->SetFixedImageRegion( fixedImageRegion );
// Transform Parameters
typedef itk::Array< double > ArrayType;
ArrayType transformParameters( (double *) TransformParameters.getValues(0), TransformParameters.getNum(), false );
metric->SetTransformParameters( transformParameters );
metric->SetComputeGradient( ComputeGradient.getValue() );
if( ComputeGradient.getValue() == TRUE )
{
metric->GetGradientImage()->Register();
mGradientImage = new SoItkDataImage( SoItkDataImage::FLOAT, 2,
FixedImage.getValue()->getModelMatrix() );
mGradientImage->ref();
mGradientImage->setPointer( metric->GetGradientImage() );
}
*/
mOutput = new SoItkDataImageMetric( SoItkDataImageMetric::FLOAT, 2 );
mOutput->ref();
mOutput->setPointer( metric );
}
break ;
case 3:
{
typedef itk::Image< float, 3 > InputImageType;
typedef itk::Image< float, 3 > OutputImageType;
typedef itk::MeanSquaresImageToImageMetric< InputImageType, OutputImageType > MetricType;
typedef itk::Transform< double, 3, 3 > TransformType;
typedef itk::InterpolateImageFunction< InputImageType, double > InterpolatorType;
MetricType::Pointer metric = MetricType::New();
metric->Register();
/*
// Fixed Image
SoItkDataImage* FixedImage_ = FixedImage.getValue();
InputImageType* itkFixedImage =
static_cast< InputImageType* >( FixedImage_->getPointer() );
if( !itkFixedImage )
return ;
metric->SetFixedImage( itkFixedImage );
// Moving Image
SoItkDataImage* MovingImage_ = MovingImage.getValue();
InputImageType* itkMovingImage =
static_cast< InputImageType* >( MovingImage_->getPointer() );
if( !itkMovingImage )
return ;
metric->SetMovingImage( itkMovingImage );
// Transform
SoItkDataTransform* Transform_ = Transform.getValue();
TransformType* itkTransform =
static_cast< TransformType* >( Transform_->getPointer() );
if( !itkTransform )
return ;
metric->SetTransform( itkTransform );
// Interpolator
SoItkDataInterpolator* Interpolator_ = Interpolator.getValue();
InterpolatorType* itkInterpolator =
static_cast< InterpolatorType* >( Interpolator_->getPointer() );
if( !itkInterpolator )
return ;
metric->SetInterpolator( itkInterpolator );
// Fixed Image Region
typedef itk::ImageRegion< 3 > ImageRegionType;
typedef itk::Index< 3 > ImageRegionIndexType;
typedef itk::Size< 3 > ImageRegionSizeType;
ImageRegionIndexType fixedImageRegionIndex;
fixedImageRegionIndex[0] = FixedImageRegionOrigin.getValue()[0];
fixedImageRegionIndex[1] = FixedImageRegionOrigin.getValue()[1];
fixedImageRegionIndex[2] = FixedImageRegionOrigin.getValue()[2];
ImageRegionSizeType fixedImageRegionSize;
fixedImageRegionSize[0] = FixedImageRegionSize.getValue()[0];
fixedImageRegionSize[1] = FixedImageRegionSize.getValue()[1];
fixedImageRegionSize[2] = FixedImageRegionSize.getValue()[2];
ImageRegionType fixedImageRegion;
fixedImageRegion.SetIndex( fixedImageRegionIndex );
fixedImageRegion.SetSize( fixedImageRegionSize );
metric->SetFixedImageRegion( fixedImageRegion );
// Transform Parameters
typedef itk::Array< double > ArrayType;
ArrayType transformParameters( (double *) TransformParameters.getValues(0), TransformParameters.getNum(), false );
metric->SetTransformParameters( transformParameters );
metric->SetComputeGradient( ComputeGradient.getValue() );
if( ComputeGradient.getValue() == TRUE )
{
metric->GetGradientImage()->Register();
mGradientImage = new SoItkDataImage( SoItkDataImage::FLOAT, 3,
FixedImage.getValue()->getModelMatrix() );
mGradientImage->ref();
mGradientImage->setPointer( metric->GetGradientImage() );
}
*/
mOutput = new SoItkDataImageMetric( SoItkDataImageMetric::FLOAT, 3 );
mOutput->ref();
mOutput->setPointer( metric );
}
break ;
}
}
break ;
case UNSIGNED_SHORT:
{
switch( Dimension.getValue() )
{
case 2:
{
typedef itk::Image< unsigned short, 2 > InputImageType;
typedef itk::Image< unsigned short, 2 > OutputImageType;
typedef itk::MeanSquaresImageToImageMetric< InputImageType, OutputImageType > MetricType;
typedef itk::Transform< double, 2, 2 > TransformType;
typedef itk::InterpolateImageFunction< InputImageType, double > InterpolatorType;
MetricType::Pointer metric = MetricType::New();
metric->Register();
/*
// Fixed Image
SoItkDataImage* FixedImage_ = FixedImage.getValue();
InputImageType* itkFixedImage =
static_cast< InputImageType* >( FixedImage_->getPointer() );
if( !itkFixedImage )
return ;
metric->SetFixedImage( itkFixedImage );
// Moving Image
SoItkDataImage* MovingImage_ = MovingImage.getValue();
InputImageType* itkMovingImage =
static_cast< InputImageType* >( MovingImage_->getPointer() );
if( !itkMovingImage )
return ;
metric->SetMovingImage( itkMovingImage );
// Transform
SoItkDataTransform* Transform_ = Transform.getValue();
TransformType* itkTransform =
static_cast< TransformType* >( Transform_->getPointer() );
if( !itkTransform )
return ;
metric->SetTransform( itkTransform );
// Interpolator
SoItkDataInterpolator* Interpolator_ = Interpolator.getValue();
InterpolatorType* itkInterpolator =
static_cast< InterpolatorType* >( Interpolator_->getPointer() );
if( !itkInterpolator )
return ;
metric->SetInterpolator( itkInterpolator );
// Fixed Image Region
typedef itk::ImageRegion< 2 > ImageRegionType;
typedef itk::Index< 2 > ImageRegionIndexType;
typedef itk::Size< 2 > ImageRegionSizeType;
ImageRegionIndexType fixedImageRegionIndex;
fixedImageRegionIndex[0] = FixedImageRegionOrigin.getValue()[0];
fixedImageRegionIndex[1] = FixedImageRegionOrigin.getValue()[1];
ImageRegionSizeType fixedImageRegionSize;
fixedImageRegionSize[0] = FixedImageRegionSize.getValue()[0];
fixedImageRegionSize[1] = FixedImageRegionSize.getValue()[1];
ImageRegionType fixedImageRegion;
fixedImageRegion.SetIndex( fixedImageRegionIndex );
fixedImageRegion.SetSize( fixedImageRegionSize );
metric->SetFixedImageRegion( fixedImageRegion );
// Transform Parameters
typedef itk::Array< double > ArrayType;
ArrayType transformParameters( (double *) TransformParameters.getValues(0), TransformParameters.getNum(), false );
metric->SetTransformParameters( transformParameters );
metric->SetComputeGradient( ComputeGradient.getValue() );
if( ComputeGradient.getValue() == TRUE )
{
metric->GetGradientImage()->Register();
mGradientImage = new SoItkDataImage( SoItkDataImage::FLOAT, 2,
FixedImage.getValue()->getModelMatrix() );
mGradientImage->ref();
mGradientImage->setPointer( metric->GetGradientImage() );
}
*/
mOutput = new SoItkDataImageMetric( SoItkDataImageMetric::UNSIGNED_SHORT, 2 );
mOutput->ref();
mOutput->setPointer( metric );
}
break ;
case 3:
{
typedef itk::Image< unsigned short, 3 > InputImageType;
typedef itk::Image< unsigned short, 3 > OutputImageType;
typedef itk::MeanSquaresImageToImageMetric< InputImageType, OutputImageType > MetricType;
typedef itk::Transform< double, 3, 3 > TransformType;
typedef itk::InterpolateImageFunction< InputImageType, double > InterpolatorType;
MetricType::Pointer metric = MetricType::New();
metric->Register();
/*
// Fixed Image
SoItkDataImage* FixedImage_ = FixedImage.getValue();
InputImageType* itkFixedImage =
static_cast< InputImageType* >( FixedImage_->getPointer() );
if( !itkFixedImage )
return ;
metric->SetFixedImage( itkFixedImage );
// Moving Image
SoItkDataImage* MovingImage_ = MovingImage.getValue();
InputImageType* itkMovingImage =
static_cast< InputImageType* >( MovingImage_->getPointer() );
if( !itkMovingImage )
return ;
metric->SetMovingImage( itkMovingImage );
// Transform
SoItkDataTransform* Transform_ = Transform.getValue();
TransformType* itkTransform =
static_cast< TransformType* >( Transform_->getPointer() );
if( !itkTransform )
return ;
metric->SetTransform( itkTransform );
// Interpolator
SoItkDataInterpolator* Interpolator_ = Interpolator.getValue();
InterpolatorType* itkInterpolator =
static_cast< InterpolatorType* >( Interpolator_->getPointer() );
if( !itkInterpolator )
return ;
metric->SetInterpolator( itkInterpolator );
// Fixed Image Region
typedef itk::ImageRegion< 3 > ImageRegionType;
typedef itk::Index< 3 > ImageRegionIndexType;
typedef itk::Size< 3 > ImageRegionSizeType;
ImageRegionIndexType fixedImageRegionIndex;
fixedImageRegionIndex[0] = FixedImageRegionOrigin.getValue()[0];
fixedImageRegionIndex[1] = FixedImageRegionOrigin.getValue()[1];
fixedImageRegionIndex[2] = FixedImageRegionOrigin.getValue()[2];
ImageRegionSizeType fixedImageRegionSize;
fixedImageRegionSize[0] = FixedImageRegionSize.getValue()[0];
fixedImageRegionSize[1] = FixedImageRegionSize.getValue()[1];
fixedImageRegionSize[2] = FixedImageRegionSize.getValue()[2];
ImageRegionType fixedImageRegion;
fixedImageRegion.SetIndex( fixedImageRegionIndex );
fixedImageRegion.SetSize( fixedImageRegionSize );
metric->SetFixedImageRegion( fixedImageRegion );
// Transform Parameters
typedef itk::Array< double > ArrayType;
ArrayType transformParameters( (double *) TransformParameters.getValues(0), TransformParameters.getNum(), false );
metric->SetTransformParameters( transformParameters );
metric->SetComputeGradient( ComputeGradient.getValue() );
if( ComputeGradient.getValue() == TRUE )
{
metric->GetGradientImage()->Register();
mGradientImage = new SoItkDataImage( SoItkDataImage::FLOAT, 3,
FixedImage.getValue()->getModelMatrix() );
mGradientImage->ref();
mGradientImage->setPointer( metric->GetGradientImage() );
}
*/
mOutput = new SoItkDataImageMetric( SoItkDataImageMetric::UNSIGNED_SHORT, 3 );
mOutput->ref();
mOutput->setPointer( metric );
}
break ;
}
}
break ;
}
}
catch(...)
{
SoDebugError::post( __FILE__, "Unknown Exception" );
return ;
}
SO_ENGINE_OUTPUT( Output, SoItkSFDataImageMetric, setValue( mOutput ) );
// SO_ENGINE_OUTPUT( GradientImage, SoItkSFDataImage, setValue( mGradientImage ) );
}
void QAngioSubstractionExtension::computeAutomateSingleImage()
{
QApplication::setOverrideCursor(Qt::WaitCursor);
const unsigned int Dimension = 2;
typedef Volume::ItkPixelType PixelType;
typedef itk::Image< PixelType, Dimension > FixedImageType;
typedef itk::Image< PixelType, Dimension > MovingImageType;
typedef float InternalPixelType;
typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
typedef itk::TranslationTransform< double, Dimension > TransformType;
typedef itk::GradientDescentOptimizer OptimizerType;
typedef itk::LinearInterpolateImageFunction<
InternalImageType,
double > InterpolatorType;
typedef itk::ImageRegistrationMethod<
InternalImageType,
InternalImageType > RegistrationType;
typedef itk::MutualInformationImageToImageMetric<
InternalImageType,
InternalImageType > MetricType;
TransformType::Pointer transform = TransformType::New();
OptimizerType::Pointer optimizer = OptimizerType::New();
InterpolatorType::Pointer interpolator = InterpolatorType::New();
RegistrationType::Pointer registration = RegistrationType::New();
registration->SetOptimizer(optimizer);
registration->SetTransform(transform);
registration->SetInterpolator(interpolator);
MetricType::Pointer metric = MetricType::New();
registration->SetMetric(metric);
metric->SetFixedImageStandardDeviation(0.4);
metric->SetMovingImageStandardDeviation(0.4);
metric->SetNumberOfSpatialSamples(50);
typedef itk::ExtractImageFilter< Volume::ItkImageType, FixedImageType > FilterType;
FilterType::Pointer extractFixedImageFilter = FilterType::New();
Volume::ItkImageType::RegionType inputRegion = m_mainVolume->getItkData()->GetLargestPossibleRegion();
Volume::ItkImageType::SizeType size = inputRegion.GetSize();
//Dividim la mida per dos per tal de quedar-nos només amb la part central
// ja que si no ens registre el background
size[0] = size[0] / 2;
size[1] = size[1] / 2;
size[2] = 0;
Volume::ItkImageType::IndexType start = inputRegion.GetIndex();
const unsigned int sliceReference = m_imageSelectorSpinBox->value();
//comencem a un quart de la imatge
start[0] = size[0] / 2;
start[1] = size[1] / 2;
start[2] = sliceReference;
Volume::ItkImageType::RegionType desiredRegion;
desiredRegion.SetSize(size);
desiredRegion.SetIndex(start);
extractFixedImageFilter->SetExtractionRegion(desiredRegion);
extractFixedImageFilter->SetInput(m_mainVolume->getItkData());
extractFixedImageFilter->Update();
FilterType::Pointer extractMovingImageFilter = FilterType::New();
Volume::ItkImageType::IndexType startMoving = inputRegion.GetIndex();
const unsigned int sliceNumber = m_2DView_1->getViewer()->getCurrentSlice();
startMoving[0] = size[0] / 2;
startMoving[1] = size[1] / 2;
startMoving[2] = sliceNumber;
Volume::ItkImageType::RegionType desiredMovingRegion;
desiredMovingRegion.SetSize(size);
desiredMovingRegion.SetIndex(startMoving);
extractMovingImageFilter->SetExtractionRegion(desiredMovingRegion);
extractMovingImageFilter->SetInput(m_mainVolume->getItkData());
extractMovingImageFilter->Update();
typedef itk::NormalizeImageFilter<
FixedImageType,
InternalImageType
> FixedNormalizeFilterType;
typedef itk::NormalizeImageFilter<
MovingImageType,
InternalImageType
> MovingNormalizeFilterType;
FixedNormalizeFilterType::Pointer fixedNormalizer =
FixedNormalizeFilterType::New();
MovingNormalizeFilterType::Pointer movingNormalizer =
MovingNormalizeFilterType::New();
typedef itk::DiscreteGaussianImageFilter<
InternalImageType,
InternalImageType
> GaussianFilterType;
GaussianFilterType::Pointer fixedSmoother = GaussianFilterType::New();
GaussianFilterType::Pointer movingSmoother = GaussianFilterType::New();
fixedSmoother->SetVariance(2.0);
movingSmoother->SetVariance(2.0);
fixedNormalizer->SetInput(extractFixedImageFilter->GetOutput());
movingNormalizer->SetInput(extractMovingImageFilter->GetOutput());
fixedSmoother->SetInput(fixedNormalizer->GetOutput());
movingSmoother->SetInput(movingNormalizer->GetOutput());
registration->SetFixedImage(fixedSmoother->GetOutput());
registration->SetMovingImage(movingSmoother->GetOutput());
fixedNormalizer->Update();
registration->SetFixedImageRegion(
fixedNormalizer->GetOutput()->GetBufferedRegion());
typedef RegistrationType::ParametersType ParametersType;
ParametersType initialParameters(transform->GetNumberOfParameters());
initialParameters[0] = 0.0; // Initial offset in mm along X
initialParameters[1] = 0.0; // Initial offset in mm along Y
registration->SetInitialTransformParameters(initialParameters);
optimizer->SetLearningRate(20.0);
optimizer->SetNumberOfIterations(200);
optimizer->MaximizeOn();
try
{
registration->Update();
}
catch(itk::ExceptionObject & err)
{
std::cout << "ExceptionObject caught !" << std::endl;
std::cout << err << std::endl;
return;
}
ParametersType finalParameters = registration->GetLastTransformParameters();
double TranslationAlongX = finalParameters[0];
double TranslationAlongY = finalParameters[1];
// Print out results
//
DEBUG_LOG(QString("Result = "));
DEBUG_LOG(QString(" Translation X = %1").arg(TranslationAlongX));
DEBUG_LOG(QString(" Translation Y = %1").arg(TranslationAlongY));
DEBUG_LOG(QString(" Iterations = %1").arg(optimizer->GetCurrentIteration()));
DEBUG_LOG(QString(" Metric value = %1").arg(optimizer->GetValue()));
double spacing[3];
m_mainVolume->getSpacing(spacing);
DEBUG_LOG(QString(" Translation X (in px) = %1").arg(TranslationAlongX / spacing[0]));
DEBUG_LOG(QString(" Translation Y (in px) = %1").arg(TranslationAlongY / spacing[1]));
//Actualitzem les dades de la transdifference tool
m_toolManager->triggerTool("TransDifferenceTool");
TransDifferenceTool* tdTool = static_cast<TransDifferenceTool*> (m_2DView_2->getViewer()->getToolProxy()->getTool("TransDifferenceTool"));
if(m_tdToolData == 0){
m_tdToolData = static_cast<TransDifferenceToolData*> (tdTool->getToolData());
}
if(m_tdToolData->getInputVolume() != m_mainVolume){
m_tdToolData->setInputVolume(m_mainVolume);
}
tdTool->setSingleDifferenceImage(TranslationAlongX / spacing[0],TranslationAlongY / spacing[1]);
m_toolManager->triggerTool("SlicingTool");
/* typedef itk::Image< PixelType, Dimension > FixedImageType;
typedef itk::Image< PixelType, Dimension > MovingImageType;
typedef itk::TranslationTransform< double, Dimension > TransformType;
typedef itk::RegularStepGradientDescentOptimizer OptimizerType;
typedef itk::MattesMutualInformationImageToImageMetric<
FixedImageType,
MovingImageType > MetricType;
typedef itk:: LinearInterpolateImageFunction<
MovingImageType,
double > InterpolatorType;
typedef itk::ImageRegistrationMethod<
FixedImageType,
MovingImageType > RegistrationType;
MetricType::Pointer metric = MetricType::New();
TransformType::Pointer transform = TransformType::New();
OptimizerType::Pointer optimizer = OptimizerType::New();
InterpolatorType::Pointer interpolator = InterpolatorType::New();
RegistrationType::Pointer registration = RegistrationType::New();
registration->SetMetric(metric);
registration->SetOptimizer(optimizer);
registration->SetTransform(transform);
registration->SetInterpolator(interpolator);
metric->SetNumberOfHistogramBins(50);
metric->SetNumberOfSpatialSamples(10000);
typedef itk::ExtractImageFilter< Volume::ItkImageType, FixedImageType > FilterType;
FilterType::Pointer extractFixedImageFilter = FilterType::New();
Volume::ItkImageType::RegionType inputRegion = m_mainVolume->getItkData()->GetLargestPossibleRegion();
Volume::ItkImageType::SizeType size = inputRegion.GetSize();
//Dividim la mida per dos per tal de quedar-nos només amb la part central
// ja que si no ens registre el background
size[0] = size[0] / 2;
size[1] = size[1] / 2;
size[2] = 0;
Volume::ItkImageType::IndexType start = inputRegion.GetIndex();
const unsigned int sliceReference = m_imageSelectorSpinBox->value();
//comencem a un quart de la imatge
start[0] = size[0] / 2;
start[1] = size[1] / 2;
start[2] = sliceReference;
Volume::ItkImageType::RegionType desiredRegion;
desiredRegion.SetSize(size);
desiredRegion.SetIndex(start);
extractFixedImageFilter->SetExtractionRegion(desiredRegion);
extractFixedImageFilter->SetInput(m_mainVolume->getItkData());
extractFixedImageFilter->Update();
FilterType::Pointer extractMovingImageFilter = FilterType::New();
Volume::ItkImageType::IndexType startMoving = inputRegion.GetIndex();
const unsigned int sliceNumber = m_2DView_1->getViewer()->getCurrentSlice();
startMoving[0] = size[0] / 2;
startMoving[1] = size[1] / 2;
startMoving[2] = sliceNumber;
Volume::ItkImageType::RegionType desiredMovingRegion;
desiredMovingRegion.SetSize(size);
desiredMovingRegion.SetIndex(startMoving);
extractMovingImageFilter->SetExtractionRegion(desiredMovingRegion);
extractMovingImageFilter->SetInput(m_mainVolume->getItkData());
extractMovingImageFilter->Update();
registration->SetFixedImage(extractFixedImageFilter->GetOutput());
registration->SetMovingImage(extractMovingImageFilter->GetOutput());
typedef RegistrationType::ParametersType ParametersType;
ParametersType initialParameters(transform->GetNumberOfParameters());
//Potser seria millor posar la transformada que té actualment
initialParameters[0] = 0.0; // Initial offset in mm along X
initialParameters[1] = 0.0; // Initial offset in mm along Y
registration->SetInitialTransformParameters(initialParameters);
optimizer->SetMaximumStepLength(4.00);
optimizer->SetMinimumStepLength(0.005);
optimizer->SetNumberOfIterations(200);
try
{
registration->StartRegistration();
}
catch(itk::ExceptionObject & err)
{
DEBUG_LOG(QString("ExceptionObject caught !"));
std::cout<<err<<std::endl;
return;
}
ParametersType finalParameters = registration->GetLastTransformParameters();
const double TranslationAlongX = finalParameters[0];
const double TranslationAlongY = finalParameters[1];
const unsigned int numberOfIterations = optimizer->GetCurrentIteration();
const double bestValue = optimizer->GetValue();
DEBUG_LOG(QString("Result = "));
DEBUG_LOG(QString(" Translation X = %1").arg(TranslationAlongX));
DEBUG_LOG(QString(" Translation Y = %1").arg(TranslationAlongY));
DEBUG_LOG(QString(" Iterations = %1").arg(numberOfIterations));
DEBUG_LOG(QString(" Metric value = %1").arg(bestValue));
typedef unsigned char OutputPixelType;
typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
typedef itk::RescaleIntensityImageFilter< FixedImageType, FixedImageType > RescaleFilterType;
typedef itk::ResampleImageFilter<
FixedImageType,
FixedImageType > ResampleFilterType;
typedef itk::CastImageFilter<
FixedImageType,
OutputImageType > CastFilterType;
typedef itk::ImageFileWriter< OutputImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
CastFilterType::Pointer caster = CastFilterType::New();
ResampleFilterType::Pointer resample = ResampleFilterType::New();
RescaleFilterType::Pointer rescaler = RescaleFilterType::New();
rescaler->SetOutputMinimum(0);
rescaler->SetOutputMaximum(255);
TransformType::Pointer finalTransform = TransformType::New();
finalTransform->SetParameters(finalParameters);
resample->SetTransform(finalTransform);
resample->SetSize(extractMovingImageFilter->GetOutput()->GetLargestPossibleRegion().GetSize());
resample->SetOutputOrigin(extractMovingImageFilter->GetOutput()->GetOrigin());
resample->SetOutputSpacing(extractMovingImageFilter->GetOutput()->GetSpacing());
resample->SetDefaultPixelValue(100);
writer->SetFileName("prova.jpg");
rescaler->SetInput(extractMovingImageFilter->GetOutput());
resample->SetInput(rescaler->GetOutput());
caster->SetInput(resample->GetOutput());
writer->SetInput(caster->GetOutput());
writer->Update();
*/
QApplication::restoreOverrideCursor();
}
