void mitk::ToFImageDownsamplingFilter::ItkImageResampling( const itk::Image<TPixel,VImageDimension>* itkImage )
{
  // declare typdef for itk image from input mitk image
 typedef itk::Image< TPixel, VImageDimension >   ItkImageType;

  //declare itk filter related typedefs (transform type, interpolater, and size type)
  typedef itk::ResampleImageFilter<ItkImageType,ItkImageType>    ResamplerFilterType;
  typedef itk::IdentityTransform<double, VImageDimension> TransformType;
  typedef itk::NearestNeighborInterpolateImageFunction<ItkImageType, double > InterpolatorType;
  typedef typename ItkImageType::SizeType::SizeValueType SizeValueType;

  //instantiate filter related parameters
  typename ResamplerFilterType::Pointer resampler = ResamplerFilterType::New();
  typename TransformType::Pointer transform = TransformType::New();
  typename InterpolatorType::Pointer interpolator = InterpolatorType::New();

  // establish size for downsampled image ( the result of this filter)
  typename ItkImageType::SizeType inputSize = itkImage->GetLargestPossibleRegion().GetSize();
  typename ItkImageType::SizeType size;

  size[0] = static_cast< SizeValueType >( m_ResampledX );
  size[1] = static_cast< SizeValueType >( m_ResampledY );
  size[2] = static_cast< SizeValueType >( m_ResampledZ );

  //establish spacing for new downsampled image ( resulting image)
  const typename ItkImageType::SpacingType& inputSpacing = itkImage->GetSpacing();
  typename ItkImageType::SpacingType outputSpacing;

  outputSpacing[0] = inputSpacing[0] * ( inputSize[0]/ m_ResampledX );
  outputSpacing[1] = inputSpacing[1] * ( inputSize[1]/ m_ResampledY );
  outputSpacing[2] = inputSpacing[2] * ( inputSize[2]/ m_ResampledZ );

  mitk::Vector3D mitkspacing;
  mitkspacing[0] = outputSpacing[0];
  mitkspacing[1] = outputSpacing[1];
  mitkspacing[2] = outputSpacing[2];

  mitk::Point3D mitkorig;
  mitkorig[0] = itkImage->GetOrigin()[0];
  mitkorig[1] = itkImage->GetOrigin()[1];
  mitkorig[2] = 0.0;

  // set filter parameters and update
  transform->SetIdentity();
  resampler->SetTransform(transform);
  resampler->SetInterpolator(interpolator);
  resampler->SetOutputSpacing(outputSpacing);
  resampler->SetOutputOrigin(itkImage->GetOrigin());
  resampler->SetSize(size);
  resampler->SetInput(itkImage);
  resampler->UpdateLargestPossibleRegion();

  // Create mitk container for resulting image
  mitk::Image::Pointer resultImage = ImageToImageFilter::GetOutput();
  resultImage->SetSpacing(mitkspacing);
  resultImage->SetOrigin(mitkorig);

  // Cast itk image to mitk image
  mitk::CastToMitkImage(resampler->GetOutput(), resultImage);
}
Example #2
0
void WorkbenchUtils::resampleImageItk(itk::Image <PixelType, ImageDimension> *itkImage, Interpolator interpolType,
                                      unsigned int *newDimensions, Image::Pointer outImage) {
    typedef itk::Image <PixelType, ImageDimension> ImageType;

    // get original image informations
    const typename ImageType::RegionType &inputRegion = itkImage->GetLargestPossibleRegion();
    const typename ImageType::SizeType &inputDimensions = inputRegion.GetSize();
    const typename ImageType::SpacingType &inputSpacing = itkImage->GetSpacing();

    // calculate spacing
    double outputSpacing[ImageDimension];
    itk::Size <ImageDimension> outputSize;
    for (unsigned int i = 0; i < ImageDimension; ++i) {
        outputSpacing[i] = inputSpacing[i] * (double) inputDimensions[i] / newDimensions[i];
        outputSize[i] = newDimensions[i];
    }

    // transform
    typedef itk::IdentityTransform<double, ImageDimension> TransformType;
    typename TransformType::Pointer transform = TransformType::New();
    transform->SetIdentity();

    // interpolator typedefs
    typedef double CoordinateType;
    typedef itk::LinearInterpolateImageFunction <ImageType, CoordinateType> LinearInterpolatorType;
    typedef itk::NearestNeighborInterpolateImageFunction <ImageType, CoordinateType> NearestNeighborInterpolatorType;
    typedef itk::GaussianInterpolateImageFunction <ImageType, CoordinateType> GaussianInterpolatorType;
    typedef itk::BSplineInterpolateImageFunction <ImageType, CoordinateType> BSplineInterpolatorType;

    // set up the filter
    typedef itk::ResampleImageFilter <ImageType, ImageType> ResampleFilterType;
    typename ResampleFilterType::Pointer resampleFilter = ResampleFilterType::New();
    resampleFilter->SetTransform(transform);
    resampleFilter->SetOutputOrigin(itkImage->GetOrigin());
    resampleFilter->SetOutputSpacing(outputSpacing);
    resampleFilter->SetSize(outputSize);
    switch (interpolType) {
        case Interpolator::LINEAR: // the default;
            resampleFilter->SetInterpolator(LinearInterpolatorType::New());
            break;
        case Interpolator::NEAREST_NEIGHBOR:
            resampleFilter->SetInterpolator(NearestNeighborInterpolatorType::New());
            break;
        case Interpolator::GAUSSIAN:
            resampleFilter->SetInterpolator(GaussianInterpolatorType::New());
            break;
        case Interpolator::BSPLINE:
            resampleFilter->SetInterpolator(BSplineInterpolatorType::New());
            break;
    }
    resampleFilter->SetInput(itkImage);
    resampleFilter->UpdateLargestPossibleRegion();

    // get the results and cast them back to mitk. return via out parameter.
    outImage->InitializeByItk(resampleFilter->GetOutput());
    CastToMitkImage(resampleFilter->GetOutput(), outImage);
}
itk::Object::Pointer QmitkTranslationTransformView::GetTransform2(itk::Image<TPixelType, VImageDimension>* /*itkImage1*/)
{
  typedef typename itk::Image< TPixelType, VImageDimension >  FixedImageType;
  typedef typename itk::Image< TPixelType, VImageDimension >  MovingImageType;
  typedef itk::AffineTransform<double, VImageDimension>  TransformType;
  typename TransformType::Pointer transform = TransformType::New();
  transform->SetIdentity();
  m_TransformObject = transform;
  return transform.GetPointer();
}
typename TImage::Pointer modelBasedImageToImageRegistration(std::string referenceFilename,
																					std::string targetFilename, 
																					typename TStatisticalModelType::Pointer model,
																					std::string outputDfFilename,
																					unsigned numberOfIterations){

	typedef itk::ImageFileReader<TImage> ImageReaderType;
	typedef itk::InterpolatingStatisticalDeformationModelTransform<TRepresenter, double, VImageDimension> TransformType;
	typedef itk::LBFGSOptimizer OptimizerType;
	typedef itk::ImageRegistrationMethod<TImage, TImage> RegistrationFilterType;
	typedef itk::WarpImageFilter< TImage, TImage, TVectorImage > WarperType;
	typedef itk::LinearInterpolateImageFunction< TImage, double > InterpolatorType;
	
	typename ImageReaderType::Pointer referenceReader = ImageReaderType::New();
	referenceReader->SetFileName(referenceFilename.c_str());
	referenceReader->Update();
	typename TImage::Pointer referenceImage = referenceReader->GetOutput();
	referenceImage->Update();

	typename ImageReaderType::Pointer targetReader = ImageReaderType::New();
	targetReader->SetFileName(targetFilename.c_str());
	targetReader->Update();
	typename TImage::Pointer targetImage = targetReader->GetOutput();
	targetImage->Update();

	// do the fitting
	typename TransformType::Pointer transform = TransformType::New();
	transform->SetStatisticalModel(model);
	transform->SetIdentity();

	// Setting up the fitting
	OptimizerType::Pointer optimizer = OptimizerType::New();
	optimizer->MinimizeOn();
	optimizer->SetMaximumNumberOfFunctionEvaluations(numberOfIterations);

	typedef  IterationStatusObserver ObserverType;
	ObserverType::Pointer observer = ObserverType::New();
	optimizer->AddObserver( itk::IterationEvent(), observer );

	typename TMetricType::Pointer metric = TMetricType::New();
	typename InterpolatorType::Pointer interpolator = InterpolatorType::New();

	typename RegistrationFilterType::Pointer registration = RegistrationFilterType::New();
	registration->SetInitialTransformParameters(transform->GetParameters());
	registration->SetMetric(metric);
	registration->SetOptimizer(   optimizer   );
	registration->SetTransform(   transform );
	registration->SetInterpolator( interpolator );
	registration->SetFixedImage( targetImage );
	registration->SetFixedImageRegion(targetImage->GetBufferedRegion() );
	registration->SetMovingImage( referenceImage );

	try {
		std::cout << "Performing registration... " << std::flush;
		registration->Update();
		std::cout << "[done]" << std::endl;

	} catch ( itk::ExceptionObject& o ) {
		std::cout << "caught exception " << o << std::endl;
	}

	typename TVectorImage::Pointer df = model->DrawSample(transform->GetCoefficients());

	// write deformation field
	if(outputDfFilename.size()>0){
		typename itk::ImageFileWriter<TVectorImage>::Pointer df_writer = itk::ImageFileWriter<TVectorImage>::New();
		df_writer->SetFileName(outputDfFilename);
		df_writer->SetInput(df);
		df_writer->Update();
	}

	
	// warp reference
	std::cout << "Warping reference... " << std::flush;
	typename WarperType::Pointer warper = WarperType::New();
	warper->SetInput(referenceImage  );
	warper->SetInterpolator( interpolator );
	warper->SetOutputSpacing( targetImage->GetSpacing() );
	warper->SetOutputOrigin( targetImage->GetOrigin() );
	warper->SetOutputDirection( targetImage->GetDirection() );
	warper->SetDisplacementField( df );
	warper->Update();
	std::cout << "[done]" << std::endl;

	return warper->GetOutput();
}