Ejemplo n.º 1
0
// perform B-spline registration for 2D image
void runBspline2D(StringVector& args) {
    typedef itk::BSplineTransform<double, 2, 3> TransformType;
    typedef itk::LBFGSOptimizer OptimizerType;
    typedef itk::MeanSquaresImageToImageMetric<RealImage2, RealImage2> MetricType;
    typedef itk:: LinearInterpolateImageFunction<RealImage2, double> InterpolatorType;
    typedef itk::ImageRegistrationMethod<RealImage2, RealImage2> RegistrationType;

    MetricType::Pointer         metric        = MetricType::New();
    OptimizerType::Pointer      optimizer     = OptimizerType::New();
    InterpolatorType::Pointer   interpolator  = InterpolatorType::New();
    RegistrationType::Pointer   registration  = RegistrationType::New();

    // The old registration framework has problems with multi-threading
    // For now, we set the number of threads to 1
    registration->SetNumberOfThreads(1);

    registration->SetMetric(        metric        );
    registration->SetOptimizer(     optimizer     );
    registration->SetInterpolator(  interpolator  );

    TransformType::Pointer  transform = TransformType::New();
    registration->SetTransform( transform );


    ImageIO<RealImage2> io;

    // Create the synthetic images
    RealImage2::Pointer  fixedImage  = io.ReadImage(args[0]);
    RealImage2::Pointer  movingImage  = io.ReadImage(args[1]);

    // Setup the registration
    registration->SetFixedImage(  fixedImage   );
    registration->SetMovingImage(   movingImage);

    RealImage2::RegionType fixedRegion = fixedImage->GetBufferedRegion();
    registration->SetFixedImageRegion( fixedRegion );

    TransformType::PhysicalDimensionsType   fixedPhysicalDimensions;
    TransformType::MeshSizeType             meshSize;
    for( unsigned int i=0; i < 2; i++ )
    {
        fixedPhysicalDimensions[i] = fixedImage->GetSpacing()[i] *
        static_cast<double>(
                            fixedImage->GetLargestPossibleRegion().GetSize()[i] - 1 );
    }
    unsigned int numberOfGridNodesInOneDimension = 18;
    meshSize.Fill( numberOfGridNodesInOneDimension - 3 );
    transform->SetTransformDomainOrigin( fixedImage->GetOrigin() );
    transform->SetTransformDomainPhysicalDimensions( fixedPhysicalDimensions );
    transform->SetTransformDomainMeshSize( meshSize );
    transform->SetTransformDomainDirection( fixedImage->GetDirection() );

    typedef TransformType::ParametersType     ParametersType;

    const unsigned int numberOfParameters =
    transform->GetNumberOfParameters();

    ParametersType parameters( numberOfParameters );

    parameters.Fill( 0.0 );

    transform->SetParameters( parameters );

    //  We now pass the parameters of the current transform as the initial
    //  parameters to be used when the registration process starts.

    registration->SetInitialTransformParameters( transform->GetParameters() );

    std::cout << "Intial Parameters = " << std::endl;
    std::cout << transform->GetParameters() << std::endl;

    //  Next we set the parameters of the LBFGS Optimizer.

    optimizer->SetGradientConvergenceTolerance( 0.005 );
    optimizer->SetLineSearchAccuracy( 0.9 );
    optimizer->SetDefaultStepLength( .1 );
    optimizer->TraceOn();
    optimizer->SetMaximumNumberOfFunctionEvaluations( 1000 );

    std::cout << std::endl << "Starting Registration" << std::endl;

    try
    {
        registration->Update();
        std::cout << "Optimizer stop condition = "
        << registration->GetOptimizer()->GetStopConditionDescription()
        << std::endl;
    }
    catch( itk::ExceptionObject & err )
    {
        std::cerr << "ExceptionObject caught !" << std::endl;
        std::cerr << err << std::endl;
        return;
    }

    OptimizerType::ParametersType finalParameters =
    registration->GetLastTransformParameters();

    std::cout << "Last Transform Parameters" << std::endl;
    std::cout << finalParameters << std::endl;

    transform->SetParameters( finalParameters );

    typedef itk::ResampleImageFilter<RealImage2, RealImage2> ResampleFilterType;

    ResampleFilterType::Pointer resample = ResampleFilterType::New();

    resample->SetTransform( transform );
    resample->SetInput( movingImage );

    resample->SetSize(    fixedImage->GetLargestPossibleRegion().GetSize() );
    resample->SetOutputOrigin(  fixedImage->GetOrigin() );
    resample->SetOutputSpacing( fixedImage->GetSpacing() );
    resample->SetOutputDirection( fixedImage->GetDirection() );
    resample->SetDefaultPixelValue( 100 );
    resample->Update();

    io.WriteImage(args[2], resample->GetOutput());
}
int main( int argc, char *argv[] )
{
if( argc < 4 )
{
std::cerr << "Missing Parameters " << std::endl;
std::cerr << "Usage: " << argv[0];
std::cerr << " fixedImageFile movingImageFile ";
std::cerr << " outputImagefile [differenceBeforeRegistration] ";
std::cerr << " [differenceAfterRegistration] ";
std::cerr << " [sliceBeforeRegistration] ";
std::cerr << " [sliceDifferenceBeforeRegistration] ";
std::cerr << " [sliceDifferenceAfterRegistration] ";
std::cerr << " [sliceAfterRegistration] " << std::endl;
return EXIT_FAILURE;
}
const unsigned int Dimension = 3;
typedef float PixelType;
typedef itk::Image< PixelType, Dimension > FixedImageType;
typedef itk::Image< PixelType, Dimension > MovingImageType;
// Software Guide : BeginLatex
//
// The Transform class is instantiated using the code below. The only
// template parameter to this class is the representation type of the
// space coordinates.
//
// \index{itk::Versor\-Rigid3D\-Transform!Instantiation}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet

// Software Guide : EndCodeSnippet


typedef itk:: LinearInterpolateImageFunction< MovingImageType, double > InterpolatorType;
typedef itk::ImageRegistrationMethod< FixedImageType, MovingImageType > RegistrationType;

MetricType::Pointer metric = MetricType::New();
OptimizerType::Pointer optimizer = OptimizerType::New();
InterpolatorType::Pointer interpolator = InterpolatorType::New();
RegistrationType::Pointer registration = RegistrationType::New();
registration->SetMetric( metric );
registration->SetOptimizer( optimizer );
registration->SetInterpolator( interpolator );
// Software Guide : BeginLatex
//
// The transform object is constructed below and passed to the registration
// method.
//
// \index{itk::Versor\-Rigid3D\-Transform!New()}
// \index{itk::Versor\-Rigid3D\-Transform!Pointer}
// \index{itk::Registration\-Method!SetTransform()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
TransformType::Pointer transform = TransformType::New();
registration->SetTransform( transform );
// Software Guide : EndCodeSnippet
typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType;
typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType;
FixedImageReaderType::Pointer fixedImageReader = FixedImageReaderType::New();
MovingImageReaderType::Pointer movingImageReader = MovingImageReaderType::New();
fixedImageReader->SetFileName( argv[1] );
movingImageReader->SetFileName( argv[2] );
registration->SetFixedImage( fixedImageReader->GetOutput() );
registration->SetMovingImage( movingImageReader->GetOutput() );
fixedImageReader->Update();
registration->SetFixedImageRegion(
fixedImageReader->GetOutput()->GetBufferedRegion() );
// Software Guide : BeginLatex
//
// The input images are taken from readers. It is not necessary here to
// explicitly call \code{Update()} on the readers since the
// \doxygen{CenteredTransformInitializer} will do it as part of its
// computations. The following code instantiates the type of the
// initializer. This class is templated over the fixed and moving image type
// as well as the transform type. An initializer is then constructed by
// calling the \code{New()} method and assigning the result to a smart
// pointer.
//
// \index{itk::Centered\-Transform\-Initializer!Instantiation}
// \index{itk::Centered\-Transform\-Initializer!New()}
// \index{itk::Centered\-Transform\-Initializer!SmartPointer}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : BeginLatex
//
// Let's execute this example over some of the images available in the ftp
// site
//
// \url{ftp://public.kitware.com/pub/itk/Data/BrainWeb}
//
// Note that the images in the ftp site are compressed in \code{.tgz} files.
// You should download these files an uncompress them in your local system.
// After decompressing and extracting the files you could take a pair of
// volumes, for example the pair:
//
// \begin{itemize}
// \item \code{brainweb1e1a10f20.mha}
// \item \code{brainweb1e1a10f20Rot10Tx15.mha}
// \end{itemize}
//
// The second image is the result of intentionally rotating the first image
// by $10$ degrees around the origin and shifting it $15mm$ in $X$. The
// registration takes $24$ iterations and produces:
//
// \begin{center}
// \begin{verbatim}
// [-6.03744e-05, 5.91487e-06, -0.0871932, 2.64659, -17.4637, -0.00232496]
// \end{verbatim}
// \end{center}
//
// That are interpreted as
//
// \begin{itemize}
// \item Versor = $(-6.03744e-05, 5.91487e-06, -0.0871932)$
// \item Translation = $(2.64659, -17.4637, -0.00232496)$ millimeters
// \end{itemize}
//
// This Versor is equivalent to a rotation of $9.98$ degrees around the $Z$
// axis.
//
// Note that the reported translation is not the translation of $(15.0,0.0,0.0)$
// that we may be naively expecting. The reason is that the
// \code{VersorRigid3DTransform} is applying the rotation around the center
// found by the \code{CenteredTransformInitializer} and then adding the
// translation vector shown above.
//
// It is more illustrative in this case to take a look at the actual
// rotation matrix and offset resulting form the $6$ parameters.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
transform->SetParameters( finalParameters );
TransformType::MatrixType matrix = transform->GetMatrix();
TransformType::OffsetType offset = transform->GetOffset();
std::cout << "Matrix = " << std::endl << matrix << std::endl;
std::cout << "Offset = " << std::endl << offset << std::endl;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The output of this print statements is
//
// \begin{center}
// \begin{verbatim}
// Matrix =
// 0.984795 0.173722 2.23132e-05
// -0.173722 0.984795 0.000119257
// -1.25621e-06 -0.00012132 1
//
// Offset =
// [-15.0105, -0.00672343, 0.0110854]
// \end{verbatim}
// \end{center}
//
// From the rotation matrix it is possible to deduce that the rotation is
// happening in the X,Y plane and that the angle is on the order of
// $\arcsin{(0.173722)}$ which is very close to 10 degrees, as we expected.
//
// Software Guide : EndLatex
// Software Guide : BeginLatex
//
// \begin{figure}
// \center
// \includegraphics[width=0.44\textwidth]{BrainProtonDensitySliceBorder20}
// \includegraphics[width=0.44\textwidth]{BrainProtonDensitySliceR10X13Y17}
// \itkcaption[CenteredTransformInitializer input images]{Fixed and moving image
// provided as input to the registration method using
// CenteredTransformInitializer.}
// \label{fig:FixedMovingImageRegistration8}
// \end{figure}
//
//
// \begin{figure}
// \center
// \includegraphics[width=0.32\textwidth]{ImageRegistration8Output}
// \includegraphics[width=0.32\textwidth]{ImageRegistration8DifferenceBefore}
// \includegraphics[width=0.32\textwidth]{ImageRegistration8DifferenceAfter}
// \itkcaption[CenteredTransformInitializer output images]{Resampled moving
// image (left). Differences between fixed and moving images, before (center)
// and after (right) registration with the
// CenteredTransformInitializer.}
// \label{fig:ImageRegistration8Outputs}
// \end{figure}
//
// Figure \ref{fig:ImageRegistration8Outputs} shows the output of the
// registration. The center image in this figure shows the differences
// between the fixed image and the resampled moving image before the
// registration. The image on the right side presents the difference between
// the fixed image and the resampled moving image after the registration has
// been performed. Note that these images are individual slices extracted
// from the actual volumes. For details, look at the source code of this
// example, where the ExtractImageFilter is used to extract a slice from the
// the center of each one of the volumes. One of the main purposes of this
// example is to illustrate that the toolkit can perform registration on
// images of any dimension. The only limitations are, as usual, the amount of
// memory available for the images and the amount of computation time that it
// will take to complete the optimization process.
//
// \begin{figure}
// \center
// \includegraphics[height=0.32\textwidth]{ImageRegistration8TraceMetric}
// \includegraphics[height=0.32\textwidth]{ImageRegistration8TraceAngle}
// \includegraphics[height=0.32\textwidth]{ImageRegistration8TraceTranslations}
// \itkcaption[CenteredTransformInitializer output plots]{Plots of the metric,
// rotation angle, center of rotation and translations during the
// registration using CenteredTransformInitializer.}
// \label{fig:ImageRegistration8Plots}
// \end{figure}
//
// Figure \ref{fig:ImageRegistration8Plots} shows the plots of the main
// output parameters of the registration process. The metric values at every
// iteration. The Z component of the versor is plotted as an indication of
// how the rotation progress. The X,Y translation components of the
// registration are plotted at every iteration too.
//
// Shell and Gnuplot scripts for generating the diagrams in
// Figure~\ref{fig:ImageRegistration8Plots} are available in the directory
//
// \code{InsightDocuments/SoftwareGuide/Art}
//
// You are strongly encouraged to run the example code, since only in this
// way you can gain a first hand experience with the behavior of the
// registration process. Once again, this is a simple reflection of the
// philosophy that we put forward in this book:
//
// \emph{If you can not replicate it, then it does not exist!}.
//
// We have seen enough published papers with pretty pictures, presenting
// results that in practice are impossible to replicate. That is vanity, not
// science.
//
// Software Guide : EndLatex
typedef itk::ResampleImageFilter<
MovingImageType,
FixedImageType > ResampleFilterType;
TransformType::Pointer finalTransform = TransformType::New();
finalTransform->SetCenter( transform->GetCenter() );
finalTransform->SetParameters( finalParameters );
finalTransform->SetFixedParameters( transform->GetFixedParameters() );
ResampleFilterType::Pointer resampler = ResampleFilterType::New();
resampler->SetTransform( finalTransform );
resampler->SetInput( movingImageReader->GetOutput() );
FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();
resampler->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );
resampler->SetOutputOrigin( fixedImage->GetOrigin() );
resampler->SetOutputSpacing( fixedImage->GetSpacing() );
resampler->SetOutputDirection( fixedImage->GetDirection() );
resampler->SetDefaultPixelValue( 100 );
typedef unsigned char OutputPixelType;
typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
typedef itk::CastImageFilter< FixedImageType, OutputImageType > CastFilterType;
typedef itk::ImageFileWriter< OutputImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
CastFilterType::Pointer caster = CastFilterType::New();
writer->SetFileName( argv[3] );
caster->SetInput( resampler->GetOutput() );
writer->SetInput( caster->GetOutput() );
writer->Update();
typedef itk::SubtractImageFilter<
FixedImageType,
FixedImageType,
FixedImageType > DifferenceFilterType;
DifferenceFilterType::Pointer difference = DifferenceFilterType::New();
typedef itk::RescaleIntensityImageFilter<
FixedImageType,
OutputImageType > RescalerType;
RescalerType::Pointer intensityRescaler = RescalerType::New();
intensityRescaler->SetInput( difference->GetOutput() );
intensityRescaler->SetOutputMinimum( 0 );
intensityRescaler->SetOutputMaximum( 255 );
difference->SetInput1( fixedImageReader->GetOutput() );
difference->SetInput2( resampler->GetOutput() );
resampler->SetDefaultPixelValue( 1 );
WriterType::Pointer writer2 = WriterType::New();
writer2->SetInput( intensityRescaler->GetOutput() );
// Compute the difference image between the
// fixed and resampled moving image.
if( argc > 5 )
{
writer2->SetFileName( argv[5] );
writer2->Update();
}
typedef itk::IdentityTransform< double, Dimension > IdentityTransformType;
IdentityTransformType::Pointer identity = IdentityTransformType::New();
// Compute the difference image between the
// fixed and moving image before registration.
if( argc > 4 )
{
resampler->SetTransform( identity );
writer2->SetFileName( argv[4] );
writer2->Update();
}
//
// Here we extract slices from the input volume, and the difference volumes
// produced before and after the registration. These slices are presented as
// figures in the Software Guide.
//
//
typedef itk::Image< OutputPixelType, 2 > OutputSliceType;
typedef itk::ExtractImageFilter<
OutputImageType,
OutputSliceType > ExtractFilterType;
ExtractFilterType::Pointer extractor = ExtractFilterType::New();
extractor->SetDirectionCollapseToSubmatrix();
extractor->InPlaceOn();
FixedImageType::RegionType inputRegion =
fixedImage->GetLargestPossibleRegion();
FixedImageType::SizeType size = inputRegion.GetSize();
FixedImageType::IndexType start = inputRegion.GetIndex();
// Select one slice as output
size[2] = 0;
start[2] = 90;
FixedImageType::RegionType desiredRegion;
desiredRegion.SetSize( size );
desiredRegion.SetIndex( start );
extractor->SetExtractionRegion( desiredRegion );
typedef itk::ImageFileWriter< OutputSliceType > SliceWriterType;
SliceWriterType::Pointer sliceWriter = SliceWriterType::New();
sliceWriter->SetInput( extractor->GetOutput() );
if( argc > 6 )
{
extractor->SetInput( caster->GetOutput() );
resampler->SetTransform( identity );
sliceWriter->SetFileName( argv[6] );
sliceWriter->Update();
}
if( argc > 7 )
{
extractor->SetInput( intensityRescaler->GetOutput() );
resampler->SetTransform( identity );
sliceWriter->SetFileName( argv[7] );
sliceWriter->Update();
}
if( argc > 8 )
{
resampler->SetTransform( finalTransform );
sliceWriter->SetFileName( argv[8] );
sliceWriter->Update();
}
if( argc > 9 )
{
extractor->SetInput( caster->GetOutput() );
resampler->SetTransform( finalTransform );
sliceWriter->SetFileName( argv[9] );
sliceWriter->Update();
}
return EXIT_SUCCESS;
}
Ejemplo n.º 3
0
    RealImage::Pointer bsplineRegistration(RealImage::Pointer srcImg, RealImage::Pointer dstImg) {

        const unsigned int SpaceDimension = ImageDimension;
        const unsigned int SplineOrder = 3;
        typedef double CoordinateRepType;

        typedef itk::BSplineTransform<CoordinateRepType, SpaceDimension, SplineOrder> TransformType;
        typedef itk::LBFGSOptimizer OptimizerType;
        typedef itk::MeanSquaresImageToImageMetric<ImageType, ImageType> MetricType;
        typedef itk::LinearInterpolateImageFunction<ImageType, double> InterpolatorType;
        typedef itk::ImageRegistrationMethod<ImageType, ImageType> RegistrationType;

        MetricType::Pointer         metric        = MetricType::New();
        OptimizerType::Pointer      optimizer     = OptimizerType::New();
        InterpolatorType::Pointer   interpolator  = InterpolatorType::New();
        RegistrationType::Pointer   registration  = RegistrationType::New();



        // The old registration framework has problems with multi-threading
        // For now, we set the number of threads to 1
//        registration->SetNumberOfThreads(1);
        registration->SetMetric(        metric        );
        registration->SetOptimizer(     optimizer     );
        registration->SetInterpolator(  interpolator  );

        TransformType::Pointer  transform = TransformType::New();
        registration->SetTransform( transform );

        // Setup the registration
        registration->SetFixedImage(  dstImg   );
        registration->SetMovingImage(   srcImg);

        ImageType::RegionType fixedRegion = srcImg->GetBufferedRegion();
        registration->SetFixedImageRegion( fixedRegion );

        //  Here we define the parameters of the BSplineDeformableTransform grid.  We
        //  arbitrarily decide to use a grid with $5 \times 5$ nodes within the image.
        //  The reader should note that the BSpline computation requires a
        //  finite support region ( 1 grid node at the lower borders and 2
        //  grid nodes at upper borders). Therefore in this example, we set
        //  the grid size to be $8 \times 8$ and place the grid origin such that
        //  grid node (1,1) coincides with the first pixel in the fixed image.

        TransformType::PhysicalDimensionsType   fixedPhysicalDimensions;
        TransformType::MeshSizeType             meshSize;
        for (unsigned int i=0; i < ImageDimension; i++) {
            fixedPhysicalDimensions[i] = dstImg->GetSpacing()[i] *
            static_cast<double>(dstImg->GetLargestPossibleRegion().GetSize()[i] - 1 );
            meshSize[i] = dstImg->GetLargestPossibleRegion().GetSize()[i] / 8 - SplineOrder;
        }
//        unsigned int numberOfGridNodesInOneDimension = 15;
//        meshSize.Fill( numberOfGridNodesInOneDimension - SplineOrder );
        transform->SetTransformDomainOrigin( dstImg->GetOrigin() );
        transform->SetTransformDomainPhysicalDimensions( fixedPhysicalDimensions );
        transform->SetTransformDomainMeshSize( meshSize );
        transform->SetTransformDomainDirection( dstImg->GetDirection() );

        typedef TransformType::ParametersType     ParametersType;

        const unsigned int numberOfParameters = transform->GetNumberOfParameters();

        ParametersType parameters( numberOfParameters );
        parameters.Fill( 0.0 );

        transform->SetParameters( parameters );

        //  We now pass the parameters of the current transform as the initial
        //  parameters to be used when the registration process starts.

        registration->SetInitialTransformParameters( transform->GetParameters() );

        std::cout << "Intial Parameters = " << std::endl;
        std::cout << transform->GetParameters() << std::endl;

        //  Next we set the parameters of the LBFGS Optimizer.
        optimizer->SetGradientConvergenceTolerance(0.1);
        optimizer->SetLineSearchAccuracy(0.09);
        optimizer->SetDefaultStepLength(.1);
        optimizer->TraceOn();
        optimizer->SetMaximumNumberOfFunctionEvaluations(1000);

        std::cout << std::endl << "Starting Registration" << std::endl;

        try {
            registration->Update();
            std::cout << "Optimizer stop condition = "
            << registration->GetOptimizer()->GetStopConditionDescription()
            << std::endl;
        } catch (itk::ExceptionObject & err) {
            std::cerr << "ExceptionObject caught !" << std::endl;
            std::cerr << err << std::endl;
            return RealImage::Pointer();
        }

        OptimizerType::ParametersType finalParameters =
        registration->GetLastTransformParameters();
        
        std::cout << "Last Transform Parameters" << std::endl;
        std::cout << finalParameters << std::endl;
        
        transform->SetParameters( finalParameters );
        
        typedef itk::ResampleImageFilter<ImageType, ImageType>    ResampleFilterType;
        
        ResampleFilterType::Pointer resample = ResampleFilterType::New();
        
        resample->SetTransform( transform );
        resample->SetInput( srcImg );
        
        resample->SetSize(    dstImg->GetLargestPossibleRegion().GetSize() );
        resample->SetOutputOrigin(  dstImg->GetOrigin() );
        resample->SetOutputSpacing( dstImg->GetSpacing() );
        resample->SetOutputDirection( dstImg->GetDirection() );
        resample->SetDefaultPixelValue( 100 );
        resample->Update();
        return resample->GetOutput();
    }
int mitkPyramidImageRegistrationMethodTest( int argc, char* argv[] )
{
  if( argc < 4 )
  {
    MITK_ERROR << "Not enough input \n Usage: <TEST_NAME> fixed moving type [output_image [output_transform]]"
               << "\n \t fixed : the path to the fixed image \n"
               << " \t moving : path to the image to be registered"
               << " \t type : Affine or Rigid defining the type of the transformation"
               << " \t output_image : output file optional, (full) path, and optionally output_transform : also (full)path to file";
    return EXIT_FAILURE;
  }

  MITK_TEST_BEGIN("PyramidImageRegistrationMethodTest");

  mitk::Image::Pointer fixedImage = dynamic_cast<mitk::Image*>(mitk::IOUtil::Load( argv[1] )[0].GetPointer());
  mitk::Image::Pointer movingImage = dynamic_cast<mitk::Image*>(mitk::IOUtil::Load( argv[2] )[0].GetPointer());

  std::string type_flag( argv[3] );

  mitk::PyramidImageRegistrationMethod::Pointer registrationMethod = mitk::PyramidImageRegistrationMethod::New();
  registrationMethod->SetFixedImage( fixedImage );
  registrationMethod->SetMovingImage( movingImage );

  if( type_flag == "Rigid" )
  {
    registrationMethod->SetTransformToRigid();
  }
  else if( type_flag == "Affine" )
  {
    registrationMethod->SetTransformToAffine();
  }
  else
  {
    MITK_WARN << " No type specified, using 'Affine' .";
  }

  registrationMethod->Update();

  bool imageOutput = false;
  bool transformOutput = false;

  std::string image_out_filename, transform_out_filename;

  std::string first_output( argv[4] );
  // check for txt, otherwise suppose it is an image
  if( first_output.find(".txt") != std::string::npos )
  {
    transformOutput = true;
    transform_out_filename = first_output;
  }
  else
  {
    imageOutput = true;
    image_out_filename = first_output;
  }

  if( argc > 4 )
  {
    std::string second_output( argv[5] );
    if( second_output.find(".txt") != std::string::npos )
    {
      transformOutput = true;
      transform_out_filename = second_output;
    }
  }

  MITK_INFO << " Selected output: " << transform_out_filename  << " " << image_out_filename;

  try{

    unsigned int paramCount = registrationMethod->GetNumberOfParameters();
    double* params = new double[ paramCount ];
    registrationMethod->GetParameters( &params[0] );

    std::cout << "Parameters: ";
    for( unsigned int i=0; i< paramCount; i++)
    {
      std::cout << params[ i ] << " ";
    }
    std::cout << std::endl;

    if( imageOutput )
    {
      mitk::IOUtil::Save( registrationMethod->GetResampledMovingImage(), image_out_filename.c_str() );
    }


    if( transformOutput )
    {

      itk::TransformFileWriter::Pointer writer = itk::TransformFileWriter::New();

      // Get transform parameter for resampling / saving
      // Affine
      if( paramCount == 12 )
      {
        typedef itk::AffineTransform< double > TransformType;
        TransformType::Pointer transform = TransformType::New();

        TransformType::ParametersType affine_params( paramCount );
        registrationMethod->GetParameters( &affine_params[0] );

        transform->SetParameters( affine_params );
        writer->SetInput( transform );
      }
      // Rigid
      else
      {
        typedef itk::Euler3DTransform< double > RigidTransformType;
        RigidTransformType::Pointer rtransform = RigidTransformType::New();

        RigidTransformType::ParametersType rigid_params( paramCount );
        registrationMethod->GetParameters( &rigid_params[0] );

        rtransform->SetParameters( rigid_params );
        writer->SetInput( rtransform );
      }

      writer->SetFileName( transform_out_filename );
      writer->Update();
    }

  }
  catch( const std::exception &e)
  {
    MITK_ERROR << "Caught exception: " << e.what();
  }


  MITK_TEST_END();
}
Ejemplo n.º 5
0
	void SetTransformParameters(TransformType::Pointer inputTransform) {
    transform->SetParameters( inputTransform->GetParameters() );
    transform->SetFixedParameters( inputTransform->GetFixedParameters() );
    buildSlices();
    buildMaskSlices();
	}