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( ¶ms[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();
}
void mitk::RegistrationWrapper::ApplyTransformationToImage(mitk::Image::Pointer img, const mitk::RegistrationWrapper::RidgidTransformType &transformation,double* offset, mitk::Image* resampleReference, bool binary)
{
typedef mitk::DiffusionImage<short> DiffusionImageType;
if (dynamic_cast<DiffusionImageType*> (img.GetPointer()) == NULL)
{
ItkImageType::Pointer itkImage = ItkImageType::New();
MITK_ERROR << "imgCopy 0 " << "/" << img->GetReferenceCount();
MITK_ERROR << "pixel type " << img->GetPixelType().GetComponentTypeAsString();
CastToItkImage(img, itkImage);
typedef itk::Euler3DTransform< double > RigidTransformType;
RigidTransformType::Pointer rtransform = RigidTransformType::New();
RigidTransformType::ParametersType parameters(RigidTransformType::ParametersDimension);
for (int i = 0; i<6;++i)
parameters[i] = transformation[i];
rtransform->SetParameters( parameters );
mitk::Point3D origin = itkImage->GetOrigin();
origin[0]-=offset[0];
origin[1]-=offset[1];
origin[2]-=offset[2];
mitk::Point3D newOrigin = rtransform->GetInverseTransform()->TransformPoint(origin);
itk::Matrix<double,3,3> dir = itkImage->GetDirection();
itk::Matrix<double,3,3> transM ( vnl_inverse(rtransform->GetMatrix().GetVnlMatrix()));
itk::Matrix<double,3,3> newDirection = transM * dir;
itkImage->SetOrigin(newOrigin);
itkImage->SetDirection(newDirection);
// Perform Resampling if reference image is provided
if (resampleReference != NULL)
{
typedef itk::ResampleImageFilter<ItkImageType, ItkImageType> ResampleFilterType;
ItkImageType::Pointer itkReference = ItkImageType::New();
CastToItkImage(resampleReference,itkReference);
typedef itk::WindowedSincInterpolateImageFunction< ItkImageType, 3> WindowedSincInterpolatorType;
WindowedSincInterpolatorType::Pointer sinc_interpolator = WindowedSincInterpolatorType::New();
typedef itk::NearestNeighborInterpolateImageFunction< ItkImageType, double > NearestNeighborInterpolatorType;
NearestNeighborInterpolatorType::Pointer nn_interpolator = NearestNeighborInterpolatorType::New();
ResampleFilterType::Pointer resampler = ResampleFilterType::New();
resampler->SetInput(itkImage);
resampler->SetReferenceImage( itkReference );
resampler->UseReferenceImageOn();
if (binary)
resampler->SetInterpolator(nn_interpolator);
else
resampler->SetInterpolator(sinc_interpolator);
resampler->Update();
GrabItkImageMemory(resampler->GetOutput(), img);
}
else
{
// !! CastToItk behaves very differently depending on the original data type
// if the target type is the same as the original, only a pointer to the data is set
// and an additional GrabItkImageMemory will cause a segfault when the image is destroyed
// GrabItkImageMemory - is not necessary in this case since we worked on the original data
// See Bug 17538.
if (img->GetPixelType().GetComponentTypeAsString() != "double")
img = GrabItkImageMemory(itkImage);
}
}
else
{
DiffusionImageType::Pointer diffImages = dynamic_cast<DiffusionImageType*>(img.GetPointer());
typedef itk::Euler3DTransform< double > RigidTransformType;
RigidTransformType::Pointer rtransform = RigidTransformType::New();
RigidTransformType::ParametersType parameters(RigidTransformType::ParametersDimension);
for (int i = 0; i<6;++i)
{
parameters[i] = transformation[i];
}
rtransform->SetParameters( parameters );
mitk::Point3D b0origin = diffImages->GetVectorImage()->GetOrigin();
b0origin[0]-=offset[0];
b0origin[1]-=offset[1];
b0origin[2]-=offset[2];
mitk::Point3D newOrigin = rtransform->GetInverseTransform()->TransformPoint(b0origin);
itk::Matrix<double,3,3> dir = diffImages->GetVectorImage()->GetDirection();
itk::Matrix<double,3,3> transM ( vnl_inverse(rtransform->GetMatrix().GetVnlMatrix()));
itk::Matrix<double,3,3> newDirection = transM * dir;
diffImages->GetVectorImage()->SetOrigin(newOrigin);
diffImages->GetVectorImage()->SetDirection(newDirection);
diffImages->Modified();
mitk::DiffusionImageCorrectionFilter<short>::Pointer correctionFilter = mitk::DiffusionImageCorrectionFilter<short>::New();
// For Diff. Images: Need to rotate the gradients (works in-place)
correctionFilter->SetImage(diffImages);
correctionFilter->CorrectDirections(transM.GetVnlMatrix());
img = diffImages;
}
}
int main(int argc, char* argv[])
{
//const char* SSMFile = argv[1];
const char* SSMFile = "D:\\Workspace\\ASM\\projects\\LiverSegbyASM\\experiments\\buidModel\\shape\\output_20140815\\StatisticalShapeModel_20140815.h5";
const char* targetMeshFile = "D:\\Workspace\\ASM\\projects\\LiverSegbyASM\\experiments\\training\\shape\\output_20140815\\liverMesh.46.vtk";
const char* configFile = "D:\\Workspace\\LiverSegByASM\\liversegbyasm-v2\\Data\\config.txt";
KM_DEBUG_INFO("Load config file...");
km::Config::loadConfig(configFile);
const int Dimension = 3;
typedef double MeshPixelType;
typedef itk::SimplexMeshRepresenter<MeshPixelType, Dimension> RepresenterType;
typedef itk::StatisticalModel<RepresenterType> StatisticalModelType;
typedef RepresenterType::MeshType MeshType;
StatisticalModelType::Pointer model = StatisticalModelType::New();
model->Load( SSMFile );
MeshType::Pointer meanShape = model->DrawMean();
MeshType::PointType centroid = km::getMeshCentroid<MeshType>(meanShape);
typedef itk::AffineTransform<double, Dimension> RigidTransformType;
typedef itk::StatisticalShapeModelTransform<RepresenterType, double, Dimension> ShapeTransformType;
ShapeTransformType::Pointer shapeTransform = ShapeTransformType::New();
shapeTransform->SetStatisticalModel(model);
shapeTransform->SetIdentity();
RigidTransformType::Pointer rigidTransform = RigidTransformType::New();
rigidTransform->SetCenter(centroid);
rigidTransform->SetIdentity();
typedef km::SSMUtils<MeshType, StatisticalModelType, RigidTransformType, ShapeTransformType> SSMUtilsType;
SSMUtilsType ssmUtils;
ssmUtils.SetSSM(model);
ssmUtils.SetRigidTransform(rigidTransform);
ssmUtils.SetShapeTransform(shapeTransform);
ssmUtils.SetNumberOfClusters(km::g_number_clusters);
ssmUtils.Initialize();
MeshType::Pointer targetMesh = km::readMesh<MeshType>(targetMeshFile);
MeshType::Pointer outputMesh = km::cloneMesh<MeshType, MeshType>(meanShape);
km::writeMesh<MeshType>("targetMesh.vtk", targetMesh);
km::writeMesh<MeshType>("unfittedMesh.vtk", meanShape);
for (int i=0;i<1;i++)
{
std::cout<<"****************iter: "<<i<<"**************"<<std::endl;
ssmUtils.Update(targetMesh, outputMesh);
char filename[1024];
sprintf(filename, "fittedMesh-%d.vtk", i);
km::writeMesh<MeshType>(filename, outputMesh);
ssmUtils.PrintTransform();
}
//km::assigneMesh<MeshType>(meanShape, 0);
//ssmUtils.cluster(1);
//for (int i=0;i<meanShape->GetNumberOfPoints();i++)
//{
// meanShape->SetPointData(i, ssmUtils.getShapeCluster(i)->clusterId);
//}
//km::writeMesh<MeshType>("clusteredMesh.vtk", meanShape);
system("pause");
return 0;
}
