ITK  4.13.0
Insight Segmentation and Registration Toolkit
WikiExamples/Registration/ImageRegistrationMethodBSpline.cxx
#if ITK_VERSION_MAJOR < 4
#else
#endif
#include "QuickView.h"
const unsigned int ImageDimension = 2;
typedef float PixelType;
static void CreateEllipseImage(ImageType::Pointer image);
static void CreateCircleImage(ImageType::Pointer image);
int main( int argc, char *argv[] )
{
const unsigned int SpaceDimension = ImageDimension;
const unsigned int SplineOrder = 3;
typedef double CoordinateRepType;
#if ITK_VERSION_MAJOR < 4
CoordinateRepType,
SpaceDimension,
SplineOrder > TransformType;
#else
CoordinateRepType,
SpaceDimension,
SplineOrder > TransformType;
#endif
typedef itk::LBFGSOptimizer OptimizerType;
ImageType,
ImageType > MetricType;
ImageType,
double > InterpolatorType;
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 );
// Create the synthetic images
ImageType::Pointer fixedImage = ImageType::New();
CreateCircleImage(fixedImage);
ImageType::Pointer movingImage = ImageType::New();
CreateEllipseImage(movingImage);
// Setup the registration
registration->SetFixedImage( fixedImage );
registration->SetMovingImage( movingImage);
ImageType::RegionType fixedRegion = fixedImage->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.
#if ITK_VERSION_MAJOR < 4
typedef TransformType::RegionType RegionType;
RegionType bsplineRegion;
RegionType::SizeType gridSizeOnImage;
RegionType::SizeType gridBorderSize;
RegionType::SizeType totalGridSize;
gridSizeOnImage.Fill( 5 );
gridBorderSize.Fill( 3 ); // Border for spline order = 3 ( 1 lower, 2 upper )
totalGridSize = gridSizeOnImage + gridBorderSize;
bsplineRegion.SetSize( totalGridSize );
typedef TransformType::SpacingType SpacingType;
SpacingType spacing = fixedImage->GetSpacing();
typedef TransformType::OriginType OriginType;
OriginType origin = fixedImage->GetOrigin();
ImageType::SizeType fixedImageSize = fixedRegion.GetSize();
for(unsigned int r=0; r<ImageDimension; r++)
{
spacing[r] *= static_cast<double>(fixedImageSize[r] - 1) /
static_cast<double>(gridSizeOnImage[r] - 1);
}
ImageType::DirectionType gridDirection = fixedImage->GetDirection();
SpacingType gridOriginOffset = gridDirection * spacing;
OriginType gridOrigin = origin - gridOriginOffset;
transform->SetGridSpacing( spacing );
transform->SetGridOrigin( gridOrigin );
transform->SetGridRegion( bsplineRegion );
transform->SetGridDirection( gridDirection );
#else
TransformType::PhysicalDimensionsType fixedPhysicalDimensions;
TransformType::MeshSizeType meshSize;
for( unsigned int i=0; i < ImageDimension; i++ )
{
fixedPhysicalDimensions[i] = fixedImage->GetSpacing()[i] *
static_cast<double>(
fixedImage->GetLargestPossibleRegion().GetSize()[i] - 1 );
}
unsigned int numberOfGridNodesInOneDimension = 5;
meshSize.Fill( numberOfGridNodesInOneDimension - SplineOrder );
transform->SetTransformDomainOrigin( fixedImage->GetOrigin() );
transform->SetTransformDomainPhysicalDimensions( fixedPhysicalDimensions );
transform->SetTransformDomainMeshSize( meshSize );
transform->SetTransformDomainDirection( fixedImage->GetDirection() );
#endif
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( 0.05 );
optimizer->SetLineSearchAccuracy( 0.9 );
optimizer->SetDefaultStepLength( .5 );
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 EXIT_FAILURE;
}
OptimizerType::ParametersType finalParameters =
registration->GetLastTransformParameters();
std::cout << "Last Transform Parameters" << std::endl;
std::cout << finalParameters << std::endl;
transform->SetParameters( finalParameters );
ImageType,
ImageType > 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 );
typedef unsigned char OutputPixelType;
ImageType,
OutputImageType > CastFilterType;
typedef itk::ImageFileWriter< OutputImageType > OutputWriterType;
OutputWriterType::Pointer writer = OutputWriterType::New();
CastFilterType::Pointer caster = CastFilterType::New();
writer->SetFileName("output.png");
caster->SetInput( resample->GetOutput() );
writer->SetInput( caster->GetOutput() );
try
{
writer->Update();
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return EXIT_FAILURE;
}
QuickView viewer;
viewer.AddImage(
fixedImage.GetPointer(),true,
"Fixed Image");
viewer.AddImage(
movingImage.GetPointer(),true,
"Moving Image");
viewer.AddImage(
resample->GetOutput(),true,
"Resampled Moving Image");
viewer.Visualize();
return EXIT_SUCCESS;
}
void CreateEllipseImage(ImageType::Pointer image)
{
EllipseType, ImageType > SpatialObjectToImageFilterType;
SpatialObjectToImageFilterType::Pointer imageFilter =
SpatialObjectToImageFilterType::New();
size[ 0 ] = 100;
size[ 1 ] = 100;
imageFilter->SetSize( size );
ImageType::SpacingType spacing;
spacing.Fill(1);
imageFilter->SetSpacing(spacing);
EllipseType::Pointer ellipse = EllipseType::New();
EllipseType::ArrayType radiusArray;
radiusArray[0] = 10;
radiusArray[1] = 20;
ellipse->SetRadius(radiusArray);
typedef EllipseType::TransformType TransformType;
TransformType::Pointer transform = TransformType::New();
transform->SetIdentity();
TransformType::OutputVectorType translation;
TransformType::CenterType center;
translation[ 0 ] = 65;
translation[ 1 ] = 45;
transform->Translate( translation, false );
ellipse->SetObjectToParentTransform( transform );
imageFilter->SetInput(ellipse);
ellipse->SetDefaultInsideValue(255);
ellipse->SetDefaultOutsideValue(0);
imageFilter->SetUseObjectValue( true );
imageFilter->SetOutsideValue( 0 );
imageFilter->Update();
image->Graft(imageFilter->GetOutput());
}
void CreateCircleImage(ImageType::Pointer image)
{
EllipseType, ImageType > SpatialObjectToImageFilterType;
SpatialObjectToImageFilterType::Pointer imageFilter =
SpatialObjectToImageFilterType::New();
size[ 0 ] = 100;
size[ 1 ] = 100;
imageFilter->SetSize( size );
ImageType::SpacingType spacing;
spacing.Fill(1);
imageFilter->SetSpacing(spacing);
EllipseType::Pointer ellipse = EllipseType::New();
EllipseType::ArrayType radiusArray;
radiusArray[0] = 10;
radiusArray[1] = 10;
ellipse->SetRadius(radiusArray);
typedef EllipseType::TransformType TransformType;
TransformType::Pointer transform = TransformType::New();
transform->SetIdentity();
TransformType::OutputVectorType translation;
TransformType::CenterType center;
translation[ 0 ] = 50;
translation[ 1 ] = 50;
transform->Translate( translation, false );
ellipse->SetObjectToParentTransform( transform );
imageFilter->SetInput(ellipse);
ellipse->SetDefaultInsideValue(255);
ellipse->SetDefaultOutsideValue(0);
imageFilter->SetUseObjectValue( true );
imageFilter->SetOutsideValue( 0 );
imageFilter->Update();
image->Graft(imageFilter->GetOutput());
}