ITK  5.0.0
Insight Segmentation and Registration Toolkit
SphinxExamples/src/Registration/Common/PerformMultiModalityRegistrationWithMutualInformation/Code.cxx
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// The following simple example illustrates how multiple imaging modalities can
// be registered using the ITK registration framework. The first difference
// between this and previous examples is the use of the
// MutualInformationImageToImageMetric as the cost-function to be
// optimized. The second difference is the use of the
// GradientDescentOptimizer. Due to the stochastic nature of the
// metric computation, the values are too noisy to work successfully with the
// RegularStepGradientDescentOptimizer. Therefore, we will use the
// simpler GradientDescentOptimizer with a user defined learning rate. The
// following headers declare the basic components of this registration method.
// One way to simplify the computation of the mutual information is
// to normalize the statistical distribution of the two input images. The
// NormalizeImageFilter is the perfect tool for this task.
// It rescales the intensities of the input images in order to produce an
// output image with zero mean and unit variance.
// Additionally, low-pass filtering of the images to be registered will also
// increase robustness against noise. In this example, we will use the
// DiscreteGaussianImageFilter for that purpose.
// The following section of code implements a Command observer
// that will monitor the evolution of the registration process.
//
#include "itkCommand.h"
class CommandIterationUpdate : public itk::Command
{
public:
using Self = CommandIterationUpdate;
using Superclass = itk::Command;
using Pointer = itk::SmartPointer<Self>;
itkNewMacro( Self );
protected:
CommandIterationUpdate() {};
public:
using OptimizerType = itk::GradientDescentOptimizer;
using OptimizerPointer = const OptimizerType *;
void Execute(itk::Object *caller, const itk::EventObject & event) override
{
Execute( (const itk::Object *)caller, event);
}
void Execute(const itk::Object * object, const itk::EventObject & event) override
{
auto optimizer = dynamic_cast< OptimizerPointer >( object );
if( ! itk::IterationEvent().CheckEvent( &event ) )
{
return;
}
std::cout << optimizer->GetCurrentIteration() << " ";
std::cout << optimizer->GetValue() << " ";
std::cout << optimizer->GetCurrentPosition() << std::endl;
}
};
int main( int argc, char *argv[] )
{
if( argc < 4 )
{
std::cerr << "Missing Parameters " << std::endl;
std::cerr << "Usage: " << argv[0];
std::cerr << " fixedImageFile";
std::cerr << " movingImageFile";
std::cerr << " outputImageFile ";
std::cerr << " [checkerBoardBefore]";
std::cerr << " [checkerBoardAfter]" << std::endl;
return EXIT_FAILURE;
}
const char * fixedImageFile = argv[1];
const char * movingImageFile = argv[2];
const char * outputImageFile = argv[3];
const char * checkerBoardBefore = argv[4];
const char * checkerBoardAfter = argv[5];
constexpr unsigned int Dimension = 2;
using PixelType = unsigned short;
using FixedImageType = itk::Image< PixelType, Dimension >;
using MovingImageType = itk::Image< PixelType, Dimension >;
// It is convenient to work with an internal image type because mutual
// information will perform better on images with a normalized statistical
// distribution. The fixed and moving images will be normalized and
// converted to this internal type.
using InternalPixelType = float;
using InternalImageType = itk::Image< InternalPixelType, Dimension >;
using OptimizerType = itk::GradientDescentOptimizer;
using InterpolatorType = itk::LinearInterpolateImageFunction<
InternalImageType,
double >;
using RegistrationType = itk::ImageRegistrationMethod<
InternalImageType,
InternalImageType >;
InternalImageType,
InternalImageType >;
TransformType::Pointer transform = TransformType::New();
OptimizerType::Pointer optimizer = OptimizerType::New();
InterpolatorType::Pointer interpolator = InterpolatorType::New();
RegistrationType::Pointer registration = RegistrationType::New();
MetricType::Pointer metric = MetricType::New();
registration->SetOptimizer( optimizer );
registration->SetTransform( transform );
registration->SetInterpolator( interpolator );
registration->SetMetric( metric );
// The metric requires a number of parameters to be selected, including
// the standard deviation of the Gaussian kernel for the fixed image
// density estimate, the standard deviation of the kernel for the moving
// image density and the number of samples use to compute the densities
// and entropy values. Experience has
// shown that a kernel standard deviation of 0.4 works well for images
// which have been normalized to a mean of zero and unit variance. We
// will follow this empirical rule in this example.
metric->SetFixedImageStandardDeviation( 0.4 );
metric->SetMovingImageStandardDeviation( 0.4 );
using FixedImageReaderType = itk::ImageFileReader< FixedImageType >;
using MovingImageReaderType = itk::ImageFileReader< MovingImageType >;
FixedImageReaderType::Pointer fixedImageReader =
FixedImageReaderType::New();
MovingImageReaderType::Pointer movingImageReader =
MovingImageReaderType::New();
fixedImageReader->SetFileName( fixedImageFile );
movingImageReader->SetFileName( movingImageFile );
FixedNormalizeFilterType::Pointer fixedNormalizer =
FixedNormalizeFilterType::New();
MovingNormalizeFilterType::Pointer movingNormalizer =
MovingNormalizeFilterType::New();
GaussianFilterType::Pointer fixedSmoother = GaussianFilterType::New();
GaussianFilterType::Pointer movingSmoother = GaussianFilterType::New();
fixedSmoother->SetVariance( 2.0 );
movingSmoother->SetVariance( 2.0 );
fixedNormalizer->SetInput( fixedImageReader->GetOutput() );
movingNormalizer->SetInput( movingImageReader->GetOutput() );
fixedSmoother->SetInput( fixedNormalizer->GetOutput() );
movingSmoother->SetInput( movingNormalizer->GetOutput() );
registration->SetFixedImage( fixedSmoother->GetOutput() );
registration->SetMovingImage( movingSmoother->GetOutput() );
fixedNormalizer->Update();
FixedImageType::RegionType fixedImageRegion =
fixedNormalizer->GetOutput()->GetBufferedRegion();
registration->SetFixedImageRegion( fixedImageRegion );
using ParametersType = RegistrationType::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 );
// We should now define the number of spatial samples to be considered in
// the metric computation. Note that we were forced to postpone this setting
// until we had done the preprocessing of the images because the number of
// samples is usually defined as a fraction of the total number of pixels in
// the fixed image.
//
// The number of spatial samples can usually be as low as $1\%$ of the total
// number of pixels in the fixed image. Increasing the number of samples
// improves the smoothness of the metric from one iteration to another and
// therefore helps when this metric is used in conjunction with optimizers
// that rely of the continuity of the metric values. The trade-off, of
// course, is that a larger number of samples result in longer computation
// times per every evaluation of the metric.
//
// It has been demonstrated empirically that the number of samples is not a
// critical parameter for the registration process. When you start fine
// tuning your own registration process, you should start using high values
// of number of samples, for example in the range of 20% to 50% of the
// number of pixels in the fixed image. Once you have succeeded to register
// your images you can then reduce the number of samples progressively until
// you find a good compromise on the time it takes to compute one evaluation
// of the Metric. Note that it is not useful to have very fast evaluations
// of the Metric if the noise in their values results in more iterations
// being required by the optimizer to converge.
// behavior of the metric values as the iterations progress.
const unsigned int numberOfPixels = fixedImageRegion.GetNumberOfPixels();
const auto numberOfSamples = static_cast< unsigned int >( numberOfPixels * 0.01 );
metric->SetNumberOfSpatialSamples( numberOfSamples );
// For consistent results when regression testing.
metric->ReinitializeSeed( 121212 );
// Since larger values of mutual information indicate better matches than
// smaller values, we need to maximize the cost function in this example.
// By default the GradientDescentOptimizer class is set to minimize the
// value of the cost-function. It is therefore necessary to modify its
// default behavior by invoking the MaximizeOn() method.
// Additionally, we need to define the optimizer's step size using the
// SetLearningRate() method.
optimizer->SetNumberOfIterations( 200 );
optimizer->MaximizeOn();
// Note that large values of the learning rate will make the optimizer
// unstable. Small values, on the other hand, may result in the optimizer
// needing too many iterations in order to walk to the extrema of the cost
// function. The easy way of fine tuning this parameter is to start with
// small values, probably in the range of {5.0, 10.0}. Once the other
// registration parameters have been tuned for producing convergence, you
// may want to revisit the learning rate and start increasing its value until
// you observe that the optimization becomes unstable. The ideal value for
// this parameter is the one that results in a minimum number of iterations
// while still keeping a stable path on the parametric space of the
// optimization. Keep in mind that this parameter is a multiplicative factor
// applied on the gradient of the Metric. Therefore, its effect on the
// optimizer step length is proportional to the Metric values themselves.
// Metrics with large values will require you to use smaller values for the
// learning rate in order to maintain a similar optimizer behavior.
optimizer->SetLearningRate( 15.0 );
CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
optimizer->AddObserver( itk::IterationEvent(), observer );
try
{
registration->Update();
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();
double TranslationAlongX = finalParameters[0];
double TranslationAlongY = finalParameters[1];
unsigned int numberOfIterations = optimizer->GetCurrentIteration();
double bestValue = optimizer->GetValue();
// Print out results
std::cout << std::endl;
std::cout << "Result = " << std::endl;
std::cout << " Translation X = " << TranslationAlongX << std::endl;
std::cout << " Translation Y = " << TranslationAlongY << std::endl;
std::cout << " Iterations = " << numberOfIterations << std::endl;
std::cout << " Metric value = " << bestValue << std::endl;
std::cout << " Numb. Samples = " << numberOfSamples << std::endl;
using ResampleFilterType = itk::ResampleImageFilter<
MovingImageType,
FixedImageType >;
TransformType::Pointer finalTransform = TransformType::New();
finalTransform->SetParameters( finalParameters );
finalTransform->SetFixedParameters( transform->GetFixedParameters() );
ResampleFilterType::Pointer resample = ResampleFilterType::New();
resample->SetTransform( finalTransform );
resample->SetInput( movingImageReader->GetOutput() );
FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();
resample->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );
resample->SetOutputOrigin( fixedImage->GetOrigin() );
resample->SetOutputSpacing( fixedImage->GetSpacing() );
resample->SetOutputDirection( fixedImage->GetDirection() );
resample->SetDefaultPixelValue( 100 );
using OutputPixelType = unsigned char;
using CastFilterType = itk::CastImageFilter<
FixedImageType,
OutputImageType >;
WriterType::Pointer writer = WriterType::New();
CastFilterType::Pointer caster = CastFilterType::New();
writer->SetFileName( outputImageFile );
caster->SetInput( resample->GetOutput() );
writer->SetInput( caster->GetOutput() );
writer->Update();
// Generate checkerboards before and after registration
using CheckerBoardFilterType = itk::CheckerBoardImageFilter< FixedImageType >;
CheckerBoardFilterType::Pointer checker = CheckerBoardFilterType::New();
checker->SetInput1( fixedImage );
checker->SetInput2( resample->GetOutput() );
caster->SetInput( checker->GetOutput() );
writer->SetInput( caster->GetOutput() );
// Before registration
TransformType::Pointer identityTransform = TransformType::New();
identityTransform->SetIdentity();
resample->SetTransform( identityTransform );
if( argc > 4 )
{
writer->SetFileName( checkerBoardBefore );
}
// After registration
resample->SetTransform( finalTransform );
if( argc > 5 )
{
writer->SetFileName( checkerBoardAfter );
}
try
{
writer->Update();
}
catch( itk::ExceptionObject & error )
{
std::cerr << "Error: " << error << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}