ITK  5.0.0
Insight Segmentation and Registration Toolkit
Examples/RegistrationITKv4/ImageRegistration15.cxx
/*=========================================================================
*
* Copyright Insight Software Consortium
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
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*=========================================================================*/
// Software Guide : BeginLatex
//
// This example illustrates how to do registration with a 2D Translation Transform,
// the Normalized Mutual Information metric and the One+One evolutionary optimizer.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// The following section of code implements a Command observer
// used to 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() {m_LastMetricValue = 0;}
public:
using OptimizerType = itk::OnePlusOneEvolutionaryOptimizer;
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 = static_cast< OptimizerPointer >( object );
if( ! itk::IterationEvent().CheckEvent( &event ) )
{
return;
}
double currentValue = optimizer->GetValue();
// Only print out when the Metric value changes
if( std::fabs( m_LastMetricValue - currentValue ) > 1e-7 )
{
std::cout << optimizer->GetCurrentIteration() << " ";
std::cout << currentValue << " ";
std::cout << optimizer->GetFrobeniusNorm() << " ";
std::cout << optimizer->GetCurrentPosition() << std::endl;
m_LastMetricValue = currentValue;
}
}
private:
double m_LastMetricValue;
};
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 [numberOfHistogramBins] ";
std::cerr << "[initialRadius] [epsilon] [initialTx] [initialTy]"
<< std::endl;
return EXIT_FAILURE;
}
constexpr unsigned int Dimension = 2;
using PixelType = unsigned char;
using FixedImageType = itk::Image< PixelType, Dimension >;
using MovingImageType = itk::Image< PixelType, Dimension >;
using OptimizerType = itk::OnePlusOneEvolutionaryOptimizer;
using InterpolatorType = itk::LinearInterpolateImageFunction<
MovingImageType,
double >;
using RegistrationType = itk::ImageRegistrationMethod<
FixedImageType,
MovingImageType >;
using MetricType =
FixedImageType,
MovingImageType >;
TransformType::Pointer transform = TransformType::New();
OptimizerType::Pointer optimizer = OptimizerType::New();
InterpolatorType::Pointer interpolator = InterpolatorType::New();
RegistrationType::Pointer registration = RegistrationType::New();
registration->SetOptimizer( optimizer );
registration->SetTransform( transform );
registration->SetInterpolator( interpolator );
MetricType::Pointer metric = MetricType::New();
registration->SetMetric( metric );
unsigned int numberOfHistogramBins = 32;
if( argc > 4 )
{
numberOfHistogramBins = std::stoi( argv[4] );
std::cout << "Using " << numberOfHistogramBins << " Histogram bins"
<< std::endl;
}
histogramSize.SetSize(2);
histogramSize[0] = numberOfHistogramBins;
histogramSize[1] = numberOfHistogramBins;
metric->SetHistogramSize( histogramSize );
const unsigned int numberOfParameters = transform->GetNumberOfParameters();
using ScalesType = MetricType::ScalesType;
ScalesType scales( numberOfParameters );
scales.Fill( 1.0 );
metric->SetDerivativeStepLengthScales(scales);
using FixedImageReaderType = itk::ImageFileReader< FixedImageType >;
using MovingImageReaderType = itk::ImageFileReader< MovingImageType >;
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();
movingImageReader->Update();
FixedImageType::ConstPointer fixedImage = fixedImageReader->GetOutput();
registration->SetFixedImageRegion( fixedImage->GetBufferedRegion() );
transform->SetIdentity();
using ParametersType = RegistrationType::ParametersType;
ParametersType initialParameters = transform->GetParameters();
initialParameters[0] = 0.0;
initialParameters[1] = 0.0;
if( argc > 8 )
{
initialParameters[0] = std::stod( argv[7] );
initialParameters[1] = std::stod( argv[8] );
}
registration->SetInitialTransformParameters( initialParameters );
std::cout << "Initial transform parameters = ";
std::cout << initialParameters << std::endl;
using OptimizerScalesType = OptimizerType::ScalesType;
OptimizerScalesType optimizerScales( transform->GetNumberOfParameters() );
FixedImageType::RegionType region = fixedImage->GetLargestPossibleRegion();
FixedImageType::SpacingType spacing = fixedImage->GetSpacing();
optimizerScales[0] = 1.0 / ( 0.1 * size[0] * spacing[0] );
optimizerScales[1] = 1.0 / ( 0.1 * size[1] * spacing[1] );
optimizer->SetScales( optimizerScales );
GeneratorType::Pointer generator = GeneratorType::New();
generator->Initialize(12345);
optimizer->MaximizeOn();
optimizer->SetNormalVariateGenerator( generator );
double initialRadius = 0.01;
if( argc > 5 )
{
initialRadius = std::stod( argv[5] );
std::cout << "Using initial radius = " << initialRadius << std::endl;
}
optimizer->Initialize( initialRadius );
double epsilon = 0.001;
if( argc > 6 )
{
epsilon = std::stod( argv[6] );
std::cout << "Using epsilon = " << epsilon << std::endl;
}
optimizer->SetEpsilon( epsilon );
optimizer->SetMaximumIteration( 2000 );
// Create the Command observer and register it with the optimizer.
//
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();
const double finalTranslationX = finalParameters[0];
const double finalTranslationY = finalParameters[1];
unsigned int numberOfIterations = optimizer->GetCurrentIteration();
const double bestValue = optimizer->GetValue();
// Print out results
std::cout << "Result = " << std::endl;
std::cout << " Translation X = " << finalTranslationX << std::endl;
std::cout << " Translation Y = " << finalTranslationY << std::endl;
std::cout << " Iterations = " << numberOfIterations << std::endl;
std::cout << " Metric value = " << bestValue << 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() );
resample->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );
resample->SetOutputOrigin( fixedImage->GetOrigin() );
resample->SetOutputSpacing( fixedImage->GetSpacing() );
resample->SetOutputDirection( fixedImage->GetDirection() );
resample->SetDefaultPixelValue( 100 );
using OutputImageType = itk::Image< PixelType, Dimension >;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName( argv[3] );
writer->SetInput( resample->GetOutput() );
writer->Update();
// Software Guide : EndCodeSnippet
return EXIT_SUCCESS;
}