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Insight Segmentation and Registration Toolkit
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RegistrationITKv4/ImageRegistration14.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.
*
*=========================================================================*/
// Software Guide : BeginLatex
//
// This example illustrates how to do registration with a 2D Rigid Transform
// and with the Normalized Mutual Information metric.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
#include "
itkImageRegistrationMethod.h
"
#include "
itkCenteredRigid2DTransform.h
"
#include "
itkCenteredTransformInitializer.h
"
#include "
itkNormalizedMutualInformationHistogramImageToImageMetric.h
"
#include "
itkOnePlusOneEvolutionaryOptimizer.h
"
#include "
itkNormalVariateGenerator.h
"
#include "
itkImageFileReader.h
"
#include "
itkImageFileWriter.h
"
#include "
itkResampleImageFilter.h
"
#include "
itkCastImageFilter.h
"
// 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
:
typedef
CommandIterationUpdate
Self
;
typedef
itk::Command
Superclass
;
typedef
itk::SmartPointer<Self>
Pointer
;
itkNewMacro( Self );
protected
:
CommandIterationUpdate() {m_LastMetricValue = 0;}
public
:
typedef
itk::OnePlusOneEvolutionaryOptimizer
OptimizerType;
typedef
const
OptimizerType * OptimizerPointer;
void
Execute
(
itk::Object
*caller,
const
itk::EventObject
& event)
{
Execute
( (
const
itk::Object
*)caller, event);
}
void
Execute
(
const
itk::Object
*
object
,
const
itk::EventObject
& event)
{
OptimizerPointer optimizer =
dynamic_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 ) > 1
e
-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]"
<< std::endl;
std::cerr <<
"[initialAngle(radians)] [initialTx] [initialTy]"
<< std::endl;
return
EXIT_FAILURE;
}
const
unsigned
int
Dimension = 2;
typedef
unsigned
char
PixelType;
typedef
itk::Image< PixelType, Dimension >
FixedImageType;
typedef
itk::Image< PixelType, Dimension >
MovingImageType;
typedef
itk::CenteredRigid2DTransform< double >
TransformType;
typedef
itk::OnePlusOneEvolutionaryOptimizer
OptimizerType;
typedef
itk::LinearInterpolateImageFunction
<
MovingImageType,
double
> InterpolatorType;
typedef
itk::ImageRegistrationMethod
<
FixedImageType,
MovingImageType > RegistrationType;
typedef
itk::NormalizedMutualInformationHistogramImageToImageMetric
<
FixedImageType,
MovingImageType > MetricType;
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 = atoi( argv[4] );
std::cout <<
"Using "
<< numberOfHistogramBins <<
" Histogram bins"
<< std::endl;
}
MetricType::HistogramType::SizeType histogramSize;
histogramSize.SetSize(2);
histogramSize[0] = numberOfHistogramBins;
histogramSize[1] = numberOfHistogramBins;
metric->SetHistogramSize( histogramSize );
const
unsigned
int
numberOfParameters = transform->GetNumberOfParameters();
typedef
MetricType::ScalesType ScalesType;
ScalesType scales( numberOfParameters );
scales.Fill( 1.0 );
metric->SetDerivativeStepLengthScales(scales);
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();
movingImageReader->Update();
FixedImageType::ConstPointer fixedImage = fixedImageReader->GetOutput();
registration->SetFixedImageRegion( fixedImage->GetBufferedRegion() );
typedef
itk::CenteredTransformInitializer
<
TransformType, FixedImageType,
MovingImageType > TransformInitializerType;
TransformInitializerType::Pointer initializer
= TransformInitializerType::New();
initializer->SetTransform( transform );
initializer->SetFixedImage( fixedImageReader->GetOutput() );
initializer->SetMovingImage( movingImageReader->GetOutput() );
initializer->GeometryOn();
initializer->InitializeTransform();
double
initialAngle = 0.0;
if
( argc > 7 )
{
initialAngle = atof( argv[7] );
}
transform->SetAngle( initialAngle );
TransformType::OutputVectorType initialTranslation
= transform->GetTranslation();
if
( argc > 9 )
{
initialTranslation[0] += atof( argv[8] );
initialTranslation[1] += atof( argv[9] );
}
transform->SetTranslation( initialTranslation );
typedef
RegistrationType::ParametersType ParametersType;
ParametersType initialParameters = transform->GetParameters();
registration->SetInitialTransformParameters( initialParameters );
std::cout <<
"Initial transform parameters = "
;
std::cout << initialParameters << std::endl;
typedef
OptimizerType::ScalesType OptimizerScalesType;
OptimizerScalesType optimizerScales( transform->GetNumberOfParameters() );
FixedImageType::RegionType region = fixedImage->GetLargestPossibleRegion();
FixedImageType::SizeType size = region.GetSize();
FixedImageType::SpacingType spacing = fixedImage->GetSpacing();
optimizerScales[0] = 1.0 / 0.1;
// make angle move slowly
optimizerScales[1] = 10000.0;
// prevent the center from moving
optimizerScales[2] = 10000.0;
// prevent the center from moving
optimizerScales[3] = 1.0 / ( 0.1 * size[0] * spacing[0] );
optimizerScales[4] = 1.0 / ( 0.1 * size[1] * spacing[1] );
std::cout <<
"optimizerScales = "
<< optimizerScales << std::endl;
optimizer->SetScales( optimizerScales );
typedef
itk::Statistics::NormalVariateGenerator
GeneratorType;
GeneratorType::Pointer generator = GeneratorType::New();
generator->Initialize(12345);
optimizer->MaximizeOn();
optimizer->SetNormalVariateGenerator( generator );
double
initialRadius = 0.05;
if
( argc > 5 )
{
initialRadius = atof( argv[5] );
std::cout <<
"Using initial radius = "
<< initialRadius << std::endl;
}
optimizer->Initialize( initialRadius );
double
epsilon = 0.001;
if
( argc > 6 )
{
epsilon = atof( 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;
}
typedef
RegistrationType::ParametersType ParametersType;
ParametersType finalParameters = registration->GetLastTransformParameters();
const
double
finalAngle = finalParameters[0];
const
double
finalRotationCenterX = finalParameters[1];
const
double
finalRotationCenterY = finalParameters[2];
const
double
finalTranslationX = finalParameters[3];
const
double
finalTranslationY = finalParameters[4];
const
unsigned
int
numberOfIterations = optimizer->GetCurrentIteration();
const
double
bestValue = optimizer->GetValue();
// Print out results
const
double
finalAngleInDegrees = finalAngle * 180.0 /
vnl_math::pi
;
std::cout <<
" Result = "
<< std::endl;
std::cout <<
" Angle (radians) "
<< finalAngle << std::endl;
std::cout <<
" Angle (degrees) "
<< finalAngleInDegrees << std::endl;
std::cout <<
" Center X = "
<< finalRotationCenterX << std::endl;
std::cout <<
" Center Y = "
<< finalRotationCenterY << 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;
typedef
itk::ResampleImageFilter
<
MovingImageType, FixedImageType > ResampleFilterType;
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 );
typedef
itk::Image< PixelType, Dimension >
OutputImageType;
typedef
itk::ImageFileWriter< OutputImageType >
WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName( argv[3] );
writer->SetInput( resample->GetOutput() );
writer->Update();
// Software Guide : EndCodeSnippet
return
EXIT_SUCCESS;
}
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