[Insight-users] registration example 2 and 9
Mr Gaffe
lagaffe74130 at yahoo.fr
Wed Nov 10 05:36:13 EST 2004
Hi all,
I try to combine registration example: ImageRegistration2 and 9 to perform an CenteredAffine+MutualInfo registration.
The code bellow compile well, but when I try with: BrainT1SliceBorder20.png and BrainProtonDensitySliceR10X13Y17S12.png I have the following error:
---------------
Initial Transform Parameters
[1, 0, 0, 1, -1.00276e+008, -4.25387e+008, 4.90708e+007, 3.85172e+008]
ExceptionObject caught !
itk::ExceptionObject (00FCFD30)
Location: "Unknown"
File: D:\InsightToolkit-1.8.1\Code\Algorithms\itkMutualInformationImageToImageMetric.txx
Line: 155
Description: itk::ERROR: MutualInformationImageToImageMetric(012F4780): All the sampled point mapped to outside of the moving image
-----------------
->The Typedef is set to float since Images are unsigned chart is it the problem ?
If I change the initialisation of the CenteredTransformInitializer as:
initializer->SetFixedImage( fixedImageReader->GetOutput() );
initializer->SetMovingImage( movingImageReader->GetOutput() );
There is no error, but the after 9 iterations it stop with a wrong image results....
Is it just a problem of initial typeddef for my fixed and moved image ?
thanks,
lagaffe
---------------------------------------------------------------------------------------------------------------------
/*
* Code from ImageRegistration2 and ImageRegistration9
*/
#include "itkImageRegistrationMethod.h"
//#include "itkMeanSquaresImageToImageMetric.h"
#include "itkMutualInformationImageToImageMetric.h"
#include "itkNormalizeImageFilter.h"
#include "itkDiscreteGaussianImageFilter.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkRegularStepGradientDescentOptimizer.h"
#include "itkImage.h"
#include "itkCenteredTransformInitializer.h"
#include "itkCenteredAffineTransform.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkResampleImageFilter.h"
#include "itkCastImageFilter.h"
#include "itkSquaredDifferenceImageFilter.h"
#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() {};
public:
typedef itk::RegularStepGradientDescentOptimizer 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( typeid( event ) != typeid( itk::IterationEvent ) )
{
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 movingImageFile " << std::endl;
std::cerr << " outputImagefile [differenceOutputfile] [differenceBeforeRegistration] " << std::endl;
std::cerr << " [stepLength] [maxNumberOfIterations] "<< std::endl;
return 1;
}
const unsigned int Dimension = 2;
typedef float PixelType;
typedef float InternalPixelType;
typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
typedef itk::Image< PixelType, Dimension > FixedImageType;
typedef itk::Image< PixelType, Dimension > MovingImageType;
typedef itk::CenteredAffineTransform<
double,
Dimension > TransformType;
typedef itk::RegularStepGradientDescentOptimizer OptimizerType;
/*
typedef itk::MeanSquaresImageToImageMetric<
FixedImageType,
MovingImageType > MetricType;
*/
typedef itk::MutualInformationImageToImageMetric<
InternalImageType,
InternalImageType > MetricType;
typedef itk:: LinearInterpolateImageFunction<
MovingImageType,
double > InterpolatorType;
typedef itk::ImageRegistrationMethod<
FixedImageType,
MovingImageType > RegistrationType;
MetricType::Pointer metric = MetricType::New();
OptimizerType::Pointer optimizer = OptimizerType::New();
InterpolatorType::Pointer interpolator = InterpolatorType::New();
RegistrationType::Pointer registration = RegistrationType::New();
TransformType::Pointer transform = TransformType::New();
registration->SetMetric( metric );
registration->SetOptimizer( optimizer );
registration->SetInterpolator( interpolator );
registration->SetTransform( transform );
metric->SetFixedImageStandardDeviation( 0.4 );
metric->SetMovingImageStandardDeviation( 0.4 );
metric->SetNumberOfSpatialSamples( 50 );
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] );
typedef itk::NormalizeImageFilter<
FixedImageType,
InternalImageType
> FixedNormalizeFilterType;
typedef itk::NormalizeImageFilter<
MovingImageType,
InternalImageType
> MovingNormalizeFilterType;
FixedNormalizeFilterType::Pointer fixedNormalizer =
FixedNormalizeFilterType::New();
MovingNormalizeFilterType::Pointer movingNormalizer =
MovingNormalizeFilterType::New();
typedef itk::DiscreteGaussianImageFilter<
InternalImageType,
InternalImageType
> GaussianFilterType;
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();
registration->SetFixedImageRegion(
fixedNormalizer->GetOutput()->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->SetFixedImage( fixedSmoother->GetOutput() );
initializer->SetMovingImage( movingSmoother->GetOutput() );
initializer->MomentsOn();
initializer->InitializeTransform();
std::cout << "Initial Transform Parameters " << std::endl;
std::cout << transform->GetParameters() << std::endl;
// -----------------------
registration->SetInitialTransformParameters(
transform->GetParameters() );
double translationScale = 1.0 / 1000.0;
if( argc > 8 )
{
translationScale = atof( argv[8] );
}
typedef OptimizerType::ScalesType OptimizerScalesType;
OptimizerScalesType optimizerScales( transform->GetNumberOfParameters() );
optimizerScales[0] = 1.0;
optimizerScales[1] = 1.0;
optimizerScales[2] = 1.0;
optimizerScales[3] = 1.0;
optimizerScales[4] = translationScale;
optimizerScales[5] = translationScale;
optimizerScales[6] = translationScale;
optimizerScales[7] = translationScale;
optimizer->SetScales( optimizerScales );
double steplength = 0.1;
if( argc > 6 )
{
steplength = atof( argv[6] );
}
unsigned int maxNumberOfIterations = 300;
if( argc > 7 )
{
maxNumberOfIterations = atoi( argv[7] );
}
optimizer->SetMaximumStepLength( steplength );
optimizer->SetMinimumStepLength( 0.001 );
optimizer->SetNumberOfIterations( maxNumberOfIterations );
optimizer->MinimizeOn();
CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
optimizer->AddObserver( itk::IterationEvent(), observer );
try
{
registration->StartRegistration();
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return -1;
}
OptimizerType::ParametersType finalParameters =
registration->GetLastTransformParameters();
const double finalRotationCenterX = finalParameters[4];
const double finalRotationCenterY = finalParameters[5];
const double finalTranslationX = finalParameters[6];
const double finalTranslationY = finalParameters[7];
const unsigned int numberOfIterations = optimizer->GetCurrentIteration();
const double bestValue = optimizer->GetValue();
// Software Guide : EndCodeSnippet
// Print out results
//
std::cout << "Result = " << 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 );
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->SetDefaultPixelValue( 100 );
typedef unsigned char OutputPixelType;
typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
typedef itk::CastImageFilter<
FixedImageType,
OutputImageType > CastFilterType;
typedef itk::ImageFileWriter< OutputImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
CastFilterType::Pointer caster = CastFilterType::New();
writer->SetFileName( argv[3] );
caster->SetInput( resample->GetOutput() );
writer->SetInput( caster->GetOutput() );
writer->Update();
typedef itk::SquaredDifferenceImageFilter<
FixedImageType,
FixedImageType,
OutputImageType > DifferenceFilterType;
DifferenceFilterType::Pointer difference = DifferenceFilterType::New();
WriterType::Pointer writer2 = WriterType::New();
writer2->SetInput( difference->GetOutput() );
if( argc > 4 )
{
difference->SetInput1( fixedImageReader->GetOutput() );
difference->SetInput2( resample->GetOutput() );
writer2->SetFileName( argv[4] );
writer2->Update();
}
if( argc > 5 )
{
writer2->SetFileName( argv[5] );
difference->SetInput1( fixedImageReader->GetOutput() );
difference->SetInput2( movingImageReader->GetOutput() );
writer2->Update();
}
return 0;
}
---------------------------------
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