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DeformableRegistration4.cxx
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DeformableRegistration4.cxx
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/*=========================================================================
*
* 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 the use of the \doxygen{BSplineTransform}
// class for performing registration of two $2D$ images. The example code is
// for the most part identical to the code presented in
// Section~\ref{sec:RigidRegistrationIn2D}. The major difference is that this
// example we replace the Transform for a more generic one endowed with a large
// number of degrees of freedom. Due to the large number of parameters, we will
// also replace the simple steepest descent optimizer with the
// \doxygen{LBFGSOptimizer}.
//
//
// \index{itk::BSplineTransform}
// \index{itk::BSplineTransform!DeformableRegistration}
// \index{itk::LBFGSOptimizer}
//
//
// Software Guide : EndLatex
#include "itkImageRegistrationMethod.h"
#include "itkMeanSquaresImageToImageMetric.h"
#include "itkTimeProbesCollectorBase.h"
#include "itkMemoryProbesCollectorBase.h"
// Software Guide : BeginLatex
//
// The following are the most relevant headers to this example.
//
// \index{itk::BSplineTransform!header}
// \index{itk::LBFGSOptimizer!header}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
#include "itkBSplineTransform.h"
#include "itkLBFGSOptimizer.h"
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The parameter space of the \code{BSplineTransform} is composed by
// the set of all the deformations associated with the nodes of the BSpline
// grid. This large number of parameters makes possible to represent a wide
// variety of deformations, but it also has the price of requiring a
// significant amount of computation time.
//
// \index{itk::BSplineTransform!header}
//
// Software Guide : EndLatex
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkResampleImageFilter.h"
#include "itkCastImageFilter.h"
#include "itkSquaredDifferenceImageFilter.h"
// NOTE: the LBFGSOptimizer does not invoke events
int main( int argc, char *argv[] )
{
if( argc < 4 )
{
std::cerr << "Missing Parameters " << std::endl;
std::cerr << "Usage: " << argv[0];
std::cerr << " fixedImageFile movingImageFile outputImagefile ";
std::cerr << " [differenceOutputfile] [differenceBeforeRegistration] ";
std::cerr << " [deformationField] ";
return EXIT_FAILURE;
}
const unsigned int ImageDimension = 2;
typedef float PixelType;
typedef itk::Image< PixelType, ImageDimension > FixedImageType;
typedef itk::Image< PixelType, ImageDimension > MovingImageType;
// Software Guide : BeginLatex
//
// We instantiate now the type of the \code{BSplineTransform} using
// as template parameters the type for coordinates representation, the
// dimension of the space, and the order of the BSpline.
//
// \index{BSplineTransform!New}
// \index{BSplineTransform!Instantiation}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
const unsigned int SpaceDimension = ImageDimension;
const unsigned int SplineOrder = 3;
typedef double CoordinateRepType;
typedef itk::BSplineTransform<
CoordinateRepType,
SpaceDimension,
SplineOrder > TransformType;
// Software Guide : EndCodeSnippet
typedef itk::LBFGSOptimizer OptimizerType;
typedef itk::MeanSquaresImageToImageMetric<
FixedImageType,
MovingImageType > 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();
registration->SetMetric( metric );
registration->SetOptimizer( optimizer );
registration->SetInterpolator( interpolator );
// Software Guide : BeginLatex
//
// The transform object is constructed below and passed to the registration
// method.
// \index{itk::RegistrationMethod!SetTransform()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
TransformType::Pointer transform = TransformType::New();
registration->SetTransform( transform );
// Software Guide : EndCodeSnippet
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] );
FixedImageType::ConstPointer fixedImage = fixedImageReader->GetOutput();
registration->SetFixedImage( fixedImage );
registration->SetMovingImage( movingImageReader->GetOutput() );
fixedImageReader->Update();
FixedImageType::RegionType fixedRegion = fixedImage->GetBufferedRegion();
registration->SetFixedImageRegion( fixedRegion );
// Software Guide : BeginCodeSnippet
TransformType::PhysicalDimensionsType fixedPhysicalDimensions;
TransformType::MeshSizeType meshSize;
TransformType::OriginType fixedOrigin;
unsigned int numberOfGridNodesInOneDimension = 8;
for( unsigned int i=0; i< SpaceDimension; i++ )
{
fixedOrigin[i] = fixedImage->GetOrigin()[i];
fixedPhysicalDimensions[i] = fixedImage->GetSpacing()[i] *
static_cast<double>(
fixedImage->GetLargestPossibleRegion().GetSize()[i] - 1 );
}
meshSize.Fill( numberOfGridNodesInOneDimension - SplineOrder );
transform->SetTransformDomainOrigin( fixedOrigin );
transform->SetTransformDomainPhysicalDimensions(
fixedPhysicalDimensions );
transform->SetTransformDomainMeshSize( meshSize );
transform->SetTransformDomainDirection( fixedImage->GetDirection() );
typedef TransformType::ParametersType ParametersType;
const unsigned int numberOfParameters =
transform->GetNumberOfParameters();
ParametersType parameters( numberOfParameters );
parameters.Fill( 0.0 );
transform->SetParameters( parameters );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We now pass the parameters of the current transform as the initial
// parameters to be used when the registration process starts.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
registration->SetInitialTransformParameters( transform->GetParameters() );
// Software Guide : EndCodeSnippet
std::cout << "Intial Parameters = " << std::endl;
std::cout << transform->GetParameters() << std::endl;
// Software Guide : BeginLatex
//
// Next we set the parameters of the LBFGS Optimizer.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
optimizer->SetGradientConvergenceTolerance( 0.05 );
optimizer->SetLineSearchAccuracy( 0.9 );
optimizer->SetDefaultStepLength( 1.5 );
optimizer->TraceOn();
optimizer->SetMaximumNumberOfFunctionEvaluations( 1000 );
// Software Guide : EndCodeSnippet
// Add time and memory probes
itk::TimeProbesCollectorBase chronometer;
itk::MemoryProbesCollectorBase memorymeter;
std::cout << std::endl << "Starting Registration" << std::endl;
try
{
memorymeter.Start( "Registration" );
chronometer.Start( "Registration" );
registration->Update();
chronometer.Stop( "Registration" );
memorymeter.Stop( "Registration" );
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;
// Report the time and memory taken by the registration
chronometer.Report( std::cout );
memorymeter.Report( std::cout );
// Software Guide : BeginLatex
//
// Let's execute this example using the rat lung images from the previous examples.
//
// \begin{itemize}
// \item \code{RatLungSlice1.mha}
// \item \code{RatLungSlice2.mha}
// \end{itemize}
//
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
transform->SetParameters( finalParameters );
// Software Guide : EndCodeSnippet
typedef itk::ResampleImageFilter<
MovingImageType,
FixedImageType > ResampleFilterType;
ResampleFilterType::Pointer resample = ResampleFilterType::New();
resample->SetTransform( transform );
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 unsigned char OutputPixelType;
typedef itk::Image< OutputPixelType, ImageDimension > 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() );
try
{
writer->Update();
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return EXIT_FAILURE;
}
typedef itk::SquaredDifferenceImageFilter<
FixedImageType,
FixedImageType,
OutputImageType > DifferenceFilterType;
DifferenceFilterType::Pointer difference = DifferenceFilterType::New();
WriterType::Pointer writer2 = WriterType::New();
writer2->SetInput( difference->GetOutput() );
// Compute the difference image between the
// fixed and resampled moving image.
if( argc >= 5 )
{
difference->SetInput1( fixedImageReader->GetOutput() );
difference->SetInput2( resample->GetOutput() );
writer2->SetFileName( argv[4] );
try
{
writer2->Update();
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return EXIT_FAILURE;
}
}
// Compute the difference image between the
// fixed and moving image before registration.
if( argc >= 6 )
{
writer2->SetFileName( argv[5] );
difference->SetInput1( fixedImageReader->GetOutput() );
difference->SetInput2( movingImageReader->GetOutput() );
try
{
writer2->Update();
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return EXIT_FAILURE;
}
}
// Generate the explicit deformation field resulting from
// the registration.
typedef itk::Vector< float, ImageDimension > VectorType;
typedef itk::Image< VectorType, ImageDimension > DisplacementFieldType;
DisplacementFieldType::Pointer field = DisplacementFieldType::New();
field->SetRegions( fixedRegion );
field->SetOrigin( fixedImage->GetOrigin() );
field->SetSpacing( fixedImage->GetSpacing() );
field->SetDirection( fixedImage->GetDirection() );
field->Allocate();
typedef itk::ImageRegionIterator< DisplacementFieldType > FieldIterator;
FieldIterator fi( field, fixedRegion );
fi.GoToBegin();
TransformType::InputPointType fixedPoint;
TransformType::OutputPointType movingPoint;
DisplacementFieldType::IndexType index;
VectorType displacement;
while( ! fi.IsAtEnd() )
{
index = fi.GetIndex();
field->TransformIndexToPhysicalPoint( index, fixedPoint );
movingPoint = transform->TransformPoint( fixedPoint );
displacement = movingPoint - fixedPoint;
fi.Set( displacement );
++fi;
}
typedef itk::ImageFileWriter< DisplacementFieldType > FieldWriterType;
FieldWriterType::Pointer fieldWriter = FieldWriterType::New();
fieldWriter->SetInput( field );
if( argc >= 7 )
{
fieldWriter->SetFileName( argv[6] );
try
{
fieldWriter->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
}
return EXIT_SUCCESS;
}