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BSplineWarping1.cxx
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BSplineWarping1.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 how to deform a 2D image using a BSplineTransform.
//
// \index{BSplineTransform}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkResampleImageFilter.h"
#include "itkBSplineTransform.h"
#include "itkTransformFileWriter.h"
// Software Guide : EndCodeSnippet
#include <fstream>
// The following section of code implements a Command observer
// used to monitor the evolution of the registration process.
//
#include "itkCommand.h"
class CommandProgressUpdate : public itk::Command
{
public:
typedef CommandProgressUpdate Self;
typedef itk::Command Superclass;
typedef itk::SmartPointer<Self> Pointer;
itkNewMacro( Self );
protected:
CommandProgressUpdate() {};
public:
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)
{
const itk::ProcessObject * filter = static_cast< const itk::ProcessObject * >( object );
if( ! itk::ProgressEvent().CheckEvent( &event ) )
{
return;
}
std::cout << filter->GetProgress() << std::endl;
}
};
int main( int argc, char * argv[] )
{
if( argc < 5 )
{
std::cerr << "Missing Parameters " << std::endl;
std::cerr << "Usage: " << argv[0];
std::cerr << " coefficientsFile fixedImage ";
std::cerr << "movingImage deformedMovingImage" << std::endl;
std::cerr << "[deformationField] [transformFile]" << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginCodeSnippet
const unsigned int ImageDimension = 2;
typedef unsigned char PixelType;
typedef itk::Image< PixelType, ImageDimension > FixedImageType;
typedef itk::Image< PixelType, ImageDimension > MovingImageType;
typedef itk::ImageFileReader< FixedImageType > FixedReaderType;
typedef itk::ImageFileReader< MovingImageType > MovingReaderType;
typedef itk::ImageFileWriter< MovingImageType > MovingWriterType;
FixedReaderType::Pointer fixedReader = FixedReaderType::New();
fixedReader->SetFileName( argv[2] );
try
{
fixedReader->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
MovingReaderType::Pointer movingReader = MovingReaderType::New();
MovingWriterType::Pointer movingWriter = MovingWriterType::New();
movingReader->SetFileName( argv[3] );
movingWriter->SetFileName( argv[4] );
FixedImageType::ConstPointer fixedImage = fixedReader->GetOutput();
typedef itk::ResampleImageFilter< MovingImageType,
FixedImageType > FilterType;
FilterType::Pointer resampler = FilterType::New();
typedef itk::LinearInterpolateImageFunction<
MovingImageType, double > InterpolatorType;
InterpolatorType::Pointer interpolator = InterpolatorType::New();
resampler->SetInterpolator( interpolator );
FixedImageType::SpacingType fixedSpacing = fixedImage->GetSpacing();
FixedImageType::PointType fixedOrigin = fixedImage->GetOrigin();
FixedImageType::DirectionType fixedDirection = fixedImage->GetDirection();
resampler->SetOutputSpacing( fixedSpacing );
resampler->SetOutputOrigin( fixedOrigin );
resampler->SetOutputDirection( fixedDirection );
FixedImageType::RegionType fixedRegion = fixedImage->GetBufferedRegion();
FixedImageType::SizeType fixedSize = fixedRegion.GetSize();
resampler->SetSize( fixedSize );
resampler->SetOutputStartIndex( fixedRegion.GetIndex() );
resampler->SetInput( movingReader->GetOutput() );
movingWriter->SetInput( resampler->GetOutput() );
// Software Guide : EndCodeSnippet
// 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 B-spline.
//
// \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;
TransformType::Pointer bsplineTransform = TransformType::New();
// Software Guide : EndCodeSnippet
// Software Guide : BeginCodeSnippet
const unsigned int numberOfGridNodes = 7;
TransformType::PhysicalDimensionsType fixedPhysicalDimensions;
TransformType::MeshSizeType meshSize;
for( unsigned int i=0; i< SpaceDimension; i++ )
{
fixedPhysicalDimensions[i] = fixedSpacing[i] * static_cast<double>(
fixedSize[i] - 1 );
}
meshSize.Fill( numberOfGridNodes - SplineOrder );
bsplineTransform->SetTransformDomainOrigin( fixedOrigin );
bsplineTransform->SetTransformDomainPhysicalDimensions(
fixedPhysicalDimensions );
bsplineTransform->SetTransformDomainMeshSize( meshSize );
bsplineTransform->SetTransformDomainDirection( fixedDirection );
typedef TransformType::ParametersType ParametersType;
const unsigned int numberOfParameters =
bsplineTransform->GetNumberOfParameters();
const unsigned int numberOfNodes = numberOfParameters / SpaceDimension;
ParametersType parameters( numberOfParameters );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The B-spline grid should now be fed with coeficients at each node. Since
// this is a two dimensional grid, each node should receive two coefficients.
// Each coefficient pair is representing a displacement vector at this node.
// The coefficients can be passed to the B-spline in the form of an array where
// the first set of elements are the first component of the displacements for
// all the nodes, and the second set of elemets is formed by the second
// component of the displacements for all the nodes.
//
// In this example we read such displacements from a file, but for convinience
// we have written this file using the pairs of $(x,y)$ displacement for every
// node. The elements read from the file should therefore be reorganized when
// assigned to the elements of the array. We do this by storing all the odd
// elements from the file in the first block of the array, and all the even
// elements from the file in the second block of the array. Finally the array
// is passed to the B-spline transform using the \code{SetParameters()}.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
std::ifstream infile;
infile.open( argv[1] );
for( unsigned int n=0; n < numberOfNodes; n++ )
{
infile >> parameters[n];
infile >> parameters[n+numberOfNodes];
}
infile.close();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Finally the array is passed to the B-spline transform using the
// \code{SetParameters()}.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
bsplineTransform->SetParameters( parameters );
// Software Guide : EndCodeSnippet
CommandProgressUpdate::Pointer observer = CommandProgressUpdate::New();
resampler->AddObserver( itk::ProgressEvent(), observer );
// Software Guide : BeginLatex
//
// At this point we are ready to use the transform as part of the resample
// filter. We trigger the execution of the pipeline by invoking
// \code{Update()} on the last filter of the pipeline, in this case writer.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
resampler->SetTransform( bsplineTransform );
try
{
movingWriter->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
// Software Guide : EndCodeSnippet
typedef itk::Vector< float, ImageDimension > VectorType;
typedef itk::Image< VectorType, ImageDimension > DisplacementFieldType;
DisplacementFieldType::Pointer field = DisplacementFieldType::New();
field->SetRegions( fixedRegion );
field->SetOrigin( fixedOrigin );
field->SetSpacing( fixedSpacing );
field->SetDirection( fixedDirection );
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 = bsplineTransform->TransformPoint( fixedPoint );
displacement = movingPoint - fixedPoint;
fi.Set( displacement );
++fi;
}
typedef itk::ImageFileWriter< DisplacementFieldType > FieldWriterType;
FieldWriterType::Pointer fieldWriter = FieldWriterType::New();
fieldWriter->SetInput( field );
if( argc >= 6 )
{
fieldWriter->SetFileName( argv[5] );
try
{
fieldWriter->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
}
if( argc >= 7 )
{
fieldWriter->SetFileName( argv[6] );
try
{
typedef itk::TransformFileWriter TransformWriterType;
TransformWriterType::Pointer transformWriter = TransformWriterType::New();
transformWriter->AddTransform( bsplineTransform );
transformWriter->SetFileName( argv[6] );
transformWriter->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
}
return EXIT_SUCCESS;
}