[Insight-users] Re: some questions on BSpline Registration
he smth
kingaza at gmail.com
Sun Jul 18 21:35:36 EDT 2004
hi Luis and all,
this is the code of BSplineRegistration using DICOM files
I has set all the argv parameters for debug
I am still confused whith the origin and spacing
thanks for any help
btw, it seems not support long file name. so I set fixedImage,
movingImage as Image1 and Image2.
/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: $RCSfile: DeformableRegistration4.cxx,v $
Language: C++
Date: $Date: 2004/05/22 01:11:13 $
Version: $Revision: 1.7 $
Copyright (c) Insight Software Consortium. All rights reserved.
See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
// Software Guide : BeginLatex
//
// This example illustrates the use of the \doxygen{BSplineDeformableTransform}
// 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::BSplineDeformableTransform}
// \index{itk::BSplineDeformableTransform!DeformableRegistration}
// \index{itk::LBFGSOptimizer}
//
//
// Software Guide : EndLatex
#include "itkImageRegistrationMethod.h"
#include "itkMeanSquaresImageToImageMetric.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkImage.h"
#include "itkDICOMImageIO2Factory.h"
#include "itkTimeProbesCollectorBase.h"
// Software Guide : BeginLatex
//
// The following are the most relevant headers to this example.
//
// \index{itk::BSplineDeformableTransform!header}
// \index{itk::LBFGSOptimizer!header}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
#include "itkBSplineDeformableTransform.h"
#include "itkLBFGSOptimizer.h"
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The parameter space of the \code{BSplineDeformableTransform} 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::BSplineDeformableTransform!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 1;
}
*/
const unsigned int ImageDimension = 2;
typedef short PixelType;
typedef itk::Image< PixelType, ImageDimension > FixedImageType;
typedef itk::Image< PixelType, ImageDimension > MovingImageType;
// Software Guide : BeginLatex
//
// We instantiate now the type of the \code{BSplineDeformableTransform} using
// as template parameters the type for coordinates representation, the
// dimension of the space, and the order of the BSpline.
//
// \index{BSplineDeformableTransform|New}
// \index{BSplineDeformableTransform|Instantiation}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
const unsigned int SpaceDimension = ImageDimension;
const unsigned int SplineOrder = 3;
typedef double CoordinateRepType;
typedef itk::BSplineDeformableTransform<
CoordinateRepType,
2,
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();
itk::DICOMImageIO2Factory::RegisterOneFactory();
fixedImageReader->SetFileName( "Image1.dcm" );
movingImageReader->SetFileName( "Image2.dcm" );
FixedImageType::ConstPointer fixedImage = fixedImageReader->GetOutput();
MovingImageType::Pointer movingImage = movingImageReader->GetOutput();
registration->SetFixedImage( fixedImage );
registration->SetMovingImage( movingImageReader->GetOutput() );
fixedImageReader->Update();
FixedImageType::RegionType fixedRegion = fixedImage->GetBufferedRegion();
registration->SetFixedImageRegion( fixedRegion );
movingImageReader->Update();
std::cout << fixedImage->GetBufferedRegion()<<std::endl;
std::cout << movingImage->GetBufferedRegion()<<std::endl;
// Software Guide : BeginLatex
//
// Here we define the parameters of the BSplineDeformableTransform grid. We
// arbitrarily decide to use a grid with $5 \times 5$ nodes within
the image.
// The reader should note that the BSpline computation requires a
// finite support region ( 1 grid node at the lower borders and 2
// grid nodes at upper borders). Therefore in this example, we set
// the grid size to be $8 \times 8$ and place the grid origin such that
// grid node (1,1) coinicides with the first pixel in the fixed image.
//
// \index{BSplineDeformableTransform}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
typedef TransformType::RegionType RegionType;
RegionType bsplineRegion;
RegionType::SizeType gridSizeOnImage;
RegionType::SizeType gridBorderSize;
RegionType::SizeType totalGridSize;
gridSizeOnImage.Fill( 5 );
gridBorderSize.Fill( 3 ); // Border for spline order = 3 ( 1
lower, 2 upper )
totalGridSize = gridSizeOnImage + gridBorderSize;
std::cout << "totalGridSize: " << totalGridSize << std::endl;
bsplineRegion.SetSize( totalGridSize );
typedef TransformType::SpacingType SpacingType;
SpacingType spacing =
fixedImage->GetSpacing();//spacing[0]=1.5625;spacing[1]=1.5625;
std::cout << "spacing: "<< spacing<<std::endl;
spacing.Fill(1);
// fixedImage->SetSpacing(spacing);
// movingImage->SetSpacing(spacing);
typedef TransformType::OriginType OriginType;
OriginType origin =
fixedImage->GetOrigin();//origin[0]=-9.0569601058959961;origin[1]=-191.00799560546875;
std::cout << "origin: "<< origin <<std::endl;
origin.Fill(0);
// fixedImage->SetOrigin(origin);
// movingImage->SetOrigin(origin);
FixedImageType::SizeType fixedImageSize = fixedRegion.GetSize();
for(unsigned int r=0; r<ImageDimension; r++)
{
spacing[r] *= floor( static_cast<double>(fixedImageSize[r] - 1) /
static_cast<double>(gridSizeOnImage[r] - 1) );
origin[r] -= spacing[r];
}
transform->SetGridSpacing( spacing );
transform->SetGridOrigin( origin );
transform->SetGridRegion( bsplineRegion );
typedef TransformType::ParametersType ParametersType;
const unsigned int numberOfParameters =
transform->GetNumberOfParameters();
std::cout << "numberOfParameters:" << numberOfParameters << std::endl;
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 );
//I think it is too big to waste time
optimizer->SetMaximumNumberOfFunctionEvaluations( 1000 );
// Software Guide : EndCodeSnippet
// Add a time probe
itk::TimeProbesCollectorBase collector;
std::cout << std::endl << "Starting Registration" << std::endl;
try
{
collector.Start( "Registration" );
registration->StartRegistration();
collector.Stop( "Registration" );
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return -1;
}
OptimizerType::ParametersType finalParameters =
registration->GetLastTransformParameters();
std::cout << "Last Transform Parameters" << std::endl;
std::cout << finalParameters << std::endl;
// Report the time taken by the registration
collector.Report();
// 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() );
// typedef TransformType::SpacingType SpacingType;
SpacingType spacing1 = fixedImage->GetSpacing(); //not used
// spacing1.Fill(1);
// typedef TransformType::OriginType OriginType;
OriginType origin1 = fixedImage->GetOrigin(); //not used
// origin1.Fill(0);
// resample->SetOutputOrigin( origin1 );
// resample->SetOutputSpacing( spacing1 );
resample->SetOutputOrigin( fixedImage->GetOrigin() );
resample->SetOutputSpacing( fixedImage->GetSpacing() );
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( "output.png" );
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 -1;
}
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( 1 )
{
difference->SetInput1( fixedImageReader->GetOutput() );
difference->SetInput2( resample->GetOutput() );
writer2->SetFileName( "Diff_fixed_resampled.png" );
try
{
writer2->Update();
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return -1;
}
}
// Compute the difference image between the
// fixed and moving image before registration.
if( 1)
{
writer2->SetFileName( "Diff_fixed_moving.png" );
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 -1;
}
}
// Generate the explicit deformation field resulting from
// the registration.
typedef itk::Vector< float, ImageDimension > VectorType;
typedef itk::Image< VectorType, ImageDimension > DeformationFieldType;
DeformationFieldType::Pointer field = DeformationFieldType::New();
field->SetRegions( fixedRegion );
field->SetOrigin( fixedImage->GetOrigin() );
field->SetSpacing( fixedImage->GetSpacing() );
std::cout << "fixedRegion " << fixedRegion << std::endl;
std::cout << "fixedImage->GetOrigin(): " << fixedImage->GetOrigin()<<
std::endl;
std::cout << "fixedImage->GetSpacing(): " << fixedImage->GetSpacing()
<< std::endl;
// origin1.Fill(0);
// spacing1.Fill(1);
// field->SetOrigin(origin);
// field->SetSpacing(spacing);
field->Allocate();
typedef itk::ImageRegionIterator< DeformationFieldType > FieldIterator;
FieldIterator fi( field, fixedRegion );
fi.GoToBegin();
TransformType::InputPointType fixedPoint;
TransformType::OutputPointType movingPoint;
DeformationFieldType::IndexType index;
VectorType displacement;
int n = 0;
while( ! fi.IsAtEnd() )
{
index = fi.GetIndex();
field->TransformIndexToPhysicalPoint( index, fixedPoint );
movingPoint = transform->TransformPoint( fixedPoint );
displacement[0] = movingPoint[0] - fixedPoint[0];
displacement[1] = movingPoint[1] - fixedPoint[1];
fi.Set( displacement );
++fi;
n++;
}
std::cout << "Iterator Number: " << n << std::endl;
typedef itk::ImageFileWriter< DeformationFieldType > FieldWriterType;
FieldWriterType::Pointer fieldWriter = FieldWriterType::New();
fieldWriter->SetInput( field );
if( 1 )
{
fieldWriter->SetFileName( "DeformationField.mhd" );
try
{
fieldWriter->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown " << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
}
return 0;
}
On Sun, 11 Jul 2004 18:21:26 +0800, he smth <kingaza at gmail.com> wrote:
> hi all,
> I have some questions in using DeformableRegistration4.
>
> 1. I run the programe DeformableRegistration4.exe and get the
> deformable field. but then I have a question when viewing the result
> and the two input file(RatLungSlice1.mha and RatLungSlice2.mha) in
> paraview: can the result be accepted? I have save it to a .png file in
> the attachment. I hope that it is my fault and please tell me why.
>
> 2. when I make it in use of dicom file registration, I am confused
> with the parameters of origin and spacing. please tell me how to set
> these values if any successful experience.
>
> 3. what the parameters means? is it the motion field of each grid
> node? I have red the code for itkBSplineDeformableTransform, and found
> that the number of parameters is defined by the size of grid node.
>
> 4. how to define the parameters of the BSplineDeformableTransform
> grid? In this example, we set gridSizeOnImage as 5 and gridBorderSize
> as 3, and so the size of grid node is 8*8.
>
> thanks for any help!
>
>
>
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