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itkFEMRegistrationFilter.txx
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itkFEMRegistrationFilter.txx
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/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: itkFEMRegistrationFilter.txx
Language: C++
Date: $Date$
Version: $Revision$
Copyright (c) Insight Software Consortium. All rights reserved.
See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for detail.
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.
=========================================================================*/
#ifndef _itkFEMRegistrationFilter_txx_
#define _itkFEMRegistrationFilter_txx_
// disable debug warnings in MS compiler
#ifdef _MSC_VER
#pragma warning(disable: 4786)
#endif
#include "itkFEMRegistrationFilter.h"
#include "itkFEMElements.h"
#include "itkFEMLoadBC.h"
#include "itkImageFileWriter.h"
#include "itkImageFileReader.h"
#include "itkCastImageFilter.h"
#include "itkDiscreteGaussianImageFilter.h"
#include "itkDerivativeImageFilter.h"
#include "itkVectorNeighborhoodOperatorImageFilter.h"
#include "itkNearestNeighborInterpolateImageFunction.h"
#include "itkBSplineInterpolateImageFunction.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkMinimumMaximumImageFilter.h"
#include "itkShiftScaleImageFilter.h"
#include "vnl/algo/vnl_determinant.h"
namespace itk {
namespace fem {
template<class TMovingImage,class TFixedImage>
FEMRegistrationFilter<TMovingImage,TFixedImage>::~FEMRegistrationFilter( )
{
}
template<class TMovingImage,class TFixedImage>
FEMRegistrationFilter<TMovingImage,TFixedImage>::FEMRegistrationFilter( )
{
m_FileCount=0;
m_MinE=0;
m_MinE=vnl_huge_val(m_MinE);
m_CurrentLevel=0;
m_DescentDirection=positive;
m_E.set_size(1);
m_Gamma.set_size(1);
m_Gamma[m_CurrentLevel]=1;
m_Rho.set_size(1);
m_E[0]=1.;
m_Rho[0]=1.;
m_Maxiters.set_size(1);
m_Maxiters[m_CurrentLevel]=1;
m_dT=1;
m_Alpha=1.0;
m_Temp=0.0;
m_MeshPixelsPerElementAtEachResolution.set_size(1);
m_NumberOfIntegrationPoints.set_size(1);
m_NumberOfIntegrationPoints[m_CurrentLevel]=4;
m_MetricWidth.set_size(1);
m_MetricWidth[m_CurrentLevel]=3;
m_DoLineSearchOnImageEnergy=1;
m_LineSearchMaximumIterations=100;
m_UseMassMatrix=true;
m_NumLevels=1;
m_MaxLevel=1;
m_MeshStep=2;
m_MeshLevels=1;
m_DoMultiRes=false;
m_UseLandmarks=false;
m_MinJacobian=1.0;
// m_FixedPyramid=NULL;
// m_MovingPyramid=NULL;
m_TotalIterations=0;
m_ReadMeshFile=false;
for (unsigned int i=0; i < ImageDimension; i++)
{
m_ImageScaling[i]=1;
m_CurrentImageScaling[i]=1;
m_FullImageSize[i]=0;
m_ImageOrigin[i]=0;
}
m_FloatImage=NULL;
m_Field=NULL;
m_TotalField=NULL;
m_WarpedImage=NULL;
// Setup the default interpolator
typename DefaultInterpolatorType::Pointer interp =
DefaultInterpolatorType::New();
m_Interpolator =
static_cast<InterpolatorType*>( interp.GetPointer() );
m_Interpolator->SetInputImage(m_Field);
m_Load = 0;
}
template<class TMovingImage,class TFixedImage>
void FEMRegistrationFilter<TMovingImage,TFixedImage>::RunRegistration(void)
{
// Solve the system in time
if (!m_DoMultiRes && m_Maxiters[m_CurrentLevel] > 0)
{
SolverType mySolver;
mySolver.SetDeltatT(m_dT);
mySolver.SetRho(m_Rho[m_CurrentLevel]);
mySolver.SetAlpha(m_Alpha);
CreateMesh(static_cast<double>(m_MeshPixelsPerElementAtEachResolution[m_CurrentLevel]),
mySolver,m_FullImageSize);
ApplyLoads(mySolver,m_FullImageSize);
const unsigned int ndofpernode=(m_Element)->GetNumberOfDegreesOfFreedomPerNode();
const unsigned int numnodesperelt=(m_Element)->GetNumberOfNodes()+1;
const unsigned int ndof=mySolver.GetNumberOfDegreesOfFreedom();
unsigned int nzelts;
if (!m_ReadMeshFile)
{
nzelts=numnodesperelt*ndofpernode*ndof;
}
else
{
nzelts=((2*numnodesperelt*ndofpernode*ndof > 25*ndof) ? 2*numnodesperelt*ndofpernode*ndof : 25*ndof);
}
LinearSystemWrapperItpack itpackWrapper;
itpackWrapper.SetMaximumNonZeroValuesInMatrix(nzelts);
itpackWrapper.SetMaximumNumberIterations(2*mySolver.GetNumberOfDegreesOfFreedom());
itpackWrapper.SetTolerance(1.e-1);
// itpackWrapper.JacobianSemiIterative();
itpackWrapper.JacobianConjugateGradient();
mySolver.SetLinearSystemWrapper(&itpackWrapper);
if( m_UseMassMatrix )
{
mySolver.AssembleKandM();
}
else
{
mySolver.InitializeForSolution();
mySolver.AssembleK();
}
IterativeSolve(mySolver);
// InterpolateVectorField(&mySolver);
}
else //if (m_Maxiters[m_CurrentLevel] > 0)
{
MultiResSolve();
}
if (m_Field)
{
if (m_TotalField) m_Field=m_TotalField;
this->ComputeJacobian(1.,m_Field,2.5);
WarpImage(m_OriginalMovingImage);
}
return;
}
template<class TMovingImage,class TFixedImage>
void FEMRegistrationFilter<TMovingImage,TFixedImage>::SetMovingImage(MovingImageType* R)
{
m_MovingImage=R;
if (m_TotalIterations == 0)
{
m_OriginalMovingImage=R;
}
}
template<class TMovingImage,class TFixedImage>
void FEMRegistrationFilter<TMovingImage,TFixedImage>::SetFixedImage(FixedImageType* T)
{
m_FixedImage=T;
m_FullImageSize = m_FixedImage->GetLargestPossibleRegion().GetSize();
VectorType disp;
for (unsigned int i=0; i < ImageDimension; i++)
{
disp[i]=0.0;
m_ImageOrigin[i]=0;
}
m_CurrentLevelImageSize=m_FullImageSize;
}
template<class TMovingImage,class TFixedImage>
void FEMRegistrationFilter<TMovingImage,TFixedImage>::ChooseMetric(float which)
{
// Choose the similarity metric
// for using the imagetoimagemetricloads
#ifdef USEIMAGEMETRIC
typedef itk::MeanSquaresImageToImageMetric<FixedImageType,MovingImageType> MetricType0;
typedef itk::NormalizedCorrelationImageToImageMetric<FixedImageType,MovingImageType> MetricType1;
typedef itk::PatternIntensityImageToImageMetric<FixedImageType,MovingImageType> MetricType2;
typedef itk::MutualInformationImageToImageMetric<FixedImageType,MovingImageType> MetricType3;
typedef itk::MattesMutualInformationImageToImageMetric<FixedImageType,MovingImageType> MetricType4;
// typedef itk::DemonsImageToImageMetric<FixedImageType,MovingImageType> MetricType5;
typedef itk::MeanSquaresImageToImageMetric<FixedImageType,MovingImageType> MetricType5;
float m_Temp=1.0;
MetricType3::Pointer m=MetricType3::New();
MetricType4::Pointer ma=MetricType4::New();
unsigned int whichmetric=(unsigned int) which;
m_WhichMetric=which;
unsigned int nsp=1;
for (int i=0; i<ImageDimension; i++)
{
nsp*=m_MetricWidth[m_CurrentLevel];
}
if (whichmetric == 3 )
{
m->SetNumberOfSpatialSamples(nsp/2);
m->SetFixedImageStandardDeviation(0.4);
m->SetMovingImageStandardDeviation(0.4);
}
else if (whichmetric == 4 )
{
ma->SetNumberOfHistogramBins( 10 );
ma->SetNumberOfSpatialSamples( nsp/2 );
}
switch (whichmetric)
{
case 0:
m_Metric=MetricType0::New();
m_Metric->SetScaleGradient(m_Temp); // this is the default(?)
//p=MetricType0::New();
//m_Function->SetInverseMetric(p);
break;
case 1:
m_Metric=MetricType1::New();
m_Metric->SetScaleGradient(m_Temp);
break;
case 2:
m_Metric=MetricType2::New();
m_Metric->SetScaleGradient(m_Temp);
break;
case 3:
m_Metric=m;
m_Metric->SetScaleGradient(m_Temp);
break;
case 4:
m_Metric=ma;
m_Metric->SetScaleGradient(m_Temp);
break;
case 5:
m_Metric=MetricType5::New();
m_Metric->SetScaleGradient(m_Temp);
break;
default:
m_Metric=MetricType0::New();
m_Metric->SetScaleGradient(m_Temp);
}
#else
typedef itk::MeanSquareRegistrationFunction<FixedImageType,MovingImageType,FieldType> MetricType0;
typedef itk::NCCRegistrationFunction<FixedImageType,MovingImageType,FieldType> MetricType1;
typedef itk::NCCRegistrationFunction<FixedImageType,MovingImageType,FieldType> MetricType2;
typedef itk::MIRegistrationFunction<FixedImageType,MovingImageType,FieldType> MetricType3;
typedef itk::MIRegistrationFunction<FixedImageType,MovingImageType,FieldType> MetricType4;
typedef itk::DemonsRegistrationFunction<FixedImageType,MovingImageType,FieldType> MetricType5;
typename MetricType3::Pointer m=MetricType3::New();
typename MetricType4::Pointer ma=MetricType4::New();
unsigned int whichmetric=(unsigned int) which;
m_WhichMetric=(unsigned int)which;
switch (whichmetric)
{
case 0:
m_Metric=MetricType0::New();
break;
case 1:
m_Metric=MetricType1::New();
break;
case 2:
m_Metric=MetricType2::New();
break;
case 3:
m_Metric=m;
break;
case 4:
m_Metric=ma;
break;
case 5:
m_Metric=MetricType5::New();
break;
default:
m_Metric=MetricType0::New();
}
m_Metric->SetGradientStep( m_Gamma[m_CurrentLevel] );
if ( m_Temp == 1.0 ) m_Metric->SetNormalizeGradient(true);
else m_Metric->SetNormalizeGradient(false);
#endif
}
template<class TMovingImage,class TFixedImage>
bool FEMRegistrationFilter<TMovingImage,TFixedImage>::ReadConfigFile(const char* fname)
// Reads the parameters necessary to configure the example & returns
// false if no configuration file is found
{
std::ifstream f;
char buffer[4096] = {'\0'};
Float fbuf = 0.0;
unsigned int ibuf = 0;
unsigned int jj;
std::cout << "Reading config file..." << fname << std::endl;
f.open(fname);
if (f)
{
this->DoMultiRes(true);
FEMLightObject::SkipWhiteSpace(f);
f >> ibuf;
this->m_NumLevels = (unsigned int) ibuf;
FEMLightObject::SkipWhiteSpace(f);
f >> ibuf;
this->m_MaxLevel = ibuf;
// get the initial scales for the pyramid
FEMLightObject::SkipWhiteSpace(f);
for (jj=0; jj<ImageDimension; jj++)
{
f >> ibuf;
m_ImageScaling[jj] = ibuf;
}
this->m_MeshPixelsPerElementAtEachResolution.set_size(m_NumLevels);
FEMLightObject::SkipWhiteSpace(f);
for (jj=0; jj<this->m_NumLevels; jj++)
{
f >> ibuf;
this->m_MeshPixelsPerElementAtEachResolution(jj) = ibuf;
}
FEMLightObject::SkipWhiteSpace(f);
this->m_E.set_size(m_NumLevels);
for (jj=0; jj<this->m_NumLevels; jj++)
{
f >> fbuf;
this->SetElasticity(fbuf,jj);
}
FEMLightObject::SkipWhiteSpace(f);
this->m_Rho.set_size(m_NumLevels);
for (jj=0; jj<this->m_NumLevels; jj++)
{
f >> fbuf;
this->SetRho(fbuf,jj);
}
FEMLightObject::SkipWhiteSpace(f);
this->m_Gamma.set_size(m_NumLevels);
for (jj=0; jj<this->m_NumLevels; jj++)
{
f >> fbuf;
this->SetGamma(fbuf,jj);
}
FEMLightObject::SkipWhiteSpace(f);
this->m_NumberOfIntegrationPoints.set_size(m_NumLevels);
for(jj=0; jj< m_NumLevels; jj++)
{
f >> ibuf;
this->SetNumberOfIntegrationPoints(ibuf,jj);
}
FEMLightObject::SkipWhiteSpace(f);
this->m_MetricWidth.set_size(m_NumLevels);
for(jj=0; jj< m_NumLevels; jj++)
{
f >> ibuf;
this->SetWidthOfMetricRegion(ibuf,jj);
}
FEMLightObject::SkipWhiteSpace(f);
this->m_Maxiters.set_size(m_NumLevels);
for (jj=0; jj<this->m_NumLevels; jj++)
{
f >> ibuf;
this->SetMaximumIterations(ibuf,jj);
}
FEMLightObject::SkipWhiteSpace(f);
float fbuf2=1.0;
f >> fbuf;
f >> fbuf2;
m_Temp=fbuf2;
this->ChooseMetric(fbuf);
FEMLightObject::SkipWhiteSpace(f);
f >> fbuf;
this->m_Alpha=fbuf;
FEMLightObject::SkipWhiteSpace(f);
f >> ibuf;
if (ibuf == 0)
{
this->SetDescentDirectionMinimize();
}
else
{
this->SetDescentDirectionMaximize();
}
FEMLightObject::SkipWhiteSpace(f);
f >> ibuf;
this->DoLineSearch(ibuf);
FEMLightObject::SkipWhiteSpace(f);
f >> fbuf;
this->SetTimeStep(fbuf);
FEMLightObject::SkipWhiteSpace(f);
f >> fbuf;
this->SetEnergyReductionFactor(fbuf);
FEMLightObject::SkipWhiteSpace(f);
f >> ibuf;
m_EmployRegridding = (unsigned int) ibuf;
FEMLightObject::SkipWhiteSpace(f);
f >> ibuf;
this->m_FullImageSize[0] = ibuf;
FEMLightObject::SkipWhiteSpace(f);
f >> ibuf;
this->m_FullImageSize[1] = ibuf;
FEMLightObject::SkipWhiteSpace(f);
f >> ibuf;
unsigned int dim=2;
if (ibuf > 0) dim=3;
if (dim == 3) this->m_FullImageSize[2] = ibuf;
FEMLightObject::SkipWhiteSpace(f);
f >> buffer;
this->SetMovingFile(buffer);
FEMLightObject::SkipWhiteSpace(f);
f >> buffer;
this->SetFixedFile(buffer);
FEMLightObject::SkipWhiteSpace(f);
f >> ibuf;
FEMLightObject::SkipWhiteSpace(f);
f >> buffer;
if (ibuf == 1)
{
this->UseLandmarks(true);
this->SetLandmarkFile(buffer);
}
else
{
this->UseLandmarks(false);
}
FEMLightObject::SkipWhiteSpace(f);
f >> buffer;
this->SetResultsFile(buffer);
FEMLightObject::SkipWhiteSpace(f);
f >> ibuf;
FEMLightObject::SkipWhiteSpace(f);
f >> buffer;
if (ibuf == 1)
{
this->SetWriteDisplacements(true);
this->SetDisplacementsFile(buffer);
}
else
{
this->SetWriteDisplacements(false);
}
FEMLightObject::SkipWhiteSpace(f);
f >> ibuf;
FEMLightObject::SkipWhiteSpace(f);
f >> buffer;
if (ibuf == 1)
{
this->m_ReadMeshFile=true;
this->m_MeshFileName=buffer;
}
else
{
this->m_ReadMeshFile=false;
}
f.close();
std::cout << "Example configured. E " << m_E << " rho " << m_Rho << std::endl;
return true;
}
else
{
std::cout << "No configuration file specified...quitting.\n";
return false;
}
}
template<class TMovingImage,class TFixedImage>
int FEMRegistrationFilter<TMovingImage,TFixedImage>::WriteDisplacementFieldMultiComponent()
// Outputs the displacement field as a multicomponent image XYZXYZXYZ...
{
std::cout << "Writing multi-component displacement vector field...";
typedef itk::ImageFileWriter< FieldType > FieldWriterType;
typename FieldWriterType::Pointer fieldWriter = FieldWriterType::New();
fieldWriter->SetInput( m_Field );
fieldWriter->SetFileName("VectorDeformationField.mhd");
try
{
fieldWriter->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Error while saving the displacement vector field" << std::endl;
std::cerr << excp << std::endl;
}
std::cout << "done" << std::endl;
return 0;
}
template<class TMovingImage,class TFixedImage>
int FEMRegistrationFilter<TMovingImage,TFixedImage>::WriteDisplacementField(unsigned int index)
// Outputs the displacement field for the index provided (0=x,1=y,2=z)
{
// Initialize the Moving to the displacement field
typename IndexSelectCasterType::Pointer fieldCaster = IndexSelectCasterType::New();
fieldCaster->SetInput( m_Field );
fieldCaster->SetIndex( index );
// Define the output of the Moving
typename FloatImageType::Pointer fieldImage = FloatImageType::New();
fieldCaster->Update();
fieldImage = fieldCaster->GetOutput();
// Set up the output filename
std::string outfile=m_DisplacementsFileName+static_cast<char>('x'+index)+std::string("vec.hdr");
std::cout << "Writing displacements to " << outfile;
typedef typename FloatImageType::PixelType FType;
typedef ImageFileWriter<FloatImageType> WriterType;
typename WriterType::Pointer writer = WriterType::New();
writer->SetInput(fieldImage);
writer->SetFileName(outfile.c_str());
writer->Write();
std::cout << " ...done" << std::endl;
return 0;
}
template<class TMovingImage,class TFixedImage>
void FEMRegistrationFilter<TMovingImage,TFixedImage>::WarpImage( const MovingImageType * ImageToWarp)
{
// -------------------------------------------------------
std::cout << "Warping image" << std::endl;
{
typename WarperType::Pointer warper = WarperType::New();
typedef typename WarperType::CoordRepType WarperCoordRepType;
typedef itk::NearestNeighborInterpolateImageFunction<MovingImageType,WarperCoordRepType>
InterpolatorType0;
typedef itk::LinearInterpolateImageFunction<MovingImageType,WarperCoordRepType>
InterpolatorType1;
typedef itk::BSplineInterpolateImageFunction<MovingImageType,WarperCoordRepType>
InterpolatorType2;
typename InterpolatorType1::Pointer interpolator = InterpolatorType1::New();
warper = WarperType::New();
warper->SetInput( ImageToWarp );
warper->SetDeformationField( m_Field );
warper->SetInterpolator( interpolator );
warper->SetOutputOrigin( m_FixedImage->GetOrigin() );
warper->SetOutputSpacing( m_FixedImage->GetSpacing() );
warper->SetOutputDirection( m_FixedImage->GetDirection() );
typename FixedImageType::PixelType padValue = 0;
warper->SetEdgePaddingValue( padValue );
warper->Update();
m_WarpedImage=warper->GetOutput();
}
}
template<class TMovingImage,class TFixedImage>
void FEMRegistrationFilter<TMovingImage,TFixedImage>::CreateMesh(double PixelsPerElement,
Solver& mySolver, ImageSizeType imagesize)
{
vnl_vector<double> MeshOriginV; MeshOriginV.set_size(ImageDimension);
vnl_vector<double> MeshSizeV; MeshSizeV.set_size(ImageDimension);
vnl_vector<double> ImageSizeV; ImageSizeV.set_size(ImageDimension);
vnl_vector<double> ElementsPerDim; ElementsPerDim.set_size(ImageDimension);
for (unsigned int i=0; i<ImageDimension; i++)
{
MeshSizeV[i]=(double)imagesize[i]; // FIX ME make more general
MeshOriginV[i]=(double)m_ImageOrigin[i];// FIX ME make more general
ImageSizeV[i]=(double) imagesize[i]+1;//to make sure all elts are inside the interpolation mesh
ElementsPerDim[i]=MeshSizeV[i]/PixelsPerElement;
}
std::cout << " ElementsPerDim " << ElementsPerDim << std::endl;
if (m_ReadMeshFile)
{
std::ifstream meshstream;
meshstream.open(m_MeshFileName.c_str());
if (!meshstream)
{
std::cout<<"File "<<m_MeshFileName<<" not found!\n";
return;
}
mySolver.Read(meshstream);
mySolver.GenerateGFN();
itk::fem::MaterialLinearElasticity::Pointer m=dynamic_cast<MaterialLinearElasticity*>(mySolver.mat.Find(0));
if (m)
{
m->E=this->GetElasticity(m_CurrentLevel); // Young modulus -- used in the membrane ///
}
// now scale the mesh to the current scale
Element::VectorType coord;
Node::ArrayType* nodes = &(mySolver.node);
Node::ArrayType::iterator node=nodes->begin();
m_Element=( *((*node)->m_elements.begin()));
for( node=nodes->begin(); node!=nodes->end(); node++)
{
coord=(*node)->GetCoordinates();
for (unsigned int ii=0; ii < ImageDimension; ii++)
{
coord[ii] = coord[ii]/(float)m_CurrentImageScaling[ii];
}
(*node)->SetCoordinates(coord);
}
}
else if (ImageDimension == 2 && dynamic_cast<Element2DC0LinearQuadrilateral*>(m_Element) != NULL)
{
m_Material->E=this->GetElasticity(m_CurrentLevel);
Generate2DRectilinearMesh(m_Element,mySolver,MeshOriginV,MeshSizeV,ElementsPerDim);
mySolver.GenerateGFN();
std::cout << " init interpolation grid : im sz " << ImageSizeV << " MeshSize " << MeshSizeV << std::endl;
mySolver.InitializeInterpolationGrid(ImageSizeV,MeshOriginV,MeshSizeV);
std::cout << " done initializing interpolation grid " << std::endl;
}
else if ( ImageDimension == 3 && dynamic_cast<Element3DC0LinearHexahedron*>(m_Element) != NULL)
{
m_Material->E=this->GetElasticity(m_CurrentLevel);
std::cout << " generating regular mesh " << std::endl;
Generate3DRectilinearMesh(m_Element,mySolver,MeshOriginV,MeshSizeV,ElementsPerDim);
mySolver.GenerateGFN();
std::cout << " generating regular mesh done " << std::endl;
// the global to local transf is too slow so don't do it.
std::cout << " DO NOT init interpolation grid : im sz " << ImageSizeV << " MeshSize " << MeshSizeV << std::endl;
//mySolver.InitializeInterpolationGrid(ImageSizeV,MeshOriginV,MeshSizeV);
//std::cout << " done initializing interpolation grid " << std::endl;
}
else
{
FEMException e(__FILE__, __LINE__);
e.SetDescription("CreateMesh - wrong image or element type");
e.SetLocation(ITK_LOCATION);
throw e;
}
}
template<class TMovingImage,class TFixedImage>
void FEMRegistrationFilter<TMovingImage,TFixedImage>
::ApplyImageLoads(SolverType& mySolver, TMovingImage* movingimg, TFixedImage* fixedimg )
{
m_Load=FEMRegistrationFilter<TMovingImage,TFixedImage>::ImageMetricLoadType::New();
m_Load->SetMovingImage(movingimg);
m_Load->SetFixedImage(fixedimg);
if (!m_Field) this->InitializeField();
#ifndef USEIMAGEMETRIC
m_Load->SetDeformationField(this->GetDeformationField());
#endif
m_Load->SetMetric(m_Metric);
m_Load->InitializeMetric();
m_Load->SetTemp(m_Temp);
m_Load->SetGamma(m_Gamma[m_CurrentLevel]);
ImageSizeType r;
for (unsigned int dd=0; dd<ImageDimension; dd++)
{
r[dd]=m_MetricWidth[m_CurrentLevel];
}
m_Load->SetMetricRadius(r);
m_Load->SetNumberOfIntegrationPoints(m_NumberOfIntegrationPoints[m_CurrentLevel]);
m_Load->GN=mySolver.load.size()+1; //NOTE SETTING GN FOR FIND LATER
m_Load->SetSign((Float)m_DescentDirection);
mySolver.load.push_back( FEMP<Load>(&*m_Load) );
m_Load=dynamic_cast<typename FEMRegistrationFilter<TMovingImage,TFixedImage>::ImageMetricLoadType*>
(&*mySolver.load.Find(mySolver.load.size()));
}
template<class TMovingImage,class TFixedImage>
void FEMRegistrationFilter<TMovingImage,TFixedImage>::ApplyLoads(SolverType& mySolver,ImageSizeType ImgSz, double* scaling)
{
//
// Apply the boundary conditions. We pin the image corners.
// First compute which elements these will be.
///
std::cout << " applying loads " << std::endl;
vnl_vector<Float> pd; pd.set_size(ImageDimension);
vnl_vector<Float> pu; pu.set_size(ImageDimension);
if (m_UseLandmarks)
{
LoadArray::iterator loaditerator;
LoadLandmark::Pointer l3;
if ( this->m_LandmarkArray.empty() )
{
// Landmark loads
std::ifstream f;
std::cout << m_LandmarkFileName << std::endl;
f.open(m_LandmarkFileName.c_str());
if (f)
{
std::cout << "Try loading landmarks..." << std::endl;
std::cout << "Try loading landmarks..." << std::endl;
try
{
mySolver.load.clear(); // NOTE: CLEARING ALL LOADS - LMS MUST BE APPLIED FIRST
mySolver.Read(f);
}
catch (itk::ExceptionObject &err)
{
std::cerr << "Exception: cannot read load landmark FEMRegistrationFilter.txx " << err;
}
f.close();
m_LandmarkArray.resize(mySolver.load.size());
unsigned int ct=0;
for(loaditerator=mySolver.load.begin(); loaditerator!=mySolver.load.end(); loaditerator++)
{
if ((l3=dynamic_cast<LoadLandmark*>( &(*(*loaditerator)) )) != 0 )
{
LoadLandmark::Pointer l4=dynamic_cast<LoadLandmark*>(l3->Clone());
m_LandmarkArray[ct]=l4;
ct++;
}
}
mySolver.load.clear(); // NOTE: CLEARING ALL LOADS - LMS MUST BE APPLIED FIRST
}
else
{
std::cout << "no landmark file specified." << std::endl;
}
}
// now scale the landmarks
std::cout << " num of LM loads " << m_LandmarkArray.size() << std::endl;
/*
* Step over all the loads again to scale them by the global landmark weight.
*/
if ( !m_LandmarkArray.empty())
{
for(unsigned int lmind=0; lmind<m_LandmarkArray.size(); lmind++)
{
m_LandmarkArray[lmind]->el[0]=NULL;
bool isFound=false;
std::cout << " prescale Pt " << m_LandmarkArray[lmind]->GetTarget() << std::endl;
if (scaling)
{
m_LandmarkArray[lmind]->ScalePointAndForce(scaling,m_EnergyReductionFactor);
std::cout << " postscale Pt " << m_LandmarkArray[lmind]->GetTarget() << " scale " << scaling[0] << std::endl;
}
pu=m_LandmarkArray[lmind]->GetSource();
pd=m_LandmarkArray[lmind]->GetPoint();
for (Element::ArrayType::const_iterator n = mySolver.el.begin();
n!=mySolver.el.end() && !isFound; n++)
{
if ( (*n)->GetLocalFromGlobalCoordinates(pu, pd ) )
{
isFound=true;
m_LandmarkArray[lmind]->SetPoint(pd);
// std::cout << " load local pt " << m_LandmarkArray[lmind]->GetPoint() << std::endl;
m_LandmarkArray[lmind]->el[0]=( ( &**n ) );
}
}
m_LandmarkArray[lmind]->GN=lmind;
LoadLandmark::Pointer l5=(dynamic_cast<LoadLandmark::Pointer>(m_LandmarkArray[lmind]->Clone()));
mySolver.load.push_back(FEMP<Load>(l5));
}
}
std::cout << " landmarks done" << std::endl;
}
// now apply the BC loads
LoadBC::Pointer l1;
//Pin one corner of image
unsigned int CornerCounter,ii,EdgeCounter=0;
Node::ArrayType* nodes = &(mySolver.node);
Element::VectorType coord;
Node::ArrayType::iterator node=nodes->begin();
bool EdgeFound;
unsigned int nodect=0;
while( node!=nodes->end() && EdgeCounter < ImageDimension )
{
coord=(*node)->GetCoordinates();
CornerCounter=0;
for (ii=0; ii < ImageDimension; ii++)
{
if (coord[ii] == m_ImageOrigin[ii] || coord[ii] == ImgSz[ii]-1 ) CornerCounter++;
}
if (CornerCounter == ImageDimension) // the node is located at a true corner
{
unsigned int ndofpernode=(*((*node)->m_elements.begin()))->GetNumberOfDegreesOfFreedomPerNode();
unsigned int numnodesperelt=(*((*node)->m_elements.begin()))->GetNumberOfNodes();
unsigned int whichnode;
unsigned int maxnode=numnodesperelt-1;
typedef typename Node::SetOfElements NodeEltSetType;
for( NodeEltSetType::iterator elt=(*node)->m_elements.begin();
elt!=(*node)->m_elements.end(); elt++)
{
for (whichnode=0; whichnode<=maxnode; whichnode++)
{
coord=(*elt)->GetNode(whichnode)->GetCoordinates();
CornerCounter=0;
for (ii=0; ii < ImageDimension; ii++)
{
if (coord[ii] == m_ImageOrigin[ii] || coord[ii] == ImgSz[ii]-1 )
{
CornerCounter++;
}
}
if (CornerCounter == ImageDimension - 1)
{
EdgeFound=true;
}
else
{
EdgeFound=false;
}
if (EdgeFound)
{
for (unsigned int jj=0; jj<ndofpernode; jj++)
{
std::cout << " which node " << whichnode << std::endl;
std::cout << " edge coord " << coord << std::endl;
l1=LoadBC::New();
// now we get the element from the node -- we assume we need fix the dof only once
// even if more than one element shares it.
l1->m_element= (*elt); // Fixed bug TS 1/17/03 ( *((*node)->m_elements.begin()));
//l1->m_element= ( *((*node)->m_elements[ect-1]));
unsigned int localdof=whichnode*ndofpernode+jj;
l1->m_dof=localdof;
l1->m_value=vnl_vector<double>(1,0.0);
mySolver.load.push_back( FEMP<Load>(&*l1) );
}
EdgeCounter++;
}
}
}//end elt loop
}
node++;
nodect++;
std::cout << " node " << nodect << std::endl;
}//
return;
}
template<class TMovingImage,class TFixedImage>
void FEMRegistrationFilter<TMovingImage,TFixedImage>::IterativeSolve(SolverType& mySolver)
{
if (!m_Load)
{
std::cout << " m_Load not initialized " << std::endl;
return;
}
bool Done=false;
unsigned int iters=0;
m_MinE=10.e99;
Float deltE=0;
while ( !Done && iters < m_Maxiters[m_CurrentLevel] )
{
const Float lastdeltE=deltE;
const unsigned int DLS=m_DoLineSearchOnImageEnergy;
// Reset the variational similarity term to zero.
Float LastE=m_Load->GetCurrentEnergy();
m_Load->SetCurrentEnergy(0.0);
m_Load->InitializeMetric();
if (!m_Field)
{
std::cout << " Big Error -- Field is NULL ";
}
// Assemble the master force vector (from the applied loads)
// if (iters == 1) // for testing
if( m_UseMassMatrix )
{
mySolver.AssembleFforTimeStep();
}
else
{
mySolver.AssembleF();
}
m_Load->PrintCurrentEnergy();
// Solve the system of equations for displacements (u=K^-1*F)
mySolver.Solve();
//mySolver.PrintDisplacements(0);
// Float ImageSimilarity=0.0;
//#ifdef USEIMAGEMETRIC