bool IbisItkVtkConverter::ConvertVtkImageToItkImage( IbisRGBImageType::Pointer itkOutputImage, vtkImageData *image, vtkMatrix4x4 *imageMatrix)
{
if( !itkOutputImage )
return false;
itkOutputImage->Initialize();
int * dimensions = image->GetDimensions();
IbisItkFloat3ImageType::SizeType size;
IbisItkFloat3ImageType::IndexType start;
IbisItkFloat3ImageType::RegionType region;
const long unsigned int numberOfPixels = dimensions[0] * dimensions[1] * dimensions[2];
for (int i = 0; i < 3; i++)
{
size[i] = dimensions[i];
}
start.Fill(0);
region.SetIndex( start );
region.SetSize( size );
itkOutputImage->SetRegions(region);
itk::Matrix< double, 3,3 > dirCosine;
itk::Vector< double, 3 > origin;
itk::Vector< double, 3 > itkOrigin;
// set direction cosines
vtkMatrix4x4 *tmpMat = vtkMatrix4x4::New();
vtkMatrix4x4::Transpose( imageMatrix, tmpMat );
double step[3], mincStartPoint[3], dirCos[3][3];
for( int i = 0; i < 3; i++ )
{
double row[4];
GetMatRow( tmpMat, i, row );
step[i] = vtkMath::Dot( row, row );
step[i] = sqrt( step[i] );
for( int j = 0; j < 3; j++ )
{
dirCos[i][j] = tmpMat->GetElement( i, j ) / step[i];
dirCosine[j][i] = dirCos[i][j];
}
}
double rotation[3][3];
vtkMath::Transpose3x3( dirCos, rotation );
double row3[4];
GetMatRow( tmpMat, 3, row3 );
vtkMath::LinearSolve3x3( rotation, row3, mincStartPoint );
tmpMat->Delete();
for( int i = 0; i < 3; i++ )
origin[i] = mincStartPoint[i];
itkOrigin = dirCosine * origin;
itkOutputImage->SetSpacing(step);
itkOutputImage->SetOrigin(itkOrigin);
itkOutputImage->SetDirection(dirCosine);
itkOutputImage->Allocate();
RGBPixelType *itkImageBuffer = itkOutputImage->GetBufferPointer();
memcpy(itkImageBuffer, image->GetScalarPointer(), numberOfPixels*sizeof(RGBPixelType));
return true;
}
void CGppe::Predict_CGppe_Laplace(double sigma, MatrixXd t, MatrixXd x, VectorXd idx_global, VectorXd ind_t, VectorXd ind_x,
MatrixXd tstar, MatrixXd test_pair)
{
int Kt_ss = 1;
double sigma_star, val;
MatrixXd Kx_star, Kx_star_star, kstar, Kss, Css;
MatrixXd Kt_star = covfunc_t->Compute(t, tstar);
Kx_star = GetMatRow(Kx, test_pair.transpose()).transpose(); //maybe need some transpose?
Kx_star_star = GetMat(Kx, test_pair.transpose(), test_pair.transpose()); // test to test
kstar = Kron(Kt_star, Kx_star);
kstar = GetMatRow(kstar, idx_global);
Kss = Kt_ss * Kx_star_star;
mustar = kstar.transpose() * Kinv * GetVec(f, idx_global);
Css = Kss - kstar.transpose() * W * llt.solve(Kinv * kstar);
sigma_star = sqrt(Css(0, 0) + Css(1, 1) - 2 * Css(0, 1) + pow(sigma, 2));
val = ( mustar(0) - mustar(1) ) / sigma_star;
p = normcdf(val);
}
void CGppe::Predictive_Utility_Distribution(MatrixXd t, MatrixXd tstar, int N, VectorXd idx_global)
{
int Kt_ss = 1;
VectorXd idx_xstar(N);
MatrixXd Kstar, Kx_star_star, Kx_star, Kss, Css, Kt_star;
for (int i = 0;i < N;i++)
{
idx_xstar(i) = i;
}
Kt_star = covfunc_t->Compute(t, tstar);
Kx_star = GetMatRow(Kx, idx_xstar);//need to check for tranpose later?
Kx_star_star = GetMat(Kx, idx_xstar, idx_xstar);
Kstar = Kron(Kt_star, Kx_star);
Kstar = GetMatRow(Kstar, idx_global);
Kss = Kt_ss * Kx_star_star;
mustar = Kstar.transpose() * Kinv * GetVec(f, idx_global);
Css = Kss - Kstar.transpose() * W * llt.solve(Kinv * Kstar);
varstar = Css.diagonal();
}
double CGppe::maximum_expected_improvement(const VectorXd & theta_t, const VectorXd& theta_x, const double& sigma,
const MatrixXd& t, const MatrixXd & x, const VectorXd& idx_global, const VectorXd& ind_t, const VectorXd& ind_x, MatrixXd tstar, int N, double fbest)
{
VectorXd idx_xstar=Nfirst(N);
int Kt_ss = 1;
double mei;
MatrixXd Kx_star, Kx_star_star, kstar, Kss, Css;
MatrixXd Kt_star = covfunc_t->Compute(t, tstar);
//dsp(GetKinv(),"Kinv");
Kx_star = GetMatRow(Kx, idx_xstar.transpose()); //maybe need some transpose?
Kx_star_star = GetMat(Kx, idx_xstar.transpose(), idx_xstar.transpose()); // test to test
kstar = Kron(Kt_star, Kx_star);
kstar = GetMatRow(kstar, idx_global);
Kss = Kt_ss * Kx_star_star;
mustar = kstar.transpose() * Kinv * GetVec(f, idx_global);
Css = Kss - kstar.transpose() * W * llt.solve(Kinv * kstar);
varstar = Css.diagonal();
VectorXd sigmastar = sqrt(varstar.array());
VectorXd z = (fbest - mustar.array()) / sigmastar.array();
VectorXd pdfval = normpdf(z);
VectorXd cdfval = normcdf(z);
VectorXd inter = z.array() * (1 - cdfval.array());
VectorXd el = sigmastar.cwiseProduct(inter - pdfval);
el=-1*el;
mei = el.maxCoeff();
//dsp(mei,"mei");
return mei;
}
bool IbisItkVtkConverter::ConvertVtkImageToItkImage( IbisItkFloat3ImageType::Pointer itkOutputImage, vtkImageData *img, vtkMatrix4x4 *imageMatrix)
{
if( !itkOutputImage )
return false;
itkOutputImage->Initialize();
int numberOfScalarComponents = img->GetNumberOfScalarComponents();
vtkImageData *grayImage = img;
vtkSmartPointer<vtkImageLuminance> luminanceFilter = vtkSmartPointer<vtkImageLuminance>::New();
if (numberOfScalarComponents > 1)
{
luminanceFilter->SetInputData(img);
luminanceFilter->Update();
grayImage = luminanceFilter->GetOutput();
}
vtkImageData * image = grayImage;
vtkSmartPointer<vtkImageShiftScale> shifter = vtkSmartPointer<vtkImageShiftScale>::New();
if (img->GetScalarType() != VTK_FLOAT)
{
shifter->SetOutputScalarType(VTK_FLOAT);
shifter->SetClampOverflow(1);
shifter->SetInputData(grayImage);
shifter->SetShift(0);
shifter->SetScale(1.0);
shifter->Update();
image = shifter->GetOutput();
}
int * dimensions = img->GetDimensions();
IbisItkFloat3ImageType::SizeType size;
IbisItkFloat3ImageType::IndexType start;
IbisItkFloat3ImageType::RegionType region;
const long unsigned int numberOfPixels = dimensions[0] * dimensions[1] * dimensions[2];
for (int i = 0; i < 3; i++)
{
size[i] = dimensions[i];
}
start.Fill(0);
region.SetIndex( start );
region.SetSize( size );
itkOutputImage->SetRegions(region);
itk::Matrix< double, 3,3 > dirCosine;
itk::Vector< double, 3 > origin;
itk::Vector< double, 3 > itkOrigin;
// set direction cosines
vtkMatrix4x4 *tmpMat = vtkMatrix4x4::New();
vtkMatrix4x4::Transpose( imageMatrix, tmpMat );
double step[3], mincStartPoint[3], dirCos[3][3];
for( int i = 0; i < 3; i++ )
{
double row[4];
GetMatRow( tmpMat, i, row );
step[i] = vtkMath::Dot( row, row );
step[i] = sqrt( step[i] );
for( int j = 0; j < 3; j++ )
{
dirCos[i][j] = tmpMat->GetElement( i, j ) / step[i];
dirCosine[j][i] = dirCos[i][j];
}
}
double rotation[3][3];
vtkMath::Transpose3x3( dirCos, rotation );
double row3[4];
GetMatRow( tmpMat, 3, row3 );
vtkMath::LinearSolve3x3( rotation, row3, mincStartPoint );
tmpMat->Delete();
for( int i = 0; i < 3; i++ )
origin[i] = mincStartPoint[i];
itkOrigin = dirCosine * origin;
itkOutputImage->SetSpacing(step);
itkOutputImage->SetOrigin(itkOrigin);
itkOutputImage->SetDirection(dirCosine);
itkOutputImage->Allocate();
float *itkImageBuffer = itkOutputImage->GetBufferPointer();
memcpy(itkImageBuffer, image->GetScalarPointer(), numberOfPixels*sizeof(float));
return true;
}
