get row from itk matrix

stnava · June 8, 2022, 4:55pm

just trying to update some code for more recent itk version (latest release)

Type definitions:

ANTsX/ANTsR/blob/master/src/reorientImage.cpp#L29

      
        
            typedef double RealType;
            Rcpp::NumericVector axis( r_axis );
            Rcpp::NumericVector axis2( r_axis2 );
            Rcpp::NumericVector doReflection( r_reflect );
            Rcpp::NumericVector doScale( r_scale );
            typedef itk::Image< float , ImageDimension > ImageType;
            if( image1.IsNotNull()  )
              {
              typedef typename itk::ImageMomentsCalculator<ImageType> ImageCalculatorType;
              typedef itk::AffineTransform<RealType, ImageDimension> AffineType;
              typedef typename ImageCalculatorType::MatrixType       MatrixType;
              typedef itk::Vector<float, ImageDimension>  VectorType;
              VectorType ccg1;
              VectorType cpm1;
              MatrixType cpa1;
              MatrixType cpa2;
              typename ImageCalculatorType::Pointer calculator1 =
                ImageCalculatorType::New();
              calculator1->SetImage(  image1 );
              typename ImageCalculatorType::VectorType fixed_center;
              fixed_center.Fill(0);

github.com

ANTsX/ANTsR/blob/master/src/reorientImage.cpp#L44-L46

      
        
            ccg1 = calculator1->GetCenterOfGravity();
            cpm1 = calculator1->GetPrincipalMoments();
            cpa1 = calculator1->GetPrincipalAxes();

github.com

ANTsX/ANTsR/blob/master/src/reorientImage.cpp#L54-L55

      
        
            typedef vnl_vector<RealType> EVectorType;
            typedef vnl_matrix<RealType> EMatrixType;

Things that don’t compile b/c they use old vnl types:

github.com

ANTsX/ANTsR/blob/master/src/reorientImage.cpp#L56-L57

      
        
            EVectorType evec1_2ndary = cpa1.GetVnlMatrix().get_row( eigind2 );
            EVectorType evec1_primary = cpa1.GetVnlMatrix().get_row( eigind1 );

github.com

ANTsX/ANTsR/blob/master/src/reorientImage.cpp#L127

      
        
            typename AffineType::Pointer affine1 = AffineType::New();
            typename AffineType::OffsetType trans = affine1->GetOffset();
            itk::Point<RealType, ImageDimension> trans2;
            trans2.Fill(0);
            for( unsigned int i = 0; i < ImageDimension; i++ )
              {
              trans2[i] =  fixed_center[i] * ( 1 );
              }
            affine1->SetIdentity();
            affine1->SetOffset( trans );
            affine1->SetMatrix( A_solution );
            affine1->SetCenter( trans2 );
            // write tx
            typedef itk::TransformFileWriter TransformWriterType;
            typename TransformWriterType::Pointer transformWriter = TransformWriterType::New();
            transformWriter->SetInput( affine1 );
            transformWriter->SetFileName( Rcpp::as< std::string >(r_txfn).c_str() );
            transformWriter->Update();
            /*
            typedef itk::ResampleImageFilter<ImageType, ImageType> ResampleFilterType;
            typename ResampleFilterType::Pointer resample = ResampleFilterType::New();

But - in brief - this is a question of how to replace old vnl operations with whatever is the right way to do wrt recent ITK.

dzenanz · June 8, 2022, 6:30pm

Unfortunately, we still use VNL under the hood for Matrix. We want to transition to Eigen, but it is a large refactoring and no one has taken it up so far.