setDiagonalMatrix

C++ Function Reference

1 Signature

void BigDataStatMeth::setDiagonalMatrix(BigDataStatMeth::hdf5Dataset *dsMat, Rcpp::NumericVector intNewDiagonal)

2 Description

Sets the diagonal elements of a matrix stored in HDF5 format.

3 Parameters

  • dsMat (BigDataStatMeth::hdf5Dataset *): Target HDF5 dataset containing the matrix
  • intNewDiagonal (Rcpp::NumericVector): Vector of new diagonal values to set

4 Details

dsMatTarget HDF5 dataset containing the matrix intNewDiagonalVector of new diagonal values to set Implementation approach:Writes diagonal elements one at a timeUses HDF5 block writing for efficient accessPreserves existing non-diagonal elements

5 Call Graph

Function dependencies

6 Source Code

File: inst/include/hdf5Algebra/matrixDiagonal.hpp • Lines 104-136

inline void setDiagonalMatrix(BigDataStatMeth::hdf5Dataset* dsMat, Rcpp::NumericVector intNewDiagonal)
    {
        try {
            const hsize_t DIAG_BLOCK_SIZE = 256;
            hsize_t matrix_size = intNewDiagonal.size();
            std::vector<hsize_t> stride = {1, 1}, block = {1, 1};
            
            for (hsize_t block_start = 0; block_start < matrix_size; block_start += DIAG_BLOCK_SIZE) {
                hsize_t current_block_size = std::min(DIAG_BLOCK_SIZE, matrix_size - block_start);
                
                // Read square block starting from diagonal position
                std::vector<hsize_t> offset = {block_start, block_start};
                std::vector<hsize_t> count = {current_block_size, current_block_size};
                
                std::vector<double> block_data(current_block_size * current_block_size);
                dsMat->readDatasetBlock(offset, count, stride, block, block_data.data());
                
                // Map to Eigen for correct R/HDF5 layout handling
                Eigen::Map<Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>> 
                    block_matrix(block_data.data(), current_block_size, current_block_size);
                
                // Use Eigen diagonal assignment - NO LOOP NEEDED
                Eigen::Map<Eigen::VectorXd> diagonal_segment(REAL(intNewDiagonal) + block_start, current_block_size);
                block_matrix.diagonal() = diagonal_segment;
                
                // Write modified block back
                dsMat->writeDatasetBlock(Rcpp::wrap(block_matrix), offset, count, stride, block, false);
            }
            
        } catch(std::exception& ex) {
            Rcpp::stop("c++ exception setDiagonalMatrix: "+ std::string(ex.what()));
        }
    }

7 Usage Example

#include "BigDataStatMeth.hpp"

// Example usage
auto result = setDiagonalMatrix(...);