load_dense_matrix.hpp

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#ifndef TATAMI_HDF5_LOAD_DENSE_MATRIX_HPP
#define TATAMI_HDF5_LOAD_DENSE_MATRIX_HPP
 
#include "H5Cpp.h"
 
#include <string>
 
#include "tatami/tatami.hpp"
#include "utils.hpp"
 
namespace tatami_hdf5 {
 
template<typename Value_, typename Index_, class ValueStorage_ = std::vector<Value_> >
std::shared_ptr<tatami::Matrix<Value_, Index_> > load_dense_matrix(const std::string& file, const std::string& name, bool transpose) {
    H5::H5File fhandle(file, H5F_ACC_RDONLY);
    auto dhandle = open_and_check_dataset<false>(fhandle, name);
 
    auto dims = get_array_dimensions<2>(dhandle, name);
    ValueStorage_ values(static_cast<size_t>(dims[0]) * static_cast<size_t>(dims[1])); // cast just in case hsize_t is something silly...
    dhandle.read(values.data(), define_mem_type<tatami::ElementType<ValueStorage_> >());
 
    if (transpose) {
        return std::make_shared<tatami::DenseMatrix<Value_, Index_, ValueStorage_> >(dims[1], dims[0], std::move(values), false);
    } else {
        return std::make_shared<tatami::DenseMatrix<Value_, Index_, ValueStorage_> >(dims[0], dims[1], std::move(values), true);
    }
}
 
}
 
#endif