dense_array.hpp

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#ifndef CHIHAYA_DENSE_ARRAY_HPP
#define CHIHAYA_DENSE_ARRAY_HPP
 
#include "H5Cpp.h"
#include "ritsuko/ritsuko.hpp"
#include "sanisizer/sanisizer.hpp"
 
#include <vector>
#include <cstdint>
#include <stdexcept>
#include <exception>
#include <cstddef>
 
#include "utils_public.hpp"
#include "utils_misc.hpp"
#include "utils_type.hpp"
#include "utils_dimensions.hpp"
 
namespace chihaya {
 
template<typename Output_>
void transplant_dimensions(std::vector<hsize_t>& src, std::vector<Output_>& output) {
    if constexpr(std::is_same<hsize_t, Output_>::value) {
        // Avoid a copy if we can.
        output = std::move(src);
    } else {
        const auto ndims = src.size();
        sanisizer::resize(output, ndims);
        for (I<decltype(ndims)> d = 0; d < ndims; ++d) {
            output[d] = sanisizer::cast<Output_>(src[d]);
        }
    }
}
inline ArrayDetails validate_dense_array(const H5::Group& group, const ritsuko::Version& version, [[maybe_unused]] const Options& options) {
    ArrayDetails output;
 
    try {
        auto dhandle = group.openDataSet("data");
        auto dspace = dhandle.getSpace();
        const auto ndims = dspace.getSimpleExtentNdims();
        if (ndims == 0) {
            throw std::runtime_error("expected at least one dimension");
        }
        auto dims = sanisizer::create<std::vector<hsize_t> >(ndims);
        dspace.getSimpleExtentDims(dims.data());
 
        if (version.lt(1, 1, 0)) {
            output.type = translate_type_0_99(dhandle.getTypeClass());
            if (is_boolean_0_99(dhandle)) {
                output.type = BOOLEAN;
            }
        } else {
            try {
                auto thandle = dhandle.openAttribute("type");
                auto type = read_scalar_string_attribute(thandle);
                output.type = translate_type_1_1(type);
                if (!options.details_only) {
                    check_type_1_1(dhandle, output.type);
                }
            } catch (...) {
                std::throw_with_nested(std::runtime_error("failed to validate the 'type' attribute"));
            }
        }
 
        if (!options.details_only) {
            validate_missing_placeholder(dhandle, version);
            if (dhandle.getTypeClass() == H5T_STRING) {
                ritsuko::hdf5::validate_nd_strings(
                    dhandle,
                    dims,
                    [&]{
                        ritsuko::hdf5::ValidateNdStringsOptions opt;
                        opt.contiguous_chunk_size = options.contiguous_chunk_size;
                        return opt;
                    }()
                );
            }
        }
 
        transplant_dimensions(dims, output.dimensions);
    } catch (...) {
        std::throw_with_nested(std::runtime_error("failed to validate 'data'"));
    }
 
    bool native;
    try {
        auto nhandle = group.openDataSet("native");
        if (nhandle.getSpace().getSimpleExtentNdims() != 0) {
            throw std::runtime_error("expected a scalar dataset");
        }
 
        if (version.lt(1, 1, 0)) {
            native = load_boolean_scalar_0_99(nhandle);
        } else {
            if (ritsuko::hdf5::exceeds_integer_limit(nhandle, 8, true)) {
                throw std::runtime_error("expected a datatype that fits into an 8-bit signed integer");
            }
            std::int8_t tmp_native;
            nhandle.read(&tmp_native, H5::PredType::NATIVE_INT);
            native = tmp_native;
        }
    } catch (...) {
        std::throw_with_nested(std::runtime_error("failed to validate 'native'"));
    }
 
    // Do this before applying the 'native' reversal.
    if (!options.details_only) {
        if (group.exists("dimnames")) {
            try {
                auto dnhandle = group.openGroup("dimnames");
                validate_dimnames_internal(dnhandle, output.dimensions, version, options.contiguous_chunk_size);
            } catch (...) {
                std::throw_with_nested(std::runtime_error("failed to validate 'dimnames'"));
            }
        }
    }
 
    if (!native) {
        std::reverse(output.dimensions.begin(), output.dimensions.end());
    }
 
    return output;
}
 
}
 
#endif