H5Slice_traits_misc.hpp

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/*
 *  Copyright (c), 2017, Adrien Devresse <adrien.devresse@epfl.ch>
 *
 *  Distributed under the Boost Software License, Version 1.0.
 *    (See accompanying file LICENSE_1_0.txt or copy at
 *          http://www.boost.org/LICENSE_1_0.txt)
 *
 */
#pragma once
 
#include <algorithm>
#include <cassert>
#include <functional>
#include <numeric>
#include <sstream>
#include <string>
 
#include "h5d_wrapper.hpp"
#include "h5s_wrapper.hpp"
 
#include "H5ReadWrite_misc.hpp"
#include "H5Converter_misc.hpp"
 
namespace HighFive {
 
namespace details {
 
// map the correct reference to the dataset depending of the layout
// dataset -> itself
// subselection -> parent dataset
inline const DataSet& get_dataset(const Selection& sel) {
    return sel.getDataset();
}
 
inline const DataSet& get_dataset(const DataSet& ds) {
    return ds;
}
 
// map the correct memspace identifier depending of the layout
// dataset -> entire memspace
// selection -> resolve space id
inline hid_t get_memspace_id(const Selection& ptr) {
    return ptr.getMemSpace().getId();
}
 
inline hid_t get_memspace_id(const DataSet&) {
    return H5S_ALL;
}
}  // namespace details
 
inline ElementSet::ElementSet(std::initializer_list<std::size_t> list)
    : _ids(list) {}
 
inline ElementSet::ElementSet(std::initializer_list<std::vector<std::size_t>> list)
    : ElementSet(std::vector<std::vector<std::size_t>>(list)) {}
 
inline ElementSet::ElementSet(const std::vector<std::size_t>& element_ids)
    : _ids(element_ids) {}
 
inline ElementSet::ElementSet(const std::vector<std::vector<std::size_t>>& element_ids) {
    for (const auto& vec: element_ids) {
        std::copy(vec.begin(), vec.end(), std::back_inserter(_ids));
    }
}
 
template <typename Derivate>
inline Selection SliceTraits<Derivate>::select(const HyperSlab& hyperslab,
                                               const DataSpace& memspace) const {
    // Note: The current limitation are that memspace must describe a
    //       packed memspace.
    //
    //       The reason for this is that we're unable to unpack general
    //       hyperslabs when the memory is not contiguous, e.g.
    //       `std::vector<std::vector<double>>`.
    const auto& slice = static_cast<const Derivate&>(*this);
    auto filespace = hyperslab.apply(slice.getSpace());
 
    return detail::make_selection(memspace, filespace, details::get_dataset(slice));
}
 
template <typename Derivate>
inline Selection SliceTraits<Derivate>::select(const HyperSlab& hyper_slab) const {
    const auto& slice = static_cast<const Derivate&>(*this);
    auto filespace = slice.getSpace();
    filespace = hyper_slab.apply(filespace);
 
    auto n_elements = detail::h5s_get_select_npoints(filespace.getId());
    auto memspace = DataSpace(std::array<size_t, 1>{size_t(n_elements)});
 
    return detail::make_selection(memspace, filespace, details::get_dataset(slice));
}
 
 
template <typename Derivate>
inline Selection SliceTraits<Derivate>::select(const std::vector<size_t>& offset,
                                               const std::vector<size_t>& count,
                                               const std::vector<size_t>& stride,
                                               const std::vector<size_t>& block) const {
    auto slab = HyperSlab(RegularHyperSlab(offset, count, stride, block));
    auto memspace = DataSpace(count);
    return select(slab, memspace);
}
 
template <typename Derivate>
inline Selection SliceTraits<Derivate>::select(const std::vector<size_t>& columns) const {
    const auto& slice = static_cast<const Derivate&>(*this);
    const DataSpace& space = slice.getSpace();
    std::vector<size_t> dims = space.getDimensions();
 
    std::vector<size_t> counts = dims;
    counts.back() = 1;
 
    std::vector<size_t> offsets(dims.size(), 0);
 
    HyperSlab slab;
    for (const auto& column: columns) {
        offsets.back() = column;
        slab |= RegularHyperSlab(offsets, counts);
    }
 
    std::vector<size_t> memdims = dims;
    memdims.back() = columns.size();
 
    return select(slab, DataSpace(memdims));
}
 
template <typename Derivate>
inline Selection SliceTraits<Derivate>::select(const ElementSet& elements) const {
    const auto& slice = static_cast<const Derivate&>(*this);
    const hsize_t* data = nullptr;
    const DataSpace space = slice.getSpace().clone();
    const std::size_t length = elements._ids.size();
    if (length % space.getNumberDimensions() != 0) {
        throw DataSpaceException(
            "Number of coordinates in elements picking "
            "should be a multiple of the dimensions.");
    }
    const std::size_t num_elements = length / space.getNumberDimensions();
    std::vector<hsize_t> raw_elements;
 
    // optimised at compile time
    // switch for data conversion on 32bits platforms
    if (std::is_same<std::size_t, hsize_t>::value) {
        // `if constexpr` can't be used, thus a reinterpret_cast is needed.
        data = reinterpret_cast<const hsize_t*>(&(elements._ids[0]));
    } else {
        raw_elements.resize(length);
        std::copy(elements._ids.begin(), elements._ids.end(), raw_elements.begin());
        data = raw_elements.data();
    }
 
    detail::h5s_select_elements(space.getId(), H5S_SELECT_SET, num_elements, data);
 
    return detail::make_selection(DataSpace(num_elements), space, details::get_dataset(slice));
}
 
 
template <typename Derivate>
template <typename T>
inline T SliceTraits<Derivate>::read(const DataTransferProps& xfer_props) const {
    T array;
    read(array, xfer_props);
    return array;
}
 
 
template <typename Derivate>
template <typename T>
inline void SliceTraits<Derivate>::read(T& array, const DataTransferProps& xfer_props) const {
    const auto& slice = static_cast<const Derivate&>(*this);
    const DataSpace& mem_space = slice.getMemSpace();
 
    auto file_datatype = slice.getDataType();
 
    const details::BufferInfo<T> buffer_info(
        file_datatype,
        [&slice]() -> std::string { return details::get_dataset(slice).getPath(); },
        details::BufferInfo<T>::Operation::read);
 
    if (!details::checkDimensions(mem_space, buffer_info.n_dimensions)) {
        std::ostringstream ss;
        ss << "Impossible to read DataSet of dimensions " << mem_space.getNumberDimensions()
           << " into arrays of dimensions " << buffer_info.n_dimensions;
        throw DataSpaceException(ss.str());
    }
    auto dims = mem_space.getDimensions();
 
    auto r = details::data_converter::get_reader<T>(dims, array, file_datatype);
    read_raw(r.getPointer(), buffer_info.data_type, xfer_props);
    // re-arrange results
    r.unserialize(array);
 
    auto t = buffer_info.data_type;
    auto c = t.getClass();
    if (c == DataTypeClass::VarLen || t.isVariableStr()) {
#if H5_VERSION_GE(1, 12, 0)
        // This one have been created in 1.12.0
        (void)
            detail::h5t_reclaim(t.getId(), mem_space.getId(), xfer_props.getId(), r.getPointer());
#else
        // This one is deprecated since 1.12.0
        (void) detail::h5d_vlen_reclaim(t.getId(),
                                        mem_space.getId(),
                                        xfer_props.getId(),
                                        r.getPointer());
#endif
    }
}
 
template <typename Derivate>
template <typename T>
inline void SliceTraits<Derivate>::read(T* array,
                                        const DataType& mem_datatype,
                                        const DataTransferProps& xfer_props) const {
    read_raw(array, mem_datatype, xfer_props);
}
 
template <typename Derivate>
template <typename T>
inline void SliceTraits<Derivate>::read(T* array, const DataTransferProps& xfer_props) const {
    read_raw(array, xfer_props);
}
 
 
template <typename Derivate>
template <typename T>
inline void SliceTraits<Derivate>::read_raw(T* array,
                                            const DataType& mem_datatype,
                                            const DataTransferProps& xfer_props) const {
    static_assert(!std::is_const<T>::value,
                  "read() requires a non-const structure to read data into");
 
    const auto& slice = static_cast<const Derivate&>(*this);
 
    detail::h5d_read(details::get_dataset(slice).getId(),
                     mem_datatype.getId(),
                     details::get_memspace_id(slice),
                     slice.getSpace().getId(),
                     xfer_props.getId(),
                     static_cast<void*>(array));
}
 
 
template <typename Derivate>
template <typename T>
inline void SliceTraits<Derivate>::read_raw(T* array, const DataTransferProps& xfer_props) const {
    using element_type = typename details::inspector<T>::base_type;
    const DataType& mem_datatype = create_and_check_datatype<element_type>();
 
    read_raw(array, mem_datatype, xfer_props);
}
 
 
template <typename Derivate>
template <typename T>
inline void SliceTraits<Derivate>::write(const T& buffer, const DataTransferProps& xfer_props) {
    const auto& slice = static_cast<const Derivate&>(*this);
    const DataSpace& mem_space = slice.getMemSpace();
 
    auto file_datatype = slice.getDataType();
 
    const details::BufferInfo<T> buffer_info(
        file_datatype,
        [&slice]() -> std::string { return details::get_dataset(slice).getPath(); },
        details::BufferInfo<T>::Operation::write);
 
    if (!details::checkDimensions(mem_space, buffer_info.n_dimensions)) {
        std::ostringstream ss;
        ss << "Impossible to write buffer of dimensions "
           << details::format_vector(mem_space.getDimensions())
           << " into dataset with n = " << buffer_info.n_dimensions << " dimensions.";
        throw DataSpaceException(ss.str());
    }
    auto w = details::data_converter::serialize<T>(buffer, file_datatype);
    write_raw(w.getPointer(), buffer_info.data_type, xfer_props);
}
 
 
template <typename Derivate>
template <typename T>
inline void SliceTraits<Derivate>::write_raw(const T* buffer,
                                             const DataType& mem_datatype,
                                             const DataTransferProps& xfer_props) {
    const auto& slice = static_cast<const Derivate&>(*this);
 
    detail::h5d_write(details::get_dataset(slice).getId(),
                      mem_datatype.getId(),
                      details::get_memspace_id(slice),
                      slice.getSpace().getId(),
                      xfer_props.getId(),
                      static_cast<const void*>(buffer));
}
 
 
template <typename Derivate>
template <typename T>
inline void SliceTraits<Derivate>::write_raw(const T* buffer, const DataTransferProps& xfer_props) {
    using element_type = typename details::inspector<T>::base_type;
    const auto& mem_datatype = create_and_check_datatype<element_type>();
 
    write_raw(buffer, mem_datatype, xfer_props);
}
 
 
}  // namespace HighFive