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)
 *
 */
#ifndef H5SLICE_TRAITS_MISC_HPP
#define H5SLICE_TRAITS_MISC_HPP
 
#include <algorithm>
#include <cassert>
#include <functional>
#include <numeric>
#include <sstream>
#include <string>
 
#ifdef H5_USE_BOOST
// starting Boost 1.64, serialization header must come before ublas
#include <boost/multi_array.hpp>
#include <boost/numeric/ublas/matrix.hpp>
#include <boost/serialization/vector.hpp>
#endif
 
#include <H5Dpublic.h>
#include <H5Ppublic.h>
 
#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 std::vector<size_t>& offset,
                                               const std::vector<size_t>& count,
                                               const std::vector<size_t>& stride) const {
    // hsize_t type conversion
    // TODO : normalize hsize_t type in HighFive namespace
    const auto& slice = static_cast<const Derivate&>(*this);
    std::vector<hsize_t> offset_local(offset.size());
    std::vector<hsize_t> count_local(count.size());
    std::vector<hsize_t> stride_local(stride.size());
    std::copy(offset.begin(), offset.end(), offset_local.begin());
    std::copy(count.begin(), count.end(), count_local.begin());
    std::copy(stride.begin(), stride.end(), stride_local.begin());
 
    DataSpace space = slice.getSpace().clone();
    if (H5Sselect_hyperslab(space.getId(), H5S_SELECT_SET, offset_local.data(),
                            stride.empty() ? NULL : stride_local.data(),
                            count_local.data(), NULL) < 0) {
        HDF5ErrMapper::ToException<DataSpaceException>("Unable to select hyperslap");
    }
 
    return Selection(DataSpace(count), space, details::get_dataset(slice));
}
 
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();
    const DataSet& dataset = details::get_dataset(slice);
    std::vector<size_t> dims = space.getDimensions();
    std::vector<hsize_t> counts(dims.size());
    std::copy(dims.begin(), dims.end(), counts.begin());
    counts[dims.size() - 1] = 1;
    std::vector<hsize_t> offsets(dims.size(), 0);
 
    H5Sselect_none(space.getId());
 
    for (const auto& column : columns) {
        offsets[offsets.size() - 1] = column;
 
        if (H5Sselect_hyperslab(space.getId(), H5S_SELECT_OR, offsets.data(), 0,
                                counts.data(), 0) < 0) {
            HDF5ErrMapper::ToException<DataSpaceException>("Unable to select hyperslap");
        }
    }
 
    dims[dims.size() - 1] = columns.size();
    return Selection(DataSpace(dims), space, dataset);
}
 
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();
    }
 
    if (H5Sselect_elements(space.getId(), H5S_SELECT_SET, num_elements, data) < 0) {
        HDF5ErrMapper::ToException<DataSpaceException>("Unable to select elements");
    }
 
    return Selection(DataSpace(num_elements), space, details::get_dataset(slice));
}
 
 
template <typename Derivate>
template <typename T>
inline void SliceTraits<Derivate>::read(T& array) const {
    const auto& slice = static_cast<const Derivate&>(*this);
    const DataSpace& mem_space = slice.getMemSpace();
    const details::BufferInfo<T> buffer_info(slice.getDataType());
 
    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());
    }
    details::data_converter<T> converter(mem_space);
    read(converter.transform_read(array), buffer_info.data_type);
    // re-arrange results
    converter.process_result(array);
}
 
 
template <typename Derivate>
template <typename T>
inline void SliceTraits<Derivate>::read(T* array, const DataType& dtype) 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);
    using element_type = typename details::type_of_array<T>::type;
 
    // Auto-detect mem datatype if not provided
    const DataType& mem_datatype =
            dtype.empty() ? create_and_check_datatype<element_type>() : dtype;
 
    if (H5Dread(details::get_dataset(slice).getId(),
                mem_datatype.getId(),
                details::get_memspace_id(slice),
                slice.getSpace().getId(), H5P_DEFAULT, static_cast<void*>(array)) < 0) {
        HDF5ErrMapper::ToException<DataSetException>("Error during HDF5 Read: ");
    }
}
 
 
template <typename Derivate>
template <typename T>
inline void SliceTraits<Derivate>::write(const T& buffer) {
    const auto& slice = static_cast<const Derivate&>(*this);
    const DataSpace& mem_space = slice.getMemSpace();
    const details::BufferInfo<T> buffer_info(slice.getDataType());
 
    if (!details::checkDimensions(mem_space, buffer_info.n_dimensions)) {
        std::ostringstream ss;
        ss << "Impossible to write buffer of dimensions " << buffer_info.n_dimensions
           << " into dataset of dimensions " << mem_space.getNumberDimensions();
        throw DataSpaceException(ss.str());
    }
    details::data_converter<T> converter(mem_space);
    write_raw(converter.transform_write(buffer), buffer_info.data_type);
}
 
 
template <typename Derivate>
template <typename T>
inline void SliceTraits<Derivate>::write_raw(const T* buffer, const DataType& dtype) {
    using element_type = typename details::type_of_array<T>::type;
    const auto& slice = static_cast<const Derivate&>(*this);
    const auto& mem_datatype =
        dtype.empty() ? create_and_check_datatype<element_type>() : dtype;
 
    if (H5Dwrite(details::get_dataset(slice).getId(),
                 mem_datatype.getId(),
                 details::get_memspace_id(slice),
                 slice.getSpace().getId(), H5P_DEFAULT,
                 static_cast<const void*>(buffer)) < 0) {
        HDF5ErrMapper::ToException<DataSetException>("Error during HDF5 Write: ");
    }
}
 
}  // namespace HighFive
 
#endif  // H5SLICE_TRAITS_MISC_HPP