H5Easy.hpp

/*
 *  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)
 *
 */

/// \brief
/// Read/dump DataSets or Attribute using a minimalistic syntax.
/// To this end, the functions are templated, and accept:
/// - Any type accepted by HighFive
/// - Eigen objects
/// - xtensor objects
/// - OpenCV objects

#pragma once

#include <string>
#include <vector>

// optionally enable xtensor plug-in and load the library
#ifdef XTENSOR_VERSION_MAJOR
#ifndef H5_USE_XTENSOR
#define H5_USE_XTENSOR
#endif
#endif

#ifdef H5_USE_XTENSOR
#include <xtensor/xarray.hpp>
#include <xtensor/xtensor.hpp>
#include "xtensor.hpp"
#endif

// optionally enable Eigen plug-in and load the library
#ifdef EIGEN_WORLD_VERSION
#ifndef H5_USE_EIGEN
#define H5_USE_EIGEN
#endif
#endif

#ifdef H5_USE_EIGEN
#include <Eigen/Eigen>
#include "eigen.hpp"
#endif

// optionally enable OpenCV plug-in and load the library
#ifdef CV_MAJOR_VERSION
#ifndef H5_USE_OPENCV
#define H5_USE_OPENCV
#endif
#endif

#ifdef H5_USE_OPENCV
#include <opencv2/opencv.hpp>
#include "experimental/opencv.hpp"
#endif

#include "H5File.hpp"

namespace H5Easy {

using HighFive::AtomicType;
using HighFive::Attribute;
using HighFive::Chunking;
using HighFive::DataSet;
using HighFive::DataSetCreateProps;
using HighFive::DataSpace;
using HighFive::Deflate;
using HighFive::Exception;
using HighFive::File;
using HighFive::ObjectType;
using HighFive::Shuffle;

///
/// \brief Write mode for DataSets
enum class DumpMode {
    Create = 0,   /*!< Dump only if DataSet does not exist, otherwise throw. */
    Overwrite = 1 /*!< Create or overwrite if DataSet of correct shape exists, otherwise throw. */
};

///
/// \brief Signal to enable/disable automatic flushing after write operations.
enum class Flush {
    False = 0, /*!< No automatic flushing. */
    True = 1   /*!< Automatic flushing. */
};

///
/// \brief Signal to set compression level for written DataSets.
class Compression {
  public:
    ///
    /// \brief Enable compression with the highest compression level (9).
    /// or disable compression (set compression level to 0).
    ///
    /// \param enable ``true`` to enable with highest compression level
    explicit Compression(bool enable = true);

    ///
    /// \brief Set compression level.
    ///
    /// \param level the compression level
    template <class T>
    Compression(T level);

    ///
    /// \brief Return compression level.
    inline unsigned get() const;

  private:
    unsigned m_compression_level;
};

///
/// \brief Define options for dumping data.
///
/// By default:
/// - DumpMode::Create
/// - Flush::True
/// - Compression: false
/// - ChunkSize: automatic
class DumpOptions {
  public:
    ///
    /// \brief Constructor: accept all default settings.
    DumpOptions() = default;

    ///
    /// \brief Constructor: overwrite (some of the) defaults.
    /// \param args any of DumpMode(), Flush(), Compression() in arbitrary number and order.
    template <class... Args>
    DumpOptions(Args... args) {
        set(args...);
    }

    ///
    /// \brief Overwrite H5Easy::DumpMode setting.
    /// \param mode: DumpMode.
    inline void set(DumpMode mode);

    ///
    /// \brief Overwrite H5Easy::Flush setting.
    /// \param mode Flush.
    inline void set(Flush mode);

    ///
    /// \brief Overwrite H5Easy::Compression setting.
    /// \param level Compression.
    inline void set(const Compression& level);

    ///
    /// \brief Overwrite any setting(s).
    /// \param arg any of DumpMode(), Flush(), Compression in arbitrary number and order.
    /// \param args any of DumpMode(), Flush(), Compression in arbitrary number and order.
    template <class T, class... Args>
    inline void set(T arg, Args... args);

    ///
    /// \brief Set chunk-size. If the input is rank (size) zero, automatic chunking is enabled.
    /// \param shape Chunk size along each dimension.
    template <class T>
    inline void setChunkSize(const std::vector<T>& shape);

    ///
    /// \brief Set chunk-size. If the input is rank (size) zero, automatic chunking is enabled.
    /// \param shape Chunk size along each dimension.
    inline void setChunkSize(std::initializer_list<size_t> shape);

    ///
    /// \brief Get overwrite-mode.
    /// \return bool
    inline bool overwrite() const;

    ///
    /// \brief Get flush-mode.
    /// \return bool
    inline bool flush() const;

    ///
    /// \brief Get compress-mode.
    /// \return bool
    inline bool compress() const;

    ///
    /// \brief Get compression level.
    /// \return [0..9]
    inline unsigned getCompressionLevel() const;

    ///
    /// \brief Get chunking mode: ``true`` is manually set, ``false`` if chunk-size should be
    /// computed automatically.
    /// \return bool
    inline bool isChunked() const;

    ///
    /// \brief Get chunk size. Use DumpOptions::getChunkSize to check if chunk-size should
    /// be automatically computed.
    inline std::vector<hsize_t> getChunkSize() const;

  private:
    bool m_overwrite = false;
    bool m_flush = true;
    unsigned m_compression_level = 0;
    std::vector<hsize_t> m_chunk_size = {};
};

///
/// \brief Get the size of an existing DataSet in an open HDF5 file.
///
/// \param file opened file (has to be readable)
/// \param path path of the DataSet
///
/// \return Size of the DataSet
inline size_t getSize(const File& file, const std::string& path);

///
/// \brief Get the shape of an existing DataSet in an readable file.
///
/// \param file opened file (has to be readable)
/// \param path Path of the DataSet
///
/// \return the shape of the DataSet
inline std::vector<size_t> getShape(const File& file, const std::string& path);

///
/// \brief Write object (templated) to a (new) DataSet in an open HDF5 file.
///
/// \param file opened file (has to be writeable)
/// \param path path of the DataSet
/// \param data the data to write (any supported type)
/// \param mode write mode
///
/// \return The newly created DataSet
///
template <class T>
inline DataSet dump(File& file,
                    const std::string& path,
                    const T& data,
                    DumpMode mode = DumpMode::Create);

///
/// \brief Write object (templated) to a (new) DataSet in an open HDF5 file.
///
/// \param file opened file (has to be writeable)
/// \param path path of the DataSet
/// \param data the data to write (any supported type)
/// \param options dump options
///
/// \return The newly created DataSet
///
template <class T>
inline DataSet dump(File& file, const std::string& path, const T& data, const DumpOptions& options);

///
/// \brief Write a scalar to a (new, extendible) DataSet in an open HDF5 file.
///
/// \param file opened file (has to be writeable)
/// \param path path of the DataSet
/// \param data the data to write (any supported type)
/// \param idx the indices to which to write
///
/// \return The newly created DataSet
///
template <class T>
inline DataSet dump(File& file,
                    const std::string& path,
                    const T& data,
                    const std::vector<size_t>& idx);

///
/// \brief Write a scalar to a (new, extendable) DataSet in an open HDF5 file.
///
/// \param file open File (has to be writeable)
/// \param path path of the DataSet
/// \param data the data to write (any supported type)
/// \param idx the indices to which to write
///
/// \return The newly created DataSet
///
template <class T>
inline DataSet dump(File& file,
                    const std::string& path,
                    const T& data,
                    const std::initializer_list<size_t>& idx);

///
/// \brief Write a scalar to a (new, extendible) DataSet in an open HDF5 file.
///
/// \param file opened file (has to be writeable)
/// \param path path of the DataSet
/// \param data the data to write (any supported type)
/// \param idx the indices to which to write
/// \param options dump options
///
/// \return The newly created DataSet
///
template <class T>
inline DataSet dump(File& file,
                    const std::string& path,
                    const T& data,
                    const std::vector<size_t>& idx,
                    const DumpOptions& options);

///
/// \brief Write a scalar to a (new, extendible) DataSet in an open HDF5 file.
///
/// \param file opened file (has to be writeable)
/// \param path path of the DataSet
/// \param data the data to write (any supported type)
/// \param idx the indices to which to write
/// \param options dump options
///
/// \return The newly created DataSet
///
template <class T>
inline DataSet dump(File& file,
                    const std::string& path,
                    const T& data,
                    const std::initializer_list<size_t>& idx,
                    const DumpOptions& options);

///
/// \brief Load entry ``{i, j, ...}`` from a DataSet in an open HDF5 file to a scalar.
///
/// \param file opened file (has to be writeable)
/// \param idx the indices to load
/// \param path path of the DataSet
///
/// \return The read data
///
template <class T>
inline T load(const File& file, const std::string& path, const std::vector<size_t>& idx);

///
/// \brief Load a DataSet in an open HDF5 file to an object (templated).
///
/// \param file opened file (has to be writeable)
/// \param path path of the DataSet
///
/// \return The read data
///
template <class T>
inline T load(const File& file, const std::string& path);

///
/// \brief Write object (templated) to a (new) Attribute in an open HDF5 file.
///
/// \param file opened file (has to be writeable)
/// \param path path of the DataSet
/// \param key name of the attribute
/// \param data the data to write (any supported type)
/// \param mode write mode
///
/// \return The newly created DataSet
///
template <class T>
inline Attribute dumpAttribute(File& file,
                               const std::string& path,
                               const std::string& key,
                               const T& data,
                               DumpMode mode = DumpMode::Create);

///
/// \brief Write object (templated) to a (new) Attribute in an open HDF5 file.
///
/// \param file opened file (has to be writeable)
/// \param path path of the DataSet
/// \param key name of the attribute
/// \param data the data to write (any supported type)
/// \param options dump options
///
/// \return The newly created DataSet
///
template <class T>
inline Attribute dumpAttribute(File& file,
                               const std::string& path,
                               const std::string& key,
                               const T& data,
                               const DumpOptions& options);

///
/// \brief Load a Attribute in an open HDF5 file to an object (templated).
///
/// \param file opened file (has to be writeable)
/// \param path path of the DataSet
/// \param key name of the attribute
///
/// \return The read data
///
template <class T>
inline T loadAttribute(const File& file, const std::string& path, const std::string& key);

}  // namespace H5Easy

#include "h5easy_bits/H5Easy_Eigen.hpp"
#include "h5easy_bits/H5Easy_misc.hpp"
#include "h5easy_bits/H5Easy_public.hpp"
#include "h5easy_bits/H5Easy_scalar.hpp"