Program Listing for File hdf5.h

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#ifndef AMICI_HDF5_H
#define AMICI_HDF5_H

#include <memory>
#include <string>
#include <vector>

#include <H5Cpp.h>

#include <gsl/gsl-lite.hpp>

/* Macros for enabling/disabling  HDF5 error auto-printing
 * AMICI_H5_SAVE_ERROR_HANDLER and AMICI_H5_RESTORE_ERROR_HANDLER must be called
 * within the same context, otherwise the stack handler is lost. */
#define AMICI_H5_SAVE_ERROR_HANDLER                                            \
    herr_t (*old_func)(void*);                                                 \
    void* old_client_data;                                                     \
    H5Eget_auto1(&old_func, &old_client_data);                                 \
    H5Eset_auto1(NULL, NULL)

#define AMICI_H5_RESTORE_ERROR_HANDLER H5Eset_auto1(old_func, old_client_data)

namespace amici {

class ReturnData;
class ExpData;
class Model;
class Solver;
struct LogItem;

namespace hdf5 {

/* Functions for reading and writing AMICI data to/from HDF5 files. */

H5::H5File create_or_open_for_writing(std::string const& hdf5filename);

void read_solver_settings_from_hdf5(
    const H5::H5File& file, Solver& solver, std::string const& datasetPath
);

void write_solver_settings_to_hdf5(
    Solver const& solver, std::string const& hdf5Filename,
    std::string const& hdf5Location
);

void write_solver_settings_to_hdf5(
    Solver const& solver, H5::H5File const& file,
    std::string const& hdf5Location
);

void read_solver_settings_from_hdf5(
    std::string const& hdffile, Solver& solver, std::string const& datasetPath
);

void read_model_data_from_hdf5(
    std::string const& hdffile, Model& model, std::string const& datasetPath
);

void read_model_data_from_hdf5(
    H5::H5File const& file, Model& model, std::string const& datasetPath
);


void write_return_data_to_hdf5(
    ReturnData const& rdata, H5::H5File const& file,
    std::string const& hdf5Location
);


void write_return_data_to_hdf5(
    ReturnData const& rdata, std::string const& hdf5Filename,
    std::string const& hdf5Location
);

void write_return_data_diagnosis(
    ReturnData const& rdata, H5::H5File const& file,
    std::string const& hdf5Location
);

void write_log_items_to_hdf5(
    H5::H5File const& file, std::vector<LogItem> const& logItems,
    std::string const& hdf5Location
);

void create_group(
    const H5::H5File& file, std::string const& groupPath,
    bool recursively = true
);


std::unique_ptr<ExpData> read_exp_data_from_hdf5(
    std::string const& hdf5Filename, std::string const& hdf5Root,
    Model const& model
);


void write_exp_data_to_hdf5(
    ExpData const& edata, H5::H5File const& file,
    std::string const& hdf5Location
);

void write_exp_data_to_hdf5(
    ExpData const& edata, std::string const& filepath,
    std::string const& hdf5Location
);

bool attribute_exists(
    H5::H5File const& file, std::string const& optionsObject,
    std::string const& attributeName
);

bool attribute_exists(
    H5::H5Object const& object, std::string const& attributeName
);

void create_and_write_int_1d_dataset(
    H5::H5File const& file, std::string const& datasetName,
    gsl::span<int const> buffer
);

void create_and_write_int_2d_dataset(
    H5::H5File const& file, std::string const& datasetName,
    gsl::span<int const> buffer, hsize_t m, hsize_t n
);

void create_and_write_double_1d_dataset(
    H5::H5File const& file, std::string const& datasetName,
    gsl::span<double const> buffer
);


void create_and_write_double_2d_dataset(
    H5::H5File const& file, std::string const& datasetName,
    gsl::span<double const> buffer, hsize_t m, hsize_t n
);


void create_and_write_double_3d_dataset(
    H5::H5File const& file, std::string const& datasetName,
    gsl::span<double const> buffer, hsize_t m, hsize_t n, hsize_t o
);

std::string get_string_attribute(
    H5::H5File const& file, std::string const& optionsObject,
    std::string const& attributeName
);

double get_double_scalar_attribute(
    const H5::H5File& file, std::string const& optionsObject,
    std::string const& attributeName
);


int get_int_scalar_attribute(
    const H5::H5File& file, std::string const& optionsObject,
    std::string const& attributeName
);

std::vector<int>
get_int_1d_dataset(const H5::H5File& file, std::string const& name);


std::vector<double>
get_double_1d_dataset(const H5::H5File& file, std::string const& name);


std::vector<double> get_double_2d_dataset(
    const H5::H5File& file, std::string const& name, hsize_t& m, hsize_t& n
);


std::vector<double> get_double_3d_dataset(
    const H5::H5File& file, std::string const& name, hsize_t& m, hsize_t& n,
    hsize_t& o
);

bool location_exists(std::string const& filename, std::string const& location);


bool location_exists(H5::H5File const& file, std::string const& location);

} // namespace hdf5
} // namespace amici

#endif