hdf5.h File Reference

HDF5 file IO. More...

#include <hdf5.h>
#include <string>
#include <vector>
#include <unordered_map>
#include <stdexcept>
#include <cstring>
#include <sstream>
#include <algorithm>
#include "./error.h"
#include "../core/constants.h"
#include "../algebra/vec.h"
#include "../algebra/mat.h"

Go to the source code of this file.

Classes
class	theoretica::io::hdf5_node
	Represents a single node (group or dataset) in the HDF5 file hierarchy. More...
class	theoretica::io::hdf5_handle
	RAII wrapper for managing HDF5 C-style handles, allowing direct API usage. More...
class	theoretica::io::hdf5_file
	High-level interface for managing an HDF5 file, its structure, and operations. More...

Namespaces
namespace	theoretica
	Main namespace of the library which contains all functions and objects.
namespace	theoretica::io
	Input and output module.

Enumerations
enum class	theoretica::io::HDF5NodeType { theoretica::io::UNKNOWN , theoretica::io::GROUP , theoretica::io::DATASET }
	Type of node inside an HDF5 file. More...

Functions
template<typename Type >
hid_t	theoretica::io::_internal::hdf5_type ()
	Helper template to map C++ types to HDF5 Native Types.
void	theoretica::io::_internal::suppress_errors ()
	Suppress HDF5 error messages by setting a custom dummy error handler.
void	theoretica::io::_internal::remove_link (const hdf5_handle &id, const std::string &path)
	Removes a link (dataset or group) if it exists at the given path.
std::string	theoretica::io::to_string (const hdf5_node &node)
	Generates a string representation of the HDF5 tree structure.
std::ostream &	theoretica::io::operator<< (std::ostream &os, const hdf5_node &node)
	Prints the HDF5 file tree to a stream.
hdf5_handle	theoretica::io::hdf5_open (const std::string &filename, bool write=false)
	Open an HDF5 file with the given filename, returning a file handle.
bool	theoretica::io::hdf5_is_valid (const hdf5_handle &handle)
	Check whether a given HDF5 handle is valid.
hdf5_node	theoretica::io::hdf5_load (const hdf5_handle &id)
	Recursively loads the structure of an active HDF5 group or file.
void	theoretica::io::hdf5_create_group (const hdf5_handle &id, const std::string &path)
	Create a new group at the given path under an already open HDF5 location.
void	theoretica::io::hdf5_delete_group (const hdf5_handle &id, const std::string &path)
	Delete a group (link) at the given path under an already open HDF5 location.
template<typename Type >
Type	theoretica::io::hdf5_read_attribute (const hdf5_handle &id, const std::string &path, const std::string &attr_name)
	Reads an attribute attached to a specific node.
void	theoretica::io::hdf5_delete_attribute (const hdf5_handle &id, const std::string &path, const std::string &attr_name)
	Deletes an attribute attached to a specific node, if it exists.
template<typename Type >
void	theoretica::io::hdf5_write_attribute (const hdf5_handle &id, const std::string &path, const std::string &attr_name, const Type &value)
	Writes or overwrites an attribute attached to a specific node.
template<typename Vector = vec<real>>
Vector &	theoretica::io::hdf5_read_vec (const hdf5_handle &id, const std::string &path, Vector &v)
	Loads a 1D dataset array into a vector.
template<typename Vector = vec<real>>
Vector	theoretica::io::hdf5_read_vec (const hdf5_handle &id, const std::string &path)
	Loads a 1D dataset array into a vector.
template<typename Vector >
void	theoretica::io::hdf5_write_vec (const hdf5_handle &id, const std::string &path, const Vector &v)
	Writes a 1D vector to an HDF5 dataset, overwriting if it exists.
void	theoretica::io::hdf5_delete_dataset (const hdf5_handle &id, const std::string &path)
	Deletes a dataset at the given path if it exists.
template<typename Matrix = mat<real>>
Matrix	theoretica::io::hdf5_read_mat (const hdf5_handle &id, const std::string &path, Matrix &m)
	Loads a 2D dataset array into a matrix.
template<typename Matrix = mat<real>>
Matrix	theoretica::io::hdf5_read_mat (const hdf5_handle &id, const std::string &path)
	Loads a 2D dataset array into a matrix.
template<typename Matrix >
void	theoretica::io::hdf5_write_mat (const hdf5_handle &id, const std::string &path, const Matrix &m)
	Writes a 2D matrix to an HDF5 dataset, overwriting if it exists.

Detailed Description

HDF5 file IO.

Note

Because of its complexity and dependencies, this header is not included automatically in 'theoretica.h'.

Function Documentation

hdf5_type()

template<typename Type >

hid_t theoretica::io::_internal::hdf5_type ( )

inline

Helper template to map C++ types to HDF5 Native Types.

Template Parameters

Type	The C++ scalar type

Returns

The equivalent HDF5 hid_t native type

remove_link()

void theoretica::io::_internal::remove_link ( const hdf5_handle &  id, const std::string &  path  )

inline

Removes a link (dataset or group) if it exists at the given path.

Parameters

id	The active file or group handle
path	The path to check and remove