Functions and classes for manipulating HDF5 files. More...

Namespaces
namespace	h5
	Contains functions and classes for manipulating HDF5 files.

Classes
class	h5::Dat
	Represents a multicolumn dat file inside an HDF5 file. More...

class	h5::H5File< Access_t >
	Opens an HDF5 file for access and allows manipulation of data. More...

class	h5::Header
	Writes header info about the build, git commit, branch, etc. More...

class	h5::Object
	Abstract base class representing an object in an HDF5 file. More...

class	h5::SourceArchive
	Writes an archive of the source tree into a dataset. More...

class	h5::StellarCollapseEos
	Reads in tabulated equation of state file from stellarcollapse.org More...

class	h5::Version
	Used to store the version of the file. More...

class	h5::VolumeData
	A volume data subfile written inside an H5 file. More...

Macros
#define	CHECK_H5(h5_status, m)
	Check if an HDF5 operation was successful. More...

Enumerations
enum class	h5::AccessType { h5::AccessType::ReadWrite , h5::AccessType::ReadOnly }
	Set the access type to the H5File. More...

Functions
template<typename T >
void	h5::write_data (hid_t group_id, const std::vector< T > &data, const std::vector< size_t > &extents, const std::string &name="scalar") noexcept
	Write a std::vector named `name` to the group `group_id`

void	h5::write_data (hid_t group_id, const DataVector &data, const std::string &name) noexcept
	Write a DataVector named `name` to the group `group_id`

template<size_t Dim>
void	h5::write_extents (hid_t group_id, const Index< Dim > &extents, const std::string &name="Extents")
	Write the extents as an attribute named `name` to the group `group_id`.

template<typename Type >
void	h5::write_to_attribute (hid_t location_id, const std::string &name, const Type &value) noexcept
	Write a value of type `Type` to an HDF5 attribute named `name`

template<typename T >
void	h5::write_to_attribute (hid_t group_id, const std::string &name, const std::vector< T > &data) noexcept
	Write the vector `data` to the attribute `attribute_name` in the group `group_id`.

template<typename Type >
Type	h5::read_value_attribute (hid_t location_id, const std::string &name) noexcept
	Read a value of type `Type` from an HDF5 attribute named `name`

template<typename Type >
std::vector< Type >	h5::read_rank1_attribute (hid_t group_id, const std::string &name) noexcept
	Read rank-1 of type `Type` from an HDF5 attribute named `name`

std::vector< std::string >	h5::get_attribute_names (hid_t file_id, const std::string &group_name)
	Get the names of all the attributes in a group.

void	h5::write_connectivity (hid_t group_id, const std::vector< int > &connectivity) noexcept
	Write the connectivity into the group in the H5 file.

std::vector< std::string >	h5::get_group_names (hid_t file_id, const std::string &group_name) noexcept
	Get the names of all the groups and datasets in a group.

bool	h5::contains_dataset_or_group (hid_t id, const std::string &group_name, const std::string &dataset_name) noexcept
	Check if `name` is a dataset or group in the subgroup `group_name` of `id`. More...

bool	h5::contains_attribute (hid_t file_id, const std::string &group_name, const std::string &attribute_name)
	Check if an attribute is in a group.

hid_t	h5::open_dataset (hid_t group_id, const std::string &dataset_name) noexcept
	Open an HDF5 dataset.

void	h5::close_dataset (hid_t dataset_id) noexcept
	Close an HDF5 dataset.

hid_t	h5::open_dataspace (hid_t dataset_id) noexcept
	Open an HDF5 dataspace.

void	h5::close_dataspace (hid_t dataspace_id) noexcept
	Close an HDF5 dataspace.

template<size_t Rank, typename T >
T	h5::read_data (hid_t group_id, const std::string &dataset_name) noexcept
	Read an array of rank 0-3 into an object. More...

template<size_t Dim>
Index< Dim >	h5::read_extents (hid_t group_id, const std::string &extents_name="Extents")
	Read the HDF5 attribute representing extents from a group.

template<typename T >
T	h5::StellarCollapseEos::get_scalar_dataset (const std::string &dataset_name) const noexcept
	reads a rank-0 dataset (contains only one element)

std::vector< double >	h5::StellarCollapseEos::get_rank1_dataset (const std::string &dataset_name) const noexcept
	reads a dataset with elements along 1 dimension

boost::multi_array< double, 3 >	h5::StellarCollapseEos::get_rank3_dataset (const std::string &dataset_name) const noexcept
	reads a dataset with elements along 3 dimensions

template<typename T >
hid_t	h5::h5_type ()
	Returns the HDF5 datatype for the corresponding type `T` More...

hid_t	h5::fortran_string () noexcept
	Create an H5 FORTRAN string.

auto	h5::h5f_acc_rdonly () noexcept

auto	h5::h5f_acc_rdwr () noexcept

auto	h5::h5p_default () noexcept

auto	h5::h5s_all () noexcept

auto	h5::h5s_unlimited () noexcept

auto	h5::h5s_scalar () noexcept

Detailed Description

Functions and classes for manipulating HDF5 files.

Macro Definition Documentation

◆ CHECK_H5

#define CHECK_H5	(	h5_status,
		m
	)

Value:

  if (h5_status < 0) {                     /*NOLINT*/ \
    ERROR("Failed HDF5 operation: " << m); /*NOLINT*/ \
  } else                                              \
    static_cast<void>(0)

Check if an HDF5 operation was successful.

Requires: h5_status is a valid HDF5 return type, m is a stringstream syntax error message.

Effects: if h5_status is set to error then aborts execution else none

Enumeration Type Documentation

◆ AccessType

enum class h5::AccessType

strong

Set the access type to the H5File.

Enumerator
ReadWrite	Allow read-write access to the file.
ReadOnly	Allow only read access to the file.

Function Documentation

◆ contains_dataset_or_group()

bool h5::contains_dataset_or_group	(	hid_t	id,
		const std::string &	group_name,
		const std::string &	dataset_name
	)

noexcept

Check if name is a dataset or group in the subgroup group_name of id.

Note: To check the current id for name, pass "" as group_name.

◆ h5_type()

template<typename T >

hid_t h5::h5_type ( )

Returns the HDF5 datatype for the corresponding type T

Requires: T is a valid type with a corresponding HDF5 datatype, i.e. a fundamental or a std::string

Returns: the HDF5 datatype for the corresponding type T

Note: For strings, the returned type must be released with H5Tclose

◆ read_data()

template<size_t Rank, typename T >

T h5::read_data	(	hid_t	group_id,
		const std::string &	dataset_name
	)

noexcept

Read an array of rank 0-3 into an object.

For each rank, the data can be read into objects of the following types: rank 0: double or int rank 1: std::vector or DataVector rank 2: boost::multiarray or DataVector rank 3: boost::multiarray or DataVector

Namespaces

Classes

Macros

Enumerations

Functions