SpECTRE  v2021.11.01
h5 Namespace Reference

Contains functions and classes for manipulating HDF5 files. More...

Classes

class  Dat
 Represents a multicolumn dat file inside an HDF5 file. More...
 
class  H5File
 Opens an HDF5 file for access and allows manipulation of data. More...
 
class  Header
 Writes header info about the build, git commit, branch, etc. More...
 
class  Object
 Abstract base class representing an object in an HDF5 file. More...
 
class  SourceArchive
 Writes an archive of the source tree into a dataset. More...
 
class  StellarCollapseEos
 Reads in tabulated equation of state file from stellarcollapse.org More...
 
class  Version
 Used to store the version of the file. More...
 
class  VolumeData
 A volume data subfile written inside an H5 file. More...
 

Enumerations

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

Functions

std::ostreamoperator<< (std::ostream &os, AccessType t)
 
template<typename T >
void write_data (hid_t group_id, const std::vector< T > &data, const std::vector< size_t > &extents, const std::string &name="scalar")
 Write a std::vector named name to the group group_id
 
void write_data (hid_t group_id, const DataVector &data, const std::string &name)
 Write a DataVector named name to the group group_id
 
template<size_t Dim>
void 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 write_to_attribute (hid_t location_id, const std::string &name, const Type &value)
 Write a value of type Type to an HDF5 attribute named name
 
template<typename T >
void write_to_attribute (hid_t group_id, const std::string &name, const std::vector< T > &data)
 Write the vector data to the attribute attribute_name in the group group_id.
 
template<typename Type >
Type read_value_attribute (hid_t location_id, const std::string &name)
 Read a value of type Type from an HDF5 attribute named name
 
template<typename Type >
std::vector< Type > read_rank1_attribute (hid_t group_id, const std::string &name)
 Read rank-1 of type Type from an HDF5 attribute named name
 
std::vector< std::stringget_attribute_names (hid_t file_id, const std::string &group_name)
 Get the names of all the attributes in a group.
 
void write_connectivity (hid_t group_id, const std::vector< int > &connectivity)
 Write the connectivity into the group in the H5 file.
 
std::vector< std::stringget_group_names (hid_t file_id, const std::string &group_name)
 Get the names of all the groups and datasets in a group.
 
bool contains_dataset_or_group (hid_t id, const std::string &group_name, const std::string &dataset_name)
 Check if name is a dataset or group in the subgroup group_name of id. More...
 
bool 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 open_dataset (hid_t group_id, const std::string &dataset_name)
 Open an HDF5 dataset.
 
void close_dataset (hid_t dataset_id)
 Close an HDF5 dataset.
 
hid_t open_dataspace (hid_t dataset_id)
 Open an HDF5 dataspace.
 
void close_dataspace (hid_t dataspace_id)
 Close an HDF5 dataspace.
 
template<size_t Rank, typename T >
read_data (hid_t group_id, const std::string &dataset_name)
 Read an array of rank 0-3 into an object. More...
 
template<size_t Dim>
Index< Dim > read_extents (hid_t group_id, const std::string &extents_name="Extents")
 Read the HDF5 attribute representing extents from a group.
 
template<typename T >
hid_t h5_type ()
 Returns the HDF5 datatype for the corresponding type T More...
 
hid_t fortran_string ()
 Create an H5 FORTRAN string.
 
std::pair< size_t, size_t > offset_and_length_for_grid (const std::string &grid_name, const std::vector< std::string > &all_grid_names, const std::vector< std::vector< size_t > > &all_extents)
 Find the interval within the contiguous dataset stored in h5::VolumeData that holds data for a particular grid_name. More...
 
auto h5f_acc_rdonly ()
 
auto h5f_acc_rdwr ()
 
auto h5f_acc_trunc ()
 
auto h5p_default ()
 
auto h5s_all ()
 
auto h5s_unlimited ()
 
auto h5s_scalar ()
 

Detailed Description

Contains functions and classes for manipulating HDF5 files.

Wraps many underlying C H5 routines making them easier to use and easier to manipulate H5 files.

Function Documentation

◆ offset_and_length_for_grid()

std::pair< size_t, size_t > h5::offset_and_length_for_grid ( const std::string grid_name,
const std::vector< std::string > &  all_grid_names,
const std::vector< std::vector< size_t > > &  all_extents 
)

Find the interval within the contiguous dataset stored in h5::VolumeData that holds data for a particular grid_name.

h5::VolumeData stores data for all grids that compose the volume contiguously. This function helps with reconstructing which part of that contiguous dataset belongs to a particular grid. See the h5::VolumeData documentation for more information on how it stores data.

To use this function, call h5::VolumeData::get_grid_names and h5::VolumeData::get_extents and pass the results for the all_grid_names and all_extents arguments, respectively. This means you can retrieve this information from an h5::VolumeData once and use it to call offset_and_length_for_grid multiple times with different grid_names.

Here is an example for using this function:

const auto all_grid_names = volume_file.get_grid_names(observation_id);
const auto all_extents = volume_file.get_extents(observation_id);
const auto first_grid_offset_and_length = h5::offset_and_length_for_grid(
grid_names.front(), all_grid_names, all_extents);
std::pair< size_t, size_t > offset_and_length_for_grid(const std::string &grid_name, const std::vector< std::string > &all_grid_names, const std::vector< std::vector< size_t > > &all_extents)
Find the interval within the contiguous dataset stored in h5::VolumeData that holds data for a partic...
See also
h5::VolumeData