A base class for reading and writing an HDF5 file. More...

#include <hdf5_file.h>

Collaboration diagram for Kratos::HDF5::File:

Public Member Functions
Life Cycle
	File (const DataCommunicator &rDataCommunicator, Parameters Settings)

	File (const File &rOther)=delete

	File (File &&rOther)

virtual	~File ()

File &	operator= (const File &rOther)=delete

File &	operator= (File &&rOther)

Public operations
bool	HasPath (const std::string &rPath) const
	Checks if the given rPath exists. More...

bool	IsGroup (const std::string &rPath) const
	Checks if rPath contains a group. More...

bool	IsDataSet (const std::string &rPath) const
	Checks if rPath is a dataset. More...

bool	HasAttribute (const std::string &rObjectPath, const std::string &rName) const
	Checks if the given rName attribute exists in rObjectPath. More...

template<class TDataType >
bool	HasAttributeType (const std::string &rObjectPath, const std::string &rName) const
	Checks if the attribute is of the specified type. More...

std::vector< hsize_t >	GetAttributeDimensions (const std::string &rObjectPath, const std::string &rName) const
	Get the Attribute Dimensions. More...

void	DeleteAttribute (const std::string &rObjectPath, const std::string &rName)
	Deletes the specified attribute from the dataset or group. More...

std::vector< std::string >	GetAttributeNames (const std::string &rObjectPath) const
	Get the Attributes' Names list. More...

void	CreateGroup (const std::string &rPath)
	Create a Group. More...

std::vector< std::string >	GetLinkNames (const std::string &rGroupPath) const
	Get the link names under a group. More...

std::vector< std::string >	GetGroupNames (const std::string &rGroupPath) const
	Get the sub group names under a group. More...

std::vector< std::string >	GetDataSetNames (const std::string &rGroupPath) const
	Get the dataset names under a group. More...

void	AddPath (const std::string &rPath)
	Add a group to the path recursively. More...

template<class TDataType >
void	WriteAttribute (const std::string &rObjectPath, const std::string &rName, const TDataType &rValue)
	Write attributes to specified group or dataset. More...

void	WriteAttribute (const std::string &rObjectPath, const Parameters Attributes)
	Write attributes in a Parameters object to dataset or group. More...

template<class TDataType >
void	WriteDataSet (const std::string &rPath, const TDataType &rData, WriteInfo &rInfo)
	Write a dataset to the hDF5 file. More...

template<class TDataType >
void	WriteDataSetIndependent (const std::string &rPath, const TDataType &rData, WriteInfo &rInfo)
	Independently write dataset to the HDF5 file. More...

std::vector< unsigned >	GetDataDimensions (const std::string &rPath) const
	Get the shape of the dataset stored at the specified path. More...

bool	HasIntDataType (const std::string &rPath) const
	Checks if the dataset at path is of int type. More...

bool	HasFloatDataType (const std::string &rPath) const
	Checks if the dataset at path is of double type. More...

template<class TDataType >
bool	HasDataType (const std::string &rPath) const
	Checks the datast at path is of TDataType. More...

void	Flush ()
	Flush the content to HDF5 file. More...

void	Close ()
	Terminate access to the HDF5 file. More...

unsigned	GetFileSize () const

std::string	GetFileName () const

int	GetEchoLevel () const

void	SetEchoLevel (int Level)

const DataCommunicator &	GetDataCommunicator () const

unsigned	GetPID () const
	Get the process rank. More...

unsigned	GetTotalProcesses () const
	Get the Total number of processes with file access. More...

template<class TDataType >
void	ReadAttribute (const std::string &rObjectPath, const std::string &rName, TDataType &rValue) const
	Read attribute from a group or dataset. More...

Parameters	ReadAttribute (const std::string &rObjectPath) const
	Read attributes from a dataset or group to a Parameters object. More...

template<class TDataType >
void	ReadDataSet (const std::string &rPath, TDataType &rData, const unsigned StartIndex, const unsigned BlockSize) const
	Read a dataset from the HDF5 file. More...

template<class TDataType >
void	ReadDataSetIndependent (const std::string &rPath, TDataType &rData, const unsigned StartIndex, const unsigned BlockSize) const
	Independently read a dataset from the HDF5 file. More...

unsigned	GetOpenObjectsCount () const

Type Definitions
template<class T >
using	Vector = HDF5::Vector< T >

template<class T >
using	Matrix = HDF5::Matrix< T >

	KRATOS_CLASS_POINTER_DEFINITION (File)
	Pointer definition. More...

Detailed Description

A base class for reading and writing an HDF5 file.

This class stores the file id and is responsible for reading and writing meta data. Reading and writing data sets is the responsibility of the derived class.

Member Typedef Documentation

◆ Matrix

template<class T >

using Kratos::HDF5::File::Matrix = HDF5::Matrix<T>

◆ Vector

template<class T >

using Kratos::HDF5::File::Vector = HDF5::Vector<T>

Constructor & Destructor Documentation

◆ File() [1/3]

Kratos::HDF5::File::File	(	const DataCommunicator &	rDataCommunicator,
		Parameters	Settings
	)

explicit

◆ File() [2/3]

Kratos::HDF5::File::File ( const File & rOther )

delete

◆ File() [3/3]

Kratos::HDF5::File::File ( File && rOther )

◆ ~File()

Kratos::HDF5::File::~File ( )

virtual

Member Function Documentation

◆ AddPath()

void Kratos::HDF5::File::AddPath ( const std::string & rPath )

Add a group to the path recursively.

This method creates all the parent groups to create the final rPath.

Exceptions

If	any of the parents in the rPath is not a group.

Parameters

rPath Path to be created.

◆ Close()

void Kratos::HDF5::File::Close ( )

Terminate access to the HDF5 file.

Exceptions

If	the underlying HDF5 call fails.

Returns: * void

◆ CreateGroup()

void Kratos::HDF5::File::CreateGroup ( const std::string & rPath )

Create a Group.

Parameters

rPath Path of the group to be created.

◆ DeleteAttribute()

void Kratos::HDF5::File::DeleteAttribute	(	const std::string &	rObjectPath,
		const std::string &	rName
	)

Deletes the specified attribute from the dataset or group.

Parameters

rObjectPath	Path of a dataset or group.
rName	Attribute name to be deleted.

◆ Flush()

void Kratos::HDF5::File::Flush ( )

Flush the content to HDF5 file.

◆ GetAttributeDimensions()

std::vector< hsize_t > Kratos::HDF5::File::GetAttributeDimensions	(	const std::string &	rObjectPath,
		const std::string &	rName
	)		const

Get the Attribute Dimensions.

Parameters

rObjectPath	Dataset or group path.
rName	Attribute name.

Returns: std::vector<hsize_t> Size in each dimension.

◆ GetAttributeNames()

std::vector< std::string > Kratos::HDF5::File::GetAttributeNames ( const std::string & rObjectPath ) const

Get the Attributes' Names list.

Parameters

rObjectPath Path of a dataset or group.

Returns: std::vector<std::string> List of attribute names.

◆ GetDataCommunicator()

const DataCommunicator & Kratos::HDF5::File::GetDataCommunicator ( ) const

◆ GetDataDimensions()

std::vector< unsigned > Kratos::HDF5::File::GetDataDimensions ( const std::string & rPath ) const

Get the shape of the dataset stored at the specified path.

Parameters

rPath Dataset path.

Returns: std::vector<unsigned> Dimensions of the dataset.

◆ GetDataSetNames()

std::vector< std::string > Kratos::HDF5::File::GetDataSetNames ( const std::string & rGroupPath ) const

Get the dataset names under a group.

Parameters

rGroupPath Group path.

Returns: std::vector<std::string> List of sub dataset names.

◆ GetEchoLevel()

int Kratos::HDF5::File::GetEchoLevel ( ) const

◆ GetFileName()

std::string Kratos::HDF5::File::GetFileName ( ) const

◆ GetFileSize()

unsigned Kratos::HDF5::File::GetFileSize ( ) const

◆ GetGroupNames()

std::vector< std::string > Kratos::HDF5::File::GetGroupNames ( const std::string & rGroupPath ) const

Get the sub group names under a group.

Parameters

rGroupPath Group path.

Returns: std::vector<std::string> List of sub group names.

◆ GetLinkNames()

std::vector< std::string > Kratos::HDF5::File::GetLinkNames ( const std::string & rGroupPath ) const

Get the link names under a group.

Parameters

rGroupPath Group path.

Returns: std::vector<std::string> List of link names.

◆ GetOpenObjectsCount()

unsigned Kratos::HDF5::File::GetOpenObjectsCount ( ) const

◆ GetPID()

unsigned Kratos::HDF5::File::GetPID ( ) const

Get the process rank.

◆ GetTotalProcesses()

unsigned Kratos::HDF5::File::GetTotalProcesses ( ) const

Get the Total number of processes with file access.

◆ HasAttribute()

bool Kratos::HDF5::File::HasAttribute	(	const std::string &	rObjectPath,
		const std::string &	rName
	)		const

Checks if the given rName attribute exists in rObjectPath.

Parameters

rObjectPath	Path of a dataset or a group.
rName	Attribute name.

Returns: true True if attribute exists in the dataset or group, otherwise false.

◆ HasAttributeType()

template<class TDataType >

bool Kratos::HDF5::File::HasAttributeType	(	const std::string &	rObjectPath,
		const std::string &	rName
	)		const

Checks if the attribute is of the specified type.

Template Parameters

TDataType Data type to check.

Parameters

rObjectPath	Dataset or group path.
rName	Attribute name.

Returns: true If the attribute has data of type TDataType.; false If the attribute does not has the data of type TDataType.

◆ HasDataType()

template<class TDataType >

bool Kratos::HDF5::File::HasDataType ( const std::string & rPath ) const

Checks the datast at path is of TDataType.

Template Parameters

TDataType Datatype to check against.

Parameters

rPath Dataset path.

Returns: true If dataset is of TDataType.; false If dataset is not of TDataType.

◆ HasFloatDataType()

bool Kratos::HDF5::File::HasFloatDataType ( const std::string & rPath ) const

Checks if the dataset at path is of double type.

Parameters

rPath Dataset path.

Returns: true If dataset of double type.; false If dataset is not of double type.

◆ HasIntDataType()

bool Kratos::HDF5::File::HasIntDataType ( const std::string & rPath ) const

Checks if the dataset at path is of int type.

Parameters

rPath Dataset path.

Returns: true If dataset of int type.; false If dataset is not of int type.

◆ HasPath()

bool Kratos::HDF5::File::HasPath ( const std::string & rPath ) const

Checks if the given rPath exists.

Exceptions

If	a string with invalid characters is given.

Parameters

rPath Path to be checked.

Returns: true True if rPath exists, otherwise false.

◆ IsDataSet()

bool Kratos::HDF5::File::IsDataSet ( const std::string & rPath ) const

Checks if rPath is a dataset.

Parameters

rPath Path to be checked for.

Returns: true True if rPath exists and it is a dataset, otherwise false.

◆ IsGroup()

bool Kratos::HDF5::File::IsGroup ( const std::string & rPath ) const

Checks if rPath contains a group.

Parameters

rPath Path to be checked for.

Returns: true True if rPath exists and it is a group., otherwise false.

◆ KRATOS_CLASS_POINTER_DEFINITION()

Kratos::HDF5::File::KRATOS_CLASS_POINTER_DEFINITION ( File )

Pointer definition.

◆ operator=() [1/2]

File& Kratos::HDF5::File::operator= ( const File & rOther )

delete

◆ operator=() [2/2]

File & Kratos::HDF5::File::operator= ( File && rOther )

◆ ReadAttribute() [1/2]

Parameters Kratos::HDF5::File::ReadAttribute ( const std::string & rObjectPath ) const

Read attributes from a dataset or group to a Parameters object.

Parameters

rObjectPath Dataset or group path.

Returns: Parameters Parameters object containing attribute name, value pairs.

◆ ReadAttribute() [2/2]

template<class TDataType >

void Kratos::HDF5::File::ReadAttribute	(	const std::string &	rObjectPath,
		const std::string &	rName,
		TDataType &	rValue
	)		const

Read attribute from a group or dataset.

Template Parameters

TDataType Datatype of the attribute.

Parameters

rObjectPath	Group or dataset path.
rName	Attribute name.
rValue	Attribute value to be written to.

◆ ReadDataSet()

template<class TDataType >

void Kratos::HDF5::File::ReadDataSet	(	const std::string &	rPath,
		TDataType &	rData,
		const unsigned	StartIndex,
		const unsigned	BlockSize
	)		const

Read a dataset from the HDF5 file.

Performs collective read in MPI. Throws if out of range.

Exceptions

if	out of range.

Template Parameters

TDataType Datatype of the read data.

Parameters

rPath	Path of the dataset.
rData	Data to be written to.
StartIndex	Starting offset of data for this rank.
BlockSize	Number of data points for this rank.

◆ ReadDataSetIndependent()

template<class TDataType >

void Kratos::HDF5::File::ReadDataSetIndependent	(	const std::string &	rPath,
		TDataType &	rData,
		const unsigned	StartIndex,
		const unsigned	BlockSize
	)		const

Independently read a dataset from the HDF5 file.

Performs independent read in MPI. Throws if out of range.

Template Parameters

TDataType Datatype of the read data.

Parameters

rPath	Path of the dataset.
rData	Data to be written to.
StartIndex	Starting offset of data for this rank.
BlockSize	Number of data points for this rank.

◆ SetEchoLevel()

void Kratos::HDF5::File::SetEchoLevel ( int Level )

◆ WriteAttribute() [1/2]

void Kratos::HDF5::File::WriteAttribute	(	const std::string &	rObjectPath,
		const Parameters	Attributes
	)

Write attributes in a Parameters object to dataset or group.

Parameters

rObjectPath	Dataset or group path.
Attributes	Attributes to be written to.

◆ WriteAttribute() [2/2]

template<class TDataType >

void Kratos::HDF5::File::WriteAttribute	(	const std::string &	rObjectPath,
		const std::string &	rName,
		const TDataType &	rValue
	)

Write attributes to specified group or dataset.

Template Parameters

TDataType Data type of the attribute.

Parameters

rObjectPath	Group or dataset path.
rName	Attribute name.
rValue	Atribute data.

◆ WriteDataSet()

template<class TDataType >

void Kratos::HDF5::File::WriteDataSet	(	const std::string &	rPath,
		const TDataType &	rData,
		WriteInfo &	rInfo
	)

Write a dataset to the hDF5 file.

Performs collective write in MPI. The data is written blockwise according to processor rank.

Template Parameters

TDataType Data type of the provided data.

Parameters

rPath	Path to which the data is written.
rData	Data to be written.
rInfo	Information about the written data (output).

◆ WriteDataSetIndependent()

template<class TDataType >

void Kratos::HDF5::File::WriteDataSetIndependent	(	const std::string &	rPath,
		const TDataType &	rData,
		WriteInfo &	rInfo
	)

Independently write dataset to the HDF5 file.

Performs independent write in MPI. Must be called collectively. Throws if more than one process has non-empty data.

Template Parameters

TDataType Data type of the Data.

Parameters

rPath	Path to which the data is written.
rData	Data to be written.
rInfo	Information about the written data (output).

The documentation for this class was generated from the following files:

/home/runner/work/Documentation/Documentation/master/applications/HDF5Application/custom_io/hdf5_file.h
/home/runner/work/Documentation/Documentation/master/applications/HDF5Application/custom_io/hdf5_file.cpp

Public Member Functions

Type Definitions

Detailed Description

Member Typedef Documentation

◆ Matrix

◆ Vector

Constructor & Destructor Documentation

◆ File() [1/3]

◆ File() [2/3]

◆ File() [3/3]

◆ ~File()

Member Function Documentation

◆ AddPath()

◆ Close()

◆ CreateGroup()

◆ DeleteAttribute()

◆ Flush()

◆ GetAttributeDimensions()

◆ GetAttributeNames()

◆ GetDataCommunicator()

◆ GetDataDimensions()

◆ GetDataSetNames()

◆ GetEchoLevel()

◆ GetFileName()

◆ GetFileSize()

◆ GetGroupNames()

◆ GetLinkNames()

◆ GetOpenObjectsCount()

◆ GetPID()

◆ GetTotalProcesses()

◆ HasAttribute()

◆ HasAttributeType()

◆ HasDataType()

◆ HasFloatDataType()

◆ HasIntDataType()

◆ HasPath()

◆ IsDataSet()

◆ IsGroup()

◆ KRATOS_CLASS_POINTER_DEFINITION()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ ReadAttribute() [1/2]

◆ ReadAttribute() [2/2]

◆ ReadDataSet()

◆ ReadDataSetIndependent()

◆ SetEchoLevel()

◆ WriteAttribute() [1/2]

◆ WriteAttribute() [2/2]

◆ WriteDataSet()

◆ WriteDataSetIndependent()