WxHdf5Io is the interface for the HDF5 implementation of HDF5. More...

#include <wxhdf5io.h>

Inheritance diagram for WxHdf5Io:

Detailed Description

WxHdf5Io is the interface for the HDF5 implementation of HDF5.

Public Member Functions
	WxHdf5Io (MPI_Comm mc, MPI_Info mi)
	Constructor creates the individual templated writers.

	WxHdf5Io (const std::string &bn, int d, MPI_Comm mc, MPI_Info mi)
	Constructor creates the individual templated writers.

virtual	~WxHdf5Io ()
	Virtual destructor.

virtual WxIoNodeType	createFile (const std::string &fileName)
	Create a file.

virtual WxIoNodeType	openFile (const std::string &fileName, const std::string &perms)
	Open a file.

virtual WxIoNodeType	createGroup (WxIoNodeType node, const std::string &dataName) const
	Create an empty group.

virtual WxIoNodeType	openGroup (WxIoNodeType node, const std::string &dataName) const
	Open a group.

virtual std::list< std::string >	getGroupNames (WxIoNodeType parentNode) const
	Get list of group names under the supplied node.

virtual WxIoNodeType	createDataSet (WxIoNodeType node, const std::string &name, const WxRange &range, const std::type_info &typeinfo) const
	Collective dataset allocation.

virtual WxIoNodeType	createDataSet (WxIoNodeType node, const std::string &dataName) const
	Create an empty node.

virtual WxIoNodeType	openDataSet (WxIoNodeType node, const std::string &dataName) const
	Open a node.

virtual void	closeFile (WxIoNodeType fileNode)
	Get the top node = file node.

virtual void	closeNode (WxIoNodeType node) const
	Close a data set.

void	writeStrAttribute (WxIoNodeType node, const std::string &attribName, const std::string &attrib) const
	Write a string attribute.

void	writeStrVecAttribute (WxIoNodeType node, const std::string &attribName, const std::vector< std::string > &stringsvector) const
	Write a vector of strings as attribute.

void	readStrAttribute (WxIoNodeType node, const std::string &attribName, std::string &attrib) const
	Read a string attribute.

std::vector< std::string >	readStrVecAttribute (WxIoNodeType node, const std::string &attribName) const
	Read a vector of strings attribute.

Public Member Functions inherited from WxIoBase
virtual	~WxIoBase ()
	Virtual destructor.

void	setBaseName (const std::string &bn)
	Set the base name.

std::string	getBaseName ()
	Get the base name.

void	setDumpNo (int d)
	Set the dump number.

int	getDumpNo ()
	Get the dump number.

virtual WxIoNodeType	createFile (const std::string &fileName)=0
	Create a file.

virtual WxIoNodeType	createDumpFile (const std::string &dataName)
	Create a file with base name prepended and dump and suffix appended.

virtual WxIoNodeType	openFile (const std::string &fileName, const std::string &perms)=0
	Open a file.

virtual WxIoNodeType	openDumpFile (const std::string &dataName, const std::string &perms)
	Open a file with the base name prepended and the dump and suffix appended.

virtual void	closeFile (WxIoNodeType fileNode)=0
	Close a file node.

virtual std::string	getDumpFileName (const std::string &dataName)
	Get the dump name for a given data name.

virtual WxIoNodeType	createGroup (WxIoNodeType node, const std::string &dataName) const =0
	Create an empty group.

virtual WxIoNodeType	openGroup (WxIoNodeType node, const std::string &dataName) const =0
	Open a group.

virtual std::list< std::string >	getGroupNames (WxIoNodeType node) const =0
	Get list of group names under the supplied node.

virtual WxIoNodeType	createDataSet (WxIoNodeType node, const std::string &name, const WxRange &range, const std::type_info &typeinfo) const =0
	Collective dataset allocation.

virtual WxIoNodeType	createDataSet (WxIoNodeType node, const std::string &dataName) const =0
	Create an empty node.

virtual WxIoNodeType	openDataSet (WxIoNodeType node, const std::string &dataName) const =0
	Open a node.

template<typename T >
WxIoNodeType	writeDataSet (WxIoNodeType node, const std::string &dataName, const std::vector< std::pair< int, int > > &fileSpaceCorners, const std::vector< std::pair< int, int > > &memorySpaceCorners, const std::vector< std::pair< int, int > > &writeSelectionCorners, const T *data) const
	Write a new data set under a node.

template<typename T >
void	writeToDataSet (WxIoNodeType node, const WxRange &memoryRange, const WxRange &memorySubRange, const WxRange &fileRange, const WxRange &fileSubRange, const T *data) const
	Write to an open dataset (independent)

template<typename T >
WxIoNodeType	readDataSet (WxIoNodeType node, const std::string &dataName, const std::vector< std::pair< int, int > > &memorySpaceCorners, const std::vector< std::pair< int, int > > &readSelectionCorners, T *data) const
	Read a new data set under a node.

template<typename T >
void	readFromDataSet (WxIoNodeType node, const WxRange &memoryRange, const WxRange &memorySubRange, const WxRange &fileRange, const WxRange &fileSubRange, T *data) const
	Read from an open dataset (independent)

WxIoNodeType	getDataShape (WxIoNodeType node, const std::string &dataSetName, WxRange &dataShape) const
	Obtain simple data shape for a data set under a node.

virtual void	closeNode (WxIoNodeType node) const =0
	Close a data set.

template<typename T >
void	writeAttribute (WxIoNodeType node, const std::string &attribName, const T *attrib)
	Write an attribute.

template<typename T >
void	writeVecAttribute (WxIoNodeType node, const std::string &attribName, const std::vector< T > &attrib)
	Write an attribute (vector).

template<typename T >
void	writeVecAttribute (WxIoNodeType node, const std::string &attribName, const T *attribStorage, int count)
	Write a vector of attributes.

virtual void	writeStrAttribute (WxIoNodeType node, const std::string &attribName, const std::string &attrib) const =0
	Write a string attribute.

virtual void	writeStrVecAttribute (WxIoNodeType node, const std::string &attribName, const std::vector< std::string > &stringsvector) const =0
	Write a vector of strings as attribute.

virtual void	readStrAttribute (WxIoNodeType node, const std::string &attribName, std::string &attrib) const =0
	Read a string attribute.

virtual std::vector< std::string >	readStrVecAttribute (WxIoNodeType node, const std::string &attribName) const =0
	Read a vector of strings attribute.

template<typename T >
void	readAttribute (WxIoNodeType node, const std::string &attribName, T *attrib)
	Read an attribute.

template<typename T >
int	readVecAttribute (WxIoNodeType node, const std::string &attribName, T *attribStorage, int count)
	Read a vector attribute.

Additional Inherited Members
Protected Member Functions inherited from WxIoBase
	WxIoBase ()
	Default constructor - no dump, basename or suffix.

	WxIoBase (const std::string &sfx)
	Constructor is protected, as this class cannot be made standalone.

	WxIoBase (const std::string &bn, int d, const std::string &sfx)
	Constructor is protected, as this class cannot be made standalone.

virtual void	addOpenFile (WxIoNodeType node)
	Add a file to the list of open files.

virtual void	removeOpenFile (WxIoNodeType node)
	Remove a file from the list of open files.

virtual void	closeOpenFiles ()
	Close any files currently open.

void	setIo (const WxIoTmpl *b)
	Sets the new io object implementation.

Protected Attributes inherited from WxIoBase
std::string	suffix

Constructor & Destructor Documentation

◆ WxHdf5Io() [1/2]

WxHdf5Io::WxHdf5Io	(	MPI_Comm	mc,
		MPI_Info	mi
	)

Constructor creates the individual templated writers.

Parameters

mc	the MPI communicator
mi	info for the MPI communicator

◆ WxHdf5Io() [2/2]

WxHdf5Io::WxHdf5Io	(	const std::string &	bn,
		int	d,
		MPI_Comm	mc,
		MPI_Info	mi
	)

Constructor creates the individual templated writers.

Parameters

bn	base name for the dump
d	the dump number
mc	the MPI communicator
mi	info for the MPI communicator

◆ ~WxHdf5Io()

virtual WxHdf5Io::~WxHdf5Io ( )

virtual

Virtual destructor.

Member Function Documentation

◆ closeFile()

virtual void WxHdf5Io::closeFile ( WxIoNodeType fileNode )

virtual

Get the top node = file node.

Implements WxIoBase.

◆ closeNode()

virtual void WxHdf5Io::closeNode ( WxIoNodeType node ) const

virtual

Close a data set.

Parameters

node	the node to be closed

Implements WxIoBase.

◆ createDataSet() [1/2]

virtual WxIoNodeType WxHdf5Io::createDataSet	(	WxIoNodeType	node,
		const std::string &	dataName
	)		const

virtual

Create an empty node.

Parameters

node	the node to write under
dataName	the name of the data

Returns: the node to the written data

Implements WxIoBase.

◆ createDataSet() [2/2]

virtual WxIoNodeType WxHdf5Io::createDataSet	(	WxIoNodeType	node,
		const std::string &	name,
		const WxRange &	range,
		const std::type_info &	typeinfo
	)		const

virtual

Collective dataset allocation.

Parameters

node	the node to write under
name	the name of the data
range	the name of the data

Returns: the node to the dataset. This is not closed.

Implements WxIoBase.

◆ createFile()

virtual WxIoNodeType WxHdf5Io::createFile ( const std::string & fileName )

virtual

Create a file.

Parameters

fileName the name for the file. (an extension of '.h5' is added to the supplied filename.) Assumed to be rw.

Returns: node for the file

Implements WxIoBase.

◆ createGroup()

virtual WxIoNodeType WxHdf5Io::createGroup	(	WxIoNodeType	node,
		const std::string &	dataName
	)		const

virtual

Create an empty group.

Parameters

node	the node to write under
dataName	the name of the data

Returns: the node to the written data

Implements WxIoBase.

◆ getGroupNames()

virtual std::list< std::string > WxHdf5Io::getGroupNames ( WxIoNodeType parentNode ) const

virtual

Get list of group names under the supplied node.

Parameters

node	the node to look in

Returns: list of group names found under the supplied node

Implements WxIoBase.

◆ openDataSet()

virtual WxIoNodeType WxHdf5Io::openDataSet	(	WxIoNodeType	node,
		const std::string &	dataName
	)		const

virtual

Open a node.

Parameters

node	the node to look in
dataName	the name of the node to open

Returns: the node to the read data

Implements WxIoBase.

◆ openFile()

virtual WxIoNodeType WxHdf5Io::openFile	(	const std::string &	fileName,
		const std::string &	perms
	)

virtual

Open a file.

Parameters

fileName	the name for the file
perms	the read and write permissions. "r" or "rw"

Returns: node for the file

Implements WxIoBase.

◆ openGroup()

virtual WxIoNodeType WxHdf5Io::openGroup	(	WxIoNodeType	node,
		const std::string &	dataName
	)		const

virtual

Open a group.

Parameters

node	the node to look in
dataName	the name of the data to open

Returns: the node to the read data

Implements WxIoBase.

◆ readStrAttribute()

void WxHdf5Io::readStrAttribute	(	WxIoNodeType	node,
		const std::string &	attribName,
		std::string &	attrib
	)		const

virtual

Read a string attribute.

The string attribute data type may be a fixed length or variable length string.

Parameters

node	the node to read under
attribName	the name of the attribute
attrib	the string value of the attribute

Implements WxIoBase.

◆ readStrVecAttribute()

std::vector< std::string > WxHdf5Io::readStrVecAttribute	(	WxIoNodeType	node,
		const std::string &	attribName
	)		const

virtual

Read a vector of strings attribute.

Parameters

node	the node to read under
attribName	the name of the attribute

Returns: the vector of string values in the attribute.

Exceptions

AtttributeNotFoundException if attribName is not found at node.

Implements WxIoBase.

◆ writeStrAttribute()

void WxHdf5Io::writeStrAttribute	(	WxIoNodeType	node,
		const std::string &	attribName,
		const std::string &	attrib
	)		const

virtual

Write a string attribute.

Note that the attribute data type will be a fixed size character string in a scalar dataspace.

Parameters

node	the node to write under
attribName	the name of the attribute
attrib	the string value of the attribute

Implements WxIoBase.

◆ writeStrVecAttribute()

void WxHdf5Io::writeStrVecAttribute	(	WxIoNodeType	node,
		const std::string &	attribName,
		const std::vector< std::string > &	stringsvector
	)		const

virtual

Write a vector of strings as attribute.

Note that the strings are written out as HDF5 variable-length strings.

Parameters

node	the node to write under
attribName	the name of the attribute
the	vector of strings for the attribute

Implements WxIoBase.

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

src/lib/wxhdf5io.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

◆ WxHdf5Io() [1/2]

◆ WxHdf5Io() [2/2]

◆ ~WxHdf5Io()

Member Function Documentation

◆ closeFile()

◆ closeNode()

◆ createDataSet() [1/2]

◆ createDataSet() [2/2]

◆ createFile()

◆ createGroup()

◆ getGroupNames()

◆ openDataSet()

◆ openFile()

◆ openGroup()

◆ readStrAttribute()

◆ readStrVecAttribute()

◆ writeStrAttribute()

◆ writeStrVecAttribute()