Provides an abstract interface for access to hierachical datasets. More...

#include <wxiobase.h>

Inheritance diagram for WxIoBase:

Detailed Description

Provides an abstract interface for access to hierachical datasets.

Classes
struct	AtttributeNotFoundException
	Exception class for reporting when an attribute does not exist. More...

Public Member Functions
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.

Protected Member Functions
	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
std::string	suffix

Constructor & Destructor Documentation

◆ ~WxIoBase()

virtual WxIoBase::~WxIoBase ( )

virtual

Virtual destructor.

◆ WxIoBase() [1/3]

WxIoBase::WxIoBase ( )

protected

Default constructor - no dump, basename or suffix.

◆ WxIoBase() [2/3]

WxIoBase::WxIoBase ( const std::string & sfx )

protected

Constructor is protected, as this class cannot be made standalone.

Construct with suffix only.

Parameters

sfx	the suffix for file names

◆ WxIoBase() [3/3]

WxIoBase::WxIoBase	(	const std::string &	bn,
		int	d,
		const std::string &	sfx
	)

protected

Constructor is protected, as this class cannot be made standalone.

Parameters

bn	the base for file names
d	the dump number for file names
sfx	the suffix for file names

Member Function Documentation

◆ addOpenFile()

virtual void WxIoBase::addOpenFile ( WxIoNodeType node )

protectedvirtual

Add a file to the list of open files.

Parameters

node	the file node

◆ closeFile()

virtual void WxIoBase::closeFile ( WxIoNodeType fileNode )

pure virtual

Close a file node.

Implemented in WxHdf5Io.

◆ closeNode()

virtual void WxIoBase::closeNode ( WxIoNodeType node ) const

pure virtual

Close a data set.

Parameters

node	the node to be closed

Implemented in WxHdf5Io.

◆ closeOpenFiles()

virtual void WxIoBase::closeOpenFiles ( )

protectedvirtual

Close any files currently open.

◆ createDataSet() [1/2]

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

pure 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. This is not closed.

Implemented in WxHdf5Io.

◆ createDataSet() [2/2]

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

pure 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.

Implemented in WxHdf5Io.

◆ createDumpFile()

virtual WxIoNodeType WxIoBase::createDumpFile ( const std::string & dataName )

virtual

Create a file with base name prepended and dump and suffix appended.

Parameters

dataName the name for the file. Assumed to be rw.

Returns: node for the file

◆ createFile()

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

pure virtual

Create a file.

Parameters

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

Returns: node for the file

Implemented in WxHdf5Io.

◆ createGroup()

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

pure 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. This is not closed.

Implemented in WxHdf5Io.

◆ getBaseName()

std::string WxIoBase::getBaseName ( )

inline

Get the base name.

Returns: the base name. Used to compose the file name.

◆ getDataShape()

WxIoNodeType WxIoBase::getDataShape	(	WxIoNodeType	node,
		const std::string &	dataSetName,
		WxRange &	dataShape
	)		const

inline

Obtain simple data shape for a data set under a node.

Parameters

node	the node under which to find the dataset
dataName	the name of the data
dataShape	the data set shape is returned by reference

Returns: the node to the dataset found

◆ getDumpFileName()

virtual std::string WxIoBase::getDumpFileName ( const std::string & dataName )

virtual

Get the dump name for a given data name.

◆ getDumpNo()

int WxIoBase::getDumpNo ( )

inline

Get the dump number.

Returns: the dump number

◆ getGroupNames()

virtual std::list< std::string > WxIoBase::getGroupNames ( WxIoNodeType node ) const

pure 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

Implemented in WxHdf5Io.

◆ openDataSet()

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

pure 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

Implemented in WxHdf5Io.

◆ openDumpFile()

virtual WxIoNodeType WxIoBase::openDumpFile	(	const std::string &	dataName,
		const std::string &	perms
	)

virtual

Open a file with the base name prepended and the dump and suffix appended.

Parameters

dataName	used to compose the name of the file
perms	the read and write permissions. "r" or "rw"

Returns: node for the file

◆ openFile()

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

pure 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

Implemented in WxHdf5Io.

◆ openGroup()

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

pure 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

Implemented in WxHdf5Io.

◆ readAttribute()

template<typename T >

void WxIoBase::readAttribute	(	WxIoNodeType	node,
		const std::string &	attribName,
		T *	attrib
	)

inline

Read an attribute.

Parameters

node	the node to write under
attribName	the name of the attribute
attrib	the attribute to be read

◆ readDataSet()

template<typename T >

WxIoNodeType WxIoBase::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

inline

Read a new data set under a node.

Parameters

node	the node to read under
dataName	the name of the data
memorySpaceCorners	vector of (start, stop) pairs for each dimension that specify local extent held in contiguous allocation
readSelectionCorners	vector of (start, stop) pairs for each dimension that specify subarea of local extent to read
data	the destination for data to be read. This is returned in ROW MAJOR ordering.

Returns: the node to the written data. The node is not closed.

◆ readFromDataSet()

template<typename T >

void WxIoBase::readFromDataSet	(	WxIoNodeType	node,
		const WxRange &	memoryRange,
		const WxRange &	memorySubRange,
		const WxRange &	fileRange,
		const WxRange &	fileSubRange,
		T *	data
	)		const

inline

Read from an open dataset (independent)

Parameters

node	the node to read under
memoryRange	Range that specifies total extent on host
memorySubRange	Range that specifies local extent on host
fileRange	Range that specifies total extent on file
fileSubRange	Range that specifies local extent on file
data	the destination for data to be read. This is returned in ROW MAJOR ordering.

◆ readStrAttribute()

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

pure virtual

Read a string attribute.

Parameters

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

Implemented in WxHdf5Io.

◆ readStrVecAttribute()

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

pure 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.
WxExcept	on all other errors

Implemented in WxHdf5Io.

◆ readVecAttribute()

template<typename T >

int WxIoBase::readVecAttribute	(	WxIoNodeType	node,
		const std::string &	attribName,
		T *	attribStorage,
		int	count
	)

inline

Read a vector attribute.

Parameters

node	the node to which this attribute belongs
attribName	the name of the attribute
attribStorage	the vector attribute to be read
count	maximum number of items to read; the amount of memory provided by attribStorage

Returns: number of items actually read

◆ removeOpenFile()

virtual void WxIoBase::removeOpenFile ( WxIoNodeType node )

protectedvirtual

Remove a file from the list of open files.

Parameters

node	the file node

◆ setBaseName()

void WxIoBase::setBaseName ( const std::string & bn )

inline

Set the base name.

Parameters

bn	the base name

◆ setDumpNo()

void WxIoBase::setDumpNo ( int d )

inline

Set the dump number.

Parameters

d	the dump number. Not used if negative.

◆ setIo()

void WxIoBase::setIo ( const WxIoTmpl * b )

inlineprotected

Sets the new io object implementation.

The derived class should call this to setup WxIoBase properly.

◆ writeAttribute()

template<typename T >

void WxIoBase::writeAttribute	(	WxIoNodeType	node,
		const std::string &	attribName,
		const T *	attrib
	)

inline

Write an attribute.

Parameters

node	the node to write under
attribName	the name of the attribute
attrib	the attribute to be written

◆ writeDataSet()

template<typename T >

WxIoNodeType WxIoBase::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

inline

Write a new data set under a node.

Parameters

node	the node to write under
dataName	the name of the data
fileSpaceCorners	vector of (start, stop) pairs for each dimension that specify the global data space extent
memorySpaceCorners	vector of (start, stop) pairs for each dimension that specify local extent held in contiguous allocation
writeSelectionCorners	vector of (start, stop) pairs for each dimension that specify subarea of local extent to write
data	the data to be written. This is expected in ROW MAJOR ordering.

Returns: the node to the written data. The node is not closed.

◆ writeStrAttribute()

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

pure virtual

Write a string attribute.

Parameters

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

Implemented in WxHdf5Io.

◆ writeStrVecAttribute()

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

pure virtual

Write a vector of strings as attribute.

Parameters

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

Implemented in WxHdf5Io.

◆ writeToDataSet()

template<typename T >

void WxIoBase::writeToDataSet	(	WxIoNodeType	node,
		const WxRange &	memoryRange,
		const WxRange &	memorySubRange,
		const WxRange &	fileRange,
		const WxRange &	fileSubRange,
		const T *	data
	)		const

inline

Write to an open dataset (independent)

Parameters

node	the node to write under
memoryRange	Range that specifies total extent on host
memorySubRange	Range that specifies local extent on host
fileRange	Range that specifies total extent on file
fileSubRange	Range that specifies local extent on file
data	the destination for data to be written. This is returned in ROW MAJOR ordering.

◆ writeVecAttribute() [1/2]

template<typename T >

void WxIoBase::writeVecAttribute	(	WxIoNodeType	node,
		const std::string &	attribName,
		const std::vector< T > &	attrib
	)

inline

Write an attribute (vector).

Parameters

node	the node to write under
attribName	the name of the attribute
attrib	the attribute vector to be written

◆ writeVecAttribute() [2/2]

template<typename T >

void WxIoBase::writeVecAttribute	(	WxIoNodeType	node,
		const std::string &	attribName,
		const T *	attribStorage,
		int	count
	)

inline

Write a vector of attributes.

Parameters

node	the node to write under
attribName	the name of the attribute
attribStorage	the vector attribute to be written
count	number of items to write

Member Data Documentation

◆ suffix

std::string WxIoBase::suffix

protected

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

src/lib/wxiobase.h

Detailed Description

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

◆ ~WxIoBase()

◆ WxIoBase() [1/3]

◆ WxIoBase() [2/3]

◆ WxIoBase() [3/3]

Member Function Documentation

◆ addOpenFile()

◆ closeFile()

◆ closeNode()

◆ closeOpenFiles()

◆ createDataSet() [1/2]

◆ createDataSet() [2/2]

◆ createDumpFile()

◆ createFile()

◆ createGroup()

◆ getBaseName()

◆ getDataShape()

◆ getDumpFileName()

◆ getDumpNo()

◆ getGroupNames()

◆ openDataSet()

◆ openDumpFile()

◆ openFile()

◆ openGroup()

◆ readAttribute()

◆ readDataSet()

◆ readFromDataSet()

◆ readStrAttribute()

◆ readStrVecAttribute()

◆ readVecAttribute()

◆ removeOpenFile()

◆ setBaseName()

◆ setDumpNo()

◆ setIo()

◆ writeAttribute()

◆ writeDataSet()

◆ writeStrAttribute()

◆ writeStrVecAttribute()

◆ writeToDataSet()

◆ writeVecAttribute() [1/2]

◆ writeVecAttribute() [2/2]

Member Data Documentation

◆ suffix