Hdf5DataWriter Class Reference

#include <Hdf5DataWriter.hpp>

Collaboration diagram for Hdf5DataWriter:

List of all members.

Public Member Functions

Hdf5DataWriter (DistributedVectorFactory &rVectorFactory, const std::string &rDirectory, const std::string &rBaseName, bool cleanDirectory=true)

virtual ~Hdf5DataWriter ()

void DefineFixedDimension (long dimensionSize)

void DefineFixedDimension (const std::vector< unsigned > &rNodesToOuput, long vecSize)

void DefineUnlimitedDimension (const std::string &rVariableName, const std::string &rVariableUnits)

void AdvanceAlongUnlimitedDimension ()

int DefineVariable (const std::string &rVariableName, const std::string &rVariableUnits)

virtual void EndDefineMode ()

void PossiblyExtend ()

void PutVector (int variableID, Vec petscVector)

void PutStripedVector (int firstVariableID, int secondVariableID, Vec petscVector)

void PutUnlimitedVariable (double value)

void Close ()

Private Member Functions

void CheckVariableName (const std::string &rName)

void CheckUnitsName (const std::string &rName)

Private Attributes

DistributedVectorFactory & mrVectorFactory

std::string mDirectory

std::string mBaseName

bool mCleanDirectory

bool mIsInDefineMode

bool mIsFixedDimensionSet

bool mIsUnlimitedDimensionSet

std::string mUnlimitedDimensionName

std::string mUnlimitedDimensionUnit

unsigned mFileFixedDimensionSize

unsigned mDataFixedDimensionSize

unsigned mLo

unsigned mHi

unsigned mNumberOwned

unsigned mOffset

bool mIsDataComplete

bool mNeedExtend

std::vector< unsigned > mIncompleteNodeIndices

std::vector< DataWriterVariable > mVariables

hid_t mFileId

hid_t mDatasetId

hid_t mTimeDatasetId

long mCurrentTimeStep

hsize_t mDatasetDims [DATASET_DIMS]

Static Private Attributes

static const unsigned DATASET_DIMS = 3

Detailed Description

A concrete HDF5 data writer class.

Definition at line 46 of file Hdf5DataWriter.hpp.

Constructor & Destructor Documentation

Hdf5DataWriter::Hdf5DataWriter	(	DistributedVectorFactory &	rVectorFactory,
		const std::string &	rDirectory,
		const std::string &	rBaseName,
		bool	cleanDirectory = `true`
	)

Constructor.

Parameters:

	rVectorFactory	the factory to use in creating PETSc Vec and DistributedVector objects.
	rDirectory	the directory in which to write the data to file
	rBaseName	the name of the file in which to write the data
	cleanDirectory	whether to clean the directory (defaults to true)

Definition at line 40 of file Hdf5DataWriter.cpp.

Hdf5DataWriter::~Hdf5DataWriter ( ) [virtual]

Destructor.

Definition at line 63 of file Hdf5DataWriter.cpp.

Member Function Documentation

void Hdf5DataWriter::CheckVariableName ( const std::string & rName ) [private]

Check name of variable is allowed, i.e. contains only alphanumeric & _, and isn't blank.

Parameters:

rName

variable name

Definition at line 166 of file Hdf5DataWriter.cpp.

References CheckUnitsName().

Referenced by DefineVariable().

void Hdf5DataWriter::CheckUnitsName ( const std::string & rName ) [private]

Check name of unit is allowed, i.e. contains only alphanumeric & _, and isn't blank.

Parameters:

rName

unit name

Definition at line 175 of file Hdf5DataWriter.cpp.

Referenced by CheckVariableName(), and DefineVariable().

void Hdf5DataWriter::DefineFixedDimension ( long dimensionSize )

Define the fixed dimension, assuming complete data output (all the nodes).

Parameters:

dimensionSize

The size of the dimension

Definition at line 67 of file Hdf5DataWriter.cpp.

References DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLocalOwnership(), DistributedVectorFactory::GetLow(), mDataFixedDimensionSize, mFileFixedDimensionSize, mHi, mIsFixedDimensionSet, mIsInDefineMode, mLo, mNumberOwned, mOffset, and mrVectorFactory.

Referenced by DefineFixedDimension(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns().

void Hdf5DataWriter::DefineFixedDimension	(	const std::vector< unsigned > &	rNodesToOuput,
		long	vecSize
	)

Define the fixed dimension, assuming incomplete data output (subset of the nodes).

Parameters:

	rNodesToOuput	Node indexes to be output (precondition: to be monotonic increasing)
	vecSize

Definition at line 92 of file Hdf5DataWriter.cpp.

References DefineFixedDimension(), mFileFixedDimensionSize, mHi, mIncompleteNodeIndices, mIsDataComplete, mLo, mNumberOwned, and mOffset.

void Hdf5DataWriter::DefineUnlimitedDimension	(	const std::string &	rVariableName,
		const std::string &	rVariableUnits
	)

Define a variable.

Parameters:

	rVariableName	The name of the dimension
	rVariableUnits	The physical units of the dimension

Returns:: The identifier of the variable

Definition at line 535 of file Hdf5DataWriter.cpp.

References mIsInDefineMode, mIsUnlimitedDimensionSet, mUnlimitedDimensionName, and mUnlimitedDimensionUnit.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns().

void Hdf5DataWriter::AdvanceAlongUnlimitedDimension ( )

Advance along the unlimited dimension. Normally this will be called when all variables in a row have been input.

Definition at line 553 of file Hdf5DataWriter.cpp.

References mCurrentTimeStep, mDatasetDims, mIsUnlimitedDimensionSet, and mNeedExtend.

Referenced by CardiacElectroMechanicsProblem< DIM >::Solve(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::Solve().

int Hdf5DataWriter::DefineVariable	(	const std::string &	rVariableName,
		const std::string &	rVariableUnits
	)

Define a variable.

Parameters:

	rVariableName	The name of the dimension
	rVariableUnits	The physical units of the dimension

Returns:: The identifier of the variable

Definition at line 131 of file Hdf5DataWriter.cpp.

References CheckUnitsName(), CheckVariableName(), mIsInDefineMode, DataWriterVariable::mVariableName, mVariables, and DataWriterVariable::mVariableUnits.

Referenced by BidomainProblem< DIM >::DefineWriterColumns(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns().

void Hdf5DataWriter::EndDefineMode ( ) [virtual]

End the define mode of the DataWriter.

Definition at line 187 of file Hdf5DataWriter.cpp.

References DATASET_DIMS, OutputFileHandler::GetOutputDirectoryFullPath(), mBaseName, mCleanDirectory, mDatasetDims, mDatasetId, mDirectory, mFileFixedDimensionSize, mFileId, mIncompleteNodeIndices, mIsDataComplete, mIsFixedDimensionSet, mIsInDefineMode, mIsUnlimitedDimensionSet, mTimeDatasetId, mUnlimitedDimensionName, mUnlimitedDimensionUnit, and mVariables.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseWriter().

void Hdf5DataWriter::PossiblyExtend ( )

Extend the dataset to the correct to the correct dimensions if needed.

Definition at line 567 of file Hdf5DataWriter.cpp.

References mDatasetDims, mDatasetId, mNeedExtend, and mTimeDatasetId.

Referenced by PutStripedVector(), PutUnlimitedVariable(), and PutVector().

void Hdf5DataWriter::PutVector	(	int	variableID,
		Vec	petscVector
	)

Write data for a given variable from a Petsc vector to the dataset.

Parameters:

	variableID	the variable
	petscVector	the data

Definition at line 340 of file Hdf5DataWriter.cpp.

References DATASET_DIMS, mCurrentTimeStep, mDataFixedDimensionSize, mDatasetId, mIncompleteNodeIndices, mIsDataComplete, mIsInDefineMode, mLo, mNumberOwned, mOffset, and PossiblyExtend().

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::WriteOneStep().

void Hdf5DataWriter::PutStripedVector	(	int	firstVariableID,
		int	secondVariableID,
		Vec	petscVector
	)

Write data for two variables from a Petsc vector to the dataset.

Parameters:

	firstVariableID	the first variable
	secondVariableID	the first variable
	petscVector	the data

Todo:: Use distributed vector functionality here?

Definition at line 405 of file Hdf5DataWriter.cpp.

References DATASET_DIMS, mCurrentTimeStep, mDataFixedDimensionSize, mDatasetId, mIncompleteNodeIndices, mIsDataComplete, mIsInDefineMode, mLo, mNumberOwned, mOffset, and PossiblyExtend().

Referenced by BidomainProblem< DIM >::WriteOneStep().

void Hdf5DataWriter::PutUnlimitedVariable ( double value )

Write a single value for the unlimited variable (e.g. time) to the dataset.

Parameters:

value

the data

Definition at line 483 of file Hdf5DataWriter.cpp.

References PetscTools::AmMaster(), mCurrentTimeStep, mIsInDefineMode, mIsUnlimitedDimensionSet, mTimeDatasetId, and PossiblyExtend().

Referenced by BidomainProblem< DIM >::WriteOneStep(), and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::WriteOneStep().

void Hdf5DataWriter::Close ( )

Close any open files.

Definition at line 519 of file Hdf5DataWriter.cpp.

References mDatasetId, mFileId, mIsInDefineMode, mIsUnlimitedDimensionSet, and mTimeDatasetId.

Referenced by AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess(), and CardiacElectroMechanicsProblem< DIM >::Solve().

Member Data Documentation

DistributedVectorFactory& Hdf5DataWriter::mrVectorFactory [private]

The factory to use in creating PETSc Vec and DistributedVector objects.

Definition at line 50 of file Hdf5DataWriter.hpp.

Referenced by DefineFixedDimension().

std::string Hdf5DataWriter::mDirectory [private]

Directory output files will be stored in.

Definition at line 51 of file Hdf5DataWriter.hpp.

Referenced by EndDefineMode().

std::string Hdf5DataWriter::mBaseName [private]

The base name for the output data files.

Definition at line 52 of file Hdf5DataWriter.hpp.

Referenced by EndDefineMode().

bool Hdf5DataWriter::mCleanDirectory [private]

Whether to wipe the output directory

Definition at line 53 of file Hdf5DataWriter.hpp.

Referenced by EndDefineMode().

bool Hdf5DataWriter::mIsInDefineMode [private]

Is the DataWriter in define mode or not

Definition at line 54 of file Hdf5DataWriter.hpp.

Referenced by Close(), DefineFixedDimension(), DefineUnlimitedDimension(), DefineVariable(), EndDefineMode(), PutStripedVector(), PutUnlimitedVariable(), and PutVector().

bool Hdf5DataWriter::mIsFixedDimensionSet [private]

Is the fixed dimension set

Definition at line 55 of file Hdf5DataWriter.hpp.

Referenced by DefineFixedDimension(), and EndDefineMode().

bool Hdf5DataWriter::mIsUnlimitedDimensionSet [private]

Is the unlimited dimension set

Definition at line 56 of file Hdf5DataWriter.hpp.

Referenced by AdvanceAlongUnlimitedDimension(), Close(), DefineUnlimitedDimension(), EndDefineMode(), and PutUnlimitedVariable().

std::string Hdf5DataWriter::mUnlimitedDimensionName [private]

The name of the unlimited dimension.

Definition at line 57 of file Hdf5DataWriter.hpp.

Referenced by DefineUnlimitedDimension(), and EndDefineMode().

std::string Hdf5DataWriter::mUnlimitedDimensionUnit [private]

The physical units of the unlimited dimension.

Definition at line 58 of file Hdf5DataWriter.hpp.

Referenced by DefineUnlimitedDimension(), and EndDefineMode().

unsigned Hdf5DataWriter::mFileFixedDimensionSize [private]

The size of the fixed dimension (number of rows)

Definition at line 59 of file Hdf5DataWriter.hpp.

Referenced by DefineFixedDimension(), and EndDefineMode().

unsigned Hdf5DataWriter::mDataFixedDimensionSize [private]

The size of the fixed dimension (size of the vector of nodes)

Definition at line 60 of file Hdf5DataWriter.hpp.

Referenced by DefineFixedDimension(), PutStripedVector(), and PutVector().

unsigned Hdf5DataWriter::mLo [private]

Local ownership of a PETSc vector of size mFileFixedDimensionSize

Definition at line 61 of file Hdf5DataWriter.hpp.

Referenced by DefineFixedDimension(), PutStripedVector(), and PutVector().

unsigned Hdf5DataWriter::mHi [private]

Local ownership of a PETSc vector of size mFileFixedDimensionSize

Definition at line 62 of file Hdf5DataWriter.hpp.

Referenced by DefineFixedDimension().

unsigned Hdf5DataWriter::mNumberOwned [private]

mNumberOwned=mHi-mLo; except with incomplete data

Definition at line 63 of file Hdf5DataWriter.hpp.

Referenced by DefineFixedDimension(), PutStripedVector(), and PutVector().

unsigned Hdf5DataWriter::mOffset [private]

mOffset=mLo; except with incomplete data

Definition at line 64 of file Hdf5DataWriter.hpp.

Referenced by DefineFixedDimension(), PutStripedVector(), and PutVector().

bool Hdf5DataWriter::mIsDataComplete [private]

Whether the data file is complete.

Definition at line 65 of file Hdf5DataWriter.hpp.

Referenced by DefineFixedDimension(), EndDefineMode(), PutStripedVector(), and PutVector().

bool Hdf5DataWriter::mNeedExtend [private]

Used so that the data set is only extended when data is written

Definition at line 66 of file Hdf5DataWriter.hpp.

Referenced by AdvanceAlongUnlimitedDimension(), and PossiblyExtend().

std::vector<unsigned> Hdf5DataWriter::mIncompleteNodeIndices [private]

Vector of node indices for which the data file does not contain data.

Definition at line 67 of file Hdf5DataWriter.hpp.

Referenced by DefineFixedDimension(), EndDefineMode(), PutStripedVector(), and PutVector().

std::vector<DataWriterVariable> Hdf5DataWriter::mVariables [private]

The data variables

Definition at line 69 of file Hdf5DataWriter.hpp.

Referenced by DefineVariable(), and EndDefineMode().

hid_t Hdf5DataWriter::mFileId [private]

The data file ID.

Definition at line 85 of file Hdf5DataWriter.hpp.

Referenced by Close(), and EndDefineMode().

hid_t Hdf5DataWriter::mDatasetId [private]

The variables data set ID.

Definition at line 86 of file Hdf5DataWriter.hpp.

Referenced by Close(), EndDefineMode(), PossiblyExtend(), PutStripedVector(), and PutVector().

hid_t Hdf5DataWriter::mTimeDatasetId [private]

The time data set ID.

Definition at line 87 of file Hdf5DataWriter.hpp.

Referenced by Close(), EndDefineMode(), PossiblyExtend(), and PutUnlimitedVariable().

long Hdf5DataWriter::mCurrentTimeStep [private]

The current time step.

Definition at line 89 of file Hdf5DataWriter.hpp.

Referenced by AdvanceAlongUnlimitedDimension(), PutStripedVector(), PutUnlimitedVariable(), and PutVector().

const unsigned Hdf5DataWriter::DATASET_DIMS = 3 [static, private]

Defined in HDF5 reader too.

Todo:: : define it once

Definition at line 91 of file Hdf5DataWriter.hpp.

Referenced by EndDefineMode(), PutStripedVector(), and PutVector().

hsize_t Hdf5DataWriter::mDatasetDims[DATASET_DIMS] [private]

The sizes of each variable data set.

Definition at line 92 of file Hdf5DataWriter.hpp.

Referenced by AdvanceAlongUnlimitedDimension(), EndDefineMode(), and PossiblyExtend().

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

/tmp/release_1.1/io/src/writer/Hdf5DataWriter.hpp
/tmp/release_1.1/io/src/writer/Hdf5DataWriter.cpp


Public Member Functions
	Hdf5DataWriter (DistributedVectorFactory &rVectorFactory, const std::string &rDirectory, const std::string &rBaseName, bool cleanDirectory=true)
virtual	~Hdf5DataWriter ()
void	DefineFixedDimension (long dimensionSize)
void	DefineFixedDimension (const std::vector< unsigned > &rNodesToOuput, long vecSize)
void	DefineUnlimitedDimension (const std::string &rVariableName, const std::string &rVariableUnits)
void	AdvanceAlongUnlimitedDimension ()
int	DefineVariable (const std::string &rVariableName, const std::string &rVariableUnits)
virtual void	EndDefineMode ()
void	PossiblyExtend ()
void	PutVector (int variableID, Vec petscVector)
void	PutStripedVector (int firstVariableID, int secondVariableID, Vec petscVector)
void	PutUnlimitedVariable (double value)
void	Close ()
Private Member Functions
void	CheckVariableName (const std::string &rName)
void	CheckUnitsName (const std::string &rName)
Private Attributes
DistributedVectorFactory &	mrVectorFactory
std::string	mDirectory
std::string	mBaseName
bool	mCleanDirectory
bool	mIsInDefineMode
bool	mIsFixedDimensionSet
bool	mIsUnlimitedDimensionSet
std::string	mUnlimitedDimensionName
std::string	mUnlimitedDimensionUnit
unsigned	mFileFixedDimensionSize
unsigned	mDataFixedDimensionSize
unsigned	mLo
unsigned	mHi
unsigned	mNumberOwned
unsigned	mOffset
bool	mIsDataComplete
bool	mNeedExtend
std::vector< unsigned >	mIncompleteNodeIndices
std::vector< DataWriterVariable >	mVariables
hid_t	mFileId
hid_t	mDatasetId
hid_t	mTimeDatasetId
long	mCurrentTimeStep
hsize_t	mDatasetDims [DATASET_DIMS]
Static Private Attributes
static const unsigned	DATASET_DIMS = 3