Hdf5DataReader Class Reference

#include <Hdf5DataReader.hpp>

Collaboration diagram for Hdf5DataReader:

List of all members.

Public Member Functions

Hdf5DataReader (const std::string &rDirectory, const std::string &rBaseName, bool makeAbsolute=true)

Hdf5DataReader (const FileFinder &rDirectory, const std::string &rBaseName)

std::vector< double > GetVariableOverTime (const std::string &rVariableName, unsigned nodeIndex)

void GetVariableOverNodes (Vec data, const std::string &rVariableName, unsigned timestep=0)

std::vector< double > GetUnlimitedDimensionValues ()

unsigned GetNumberOfRows ()

std::vector< std::string > GetVariableNames ()

std::string GetUnit (const std::string &rVariableName)

bool IsDataComplete ()

std::vector< unsigned > GetIncompleteNodeMap ()

void Close ()

~Hdf5DataReader ()

Private Member Functions

void CommonConstructor (const FileFinder &rDirectory, const std::string &rBaseName)

Private Attributes

std::string mDirectory

std::string mBaseName

hid_t mFileId

hid_t mVariablesDatasetId

unsigned mVariablesDatasetRank

hsize_t mVariablesDatasetSizes [MAX_DATASET_RANK]

bool mIsUnlimitedDimensionSet

hid_t mTimeDatasetId

hsize_t mNumberTimesteps

std::vector< std::string > mVariableNames

std::map< std::string, unsigned > mVariableToColumnIndex

std::map< std::string,
std::string > mVariableToUnit

bool mIsDataComplete

std::vector< unsigned > mIncompleteNodeIndices

Static Private Attributes

static const unsigned MAX_DATASET_RANK = 3

Detailed Description

Todo:: : magic number

A concrete HDF5 data reader class.

Definition at line 46 of file Hdf5DataReader.hpp.

Constructor & Destructor Documentation

Hdf5DataReader::Hdf5DataReader	(	const std::string &	rDirectory,
		const std::string &	rBaseName,
		bool	makeAbsolute = `true`
	)

Read data from the given files into memory.

Parameters:

	rDirectory	The directory the files are stored in
	rBaseName	The base name of the files to read (i.e. without the extensions)
	makeAbsolute	Whether to convert directory to an absolute path using the OutputFileHandler (defaults to true)

Definition at line 35 of file Hdf5DataReader.cpp.

References RelativeTo::Absolute, RelativeTo::ChasteTestOutput, and CommonConstructor().

Hdf5DataReader::Hdf5DataReader	(	const FileFinder &	rDirectory,
		const std::string &	rBaseName
	)

Alternative constructor taking a FileFinder to specify the directory.

Parameters:

	rDirectory	The directory the files are stored in
	rBaseName	The base name of the files to read (i.e. without the extensions)

Definition at line 56 of file Hdf5DataReader.cpp.

References CommonConstructor().

Hdf5DataReader::~Hdf5DataReader ( )

Destructor just calls Close.

Definition at line 360 of file Hdf5DataReader.cpp.

References Close().

Member Function Documentation

void Hdf5DataReader::CommonConstructor	(	const FileFinder &	rDirectory,
		const std::string &	rBaseName
	)			`[private]`

Contains functionality common to both constructors.

Parameters:

	rDirectory	The directory the files are stored in
	rBaseName	The base name of the files to read (i.e. without the extensions)

Definition at line 66 of file Hdf5DataReader.cpp.

References EXCEPTION, FileFinder::Exists(), FileFinder::GetAbsolutePath(), FileFinder::IsDir(), MAX_DATASET_RANK, mBaseName, mDirectory, mFileId, mIncompleteNodeIndices, mIsDataComplete, mIsUnlimitedDimensionSet, mNumberTimesteps, mTimeDatasetId, mVariableNames, mVariablesDatasetId, mVariablesDatasetRank, mVariablesDatasetSizes, mVariableToColumnIndex, and mVariableToUnit.

Referenced by Hdf5DataReader().

std::vector< double > Hdf5DataReader::GetVariableOverTime	(	const std::string &	rVariableName,
		unsigned	nodeIndex
	)

Get the values of a given variable at each time step at a given node.

Parameters:

	rVariableName	name of a variable in the data file
	nodeIndex	the index of the node for which the data is obtained

Definition at line 196 of file Hdf5DataReader.cpp.

References EXCEPTION, mIncompleteNodeIndices, mIsDataComplete, mIsUnlimitedDimensionSet, mVariablesDatasetId, mVariablesDatasetSizes, and mVariableToColumnIndex.

void Hdf5DataReader::GetVariableOverNodes	(	Vec	data,
		const std::string &	rVariableName,
		unsigned	timestep = `0`
	)

Get the values of a given variable at each node at a given time step.

Parameters:

	data	Petsc vec to hold the data
	rVariableName	name of a variable in the data file
	timestep	the time step for which the data is obtained (defaults to 0)

Todo:: Use DistributedVector?

Definition at line 258 of file Hdf5DataReader.cpp.

References EXCEPTION, mIsDataComplete, mIsUnlimitedDimensionSet, mNumberTimesteps, mVariablesDatasetId, mVariablesDatasetSizes, and mVariableToColumnIndex.

Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputePseudoEcgAtOneTimeStep(), Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::load(), VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Write(), and Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Write().

std::vector< double > Hdf5DataReader::GetUnlimitedDimensionValues ( )

Get the unlimited dimension values.

Definition at line 320 of file Hdf5DataReader.cpp.

References mIsUnlimitedDimensionSet, mNumberTimesteps, and mTimeDatasetId.

unsigned Hdf5DataReader::GetNumberOfRows ( )

Get the number of rows in the data file.

Definition at line 365 of file Hdf5DataReader.cpp.

References mVariablesDatasetSizes.

Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter(), Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::PostProcessingWriter(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Write(), and Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Write().

std::vector< std::string > Hdf5DataReader::GetVariableNames ( )

Get the variable names.

Definition at line 370 of file Hdf5DataReader.cpp.

References mVariableNames.

Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToCmguiConverter(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToMeshalyzerConverter(), Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), and Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Write().

std::string Hdf5DataReader::GetUnit ( const std::string & rVariableName )

Get the units in which a given variable is measured.

Parameters:

rVariableName

name of a variable in the data file

Definition at line 375 of file Hdf5DataReader.cpp.

References mVariableToUnit.

bool Hdf5DataReader::IsDataComplete ( )

Get method for mIsDataComplete.

Definition at line 380 of file Hdf5DataReader.cpp.

References mIsDataComplete.

std::vector< unsigned > Hdf5DataReader::GetIncompleteNodeMap ( )

Get method for mIncompleteNodeIndices.

Definition at line 385 of file Hdf5DataReader.cpp.

References mIncompleteNodeIndices.

void Hdf5DataReader::Close ( )

Close any open files.

Todo:: : move code to the destructor???

Definition at line 347 of file Hdf5DataReader.cpp.

References mFileId, mIsUnlimitedDimensionSet, mTimeDatasetId, and mVariablesDatasetId.

Referenced by ~Hdf5DataReader().

Member Data Documentation

const unsigned Hdf5DataReader::MAX_DATASET_RANK = 3 [static, private]

Defined in HDF5 writer too.

Todo:: : define it once

Definition at line 50 of file Hdf5DataReader.hpp.

Referenced by CommonConstructor().

std::string Hdf5DataReader::mDirectory [private]

Directory output files will be stored in (absolute path).

Definition at line 52 of file Hdf5DataReader.hpp.

Referenced by CommonConstructor().

std::string Hdf5DataReader::mBaseName [private]

The base name for the output data files.

Definition at line 53 of file Hdf5DataReader.hpp.

Referenced by CommonConstructor().

hid_t Hdf5DataReader::mFileId [private]

The data file ID.

Definition at line 55 of file Hdf5DataReader.hpp.

Referenced by Close(), and CommonConstructor().

hid_t Hdf5DataReader::mVariablesDatasetId [private]

The variables data set ID.

Definition at line 57 of file Hdf5DataReader.hpp.

Referenced by Close(), CommonConstructor(), GetVariableOverNodes(), and GetVariableOverTime().

unsigned Hdf5DataReader::mVariablesDatasetRank [private]

The rank of the variables data set.

Definition at line 58 of file Hdf5DataReader.hpp.

Referenced by CommonConstructor().

hsize_t Hdf5DataReader::mVariablesDatasetSizes[MAX_DATASET_RANK] [private]

The sizes of each variable data set.

Definition at line 59 of file Hdf5DataReader.hpp.

Referenced by CommonConstructor(), GetNumberOfRows(), GetVariableOverNodes(), and GetVariableOverTime().

bool Hdf5DataReader::mIsUnlimitedDimensionSet [private]

Is the unlimited dimension set

Definition at line 61 of file Hdf5DataReader.hpp.

Referenced by Close(), CommonConstructor(), GetUnlimitedDimensionValues(), GetVariableOverNodes(), and GetVariableOverTime().

hid_t Hdf5DataReader::mTimeDatasetId [private]

The time data set ID.

Definition at line 62 of file Hdf5DataReader.hpp.

Referenced by Close(), CommonConstructor(), and GetUnlimitedDimensionValues().

hsize_t Hdf5DataReader::mNumberTimesteps [private]

The number of time steps recorded in the data file.

Definition at line 63 of file Hdf5DataReader.hpp.

Referenced by CommonConstructor(), GetUnlimitedDimensionValues(), and GetVariableOverNodes().

std::vector<std::string> Hdf5DataReader::mVariableNames [private]

The variable names.

Definition at line 65 of file Hdf5DataReader.hpp.

Referenced by CommonConstructor(), and GetVariableNames().

std::map<std::string, unsigned> Hdf5DataReader::mVariableToColumnIndex [private]

Map between variable names and data column numbers.

Definition at line 66 of file Hdf5DataReader.hpp.

Referenced by CommonConstructor(), GetVariableOverNodes(), and GetVariableOverTime().

std::map<std::string, std::string> Hdf5DataReader::mVariableToUnit [private]

Map between variable names and variable units.

Definition at line 67 of file Hdf5DataReader.hpp.

Referenced by CommonConstructor(), and GetUnit().

bool Hdf5DataReader::mIsDataComplete [private]

Whether the data file is complete.

Definition at line 69 of file Hdf5DataReader.hpp.

Referenced by CommonConstructor(), GetVariableOverNodes(), GetVariableOverTime(), and IsDataComplete().

std::vector<unsigned> Hdf5DataReader::mIncompleteNodeIndices [private]

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

Definition at line 70 of file Hdf5DataReader.hpp.

Referenced by CommonConstructor(), GetIncompleteNodeMap(), and GetVariableOverTime().

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

io/src/reader/Hdf5DataReader.hpp
io/src/reader/Hdf5DataReader.cpp


Public Member Functions
	Hdf5DataReader (const std::string &rDirectory, const std::string &rBaseName, bool makeAbsolute=true)
	Hdf5DataReader (const FileFinder &rDirectory, const std::string &rBaseName)
std::vector< double >	GetVariableOverTime (const std::string &rVariableName, unsigned nodeIndex)
void	GetVariableOverNodes (Vec data, const std::string &rVariableName, unsigned timestep=0)
std::vector< double >	GetUnlimitedDimensionValues ()
unsigned	GetNumberOfRows ()
std::vector< std::string >	GetVariableNames ()
std::string	GetUnit (const std::string &rVariableName)
bool	IsDataComplete ()
std::vector< unsigned >	GetIncompleteNodeMap ()
void	Close ()
	~Hdf5DataReader ()
Private Member Functions
void	CommonConstructor (const FileFinder &rDirectory, const std::string &rBaseName)
Private Attributes
std::string	mDirectory
std::string	mBaseName
hid_t	mFileId
hid_t	mVariablesDatasetId
unsigned	mVariablesDatasetRank
hsize_t	mVariablesDatasetSizes [MAX_DATASET_RANK]
bool	mIsUnlimitedDimensionSet
hid_t	mTimeDatasetId
hsize_t	mNumberTimesteps
std::vector< std::string >	mVariableNames
std::map< std::string, unsigned >	mVariableToColumnIndex
std::map< std::string, std::string >	mVariableToUnit
bool	mIsDataComplete
std::vector< unsigned >	mIncompleteNodeIndices
Static Private Attributes
static const unsigned	MAX_DATASET_RANK = 3