ColumnDataWriter Class Reference

#include <ColumnDataWriter.hpp>

Inheritance diagram for ColumnDataWriter:

Collaboration diagram for ColumnDataWriter:

List of all members.

Public Member Functions

ColumnDataWriter (const std::string &rDirectory, const std::string &rBaseName, bool cleanDirectory=true, unsigned precision=8)

virtual ~ColumnDataWriter ()

int DefineUnlimitedDimension (const std::string &rDimensionName, const std::string &rDimensionUnits)

int DefineFixedDimension (const std::string &rDimensionName, const std::string &rDimensionUnits, long dimensionSize)

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

void SetCommentForInfoFile (std::string comment)

virtual void EndDefineMode ()

virtual void AdvanceAlongUnlimitedDimension ()

virtual void PutVariable (int variableID, double variableValue, long dimensionPosition=-1)

virtual void Close ()

std::string GetOutputDirectory ()

Protected Member Functions

void CreateFixedDimensionFile (const std::string &rFileName)

void CreateInfoFile (const std::string &rFileName)

void CheckVariableName (const std::string &rName)

void CheckUnitsName (const std::string &rName)

void DoAdvanceAlongUnlimitedDimension ()

Protected Attributes

OutputFileHandler mOutputFileHandler

std::string mDirectory

std::string mBaseName

bool mIsInDefineMode

bool mIsFixedDimensionSet

bool mIsUnlimitedDimensionSet

long mUnlimitedDimensionPosition

long mFixedDimensionSize

out_stream mpCurrentOutputFile

out_stream mpCurrentAncillaryFile

DataWriterVariable * mpUnlimitedDimensionVariable

DataWriterVariable * mpFixedDimensionVariable

std::string mUnlimitedDimensionName

std::string mUnlimitedDimensionUnits

std::string mFixedDimensionName

std::string mFixedDimensionUnits

std::vector< DataWriterVariable > mVariables

const unsigned mFieldWidth

const unsigned mPrecision

std::string mFileExtension

int mRowStartPosition

int mRowWidth

int mAncillaryRowStartPosition

int mAncillaryRowWidth

bool mHasPutVariable

bool mNeedAdvanceAlongUnlimitedDimension

std::string mCommentForInfoFile

Static Protected Attributes

static const int SPACING = 2

static const int FIXED_DIMENSION_VAR_ID = -1

static const int UNLIMITED_DIMENSION_VAR_ID = -2

Detailed Description

A concrete column data writer class. Writes grid-formatted data in space separated column form. Each file has a header row with names and optional units for each column.

Definition at line 45 of file ColumnDataWriter.hpp.

Constructor & Destructor Documentation

ColumnDataWriter::ColumnDataWriter	(	const std::string &	rDirectory,
		const std::string &	rBaseName,
		bool	cleanDirectory = `true`,
		unsigned	precision = `8`
	)

Constructor.

Parameters:

	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)
	precision	the precision with which to write the data (i.e. exactly how many digits to display after the decimal point). Defaults to 8. Must be between 2 and 20 (inclusive).

Implementation file for ColumnDataWriter class.

Definition at line 46 of file ColumnDataWriter.cpp.

References EXCEPTION.

ColumnDataWriter::~ColumnDataWriter ( ) [virtual]

Destructor. Closes any open files.

Definition at line 74 of file ColumnDataWriter.cpp.

References Close(), mpFixedDimensionVariable, and mpUnlimitedDimensionVariable.

Member Function Documentation

void ColumnDataWriter::CreateFixedDimensionFile ( const std::string & rFileName ) [protected]

Create the output file and write out the header for it.

Parameters:

rFileName

the name of the file to write to, relative to the output directory

Definition at line 314 of file ColumnDataWriter.cpp.

References mFixedDimensionSize, mOutputFileHandler, mpCurrentOutputFile, mpFixedDimensionVariable, mPrecision, mRowStartPosition, mRowWidth, DataWriterVariable::mVariableName, mVariables, DataWriterVariable::mVariableUnits, and OutputFileHandler::OpenOutputFile().

Referenced by DoAdvanceAlongUnlimitedDimension(), and EndDefineMode().

void ColumnDataWriter::CreateInfoFile ( const std::string & rFileName ) [protected]

Create the info file.

Parameters:

rFileName

the name of the file to create, relative to the output directory

Definition at line 343 of file ColumnDataWriter.cpp.

References ChasteBuildInfo::GetProvenanceString(), mCommentForInfoFile, mFixedDimensionSize, mIsUnlimitedDimensionSet, mOutputFileHandler, mVariables, and OutputFileHandler::OpenOutputFile().

Referenced by EndDefineMode().

void ColumnDataWriter::CheckVariableName ( const std::string & rName ) [protected]

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

Parameters:

rName

variable name

Definition at line 110 of file ColumnDataWriter.cpp.

References CheckUnitsName(), and EXCEPTION.

Referenced by DefineFixedDimension(), DefineUnlimitedDimension(), and DefineVariable().

void ColumnDataWriter::CheckUnitsName ( const std::string & rName ) [protected]

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

Parameters:

rName

unit name

Definition at line 119 of file ColumnDataWriter.cpp.

References EXCEPTION.

Referenced by CheckVariableName(), DefineFixedDimension(), DefineUnlimitedDimension(), and DefineVariable().

void ColumnDataWriter::DoAdvanceAlongUnlimitedDimension ( ) [protected]

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

Definition at line 358 of file ColumnDataWriter.cpp.

References CreateFixedDimensionFile(), EXCEPTION, FILE_SUFFIX_WIDTH, mBaseName, mHasPutVariable, mIsFixedDimensionSet, mIsUnlimitedDimensionSet, mNeedAdvanceAlongUnlimitedDimension, mpCurrentOutputFile, mRowStartPosition, mRowWidth, and mUnlimitedDimensionPosition.

Referenced by ParallelColumnDataWriter::AdvanceAlongUnlimitedDimension(), and PutVariable().

int ColumnDataWriter::DefineUnlimitedDimension	(	const std::string &	rDimensionName,
		const std::string &	rDimensionUnits
	)			`[virtual]`

Define the unlimited dimension, i.e. the dimension that increases as the simulation progresses.

Parameters:

	rDimensionName	The name of the unlimited dimension
	rDimensionUnits	The physical units of the unlimited dimension

Returns:: The identifier of the variable

Implements AbstractDataWriter.

Definition at line 131 of file ColumnDataWriter.cpp.

References CheckUnitsName(), CheckVariableName(), EXCEPTION, mIsInDefineMode, mIsUnlimitedDimensionSet, mpUnlimitedDimensionVariable, mUnlimitedDimensionName, mUnlimitedDimensionUnits, DataWriterVariable::mVariableName, DataWriterVariable::mVariableUnits, and UNLIMITED_DIMENSION_VAR_ID.

Referenced by OdeSolution::WriteToFile().

int ColumnDataWriter::DefineFixedDimension	(	const std::string &	rDimensionName,
		const std::string &	rDimensionUnits,
		long	dimensionSize
	)			`[virtual]`

Define the fixed dimension.

Parameters:

	rDimensionName	The name of the dimension
	rDimensionUnits	The physical units of the dimension
	dimensionSize	The size of the dimension

Returns:: The identifier of the variable

Implements AbstractDataWriter.

Definition at line 159 of file ColumnDataWriter.cpp.

References CheckUnitsName(), CheckVariableName(), EXCEPTION, FIXED_DIMENSION_VAR_ID, mFixedDimensionName, mFixedDimensionSize, mFixedDimensionUnits, mIsFixedDimensionSet, mIsInDefineMode, mpFixedDimensionVariable, DataWriterVariable::mVariableName, and DataWriterVariable::mVariableUnits.

int ColumnDataWriter::DefineVariable	(	const std::string &	rVariableName,
		const std::string &	rVariableUnits
	)			`[virtual]`

Define a variable.

Parameters:

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

Returns:: The identifier of the variable

Implements AbstractDataWriter.

Definition at line 187 of file ColumnDataWriter.cpp.

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

Referenced by OdeSolution::WriteToFile().

void ColumnDataWriter::SetCommentForInfoFile ( std::string comment ) [inline]

Set a comment to be written in the info file (optional). This needs to be called before EndDefineMode().

Parameters:

comment

the comment

Definition at line 190 of file ColumnDataWriter.hpp.

References mCommentForInfoFile.

Referenced by OdeSolution::WriteToFile().

void ColumnDataWriter::EndDefineMode ( ) [virtual]

End the define mode of the DataWriter.

Implements AbstractDataWriter.

Reimplemented in ParallelColumnDataWriter.

Definition at line 224 of file ColumnDataWriter.cpp.

References CreateFixedDimensionFile(), CreateInfoFile(), EXCEPTION, FILE_SUFFIX_WIDTH, mAncillaryRowStartPosition, mAncillaryRowWidth, mBaseName, mFieldWidth, mIsFixedDimensionSet, mIsInDefineMode, mIsUnlimitedDimensionSet, mOutputFileHandler, mpCurrentAncillaryFile, mpCurrentOutputFile, mpFixedDimensionVariable, mPrecision, mpUnlimitedDimensionVariable, mRowStartPosition, mRowWidth, mUnlimitedDimensionPosition, DataWriterVariable::mVariableName, mVariables, DataWriterVariable::mVariableUnits, OutputFileHandler::OpenOutputFile(), and SPACING.

Referenced by ParallelColumnDataWriter::EndDefineMode(), and OdeSolution::WriteToFile().

void ColumnDataWriter::AdvanceAlongUnlimitedDimension ( ) [virtual]

Dummy function for DoAdvanceAlongUnlimitedDimension.

Implements AbstractDataWriter.

Reimplemented in ParallelColumnDataWriter.

Definition at line 392 of file ColumnDataWriter.cpp.

References mHasPutVariable, and mNeedAdvanceAlongUnlimitedDimension.

Referenced by OdeSolution::WriteToFile().

void ColumnDataWriter::PutVariable	(	int	variableID,
		double	variableValue,
		long	dimensionPosition = `-1`
	)			`[virtual]`

Input the variable value to the output file or ancillary file.

Parameters:

	variableID
	variableValue
	dimensionPosition	The position in column (defaults to -1). This is required if there is a fixed dimension, and will be the position along that dimension

Implements AbstractDataWriter.

Reimplemented in ParallelColumnDataWriter.

Definition at line 400 of file ColumnDataWriter.cpp.

References DoAdvanceAlongUnlimitedDimension(), EXCEPTION, FIXED_DIMENSION_VAR_ID, mFieldWidth, mFixedDimensionSize, mHasPutVariable, mIsFixedDimensionSet, mIsInDefineMode, mIsUnlimitedDimensionSet, mNeedAdvanceAlongUnlimitedDimension, mpCurrentAncillaryFile, mpCurrentOutputFile, mpFixedDimensionVariable, mpUnlimitedDimensionVariable, mRowStartPosition, mRowWidth, mVariables, SPACING, and UNLIMITED_DIMENSION_VAR_ID.

Referenced by ParallelColumnDataWriter::PutVariable(), ParallelColumnDataWriter::PutVector(), and OdeSolution::WriteToFile().

void ColumnDataWriter::Close ( ) [virtual]

Close any open files.

Implements AbstractDataWriter.

Reimplemented in ParallelColumnDataWriter.

Definition at line 95 of file ColumnDataWriter.cpp.

References mpCurrentAncillaryFile, and mpCurrentOutputFile.

Referenced by ParallelColumnDataWriter::Close(), OdeSolution::WriteToFile(), and ~ColumnDataWriter().

std::string ColumnDataWriter::GetOutputDirectory ( )

Return the full pathname of the directory where we're writing files.

Definition at line 90 of file ColumnDataWriter.cpp.

References OutputFileHandler::GetOutputDirectoryFullPath(), and mOutputFileHandler.

Member Data Documentation

OutputFileHandler ColumnDataWriter::mOutputFileHandler [protected]

For opening data files.

Definition at line 49 of file ColumnDataWriter.hpp.

Referenced by CreateFixedDimensionFile(), CreateInfoFile(), EndDefineMode(), and GetOutputDirectory().

std::string ColumnDataWriter::mDirectory [protected]

Directory output files will be stored in.

Definition at line 51 of file ColumnDataWriter.hpp.

std::string ColumnDataWriter::mBaseName [protected]

The base name for the output data files.

Definition at line 52 of file ColumnDataWriter.hpp.

Referenced by DoAdvanceAlongUnlimitedDimension(), and EndDefineMode().

bool ColumnDataWriter::mIsInDefineMode [protected]

Is the DataWriter in define mode or not

Definition at line 53 of file ColumnDataWriter.hpp.

Referenced by DefineFixedDimension(), DefineUnlimitedDimension(), DefineVariable(), ParallelColumnDataWriter::EndDefineMode(), EndDefineMode(), and PutVariable().

bool ColumnDataWriter::mIsFixedDimensionSet [protected]

Is the fixed dimension set

Definition at line 54 of file ColumnDataWriter.hpp.

Referenced by DefineFixedDimension(), DoAdvanceAlongUnlimitedDimension(), EndDefineMode(), and PutVariable().

bool ColumnDataWriter::mIsUnlimitedDimensionSet [protected]

Is the unlimited dimension set

Definition at line 55 of file ColumnDataWriter.hpp.

Referenced by CreateInfoFile(), DefineUnlimitedDimension(), DoAdvanceAlongUnlimitedDimension(), EndDefineMode(), and PutVariable().

long ColumnDataWriter::mUnlimitedDimensionPosition [protected]

The position along the unlimited dimension that writing of variables will take place

Definition at line 56 of file ColumnDataWriter.hpp.

Referenced by DoAdvanceAlongUnlimitedDimension(), and EndDefineMode().

long ColumnDataWriter::mFixedDimensionSize [protected]

The size of the fixed dimension

Definition at line 57 of file ColumnDataWriter.hpp.

Referenced by CreateFixedDimensionFile(), CreateInfoFile(), DefineFixedDimension(), PutVariable(), and ParallelColumnDataWriter::PutVector().

out_stream ColumnDataWriter::mpCurrentOutputFile [protected]

Filestream currently being addressed

Definition at line 58 of file ColumnDataWriter.hpp.

Referenced by Close(), CreateFixedDimensionFile(), DoAdvanceAlongUnlimitedDimension(), EndDefineMode(), and PutVariable().

out_stream ColumnDataWriter::mpCurrentAncillaryFile [protected]

Ancillary filestream currently being addressed (required for two dimensional output) eg. time file

Definition at line 59 of file ColumnDataWriter.hpp.

Referenced by Close(), EndDefineMode(), and PutVariable().

DataWriterVariable* ColumnDataWriter::mpUnlimitedDimensionVariable [protected]

The variable corresponding to the unlimited dimension

Definition at line 60 of file ColumnDataWriter.hpp.

Referenced by DefineUnlimitedDimension(), EndDefineMode(), PutVariable(), and ~ColumnDataWriter().

DataWriterVariable* ColumnDataWriter::mpFixedDimensionVariable [protected]

The variable corresponding to the fixed dimension

Definition at line 61 of file ColumnDataWriter.hpp.

Referenced by CreateFixedDimensionFile(), DefineFixedDimension(), EndDefineMode(), PutVariable(), and ~ColumnDataWriter().

std::string ColumnDataWriter::mUnlimitedDimensionName [protected]

The name of the unlimited dimension.

Definition at line 63 of file ColumnDataWriter.hpp.

Referenced by DefineUnlimitedDimension(), and DefineVariable().

std::string ColumnDataWriter::mUnlimitedDimensionUnits [protected]

The physical units of the unlimited dimension.

Definition at line 64 of file ColumnDataWriter.hpp.

Referenced by DefineUnlimitedDimension().

std::string ColumnDataWriter::mFixedDimensionName [protected]

The name of the fixed dimension

Definition at line 66 of file ColumnDataWriter.hpp.

Referenced by DefineFixedDimension(), and DefineVariable().

std::string ColumnDataWriter::mFixedDimensionUnits [protected]

The units of the fixed dimension

Definition at line 67 of file ColumnDataWriter.hpp.

Referenced by DefineFixedDimension().

std::vector<DataWriterVariable> ColumnDataWriter::mVariables [protected]

The data variables

Definition at line 69 of file ColumnDataWriter.hpp.

Referenced by CreateFixedDimensionFile(), CreateInfoFile(), DefineVariable(), EndDefineMode(), and PutVariable().

const unsigned ColumnDataWriter::mFieldWidth [protected]

Width of each column in the text file (excludes column headers)

Definition at line 71 of file ColumnDataWriter.hpp.

Referenced by EndDefineMode(), and PutVariable().

const unsigned ColumnDataWriter::mPrecision [protected]

Precision used in writing the data

Definition at line 72 of file ColumnDataWriter.hpp.

Referenced by CreateFixedDimensionFile(), and EndDefineMode().

const int ColumnDataWriter::SPACING = 2 [static, protected]

Space between columns (includes minus sign)

Definition at line 73 of file ColumnDataWriter.hpp.

Referenced by EndDefineMode(), and PutVariable().

const int ColumnDataWriter::FIXED_DIMENSION_VAR_ID = -1 [static, protected]

id of fixed dimension variable

Definition at line 74 of file ColumnDataWriter.hpp.

Referenced by DefineFixedDimension(), and PutVariable().

const int ColumnDataWriter::UNLIMITED_DIMENSION_VAR_ID = -2 [static, protected]

id of unlimited dimension variable

Definition at line 75 of file ColumnDataWriter.hpp.

Referenced by DefineUnlimitedDimension(), and PutVariable().

std::string ColumnDataWriter::mFileExtension [protected]

Extension of output files

Definition at line 77 of file ColumnDataWriter.hpp.

int ColumnDataWriter::mRowStartPosition [protected]

The position of the file pointer when it's at the beginning of the current row

Definition at line 79 of file ColumnDataWriter.hpp.

Referenced by CreateFixedDimensionFile(), DoAdvanceAlongUnlimitedDimension(), EndDefineMode(), and PutVariable().

int ColumnDataWriter::mRowWidth [protected]

The width in characters of a row in the file

Definition at line 80 of file ColumnDataWriter.hpp.

Referenced by CreateFixedDimensionFile(), DoAdvanceAlongUnlimitedDimension(), EndDefineMode(), and PutVariable().

int ColumnDataWriter::mAncillaryRowStartPosition [protected]

The position of the ancillary file pointer when it's at the beginning of the current row

Definition at line 82 of file ColumnDataWriter.hpp.

Referenced by EndDefineMode().

int ColumnDataWriter::mAncillaryRowWidth [protected]

The width in characters of a row in the ancillary file

Definition at line 83 of file ColumnDataWriter.hpp.

Referenced by EndDefineMode().

bool ColumnDataWriter::mHasPutVariable [protected]

Whether a variable value has been output to a file.

Definition at line 85 of file ColumnDataWriter.hpp.

Referenced by AdvanceAlongUnlimitedDimension(), DoAdvanceAlongUnlimitedDimension(), and PutVariable().

bool ColumnDataWriter::mNeedAdvanceAlongUnlimitedDimension [protected]

Whether we need to advance along the unlimited dimension.

Definition at line 86 of file ColumnDataWriter.hpp.

Referenced by AdvanceAlongUnlimitedDimension(), DoAdvanceAlongUnlimitedDimension(), and PutVariable().

std::string ColumnDataWriter::mCommentForInfoFile [protected]

(Optional) comment that can be set and will be written to the info file when CreateInfoFile() is called in EndDefineMode()

Definition at line 92 of file ColumnDataWriter.hpp.

Referenced by CreateInfoFile(), and SetCommentForInfoFile().

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

io/src/writer/ColumnDataWriter.hpp
io/src/writer/ColumnDataWriter.cpp


Public Member Functions
	ColumnDataWriter (const std::string &rDirectory, const std::string &rBaseName, bool cleanDirectory=true, unsigned precision=8)
virtual	~ColumnDataWriter ()
int	DefineUnlimitedDimension (const std::string &rDimensionName, const std::string &rDimensionUnits)
int	DefineFixedDimension (const std::string &rDimensionName, const std::string &rDimensionUnits, long dimensionSize)
int	DefineVariable (const std::string &rVariableName, const std::string &rVariableUnits)
void	SetCommentForInfoFile (std::string comment)
virtual void	EndDefineMode ()
virtual void	AdvanceAlongUnlimitedDimension ()
virtual void	PutVariable (int variableID, double variableValue, long dimensionPosition=-1)
virtual void	Close ()
std::string	GetOutputDirectory ()
Protected Member Functions
void	CreateFixedDimensionFile (const std::string &rFileName)
void	CreateInfoFile (const std::string &rFileName)
void	CheckVariableName (const std::string &rName)
void	CheckUnitsName (const std::string &rName)
void	DoAdvanceAlongUnlimitedDimension ()
Protected Attributes
OutputFileHandler	mOutputFileHandler
std::string	mDirectory
std::string	mBaseName
bool	mIsInDefineMode
bool	mIsFixedDimensionSet
bool	mIsUnlimitedDimensionSet
long	mUnlimitedDimensionPosition
long	mFixedDimensionSize
out_stream	mpCurrentOutputFile
out_stream	mpCurrentAncillaryFile
DataWriterVariable *	mpUnlimitedDimensionVariable
DataWriterVariable *	mpFixedDimensionVariable
std::string	mUnlimitedDimensionName
std::string	mUnlimitedDimensionUnits
std::string	mFixedDimensionName
std::string	mFixedDimensionUnits
std::vector< DataWriterVariable >	mVariables
const unsigned	mFieldWidth
const unsigned	mPrecision
std::string	mFileExtension
int	mRowStartPosition
int	mRowWidth
int	mAncillaryRowStartPosition
int	mAncillaryRowWidth
bool	mHasPutVariable
bool	mNeedAdvanceAlongUnlimitedDimension
std::string	mCommentForInfoFile
Static Protected Attributes
static const int	SPACING = 2
static const int	FIXED_DIMENSION_VAR_ID = -1
static const int	UNLIMITED_DIMENSION_VAR_ID = -2