#include <ColumnDataWriter.hpp>

Inheritance diagram for ColumnDataWriter:

Collaboration diagram for ColumnDataWriter:

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 ()

Public Member Functions inherited from AbstractDataWriter
virtual	~AbstractDataWriter ()

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 = 1

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 51 of file ColumnDataWriter.hpp.

Constructor & Destructor Documentation

◆ ColumnDataWriter()

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 52 of file ColumnDataWriter.cpp.

References EXCEPTION.

◆ ~ColumnDataWriter()

ColumnDataWriter::~ColumnDataWriter ( )

virtual

Destructor. Closes any open files.

Definition at line 80 of file ColumnDataWriter.cpp.

References Close(), mpFixedDimensionVariable, and mpUnlimitedDimensionVariable.

Member Function Documentation

◆ AdvanceAlongUnlimitedDimension()

void ColumnDataWriter::AdvanceAlongUnlimitedDimension ( )

virtual

Dummy function for DoAdvanceAlongUnlimitedDimension.

Implements AbstractDataWriter.

Reimplemented in ParallelColumnDataWriter.

Definition at line 400 of file ColumnDataWriter.cpp.

References mHasPutVariable, and mNeedAdvanceAlongUnlimitedDimension.

Referenced by OdeSolution::WriteToFile().

◆ CheckUnitsName()

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 125 of file ColumnDataWriter.cpp.

References EXCEPTION.

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

◆ CheckVariableName()

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 116 of file ColumnDataWriter.cpp.

References CheckUnitsName(), and EXCEPTION.

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

◆ Close()

void ColumnDataWriter::Close ( )

virtual

Close any open files.

Implements AbstractDataWriter.

Reimplemented in ParallelColumnDataWriter.

Definition at line 101 of file ColumnDataWriter.cpp.

References mpCurrentAncillaryFile, and mpCurrentOutputFile.

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

◆ CreateFixedDimensionFile()

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 322 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().

◆ CreateInfoFile()

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 351 of file ColumnDataWriter.cpp.

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

Referenced by EndDefineMode().

◆ DefineFixedDimension()

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 165 of file ColumnDataWriter.cpp.

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

◆ DefineUnlimitedDimension()

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 137 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().

◆ DefineVariable()

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 193 of file ColumnDataWriter.cpp.

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

Referenced by OdeSolution::WriteToFile().

◆ DoAdvanceAlongUnlimitedDimension()

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 366 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().

◆ EndDefineMode()

void ColumnDataWriter::EndDefineMode ( )

virtual

End the define mode of the DataWriter.

Implements AbstractDataWriter.

Reimplemented in ParallelColumnDataWriter.

Definition at line 230 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().

◆ GetOutputDirectory()

std::string ColumnDataWriter::GetOutputDirectory ( )

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

Definition at line 96 of file ColumnDataWriter.cpp.

References OutputFileHandler::GetOutputDirectoryFullPath(), and mOutputFileHandler.

◆ PutVariable()

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 408 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().

◆ SetCommentForInfoFile()

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 197 of file ColumnDataWriter.hpp.

References mCommentForInfoFile.

Referenced by OdeSolution::WriteToFile().

Member Data Documentation

◆ FIXED_DIMENSION_VAR_ID

const int ColumnDataWriter::FIXED_DIMENSION_VAR_ID = -1

staticprotected

id of fixed dimension variable

Definition at line 80 of file ColumnDataWriter.hpp.

Referenced by DefineFixedDimension(), and PutVariable().

◆ mAncillaryRowStartPosition

int ColumnDataWriter::mAncillaryRowStartPosition

protected

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

Definition at line 88 of file ColumnDataWriter.hpp.

Referenced by EndDefineMode().

◆ mAncillaryRowWidth

int ColumnDataWriter::mAncillaryRowWidth

protected

The width in characters of a row in the ancillary file

Definition at line 89 of file ColumnDataWriter.hpp.

Referenced by EndDefineMode().

◆ mBaseName

std::string ColumnDataWriter::mBaseName

protected

The base name for the output data files.

Definition at line 58 of file ColumnDataWriter.hpp.

Referenced by DoAdvanceAlongUnlimitedDimension(), and EndDefineMode().

◆ mCommentForInfoFile

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 98 of file ColumnDataWriter.hpp.

Referenced by CreateInfoFile(), and SetCommentForInfoFile().

◆ mDirectory

std::string ColumnDataWriter::mDirectory

protected

Directory output files will be stored in.

Definition at line 57 of file ColumnDataWriter.hpp.

◆ mFieldWidth

const unsigned ColumnDataWriter::mFieldWidth

protected

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

Definition at line 77 of file ColumnDataWriter.hpp.

Referenced by EndDefineMode(), and PutVariable().

◆ mFileExtension

std::string ColumnDataWriter::mFileExtension

protected

Extension of output files

Definition at line 83 of file ColumnDataWriter.hpp.

◆ mFixedDimensionName

std::string ColumnDataWriter::mFixedDimensionName

protected

The name of the fixed dimension

Definition at line 72 of file ColumnDataWriter.hpp.

Referenced by DefineFixedDimension(), and DefineVariable().

◆ mFixedDimensionSize

long ColumnDataWriter::mFixedDimensionSize

protected

The size of the fixed dimension

Definition at line 63 of file ColumnDataWriter.hpp.

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

◆ mFixedDimensionUnits

std::string ColumnDataWriter::mFixedDimensionUnits

protected

The units of the fixed dimension

Definition at line 73 of file ColumnDataWriter.hpp.

Referenced by DefineFixedDimension().

◆ mHasPutVariable

bool ColumnDataWriter::mHasPutVariable

protected

Whether a variable value has been output to a file.

Definition at line 91 of file ColumnDataWriter.hpp.

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

◆ mIsFixedDimensionSet

bool ColumnDataWriter::mIsFixedDimensionSet

protected

Is the fixed dimension set

Definition at line 60 of file ColumnDataWriter.hpp.

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

◆ mIsInDefineMode

bool ColumnDataWriter::mIsInDefineMode

protected

Is the DataWriter in define mode or not

Definition at line 59 of file ColumnDataWriter.hpp.

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

◆ mIsUnlimitedDimensionSet

bool ColumnDataWriter::mIsUnlimitedDimensionSet

protected

Is the unlimited dimension set

Definition at line 61 of file ColumnDataWriter.hpp.

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

◆ mNeedAdvanceAlongUnlimitedDimension

bool ColumnDataWriter::mNeedAdvanceAlongUnlimitedDimension

protected

Whether we need to advance along the unlimited dimension.

Definition at line 92 of file ColumnDataWriter.hpp.

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

◆ mOutputFileHandler

OutputFileHandler ColumnDataWriter::mOutputFileHandler

protected

For opening data files.

Definition at line 55 of file ColumnDataWriter.hpp.

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

◆ mpCurrentAncillaryFile

out_stream ColumnDataWriter::mpCurrentAncillaryFile

protected

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

Definition at line 65 of file ColumnDataWriter.hpp.

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

◆ mpCurrentOutputFile

out_stream ColumnDataWriter::mpCurrentOutputFile

protected

Filestream currently being addressed

Definition at line 64 of file ColumnDataWriter.hpp.

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

◆ mpFixedDimensionVariable

DataWriterVariable* ColumnDataWriter::mpFixedDimensionVariable

protected

The variable corresponding to the fixed dimension

Definition at line 67 of file ColumnDataWriter.hpp.

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

◆ mPrecision

const unsigned ColumnDataWriter::mPrecision

protected

Precision used in writing the data

Definition at line 78 of file ColumnDataWriter.hpp.

Referenced by CreateFixedDimensionFile(), and EndDefineMode().

◆ mpUnlimitedDimensionVariable

DataWriterVariable* ColumnDataWriter::mpUnlimitedDimensionVariable

protected

The variable corresponding to the unlimited dimension

Definition at line 66 of file ColumnDataWriter.hpp.

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

◆ mRowStartPosition

int ColumnDataWriter::mRowStartPosition

protected

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

Definition at line 85 of file ColumnDataWriter.hpp.

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

◆ mRowWidth

int ColumnDataWriter::mRowWidth

protected

The width in characters of a row in the file

Definition at line 86 of file ColumnDataWriter.hpp.

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

◆ mUnlimitedDimensionName

std::string ColumnDataWriter::mUnlimitedDimensionName

protected

The name of the unlimited dimension.

Definition at line 69 of file ColumnDataWriter.hpp.

Referenced by DefineUnlimitedDimension(), and DefineVariable().

◆ mUnlimitedDimensionPosition

long ColumnDataWriter::mUnlimitedDimensionPosition

protected

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

Definition at line 62 of file ColumnDataWriter.hpp.

Referenced by DoAdvanceAlongUnlimitedDimension(), and EndDefineMode().

◆ mUnlimitedDimensionUnits

std::string ColumnDataWriter::mUnlimitedDimensionUnits

protected

The physical units of the unlimited dimension.

Definition at line 70 of file ColumnDataWriter.hpp.

Referenced by DefineUnlimitedDimension().

◆ mVariables

std::vector<DataWriterVariable> ColumnDataWriter::mVariables

protected

The data variables

Definition at line 75 of file ColumnDataWriter.hpp.

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

◆ SPACING

const int ColumnDataWriter::SPACING = 1

staticprotected

Space between columns (includes minus sign)

Definition at line 79 of file ColumnDataWriter.hpp.

Referenced by EndDefineMode(), and PutVariable().

◆ UNLIMITED_DIMENSION_VAR_ID

const int ColumnDataWriter::UNLIMITED_DIMENSION_VAR_ID = -2

staticprotected

id of unlimited dimension variable

Definition at line 81 of file ColumnDataWriter.hpp.

Referenced by DefineUnlimitedDimension(), and PutVariable().

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

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

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ColumnDataWriter()

◆ ~ColumnDataWriter()

Member Function Documentation

◆ AdvanceAlongUnlimitedDimension()

◆ CheckUnitsName()

◆ CheckVariableName()

◆ Close()

◆ CreateFixedDimensionFile()

◆ CreateInfoFile()

◆ DefineFixedDimension()

◆ DefineUnlimitedDimension()

◆ DefineVariable()

◆ DoAdvanceAlongUnlimitedDimension()

◆ EndDefineMode()

◆ GetOutputDirectory()

◆ PutVariable()

◆ SetCommentForInfoFile()

Member Data Documentation

◆ FIXED_DIMENSION_VAR_ID

◆ mAncillaryRowStartPosition

◆ mAncillaryRowWidth

◆ mBaseName

◆ mCommentForInfoFile

◆ mDirectory

◆ mFieldWidth

◆ mFileExtension

◆ mFixedDimensionName

◆ mFixedDimensionSize

◆ mFixedDimensionUnits

◆ mHasPutVariable

◆ mIsFixedDimensionSet

◆ mIsInDefineMode

◆ mIsUnlimitedDimensionSet

◆ mNeedAdvanceAlongUnlimitedDimension

◆ mOutputFileHandler

◆ mpCurrentAncillaryFile

◆ mpCurrentOutputFile

◆ mpFixedDimensionVariable

◆ mPrecision

◆ mpUnlimitedDimensionVariable

◆ mRowStartPosition

◆ mRowWidth

◆ mUnlimitedDimensionName

◆ mUnlimitedDimensionPosition

◆ mUnlimitedDimensionUnits

◆ mVariables

◆ SPACING

◆ UNLIMITED_DIMENSION_VAR_ID