ColumnDataReader Class Reference

#include <ColumnDataReader.hpp>

Inheritance diagram for ColumnDataReader:

Collaboration diagram for ColumnDataReader:

List of all members.

Public Member Functions

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

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

std::vector< double > GetValues (const std::string &rVariableName)

std::vector< double > GetValues (const std::string &rVariableName, int fixedDimension)

std::vector< double > GetUnlimitedDimensionValues ()

bool HasValues (const std::string &rVariableName)

unsigned GetFieldWidth ()

Private Member Functions

void PushColumnEntryFromLine (const std::string &rLine, int col)

void ReadColumnFromFile (const std::string &rFilename, int col)

void ReadValueFromFile (const std::string &rFilename, int col, int row)

void CheckFiles (const std::string &rDirectory, const std::string &rBaseName)

Private Attributes

std::map< std::string, int > mVariablesToColumns

std::map< std::string,
std::string > mVariablesToUnits

int mNumFixedDimensions

bool mHasUnlimitedDimension

int mNumVariables

std::string mInfoFilename

std::string mDataFilename

std::string mAncillaryFilename

std::vector< double > mValues

unsigned mFieldWidth

Static Private Attributes

static const int SPACING = 2

Detailed Description

A concrete column data reader class.

Definition at line 42 of file ColumnDataReader.hpp.

Constructor & Destructor Documentation

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

Read data from the given files into memory. The files should be formatted as if written by ColumnDataWriter, with fixed width columns (except for the header line) and fields in scientific notation.

This will attempt to determine the field width from the input file. However, it needs some data to work with in order to do so. Provided at least one correctly formatted entry exists, it will be able to determine the field width, assuming that space is allowed for 3 digits in the exponent. Release 1.1 and earlier of Chaste only allowed 2 digits for the exponent; we can cope with this provided that the first data entry in the file has another entry immediately to the right of it.

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 52 of file ColumnDataReader.cpp.

References CheckFiles(), and OutputFileHandler::GetOutputDirectoryFullPath().

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

Alternative constructor using FileFinder to specify the directory files are stored in.

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 74 of file ColumnDataReader.cpp.

References CheckFiles(), EXCEPTION, FileFinder::Exists(), FileFinder::GetAbsolutePath(), and FileFinder::IsDir().

Member Function Documentation

void ColumnDataReader::PushColumnEntryFromLine	(	const std::string &	rLine,
		int	col
	)			`[private]`

Push back an entry from the data file into mValues.

Parameters:

	rLine	the line of the data file
	col	the column number

Definition at line 377 of file ColumnDataReader.cpp.

References mFieldWidth, mValues, and SPACING.

Referenced by ReadColumnFromFile(), and ReadValueFromFile().

void ColumnDataReader::ReadColumnFromFile	(	const std::string &	rFilename,
		int	col
	)			`[private]`

Read in a given column from a data file into mValues.

Parameters:

	rFilename	the file name
	col	the column number

Definition at line 351 of file ColumnDataReader.cpp.

References mValues, and PushColumnEntryFromLine().

Referenced by GetUnlimitedDimensionValues(), and GetValues().

void ColumnDataReader::ReadValueFromFile	(	const std::string &	rFilename,
		int	col,
		int	row
	)			`[private]`

Push back an entry from a file into mValues.

Parameters:

	rFilename	the file name
	col	the column number
	row	the row number

Definition at line 331 of file ColumnDataReader.cpp.

References EXCEPTION, and PushColumnEntryFromLine().

Referenced by GetValues().

void ColumnDataReader::CheckFiles	(	const std::string &	rDirectory,
		const std::string &	rBaseName
	)			`[private]`

Set up internal data structures based on file structure, checking that they contain data in roughly the expected format.

Parameters:

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

Definition at line 84 of file ColumnDataReader.cpp.

References EXCEPTION, FILE_SUFFIX_WIDTH, mAncillaryFilename, mDataFilename, mFieldWidth, mHasUnlimitedDimension, mInfoFilename, mNumFixedDimensions, mNumVariables, mVariablesToColumns, mVariablesToUnits, NOT_READ, and SPACING.

Referenced by ColumnDataReader().

std::vector< double > ColumnDataReader::GetValues ( const std::string & rVariableName ) [virtual]

Get the entries for a given variable.

Parameters:

rVariableName

Implements AbstractDataReader.

Definition at line 233 of file ColumnDataReader.cpp.

References EXCEPTION, mDataFilename, mNumFixedDimensions, mValues, mVariablesToColumns, and ReadColumnFromFile().

std::vector< double > ColumnDataReader::GetValues	(	const std::string &	rVariableName,
		int	fixedDimension
	)			`[virtual]`

Get the entries for a given variable with fixed dimension.

Parameters:

	rVariableName
	fixedDimension

Implements AbstractDataReader.

Definition at line 254 of file ColumnDataReader.cpp.

References EXCEPTION, FILE_SUFFIX_WIDTH, mDataFilename, mHasUnlimitedDimension, mNumFixedDimensions, mValues, mVariablesToColumns, and ReadValueFromFile().

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

Get the entries for a given variable with unlimited dimension.

Definition at line 311 of file ColumnDataReader.cpp.

References EXCEPTION, mAncillaryFilename, mDataFilename, mHasUnlimitedDimension, mNumFixedDimensions, mValues, and ReadColumnFromFile().

bool ColumnDataReader::HasValues ( const std::string & rVariableName )

Determine whether the data file has entries for a given variable.

Parameters:

rVariableName

Definition at line 392 of file ColumnDataReader.cpp.

References mVariablesToColumns.

unsigned ColumnDataReader::GetFieldWidth ( )

Get the field width (the number of characters (excl. preceding '+' or '-') printed for each data entry in the file).

Definition at line 398 of file ColumnDataReader.cpp.

References mFieldWidth.

Member Data Documentation

std::map<std::string, int> ColumnDataReader::mVariablesToColumns [private]

Map between variable names and data column numbers.

Todo:: Change int to unsigned? (#991)

Definition at line 46 of file ColumnDataReader.hpp.

Referenced by CheckFiles(), GetValues(), and HasValues().

std::map<std::string, std::string> ColumnDataReader::mVariablesToUnits [private]

Map between variable names and variable units.

Definition at line 47 of file ColumnDataReader.hpp.

Referenced by CheckFiles().

int ColumnDataReader::mNumFixedDimensions [private]

The number of fixed dimensions in data file.

Definition at line 48 of file ColumnDataReader.hpp.

Referenced by CheckFiles(), GetUnlimitedDimensionValues(), and GetValues().

bool ColumnDataReader::mHasUnlimitedDimension [private]

Whether the data file has an unlimited dimension.

Definition at line 49 of file ColumnDataReader.hpp.

Referenced by CheckFiles(), GetUnlimitedDimensionValues(), and GetValues().

int ColumnDataReader::mNumVariables [private]

The number of variables in the data file.

Definition at line 50 of file ColumnDataReader.hpp.

Referenced by CheckFiles().

std::string ColumnDataReader::mInfoFilename [private]

The name of the info file.

Definition at line 51 of file ColumnDataReader.hpp.

Referenced by CheckFiles().

std::string ColumnDataReader::mDataFilename [private]

The name of the data file.

Definition at line 52 of file ColumnDataReader.hpp.

Referenced by CheckFiles(), GetUnlimitedDimensionValues(), and GetValues().

std::string ColumnDataReader::mAncillaryFilename [private]

The name of the ancillary file.

Definition at line 53 of file ColumnDataReader.hpp.

Referenced by CheckFiles(), and GetUnlimitedDimensionValues().

std::vector<double> ColumnDataReader::mValues [private]

Vector to hold values for a variable.

Definition at line 54 of file ColumnDataReader.hpp.

Referenced by GetUnlimitedDimensionValues(), GetValues(), PushColumnEntryFromLine(), and ReadColumnFromFile().

unsigned ColumnDataReader::mFieldWidth [private]

Width of each column in the text file (excludes column headers). Determined from the first data entry

Definition at line 55 of file ColumnDataReader.hpp.

Referenced by CheckFiles(), GetFieldWidth(), and PushColumnEntryFromLine().

const int ColumnDataReader::SPACING = 2 [static, private]

Space between columns (includes minus sign)

Definition at line 56 of file ColumnDataReader.hpp.

Referenced by CheckFiles(), and PushColumnEntryFromLine().

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

io/src/reader/ColumnDataReader.hpp
io/src/reader/ColumnDataReader.cpp


Public Member Functions
	ColumnDataReader (const std::string &rDirectory, const std::string &rBaseName, bool makeAbsolute=true)
	ColumnDataReader (const FileFinder &rDirectory, const std::string &rBaseName)
std::vector< double >	GetValues (const std::string &rVariableName)
std::vector< double >	GetValues (const std::string &rVariableName, int fixedDimension)
std::vector< double >	GetUnlimitedDimensionValues ()
bool	HasValues (const std::string &rVariableName)
unsigned	GetFieldWidth ()
Private Member Functions
void	PushColumnEntryFromLine (const std::string &rLine, int col)
void	ReadColumnFromFile (const std::string &rFilename, int col)
void	ReadValueFromFile (const std::string &rFilename, int col, int row)
void	CheckFiles (const std::string &rDirectory, const std::string &rBaseName)
Private Attributes
std::map< std::string, int >	mVariablesToColumns
std::map< std::string, std::string >	mVariablesToUnits
int	mNumFixedDimensions
bool	mHasUnlimitedDimension
int	mNumVariables
std::string	mInfoFilename
std::string	mDataFilename
std::string	mAncillaryFilename
std::vector< double >	mValues
unsigned	mFieldWidth
Static Private Attributes
static const int	SPACING = 2