#include <ColumnDataReader.hpp>

Inheritance diagram for ColumnDataReader:

Collaboration diagram for ColumnDataReader:

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 ()

Public Member Functions inherited from AbstractDataReader
virtual	~AbstractDataReader ()

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

Detailed Description

A concrete column data reader class.

Definition at line 50 of file ColumnDataReader.hpp.

Constructor & Destructor Documentation

◆ ColumnDataReader() [1/2]

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 60 of file ColumnDataReader.cpp.

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

◆ ColumnDataReader() [2/2]

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 86 of file ColumnDataReader.cpp.

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

Member Function Documentation

◆ CheckFiles()

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 96 of file ColumnDataReader.cpp.

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

Referenced by ColumnDataReader(), and ColumnDataReader().

◆ GetFieldWidth()

unsigned ColumnDataReader::GetFieldWidth ( )

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

Definition at line 440 of file ColumnDataReader.cpp.

References mFieldWidth.

◆ GetUnlimitedDimensionValues()

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

Returns: the entries for a given variable with unlimited dimension.

Definition at line 342 of file ColumnDataReader.cpp.

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

◆ GetValues() [1/2]

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

virtual

Returns: the entries for a given variable.

Parameters

rVariableName

Implements AbstractDataReader.

Definition at line 264 of file ColumnDataReader.cpp.

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

◆ GetValues() [2/2]

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

virtual

Returns: the entries for a given variable with fixed dimension.

Parameters

rVariableName
fixedDimension

Implements AbstractDataReader.

Definition at line 285 of file ColumnDataReader.cpp.

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

◆ HasValues()

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

Returns: true if the data file has entries for a given variable.

Parameters

rVariableName

Definition at line 434 of file ColumnDataReader.cpp.

References mVariablesToColumns.

◆ PushColumnEntryFromLine()

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 408 of file ColumnDataReader.cpp.

References mFieldWidth, and mValues.

Referenced by ReadColumnFromFile(), and ReadValueFromFile().

◆ ReadColumnFromFile()

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 382 of file ColumnDataReader.cpp.

References mValues, and PushColumnEntryFromLine().

Referenced by GetUnlimitedDimensionValues(), and GetValues().

◆ ReadValueFromFile()

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 362 of file ColumnDataReader.cpp.

References EXCEPTION, and PushColumnEntryFromLine().

Referenced by GetValues().

Member Data Documentation

◆ mAncillaryFilename

std::string ColumnDataReader::mAncillaryFilename

private

The name of the ancillary file.

Definition at line 61 of file ColumnDataReader.hpp.

Referenced by CheckFiles(), and GetUnlimitedDimensionValues().

◆ mDataFilename

std::string ColumnDataReader::mDataFilename

private

The name of the data file.

Definition at line 60 of file ColumnDataReader.hpp.

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

◆ mFieldWidth

unsigned ColumnDataReader::mFieldWidth

private

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

Definition at line 63 of file ColumnDataReader.hpp.

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

◆ mHasUnlimitedDimension

bool ColumnDataReader::mHasUnlimitedDimension

private

Whether the data file has an unlimited dimension.

Definition at line 57 of file ColumnDataReader.hpp.

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

◆ mInfoFilename

std::string ColumnDataReader::mInfoFilename

private

The name of the info file.

Definition at line 59 of file ColumnDataReader.hpp.

Referenced by CheckFiles().

◆ mNumFixedDimensions

int ColumnDataReader::mNumFixedDimensions

private

The number of fixed dimensions in data file.

Definition at line 56 of file ColumnDataReader.hpp.

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

◆ mNumVariables

int ColumnDataReader::mNumVariables

private

The number of variables in the data file.

Definition at line 58 of file ColumnDataReader.hpp.

Referenced by CheckFiles().

◆ mValues

std::vector<double> ColumnDataReader::mValues

private

Vector to hold values for a variable.

Definition at line 62 of file ColumnDataReader.hpp.

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

◆ mVariablesToColumns

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 54 of file ColumnDataReader.hpp.

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

◆ mVariablesToUnits

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

private

Map between variable names and variable units.

Definition at line 55 of file ColumnDataReader.hpp.

Referenced by CheckFiles().

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

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

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ColumnDataReader() [1/2]

◆ ColumnDataReader() [2/2]

Member Function Documentation

◆ CheckFiles()

◆ GetFieldWidth()

◆ GetUnlimitedDimensionValues()

◆ GetValues() [1/2]

◆ GetValues() [2/2]

◆ HasValues()

◆ PushColumnEntryFromLine()

◆ ReadColumnFromFile()

◆ ReadValueFromFile()

Member Data Documentation

◆ mAncillaryFilename

◆ mDataFilename

◆ mFieldWidth

◆ mHasUnlimitedDimension

◆ mInfoFilename

◆ mNumFixedDimensions

◆ mNumVariables

◆ mValues

◆ mVariablesToColumns

◆ mVariablesToUnits