Chaste  Release::2018.1
Public Member Functions | Private Member Functions | Private Attributes | List of all members
ColumnDataReader Class Reference

#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::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
rDirectoryThe directory the files are stored in
rBaseNameThe base name of the files to read (i.e. without the extensions)
makeAbsoluteWhether 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::ColumnDataReader ( const FileFinder &  rDirectory,
const std::string &  rBaseName 
)

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

Parameters
rDirectoryThe directory the files are stored in
rBaseNameThe 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

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
rDirectoryAbsolute path of the directory the files are stored in
rBaseNameThe 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().

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.

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().

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().

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().

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.

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

Push back an entry from the data file into mValues.

Parameters
rLinethe line of the data file
colthe column number

Definition at line 408 of file ColumnDataReader.cpp.

References mFieldWidth, and mValues.

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
rFilenamethe file name
colthe column number

Definition at line 382 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
rFilenamethe file name
colthe column number
rowthe row number

Definition at line 362 of file ColumnDataReader.cpp.

References EXCEPTION, and PushColumnEntryFromLine().

Referenced by GetValues().

Member Data Documentation

std::string ColumnDataReader::mAncillaryFilename
private

The name of the ancillary file.

Definition at line 61 of file ColumnDataReader.hpp.

Referenced by CheckFiles(), and GetUnlimitedDimensionValues().

std::string ColumnDataReader::mDataFilename
private

The name of the data file.

Definition at line 60 of file ColumnDataReader.hpp.

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

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().

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().

std::string ColumnDataReader::mInfoFilename
private

The name of the info file.

Definition at line 59 of file ColumnDataReader.hpp.

Referenced by CheckFiles().

int ColumnDataReader::mNumFixedDimensions
private

The number of fixed dimensions in data file.

Definition at line 56 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 58 of file ColumnDataReader.hpp.

Referenced by CheckFiles().

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(), PushColumnEntryFromLine(), and ReadColumnFromFile().

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(), and HasValues().

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: