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Chaste Commit::333233612e3dcc941d260418acd7b5ccdc30390e
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#include <ColumnDataReader.hpp>
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 () |
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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 |
A concrete column data reader class.
Definition at line 50 of file ColumnDataReader.hpp.
ColumnDataReader::ColumnDataReader | ( | const std::string & | rDirectory, |
const std::string & | rBaseName, | ||
bool | makeAbsolute = true |
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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.
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::ColumnDataReader | ( | const FileFinder & | rDirectory, |
const std::string & | rBaseName | ||
) |
Alternative constructor using FileFinder to specify the directory files are stored in.
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().
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private |
Set up internal data structures based on file structure, checking that they contain data in roughly the expected format.
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().
unsigned ColumnDataReader::GetFieldWidth | ( | ) |
Definition at line 440 of file ColumnDataReader.cpp.
References mFieldWidth.
std::vector< double > ColumnDataReader::GetUnlimitedDimensionValues | ( | ) |
Definition at line 342 of file ColumnDataReader.cpp.
References EXCEPTION, mAncillaryFilename, mDataFilename, mHasUnlimitedDimension, mNumFixedDimensions, mValues, and ReadColumnFromFile().
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virtual |
rVariableName |
Implements AbstractDataReader.
Definition at line 264 of file ColumnDataReader.cpp.
References EXCEPTION, mDataFilename, mNumFixedDimensions, mValues, mVariablesToColumns, and ReadColumnFromFile().
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virtual |
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 | ) |
rVariableName |
Definition at line 434 of file ColumnDataReader.cpp.
References mVariablesToColumns.
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private |
Push back an entry from the data file into mValues.
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().
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private |
Read in a given column from a data file into mValues.
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().
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private |
Push back an entry from a file into mValues.
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().
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The name of the ancillary file.
Definition at line 61 of file ColumnDataReader.hpp.
Referenced by CheckFiles(), and GetUnlimitedDimensionValues().
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The name of the data file.
Definition at line 60 of file ColumnDataReader.hpp.
Referenced by CheckFiles(), GetUnlimitedDimensionValues(), GetValues(), and GetValues().
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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().
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Whether the data file has an unlimited dimension.
Definition at line 57 of file ColumnDataReader.hpp.
Referenced by CheckFiles(), GetUnlimitedDimensionValues(), and GetValues().
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The name of the info file.
Definition at line 59 of file ColumnDataReader.hpp.
Referenced by CheckFiles().
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The number of fixed dimensions in data file.
Definition at line 56 of file ColumnDataReader.hpp.
Referenced by CheckFiles(), GetUnlimitedDimensionValues(), GetValues(), and GetValues().
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The number of variables in the data file.
Definition at line 58 of file ColumnDataReader.hpp.
Referenced by CheckFiles().
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Vector to hold values for a variable.
Definition at line 62 of file ColumnDataReader.hpp.
Referenced by GetUnlimitedDimensionValues(), GetValues(), GetValues(), PushColumnEntryFromLine(), and ReadColumnFromFile().
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Map between variable names and data column numbers.
Definition at line 54 of file ColumnDataReader.hpp.
Referenced by CheckFiles(), GetValues(), GetValues(), and HasValues().
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Map between variable names and variable units.
Definition at line 55 of file ColumnDataReader.hpp.
Referenced by CheckFiles().