Chaste  Release::3.4
Public Member Functions | Private Member Functions | Private Attributes | List of all members
FibreReader< DIM > Class Template Reference

#include <FibreReader.hpp>

+ Collaboration diagram for FibreReader< DIM >:

Public Member Functions

 FibreReader (const FileFinder &rFileFinder, FibreFileType fibreFileType)
 
 ~FibreReader ()
 
void GetFibreSheetAndNormalMatrix (unsigned fibreIndex, c_matrix< double, DIM, DIM > &rFibreMatrix, bool checkOrthogonality=true)
 
void GetFibreVector (unsigned fibreIndex, c_vector< double, DIM > &rFibreVector, bool checkNormalised=true)
 
unsigned GetNumLinesOfData ()
 
void GetAllAxi (std::vector< c_vector< double, DIM > > &direction)
 
void GetAllOrtho (std::vector< c_vector< double, DIM > > &first_direction, std::vector< c_vector< double, DIM > > &second_direction, std::vector< c_vector< double, DIM > > &third_direction)
 
bool IsBinary ()
 

Private Member Functions

unsigned GetTokensAtNextLine ()
 
void ReadNumLinesOfDataFromFile ()
 

Private Attributes

std::ifstream mDataFile
 
std::string mFilePath
 
unsigned mNumLinesOfData
 
bool mFileIsBinary
 
unsigned mNumItemsPerLine
 
unsigned mNextIndex
 
std::vector< double > mTokens
 

Detailed Description

template<unsigned DIM>
class FibreReader< DIM >

A class for reading .axi files (files which define the fibre direction for each element) and .ortho files (files which define the fibre, sheet and normal directions for each element.

Definition at line 61 of file FibreReader.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>
FibreReader< DIM >::FibreReader ( const FileFinder &  rFileFinder,
FibreFileType  fibreFileType 
)

Create a new FibreReader.

Parameters
rFileFinderthe path to the fibre direction file
fibreFileTypeAXISYM or ORTHO depending on type of file to be read

Definition at line 42 of file FibreReader.cpp.

References EXCEPTION, FileFinder::GetAbsolutePath(), FibreReader< DIM >::mDataFile, FibreReader< DIM >::mFilePath, FibreReader< DIM >::mNumItemsPerLine, FibreReader< DIM >::mTokens, and FibreReader< DIM >::ReadNumLinesOfDataFromFile().

template<unsigned DIM>
FibreReader< DIM >::~FibreReader ( )

Destructor closes file.

Definition at line 68 of file FibreReader.cpp.

Member Function Documentation

template<unsigned DIM>
void FibreReader< DIM >::GetAllAxi ( std::vector< c_vector< double, DIM > > &  direction)

Get every line of a fibre file (axi-symmetric) in vector of vectors format. This is useful for adding to a visualizer. (Do not use with GetNext...)

Parameters
directionan empty vector which will be filled with data from file

Definition at line 74 of file FibreReader.cpp.

References EXCEPTION.

Referenced by FibreConverter::Convert().

template<unsigned DIM>
void FibreReader< DIM >::GetAllOrtho ( std::vector< c_vector< double, DIM > > &  first_direction,
std::vector< c_vector< double, DIM > > &  second_direction,
std::vector< c_vector< double, DIM > > &  third_direction 
)

Get every line of a fibre file (orthotropic) in vector of vectors format. This is useful for adding to a visualizer. (Do not use with GetNext...)

Parameters
first_directionan empty vector which will be filled with data from file
second_directionan empty vector which will be filled with data from file
third_directionan empty vector which will be filled with data from file (or will remain empty in 2D)

Definition at line 91 of file FibreReader.cpp.

References EXCEPTION.

Referenced by FibreConverter::Convert().

template<unsigned DIM>
void FibreReader< DIM >::GetFibreSheetAndNormalMatrix ( unsigned  fibreIndex,
c_matrix< double, DIM, DIM > &  rFibreMatrix,
bool  checkOrthogonality = true 
)

Read a fibre direction matrix from the file. Must only be used when reading an orthotropic file. These have lines of the form

fibre0 fibre1 fibre2 sheet0 sheet1 sheet2 normal0 normal1 normal2

which are converted to the matrix

[ fibre0 sheet0 normal0 ]
[ fibre1 sheet1 normal1 ]
[ fibre2 sheet2 normal2 ]
Parameters
fibreIndexwhich fibre vector to read. Note that vectors must be read in monotonically increasing order, so subsequent calls to this method must always pass a strictly greater index. They may skip vectors, however.
rFibreMatrixmatrix to be filled in
checkOrthogonalityif true, checks if the matrix is orthogonal and throws an exception if not

Definition at line 125 of file FibreReader.cpp.

References EXCEPTION.

Referenced by AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::SetVariableFibreSheetDirections().

template<unsigned DIM>
void FibreReader< DIM >::GetFibreVector ( unsigned  fibreIndex,
c_vector< double, DIM > &  rFibreVector,
bool  checkNormalised = true 
)

Read a fibre direction vector from the file. Must only be used when reading an axisymmetric file. These have lines of the form

fibre0 fibre1 fibre2
Parameters
fibreIndexwhich fibre vector to read. Note that vectors must be read in monotonically increasing order, so subsequent calls to this method must always pass a strictly greater index. They may skip vectors, however.
rFibreVectorvector to be filled in
checkNormalisedif true, checks if the read vector is normalised and throws an exception if not

Definition at line 197 of file FibreReader.cpp.

References EXCEPTION.

template<unsigned DIM>
unsigned FibreReader< DIM >::GetNumLinesOfData ( )
inline
Returns
the number of lines of data in the file - this is the value read from the first line.

Definition at line 155 of file FibreReader.hpp.

References FibreReader< DIM >::mNumLinesOfData.

Referenced by AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::SetVariableFibreSheetDirections().

template<unsigned DIM>
unsigned FibreReader< DIM >::GetTokensAtNextLine ( )
private

Read a line of numbers from mDataFile. Sets up the member variable mTokens with the data in the next line.

Returns
the number of data entries put into mTokens

Definition at line 248 of file FibreReader.cpp.

References EXCEPTION.

template<unsigned DIM>
bool FibreReader< DIM >::IsBinary ( )
inline
Returns
Whether the fibre file contains binary data.

Definition at line 185 of file FibreReader.hpp.

References FibreReader< DIM >::mFileIsBinary.

template<unsigned DIM>
void FibreReader< DIM >::ReadNumLinesOfDataFromFile ( )
private

Read number of elements from mDataFile. Note: Must be called before GetTokensAtNextLine (it assumes that it's reading the first line).

Definition at line 305 of file FibreReader.cpp.

References EXCEPTION.

Referenced by FibreReader< DIM >::FibreReader().

Member Data Documentation

template<unsigned DIM>
std::ifstream FibreReader< DIM >::mDataFile
private

File stream to use for GetTokensAtNextLine

Definition at line 65 of file FibreReader.hpp.

Referenced by FibreReader< DIM >::FibreReader().

template<unsigned DIM>
bool FibreReader< DIM >::mFileIsBinary
private

Whether the data file has binary entries

Definition at line 73 of file FibreReader.hpp.

Referenced by FibreReader< DIM >::IsBinary().

template<unsigned DIM>
std::string FibreReader< DIM >::mFilePath
private

Absolute path of the file being read

Definition at line 68 of file FibreReader.hpp.

Referenced by FibreReader< DIM >::FibreReader().

template<unsigned DIM>
unsigned FibreReader< DIM >::mNextIndex
private

The next index we expect to read from the file.

Definition at line 79 of file FibreReader.hpp.

template<unsigned DIM>
unsigned FibreReader< DIM >::mNumItemsPerLine
private

How many items we expect to find per line: DIM for axisymmetric, DIM*DIM for orthotropic

Definition at line 76 of file FibreReader.hpp.

Referenced by FibreReader< DIM >::FibreReader().

template<unsigned DIM>
unsigned FibreReader< DIM >::mNumLinesOfData
private

Number of lines of data in the file, read from the first line of the file

Definition at line 71 of file FibreReader.hpp.

Referenced by FibreReader< DIM >::GetNumLinesOfData().

template<unsigned DIM>
std::vector<double> FibreReader< DIM >::mTokens
private

Vector which entries read from a line in a file is put into.

Definition at line 82 of file FibreReader.hpp.

Referenced by FibreReader< DIM >::FibreReader().

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