#include <FibreReader.hpp>

Inheritance diagram for FibreReader< DIM >:

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

◆ FibreReader()

template<unsigned DIM>

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

Create a new FibreReader.

Parameters

rFileFinder	the path to the fibre direction file
fibreFileType	AXISYM 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().

◆ ~FibreReader()

template<unsigned DIM>

FibreReader< DIM >::~FibreReader ( )

Destructor closes file.

Definition at line 68 of file FibreReader.cpp.

Member Function Documentation

◆ GetAllAxi()

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

direction an empty vector which will be filled with data from file

Definition at line 74 of file FibreReader.cpp.

References EXCEPTION.

Referenced by FibreConverter::Convert().

◆ GetAllOrtho()

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_direction	an empty vector which will be filled with data from file
second_direction	an empty vector which will be filled with data from file
third_direction	an empty vector which will be filled with data from file (or will remain empty in 2D)

Definition at line 91 of file FibreReader.cpp.

Referenced by FibreConverter::Convert().

◆ GetFibreSheetAndNormalMatrix()

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

fibreIndex	which 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.
rFibreMatrix	matrix to be filled in
checkOrthogonality	if 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().

◆ GetFibreVector()

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

fibreIndex	which 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.
rFibreVector	vector to be filled in
checkNormalised	if true, checks if the read vector is normalised and throws an exception if not

Definition at line 196 of file FibreReader.cpp.

References EXCEPTION.

◆ GetNumLinesOfData()

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().

◆ GetTokensAtNextLine()

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 246 of file FibreReader.cpp.

References EXCEPTION.

◆ IsBinary()

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.

◆ ReadNumLinesOfDataFromFile()

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 302 of file FibreReader.cpp.

References EXCEPTION.

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

Member Data Documentation

◆ mDataFile

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().

◆ mFileIsBinary

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().

◆ mFilePath

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().

◆ mNextIndex

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.

◆ mNumItemsPerLine

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().

◆ mNumLinesOfData

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().

◆ mTokens

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:

heart/src/io/FibreReader.hpp
heart/src/io/FibreReader.cpp

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ FibreReader()

◆ ~FibreReader()

Member Function Documentation

◆ GetAllAxi()

◆ GetAllOrtho()

◆ GetFibreSheetAndNormalMatrix()

◆ GetFibreVector()

◆ GetNumLinesOfData()

◆ GetTokensAtNextLine()

◆ IsBinary()

◆ ReadNumLinesOfDataFromFile()

Member Data Documentation

◆ mDataFile

◆ mFileIsBinary

◆ mFilePath

◆ mNextIndex

◆ mNumItemsPerLine

◆ mNumLinesOfData

◆ mTokens