#include <StreeterFibreGenerator.hpp>

Inheritance diagram for StreeterFibreGenerator< SPACE_DIM >:

Collaboration diagram for StreeterFibreGenerator< SPACE_DIM >:

Public Member Functions
	StreeterFibreGenerator (AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > &rMesh)

	~StreeterFibreGenerator ()

void	SetSurfaceFiles (const std::string &rEpicardiumFile, const std::string &rRightVentricleFile, const std::string &rLeftVentricleFile, bool indexFromZero)

void	SetApexToBase (const c_vector< double, SPACE_DIM > &apexToBase)

void	SetApexToBase (unsigned axis)

void	SetLogInfo (bool logInfo=true)

Public Member Functions inherited from AbstractPerElementWriter< SPACE_DIM, SPACE_DIM, SPACE_DIM *SPACE_DIM >
	AbstractPerElementWriter (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)

void	WriteData (OutputFileHandler &rHandler, const std::string &rFileName)

void	SetWriteFileAsBinary (bool binary=true)

virtual	~AbstractPerElementWriter ()

Protected Member Functions
void	Visit (Element< SPACE_DIM, SPACE_DIM > pElement, unsigned localElementIndex, c_vector< double, SPACE_DIM SPACE_DIM > &rData)

void	WriteHeaderOnMaster ()

void	PreWriteCalculations (OutputFileHandler &rOutputDirectory)

Protected Member Functions inherited from AbstractPerElementWriter< SPACE_DIM, SPACE_DIM, SPACE_DIM *SPACE_DIM >
virtual void	Visit (Element< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned localElementIndex, c_vector< double, DATA_SIZE > &rData)=0

virtual void	WriteElementOnMaster (const c_vector< double, DATA_SIZE > &rData)

Private Member Functions
double	GetAveragedThicknessLocalNode (const unsigned nodeIndex, const std::vector< double > &wallThickness) const

double	GetFibreMaxAngle (const c_vector< HeartRegionType, SPACE_DIM+1 > &nodesRegionsForElement) const

Private Attributes
HeartGeometryInformation< SPACE_DIM > *	mpGeometryInfo

c_vector< double, SPACE_DIM >	mApexToBase

std::vector< double >	mWallThickness

std::vector< double >	mAveragedWallThickness

bool	mLogInfo

Additional Inherited Members
Protected Attributes inherited from AbstractPerElementWriter< SPACE_DIM, SPACE_DIM, SPACE_DIM *SPACE_DIM >
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	mpMesh

out_stream	mpMasterFile

Detailed Description

template<unsigned SPACE_DIM>
class StreeterFibreGenerator< SPACE_DIM >

Generate fibre in a ventricular mesh using the description in Streeter DD, Jr, Spotnitz HM, Patel DP, Ross J, Jr, Sonnenblick EH. Fiber orientation in the canine left ventricle during diastole and systole. Circ Res. 1969 Mar;24(3):339–347.

Formulae used to generate the fibre orientations are in A Comparison of Monodomain and Bidomain Reaction-Diffusion Models for Action Potential Propagation in the Human Heart Mark Potse, Bruno Dubé, Jacques Richer, Alain Vinet, and Ramesh M. Gulrajani IEEE Trans. Biomed. Eng. 53(12):2425-2435, 2006.

Output file format: The first line indicates the number of elements. Each of the following lines contain SPACE_DIM vectors of SPACE_DIM elements for the direction of the myofibre, the transverse to it in the plane of the myocyte laminae and the normal to this laminae.

Definition at line 64 of file StreeterFibreGenerator.hpp.

Constructor & Destructor Documentation

template<unsigned SPACE_DIM>

StreeterFibreGenerator< SPACE_DIM >::StreeterFibreGenerator ( AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > & rMesh )

Constructor

Parameters

rMesh Reference to the tetrahedral mesh of the ventricles.

Definition at line 149 of file StreeterFibreGenerator.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), StreeterFibreGenerator< SPACE_DIM >::mAveragedWallThickness, StreeterFibreGenerator< SPACE_DIM >::mWallThickness, and Citations::Register().

template<unsigned SPACE_DIM>

StreeterFibreGenerator< SPACE_DIM >::~StreeterFibreGenerator ( )

Destructor

Definition at line 163 of file StreeterFibreGenerator.cpp.

References StreeterFibreGenerator< SPACE_DIM >::mpGeometryInfo.

Member Function Documentation

template<unsigned SPACE_DIM>

double StreeterFibreGenerator< SPACE_DIM >::GetAveragedThicknessLocalNode	(	const unsigned	nodeIndex,
		const std::vector< double > &	wallThickness
	)		const

private

Compute the wall thickness of a given node based on a neighbourhood average of its thickness and of those in the forward star.

Parameters

nodeIndex	The index of the node in question
wallThickness	vector of thickness of all nodes in node index order

Returns: Neighbourhood average thickness (will return 0 if the node is not local to this process)

Definition at line 62 of file StreeterFibreGenerator.cpp.

References Node< SPACE_DIM >::ContainingElementsBegin(), Node< SPACE_DIM >::ContainingElementsEnd(), Node< SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

Referenced by StreeterFibreGenerator< SPACE_DIM >::PreWriteCalculations().

template<unsigned SPACE_DIM>

double StreeterFibreGenerator< SPACE_DIM >::GetFibreMaxAngle ( const c_vector< HeartRegionType, SPACE_DIM+1 > & nodesRegionsForElement ) const

private

R is the maximum angle between the fibre and the v axis (heart region dependant)

Parameters

nodesRegionsForElement is a small vector containing the region tags of the element's nodes

Returns: Pi/4 (if the element is in RV), Pi/3 otherwise

Definition at line 111 of file StreeterFibreGenerator.cpp.

References NEVER_REACHED.

Referenced by StreeterFibreGenerator< SPACE_DIM >::Visit().

template<unsigned SPACE_DIM>

void StreeterFibreGenerator< SPACE_DIM >::PreWriteCalculations ( OutputFileHandler & rOutputDirectory )

protectedvirtual

Does calculations to generate an orthotropic fibre orientation model of the ventricular mesh provided. In particular - populates the member variables mWallThickness and mAveragedWallThickness.

Also writes these to file if SetLogInfo() has been called.

Assumes that the base-apex axis is x. Based on Streeter 1969 and Potse 2006

Parameters

rOutputDirectory Handler for output directory

Reimplemented from AbstractPerElementWriter< SPACE_DIM, SPACE_DIM, SPACE_DIM *SPACE_DIM >.

Definition at line 187 of file StreeterFibreGenerator.cpp.

References PetscTools::AmMaster(), EXCEPTION, StreeterFibreGenerator< SPACE_DIM >::GetAveragedThicknessLocalNode(), StreeterFibreGenerator< SPACE_DIM >::mApexToBase, StreeterFibreGenerator< SPACE_DIM >::mAveragedWallThickness, StreeterFibreGenerator< SPACE_DIM >::mLogInfo, StreeterFibreGenerator< SPACE_DIM >::mpGeometryInfo, AbstractPerElementWriter< SPACE_DIM, SPACE_DIM, SPACE_DIM *SPACE_DIM >::mpMesh, StreeterFibreGenerator< SPACE_DIM >::mWallThickness, NEVER_REACHED, and OutputFileHandler::OpenOutputFile().

template<unsigned SPACE_DIM>

void StreeterFibreGenerator< SPACE_DIM >::SetApexToBase ( const c_vector< double, SPACE_DIM > & apexToBase )

Set the direction from apex to base

Parameters

apexToBase is a non-zero vector. It will be stored in normalised form

Definition at line 447 of file StreeterFibreGenerator.cpp.

References EXCEPTION, and StreeterFibreGenerator< SPACE_DIM >::mApexToBase.

template<unsigned SPACE_DIM>

void StreeterFibreGenerator< SPACE_DIM >::SetApexToBase ( unsigned axis )

Set the direction from apex to base

Parameters

axis	is the Cartesian axis from apex to base.

Definition at line 458 of file StreeterFibreGenerator.cpp.

References EXCEPTION, and StreeterFibreGenerator< SPACE_DIM >::mApexToBase.

template<unsigned SPACE_DIM>

void StreeterFibreGenerator< SPACE_DIM >::SetLogInfo ( bool logInfo = true )

Tells the WriteData method to output extra debug info on nodes in particular regions, and wall thicknesses.

Parameters

logInfo whether or not to write log files.

Definition at line 469 of file StreeterFibreGenerator.cpp.

References StreeterFibreGenerator< SPACE_DIM >::mLogInfo.

template<unsigned SPACE_DIM>

void StreeterFibreGenerator< SPACE_DIM >::SetSurfaceFiles	(	const std::string &	rEpicardiumFile,
		const std::string &	rRightVentricleFile,
		const std::string &	rLeftVentricleFile,
		bool	indexFromZero
	)

Uses the names of files defining the different surfaces of the mesh to construct the geometry information class File formats: list of nodes, either one per line or multiple (e.g. nodes in each boundary element on surface).

Parameters

rEpicardiumFile	Epicardium surface nodes (global indices).
rRightVentricleFile	Right Ventricle surface nodes (global indices).
rLeftVentricleFile	Left Ventricle surface nodes (global indices).
indexFromZero	Are the nodes in the original mesh file/surface files indexed from 0?

If either rRightVentricleFile or rLeftVentricleFile are the empty string, then it is assumed that this is a wedge preparation for left or right ventricle, respectively. That is, the ventricle with a non-empty string. If both are empty strings then throws exception in HeartGeometryInformation.

Definition at line 169 of file StreeterFibreGenerator.cpp.

References StreeterFibreGenerator< SPACE_DIM >::mpGeometryInfo, and AbstractPerElementWriter< SPACE_DIM, SPACE_DIM, SPACE_DIM *SPACE_DIM >::mpMesh.

template<unsigned SPACE_DIM>

void StreeterFibreGenerator< SPACE_DIM >::Visit	(	Element< SPACE_DIM, SPACE_DIM > *	pElement,
		unsigned	localElementIndex,
		c_vector< double, SPACE_DIM *SPACE_DIM > &	rData
	)

protected

Associate an element with a fibre direction.

This is only called (by abstract class) on processes which own pElement.

Parameters

pElement	a locally-owned element for which to calculate or lookup some data
localElementIndex	the index of pElement in the local vector.
rData	the double-precision data to write to file (output from the method). Gives Fibre x 3 (space dim), sheet(3), normal(3) in one vector.

Definition at line 314 of file StreeterFibreGenerator.cpp.

References StreeterFibreGenerator< SPACE_DIM >::GetFibreMaxAngle(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), StreeterFibreGenerator< SPACE_DIM >::mApexToBase, StreeterFibreGenerator< SPACE_DIM >::mAveragedWallThickness, StreeterFibreGenerator< SPACE_DIM >::mpGeometryInfo, AbstractPerElementWriter< SPACE_DIM, SPACE_DIM, SPACE_DIM *SPACE_DIM >::mpMesh, StreeterFibreGenerator< SPACE_DIM >::mWallThickness, SmallPow(), and VectorProduct().