StreeterFibreGenerator< SPACE_DIM > Class Template Reference

#include <StreeterFibreGenerator.hpp>

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	GenerateOrthotropicFibreOrientation (std::string outputDirectory, std::string fibreOrientationFile, bool logInfo=false)
void	SetApexToBase (const c_vector< double, SPACE_DIM > &apexToBase)
void	SetApexToBase (unsigned axis)
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
AbstractTetrahedralMesh < SPACE_DIM, SPACE_DIM > &	mrMesh
HeartGeometryInformation < SPACE_DIM > *	mpGeometryInfo
c_vector< double, SPACE_DIM >	mApexToBase

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.

Definition at line 50 of file StreeterFibreGenerator.hpp.

Constructor & Destructor Documentation

template<unsigned SPACE_DIM>

StreeterFibreGenerator< SPACE_DIM >::StreeterFibreGenerator ( AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > & rMesh ) [inline]

Constructor

Parameters:

rMesh

reference to the tetrahedral mesh of the ventricles

Definition at line 131 of file StreeterFibreGenerator.cpp.

template<unsigned SPACE_DIM>

StreeterFibreGenerator< SPACE_DIM >::~StreeterFibreGenerator ( ) [inline]

Destructor

Definition at line 139 of file StreeterFibreGenerator.cpp.

References StreeterFibreGenerator< SPACE_DIM >::mpGeometryInfo.

Member Function Documentation

template<unsigned SPACE_DIM>

void StreeterFibreGenerator< SPACE_DIM >::GenerateOrthotropicFibreOrientation	(	std::string	outputDirectory,
		std::string	fibreOrientationFile,
		bool	logInfo = `false`
	)			`[inline]`

Generates an orthotropic fibre orientation model of the ventricular mesh provided. Assumes that the base-apex axis is x. Based on Streeter 1969 and Potse 2006

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 myocite laminae and the normal to this laminae.

Parameters:

	outputDirectory	Output directory
	fibreOrientationFile	Output file
	logInfo	Tells the method to output extra debug info. To be eliminated once it's fully tested

Definition at line 156 of file StreeterFibreGenerator.cpp.

References PetscTools::AmMaster(), PetscTools::Barrier(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfElement(), EXCEPTION, StreeterFibreGenerator< SPACE_DIM >::GetAveragedThicknessLocalNode(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), StreeterFibreGenerator< SPACE_DIM >::GetFibreMaxAngle(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetInverseJacobianForElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), StreeterFibreGenerator< SPACE_DIM >::mApexToBase, StreeterFibreGenerator< SPACE_DIM >::mpGeometryInfo, StreeterFibreGenerator< SPACE_DIM >::mrMesh, NEVER_REACHED, OutputFileHandler::OpenOutputFile(), and VectorProduct().

template<unsigned SPACE_DIM>

double StreeterFibreGenerator< SPACE_DIM >::GetAveragedThicknessLocalNode	(	const unsigned	nodeIndex,
		const std::vector< double > &	wallThickness
	)			const `[inline, private]`

Compute the wallthickness 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 41 of file StreeterFibreGenerator.cpp.

References Node< SPACE_DIM >::ContainingElementsBegin(), Node< SPACE_DIM >::ContainingElementsEnd(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), DistributedVectorFactory::GetHigh(), Node< SPACE_DIM >::GetIndex(), DistributedVectorFactory::GetLow(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), and StreeterFibreGenerator< SPACE_DIM >::mrMesh.

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

template<unsigned SPACE_DIM>

double StreeterFibreGenerator< SPACE_DIM >::GetFibreMaxAngle ( const c_vector< HeartRegionType, SPACE_DIM+1 > & nodesRegionsForElement ) const [inline, 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 93 of file StreeterFibreGenerator.cpp.

References NEVER_REACHED.

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

template<unsigned SPACE_DIM>

void StreeterFibreGenerator< SPACE_DIM >::SetApexToBase ( unsigned axis ) [inline]

Set the direction from apex to base

Parameters:

axis

is the Cartesian axis from apex to base.

Definition at line 481 of file StreeterFibreGenerator.cpp.

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

template<unsigned SPACE_DIM>

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

Set the direction from apex to base

Parameters:

apexToBase

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

Definition at line 471 of file StreeterFibreGenerator.cpp.

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

template<unsigned SPACE_DIM>

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

Uses the names of files defining the diferent surfaces of the mesh to construct the geometry information class File format: list of triangles

Parameters:

	rEpicardiumFile	Epicardium surface
	rRightVentricleFile	Right Ventricle surface.
	rLeftVentricleFile	Left Ventricle surface
	indexFromZero	Are the nodes in the original mesh file/surfaces 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 145 of file StreeterFibreGenerator.cpp.

References StreeterFibreGenerator< SPACE_DIM >::mpGeometryInfo, and StreeterFibreGenerator< SPACE_DIM >::mrMesh.