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 &epicardiumFile, const std::string &rightVentricleFile, const std::string &leftVentricleFile)
void	GenerateOrthotropicFibreOrientation (std::string outputDirectory, std::string fibreOrientationFile, bool logInfo=false)
void	CheckVentricleAlignment ()
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

Detailed Description

template<unsigned SPACE_DIM>
class StreeterFibreGenerator< SPACE_DIM >

Generate fibre in a ventricular mesh using the formulae from 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.

Definition at line 45 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 138 of file StreeterFibreGenerator.cpp.

References StreeterFibreGenerator< SPACE_DIM >::mpGeometryInfo.

Member Function Documentation

template<unsigned SPACE_DIM>

void StreeterFibreGenerator< SPACE_DIM >::CheckVentricleAlignment ( ) [inline]

Check that the two ventricles are separated in the y-axis The heart ought to have x: apex to base y: right to left z: front to back

Note this method only covers some of the possible missalignments of the mesh

Definition at line 464 of file StreeterFibreGenerator.cpp.

References StreeterFibreGenerator< SPACE_DIM >::mpGeometryInfo, ChasteCuboid< SPACE_DIM >::rGetLowerCorner(), and ChasteCuboid< SPACE_DIM >::rGetUpperCorner().

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

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 154 of file StreeterFibreGenerator.cpp.

References PetscTools::AmMaster(), PetscTools::Barrier(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfElement(), StreeterFibreGenerator< SPACE_DIM >::CheckVentricleAlignment(), 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(), HeartRegionCode::LEFT_SEPTUM, HeartRegionCode::LEFT_VENTRICLE_SURFACE, HeartRegionCode::LEFT_VENTRICLE_WALL, StreeterFibreGenerator< SPACE_DIM >::mpGeometryInfo, StreeterFibreGenerator< SPACE_DIM >::mrMesh, OutputFileHandler::OpenOutputFile(), HeartRegionCode::RIGHT_SEPTUM, HeartRegionCode::RIGHT_VENTRICLE_SURFACE, HeartRegionCode::RIGHT_VENTRICLE_WALL, and HeartRegionCode::UNKNOWN.

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 HeartRegionCode::LEFT_SEPTUM, HeartRegionCode::LEFT_VENTRICLE_SURFACE, HeartRegionCode::LEFT_VENTRICLE_WALL, HeartRegionCode::RIGHT_SEPTUM, HeartRegionCode::RIGHT_VENTRICLE_SURFACE, HeartRegionCode::RIGHT_VENTRICLE_WALL, and HeartRegionCode::UNKNOWN.

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

template<unsigned SPACE_DIM>

void StreeterFibreGenerator< SPACE_DIM >::SetSurfaceFiles	(	const std::string &	epicardiumFile,
		const std::string &	rightVentricleFile,
		const std::string &	leftVentricleFile
	)			`[inline]`