StreeterFibreGenerator< SPACE_DIM > Class Template Reference
#include <StreeterFibreGenerator.hpp>
Public Member Functions | |
| StreeterFibreGenerator (TetrahedralMesh< 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 | GetAveragedThickness (const unsigned nodeIndex, const std::vector< double > &wallThickness) const |
| double | GetFibreMaxAngle (const c_vector< HeartRegionType, SPACE_DIM+1 > &nodesRegionsForElement) const |
Private Attributes | |
| TetrahedralMesh< 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
| StreeterFibreGenerator< SPACE_DIM >::StreeterFibreGenerator | ( | TetrahedralMesh< SPACE_DIM, SPACE_DIM > & | rMesh | ) | [inline] |
Constructor
- Parameters:
-
rMesh reference to the tetrahedral mesh of the ventricles
Definition at line 127 of file StreeterFibreGenerator.cpp.
| StreeterFibreGenerator< SPACE_DIM >::~StreeterFibreGenerator | ( | ) | [inline] |
Destructor
Definition at line 134 of file StreeterFibreGenerator.cpp.
References StreeterFibreGenerator< SPACE_DIM >::mpGeometryInfo.
Member Function Documentation
| double StreeterFibreGenerator< SPACE_DIM >::GetAveragedThickness | ( | 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
- Todo:
- The following nested loops appear in DistanceMapCalculator as well, refactor it. Idea: create an iterator over the neighbour nodes in class Node
Definition at line 41 of file StreeterFibreGenerator.cpp.
References Node< SPACE_DIM >::ContainingElementsBegin(), Node< SPACE_DIM >::ContainingElementsEnd(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), Node< SPACE_DIM >::GetIndex(), 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().
| 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 89 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().
| void StreeterFibreGenerator< SPACE_DIM >::SetSurfaceFiles | ( | const std::string & | epicardiumFile, | |
| const std::string & | rightVentricleFile, | |||
| const std::string & | leftVentricleFile | |||
| ) | [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:
-
epicardiumFile Epicardium surface rightVentricleFile Right Ventricle surface leftVentricleFile Left Ventricle surface
Definition at line 140 of file StreeterFibreGenerator.cpp.
References StreeterFibreGenerator< SPACE_DIM >::mpGeometryInfo, and StreeterFibreGenerator< SPACE_DIM >::mrMesh.
| 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
- Todo:
- basis_functions matrix is 3D specific, work out the generic expression
Definition at line 150 of file StreeterFibreGenerator.cpp.
References StreeterFibreGenerator< SPACE_DIM >::CheckVentricleAlignment(), StreeterFibreGenerator< SPACE_DIM >::GetAveragedThickness(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), StreeterFibreGenerator< SPACE_DIM >::GetFibreMaxAngle(), TetrahedralMesh< 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.
| 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 416 of file StreeterFibreGenerator.cpp.
References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), StreeterFibreGenerator< SPACE_DIM >::mpGeometryInfo, and StreeterFibreGenerator< SPACE_DIM >::mrMesh.
Referenced by StreeterFibreGenerator< SPACE_DIM >::GenerateOrthotropicFibreOrientation().
Member Data Documentation
TetrahedralMesh<SPACE_DIM,SPACE_DIM>& StreeterFibreGenerator< SPACE_DIM >::mrMesh [private] |
Reference to the mesh (used for calculating distances to epi and endo surfaces)
Definition at line 48 of file StreeterFibreGenerator.hpp.
Referenced by StreeterFibreGenerator< SPACE_DIM >::CheckVentricleAlignment(), StreeterFibreGenerator< SPACE_DIM >::GenerateOrthotropicFibreOrientation(), StreeterFibreGenerator< SPACE_DIM >::GetAveragedThickness(), and StreeterFibreGenerator< SPACE_DIM >::SetSurfaceFiles().
HeartGeometryInformation<SPACE_DIM>* StreeterFibreGenerator< SPACE_DIM >::mpGeometryInfo [private] |
Provides a method to calculate the relative position of a node with respect to two (or three) given surfaces
Definition at line 50 of file StreeterFibreGenerator.hpp.
Referenced by StreeterFibreGenerator< SPACE_DIM >::CheckVentricleAlignment(), StreeterFibreGenerator< SPACE_DIM >::GenerateOrthotropicFibreOrientation(), StreeterFibreGenerator< SPACE_DIM >::SetSurfaceFiles(), and StreeterFibreGenerator< SPACE_DIM >::~StreeterFibreGenerator().
The documentation for this class was generated from the following files:
- /tmp/release_1.1/heart/src/problem/StreeterFibreGenerator.hpp
- /tmp/release_1.1/heart/src/problem/StreeterFibreGenerator.cpp
