Chaste  Build::
DiscreteContinuumMesh.hpp
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35 
36 #ifndef DISCRETECONTINUUMMESH_HPP_
37 #define DISCRETECONTINUUMMESH_HPP_
38 
39 #include <vector>
40 #include "SmartPointers.hpp"
41 #include "ChastePoint.hpp"
42 #include "TetrahedralMesh.hpp"
43 #define _BACKWARD_BACKWARD_WARNING_H 1 //Cut out the vtk deprecated warning
44 #include <vtkSmartPointer.h>
45 #include <vtkUnstructuredGrid.h>
46 #include <vtkCellLocator.h>
47 #include "Part.hpp"
48 #include "Cell.hpp"
49 #include "Element.hpp"
50 #include "DimensionalChastePoint.hpp"
51 #include "DiscreteContinuumMeshGenerator.hpp"
52 #include "VesselSegment.hpp"
53 #include "VesselNetwork.hpp"
54 #include "AbstractCellPopulation.hpp"
55 #include "UnitCollection.hpp"
56 
57 // Forward declaration
58 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
60 
66 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
67 class DiscreteContinuumMesh : public TetrahedralMesh<ELEMENT_DIM, SPACE_DIM>
68 {
72  friend class DiscreteContinuumMeshGenerator<ELEMENT_DIM, SPACE_DIM>;
73 
77  std::vector<unsigned> mAttributes;
78 
82  units::quantity<unit::length> mReferenceLength;
83 
87  vtkSmartPointer<vtkUnstructuredGrid> mpVtkMesh;
88 
92  vtkSmartPointer<vtkCellLocator> mpVtkCellLocator;
93 
98 
102  std::vector<std::vector<unsigned> > mPointElementMap;
103 
107  std::vector<std::vector<boost::shared_ptr<VesselSegment<SPACE_DIM> > > > mSegmentElementMap;
108 
112  std::vector<std::vector<CellPtr > > mCellElementMap;
113 
117  boost::shared_ptr<VesselNetwork<SPACE_DIM> > mpNetwork;
118 
122  AbstractCellPopulation<SPACE_DIM>* mpCellPopulation;
123 
127  units::quantity<unit::length> mCellPopulationReferenceLength;
128 
129 public:
130 
135 
140 
145  static boost::shared_ptr<DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM> > Create();
146 
151  std::vector<std::vector<unsigned> > GetConnectivity();
152 
157  std::vector<c_vector<double, SPACE_DIM> > GetNodeLocations();
158 
163  std::vector<c_vector<double, SPACE_DIM> > GetElementCentroids();
164 
169  std::vector<DimensionalChastePoint<SPACE_DIM> > GetNodeLocationsAsPoints();
170 
175  std::vector<unsigned> GetElementRegionMarkers();
176 
181  units::quantity<unit::length> GetReferenceLengthScale();
182 
188  std::vector<std::vector<unsigned> > GetPointElementMap(std::vector<DimensionalChastePoint<SPACE_DIM> > points);
189 
195  const std::vector<std::vector<CellPtr> >& GetElementCellMap(bool update = true);
196 
203  std::vector<std::vector<boost::shared_ptr<VesselSegment<SPACE_DIM> > > > GetElementSegmentMap(bool update = true,
204  bool useVesselSurface = false);
205 
210  vtkSmartPointer<vtkUnstructuredGrid> GetAsVtkUnstructuredGrid();
211 
216  void SetAttributes(std::vector<unsigned> attributes);
217 
222  void SetCellPopulation(AbstractCellPopulation<SPACE_DIM>& rCellPopulation, units::quantity<unit::length> cellLengthScale);
223 
228  void SetVesselNetwork(boost::shared_ptr<VesselNetwork<SPACE_DIM> > pNetwork);
229 
239  void ImportDiscreteContinuumMeshFromTetgen(tetgen::tetgenio& mesherOutput, unsigned numberOfElements, int *elementList,
240  unsigned numberOfFaces, int *faceList, int *edgeMarkerList);
241 
242 };
243 
244 #endif /* DISCRETECONTINUUMMESH_HPP_*/
vtkSmartPointer< vtkUnstructuredGrid > mpVtkMesh
std::vector< c_vector< double, SPACE_DIM > > GetElementCentroids()
std::vector< c_vector< double, SPACE_DIM > > GetNodeLocations()
std::vector< unsigned > GetElementRegionMarkers()
units::quantity< unit::length > mCellPopulationReferenceLength
std::vector< std::vector< unsigned > > GetConnectivity()
std::vector< std::vector< CellPtr > > mCellElementMap
boost::shared_ptr< VesselNetwork< SPACE_DIM > > mpNetwork
const std::vector< std::vector< CellPtr > > & GetElementCellMap(bool update=true)
std::vector< std::vector< boost::shared_ptr< VesselSegment< SPACE_DIM > > > > mSegmentElementMap
std::vector< std::vector< boost::shared_ptr< VesselSegment< SPACE_DIM > > > > GetElementSegmentMap(bool update=true, bool useVesselSurface=false)
void ImportDiscreteContinuumMeshFromTetgen(tetgen::tetgenio &mesherOutput, unsigned numberOfElements, int *elementList, unsigned numberOfFaces, int *faceList, int *edgeMarkerList)
vtkSmartPointer< vtkUnstructuredGrid > GetAsVtkUnstructuredGrid()
units::quantity< unit::length > mReferenceLength
std::vector< std::vector< unsigned > > GetPointElementMap(std::vector< DimensionalChastePoint< SPACE_DIM > > points)
void SetCellPopulation(AbstractCellPopulation< SPACE_DIM > &rCellPopulation, units::quantity< unit::length > cellLengthScale)
vtkSmartPointer< vtkCellLocator > mpVtkCellLocator
std::vector< DimensionalChastePoint< SPACE_DIM > > GetNodeLocationsAsPoints()
void SetAttributes(std::vector< unsigned > attributes)
units::quantity< unit::length > GetReferenceLengthScale()
static boost::shared_ptr< DiscreteContinuumMesh< ELEMENT_DIM, SPACE_DIM > > Create()
void SetVesselNetwork(boost::shared_ptr< VesselNetwork< SPACE_DIM > > pNetwork)
std::vector< std::vector< unsigned > > mPointElementMap
std::vector< unsigned > mAttributes
AbstractCellPopulation< SPACE_DIM > * mpCellPopulation