Chaste  Release::2018.1
CellPopulationAreaWriter.cpp
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35 
36 #include "CellPopulationAreaWriter.hpp"
37 #include "AbstractCellPopulation.hpp"
38 #include "MeshBasedCellPopulation.hpp"
39 #include "CaBasedCellPopulation.hpp"
40 #include "NodeBasedCellPopulation.hpp"
41 #include "PottsBasedCellPopulation.hpp"
42 #include "VertexBasedCellPopulation.hpp"
43 #include "ApoptoticCellProperty.hpp"
44 
45 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
47  : AbstractCellPopulationWriter<ELEMENT_DIM, SPACE_DIM>("cellpopulationareas.dat")
48 {
49 }
50 
51 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
53 {
54  assert(SPACE_DIM==2 || SPACE_DIM==3); // LCOV_EXCL_LINE
55 
56  VertexMesh<ELEMENT_DIM, SPACE_DIM>* voronoi_tessellation = pCellPopulation->GetVoronoiTessellation();
57 
58  assert (voronoi_tessellation != nullptr);
59 
60  // Don't use the Voronoi tessellation to calculate the total area of the mesh because it gives huge areas for boundary cells
61  double total_area = static_cast<MutableMesh<ELEMENT_DIM,SPACE_DIM>&>((pCellPopulation->rGetMesh())).GetVolume();
62  double apoptotic_area = 0.0;
63 
64  // Loop over elements of mpVoronoiTessellation
65  for (typename VertexMesh<ELEMENT_DIM,SPACE_DIM>::VertexElementIterator elem_iter = voronoi_tessellation->GetElementIteratorBegin();
66  elem_iter != voronoi_tessellation->GetElementIteratorEnd();
67  ++elem_iter)
68  {
69  // Get index of this element in mpVoronoiTessellation
70  unsigned elem_index = elem_iter->GetIndex();
71 
72  // Get the index of the corresponding node in mrMesh
73  unsigned node_index = voronoi_tessellation->GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(elem_index);
74 
75  // Discount ghost nodes
76  if (!pCellPopulation->IsGhostNode(node_index))
77  {
78  // Get the cell corresponding to this node
79  CellPtr p_cell = pCellPopulation->GetCellUsingLocationIndex(node_index);
80 
81  // Only bother calculating the area/volume of apoptotic cells
82  bool cell_is_apoptotic = p_cell->HasCellProperty<ApoptoticCellProperty>();
83  if (cell_is_apoptotic)
84  {
85  double cell_volume = voronoi_tessellation->GetVolumeOfElement(elem_index);
86  apoptotic_area += cell_volume;
87  }
88  }
89  }
90  *this->mpOutStream << total_area << " " << apoptotic_area;
91 }
92 
93 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
95 {
96  EXCEPTION("CellPopulationAreaWriter cannot be used with a CaBasedCellPopulation");
97 }
98 
99 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
101 {
102  EXCEPTION("CellPopulationAreaWriter cannot be used with a NodeBasedCellPopulation");
103 }
104 
105 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
107 {
108  EXCEPTION("CellPopulationAreaWriter cannot be used with a PottsBasedCellPopulation");
109 }
110 
111 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
113 {
114  EXCEPTION("CellPopulationAreaWriter cannot be used with a VertexBasedCellPopulation");
115 }
116 
117 // Explicit instantiation
118 template class CellPopulationAreaWriter<1,1>;
119 template class CellPopulationAreaWriter<1,2>;
120 template class CellPopulationAreaWriter<2,2>;
121 template class CellPopulationAreaWriter<1,3>;
122 template class CellPopulationAreaWriter<2,3>;
123 template class CellPopulationAreaWriter<3,3>;
124 
126 // Declare identifier for the serializer
unsigned GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(unsigned elementIndex)
Definition: VertexMesh.cpp:503
virtual CellPtr GetCellUsingLocationIndex(unsigned index)
#define EXCEPTION(message)
Definition: Exception.hpp:143
MutableMesh< ELEMENT_DIM, SPACE_DIM > & rGetMesh()
VertexElementIterator GetElementIteratorBegin(bool skipDeletedElements=true)
Definition: VertexMesh.hpp:679
virtual double GetVolumeOfElement(unsigned index)
#define EXPORT_TEMPLATE_CLASS_ALL_DIMS(CLASS)
VertexMesh< ELEMENT_DIM, SPACE_DIM > * GetVoronoiTessellation()
VertexElementIterator GetElementIteratorEnd()
Definition: VertexMesh.hpp:686
virtual void Visit(MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM > *pCellPopulation)