Chaste  Release::2018.1
CryptShovingCaBasedDivisionRule.cpp
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35 
36 #include "CryptShovingCaBasedDivisionRule.hpp"
37 #include "RandomNumberGenerator.hpp"
38 #include "StemCellProliferativeType.hpp"
39 
40 bool CryptShovingCaBasedDivisionRule::IsNodeOnBase(unsigned NodeIndex, PottsMesh<2>* pPottsMesh)
41 {
42  std::set<unsigned> neighbouring_node_indices = pPottsMesh->GetVonNeumannNeighbouringNodeIndices(NodeIndex);
43  unsigned num_neighbours = neighbouring_node_indices.size();
44 
45  // No strange neighbourhoods and in 2D so need 3 or 4 neighbours
46  if (num_neighbours == 4)
47  {
48  return true;
49  }
50  else if (num_neighbours == 3)
51  {
52  // Quick and dirty check to see if cells are in bottom or top half of the domain
53  if (NodeIndex < 0.5*pPottsMesh->GetNumNodes())
54  {
55  return false;
56  }
57  else
58  {
59  EXCEPTION("Cells reaching the top of the crypt need to increase length to at least double the sloughing height.");
60  }
61  }
62  else
63  {
64  // If here then have <2 or >4 neighbours and not possible for 2d periodic crypt
66  }
67 }
68 
70 {
71  return true;
72 }
73 
75  CellPtr pParentCell,
76  CaBasedCellPopulation<2>& rCellPopulation)
77 {
78  // Get node index corresponding to the parent cell
79  unsigned parent_node_index = rCellPopulation.GetLocationIndexUsingCell(pParentCell);
80 
81  PottsMesh<2>* static_cast_mesh = static_cast<PottsMesh<2>*>(&(rCellPopulation.rGetMesh()));
82 
83  // This tracks if the cell is on the base of the crypt, and offsets the neighbours accordingly
84  bool is_not_on_base = IsNodeOnBase(parent_node_index,static_cast_mesh);
85 
86  /*
87  * Select a neighbour at random.
88  * Sample random number to specify which move to make either 1 (E) 2 (W) or 3 (N)
89  * This is as they are ordered in node index and that moves from south west to north east.
90  */
92  unsigned direction = p_gen->randMod(3)+ (unsigned) is_not_on_base;
93 
94  // Stem Cells only divide vertically
95  if (pParentCell->GetCellProliferativeType()->IsType<StemCellProliferativeType>())
96  {
97  direction = 2;
98  }
99 
100 
101  std::set<unsigned> neighbouring_node_indices = static_cast_mesh->GetVonNeumannNeighbouringNodeIndices(parent_node_index);
102 
103  std::set<unsigned>::iterator neighbour_iter = neighbouring_node_indices.begin();
104  for (unsigned i=0; i<direction; i++)
105  {
106  ++neighbour_iter;
107  }
108  assert(neighbour_iter != neighbouring_node_indices.end());
109 
110  unsigned daughter_node_index = *neighbour_iter;
111 
112  assert(daughter_node_index < static_cast_mesh->GetNumNodes());
113 
114  // If daughter node is occupied then move the cell north (which is always the last one in the set of neighbours)
115  if (!(rCellPopulation.IsSiteAvailable(daughter_node_index, pNewCell)))
116  {
117  std::list<std::pair<unsigned,unsigned> > cell_moves;
118 
119  bool is_neighbour_occupied = true;
120 
121  unsigned current_node_index = parent_node_index;
122  unsigned target_node_index = daughter_node_index;
123  while (is_neighbour_occupied)
124  {
125  current_node_index = target_node_index;
126 
127  std::set<unsigned> neighbouring_node_indices = static_cast_mesh->GetVonNeumannNeighbouringNodeIndices(current_node_index);
128  unsigned num_neighbours = neighbouring_node_indices.size();
129 
130  // Check to see if the current node is on the boundary
131  IsNodeOnBase(current_node_index, static_cast_mesh);
132 
133  // Select the appropriate neighbour
134  std::set<unsigned>::iterator neighbour_iter = neighbouring_node_indices.begin();
135  for (unsigned i=0; i<num_neighbours-1; i++)
136  {
137  ++neighbour_iter;
138  }
139  assert(neighbour_iter != neighbouring_node_indices.end());
140 
141  target_node_index = *neighbour_iter;
142 
143  std::pair<unsigned, unsigned> new_move(current_node_index, target_node_index);
144 
145  cell_moves.push_back(new_move);
146 
147  // If target node is unoccupied move the cell on the current node to the target node and stop shoving cells
148  if (rCellPopulation.IsSiteAvailable(target_node_index, pNewCell))
149  {
150  is_neighbour_occupied = false;
151  }
152 
153  // If target node is occupied then keep shoving the cells out of the way
154  current_node_index = target_node_index;
155  }
156 
157  // Do moves to free up the daughter node index
158  for (std::list<std::pair<unsigned, unsigned> >::reverse_iterator reverse_iter = cell_moves.rbegin();
159  reverse_iter != cell_moves.rend();
160  ++reverse_iter)
161  {
162  assert(rCellPopulation.IsSiteAvailable(reverse_iter->second, pNewCell));
163  assert(!(rCellPopulation.IsSiteAvailable(reverse_iter->first, pNewCell)));
164 
165  // Move cell from first() to second()
166  rCellPopulation.MoveCellInLocationMap(rCellPopulation.GetCellUsingLocationIndex(reverse_iter->first), reverse_iter->first, reverse_iter->second);
167  }
168 
169  // Check daughter site is now free
170  assert(rCellPopulation.IsSiteAvailable(daughter_node_index, pNewCell));
171 
172  }
173  return daughter_node_index;
174 }
175 
176 // Serialization for Boost >= 1.36
virtual bool IsRoomToDivide(CellPtr pParentCell, CaBasedCellPopulation< 2 > &rCellPopulation)
unsigned randMod(unsigned base)
virtual CellPtr GetCellUsingLocationIndex(unsigned index)
PottsMesh< DIM > & rGetMesh()
unsigned GetLocationIndexUsingCell(CellPtr pCell)
bool IsNodeOnBase(unsigned NodeIndex, PottsMesh< 2 > *pPottsMesh)
#define EXCEPTION(message)
Definition: Exception.hpp:143
virtual bool IsSiteAvailable(unsigned index, CellPtr pCell)
std::set< unsigned > GetVonNeumannNeighbouringNodeIndices(unsigned nodeIndex)
Definition: PottsMesh.cpp:239
#define NEVER_REACHED
Definition: Exception.hpp:206
void MoveCellInLocationMap(CellPtr pCell, unsigned old_index, unsigned new_index)
static RandomNumberGenerator * Instance()
virtual unsigned CalculateDaughterNodeIndex(CellPtr pNewCell, CellPtr pParentCell, CaBasedCellPopulation< 2 > &rCellPopulation)
#define CHASTE_CLASS_EXPORT(T)