CryptShovingCaBasedDivisionRule.cpp

/*

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*/

#include "CryptShovingCaBasedDivisionRule.hpp"
#include "RandomNumberGenerator.hpp"
#include "StemCellProliferativeType.hpp"

bool CryptShovingCaBasedDivisionRule::IsNodeOnBase(unsigned NodeIndex, PottsMesh<2>* pPottsMesh)
{
    std::set<unsigned> neighbouring_node_indices = pPottsMesh->GetVonNeumannNeighbouringNodeIndices(NodeIndex);
    unsigned num_neighbours = neighbouring_node_indices.size();

    // No strange neighbourhoods and in 2D so need 3 or 4 neighbours
    if (num_neighbours == 4)
    {
        return true;
    }
    else if (num_neighbours == 3)
    {
        // Quick and dirty check to see if cells are in bottom or top half of the domain
        if (NodeIndex < 0.5*pPottsMesh->GetNumNodes())
        {
            return false;
        }
        else
        {
            EXCEPTION("Cells reaching the top of the crypt need to increase length to at least double the sloughing height.");
        }
    }
    else
    {
        // If here then have <2 or >4 neighbours and not possible for 2d periodic crypt
        NEVER_REACHED;
    }
}

bool CryptShovingCaBasedDivisionRule::IsRoomToDivide(CellPtr pParentCell, CaBasedCellPopulation<2>& rCellPopulation)
{
    return true;
}

unsigned CryptShovingCaBasedDivisionRule::CalculateDaughterNodeIndex(CellPtr pNewCell,
    CellPtr pParentCell,
    CaBasedCellPopulation<2>& rCellPopulation)
{
    // Get node index corresponding to the parent cell
    unsigned parent_node_index = rCellPopulation.GetLocationIndexUsingCell(pParentCell);

    PottsMesh<2>* static_cast_mesh = static_cast<PottsMesh<2>*>(&(rCellPopulation.rGetMesh()));

    // This tracks if the cell is on the base of the crypt, and offsets the neighbours accordingly
    bool is_not_on_base = IsNodeOnBase(parent_node_index,static_cast_mesh);

    /*
     * Select a neighbour at random.
     * Sample random number to specify which move to make either 1 (E) 2 (W) or 3 (N)
     * This is as they are ordered in node index and that moves from south west to north east.
     */
    RandomNumberGenerator* p_gen = RandomNumberGenerator::Instance();
    unsigned direction = p_gen->randMod(3)+ (unsigned) is_not_on_base;

    // Stem Cells only divide vertically
    if (pParentCell->GetCellProliferativeType()->IsType<StemCellProliferativeType>())
    {
        direction = 2;
    }


    std::set<unsigned> neighbouring_node_indices = static_cast_mesh->GetVonNeumannNeighbouringNodeIndices(parent_node_index);

    std::set<unsigned>::iterator neighbour_iter = neighbouring_node_indices.begin();
    for (unsigned  i=0; i<direction; i++)
    {
        ++neighbour_iter;
    }
    assert(neighbour_iter != neighbouring_node_indices.end());

    unsigned daughter_node_index = *neighbour_iter;

    assert(daughter_node_index < static_cast_mesh->GetNumNodes());

    // If daughter node is occupied then move the cell north (which is always the last one in the set of neighbours)
    if (!(rCellPopulation.IsSiteAvailable(daughter_node_index, pNewCell)))
    {
        std::list<std::pair<unsigned,unsigned> > cell_moves;

        bool is_neighbour_occupied = true;

        unsigned current_node_index = parent_node_index;
        unsigned target_node_index = daughter_node_index;
        while (is_neighbour_occupied)
        {
            current_node_index = target_node_index;

            std::set<unsigned> neighbouring_node_indices = static_cast_mesh->GetVonNeumannNeighbouringNodeIndices(current_node_index);
            unsigned num_neighbours = neighbouring_node_indices.size();

            // Check to see if the current node is on the boundary
            IsNodeOnBase(current_node_index, static_cast_mesh);

            // Select the appropriate neighbour
            std::set<unsigned>::iterator neighbour_iter = neighbouring_node_indices.begin();
            for (unsigned i=0; i<num_neighbours-1; i++)
            {
                ++neighbour_iter;
            }
            assert(neighbour_iter != neighbouring_node_indices.end());

            target_node_index = *neighbour_iter;

            std::pair<unsigned, unsigned> new_move(current_node_index, target_node_index);

            cell_moves.push_back(new_move);

            // If target node is unoccupied move the cell on the current node to the target node and stop shoving cells
            if (rCellPopulation.IsSiteAvailable(target_node_index, pNewCell))
            {
                is_neighbour_occupied = false;
            }

            // If target node is occupied then keep shoving the cells out of the way
            current_node_index = target_node_index;
        }

        // Do moves to free up the daughter node index
        for (std::list<std::pair<unsigned, unsigned> >::reverse_iterator reverse_iter = cell_moves.rbegin();
             reverse_iter != cell_moves.rend();
             ++reverse_iter)
        {
            assert(rCellPopulation.IsSiteAvailable(reverse_iter->second, pNewCell));
            assert(!(rCellPopulation.IsSiteAvailable(reverse_iter->first, pNewCell)));

            // Move cell from first() to second()
            rCellPopulation.MoveCellInLocationMap(rCellPopulation.GetCellUsingLocationIndex(reverse_iter->first), reverse_iter->first, reverse_iter->second);
        }

        // Check daughter site is now free
        assert(rCellPopulation.IsSiteAvailable(daughter_node_index, pNewCell));

    }
    return daughter_node_index;
}

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(CryptShovingCaBasedDivisionRule)