CellPopulationMigrationRule.cpp

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#include "GeometryTools.hpp"
#include "CellPopulationMigrationRule.hpp"
#include "RandomNumberGenerator.hpp"

template<unsigned DIM>
CellPopulationMigrationRule<DIM>::CellPopulationMigrationRule()
    : LatticeBasedMigrationRule<DIM>(),
      mVolumeFractionMap(),
      mPointCellMap()
{

}

template <unsigned DIM>
boost::shared_ptr<CellPopulationMigrationRule<DIM> > CellPopulationMigrationRule<DIM>::Create()
{
    MAKE_PTR(CellPopulationMigrationRule<DIM>, pSelf);
    return pSelf;
}

template<unsigned DIM>
CellPopulationMigrationRule<DIM>::~CellPopulationMigrationRule()
{

}

template<unsigned DIM>
void CellPopulationMigrationRule<DIM>::SetVolumeFraction(boost::shared_ptr<AbstractCellMutationState> mutation_state, double volume_fraction)
{
    if(volume_fraction >1.0)
    {
        EXCEPTION("Specified volume fractions should not be greater than 1.");
    }

    typedef std::map<boost::shared_ptr<AbstractCellMutationState> , double>::iterator it_type; it_type iterator;
    for(iterator = mVolumeFractionMap.begin(); iterator != mVolumeFractionMap.end(); iterator++)
    {
        if (iterator->first->IsSame(mutation_state))
        {
            iterator->second = volume_fraction;
            break;
        }
    }

    // if mutation state does not exist in map yet then add it to the map
    if (iterator == mVolumeFractionMap.end())
    {
        mVolumeFractionMap[mutation_state] = volume_fraction;
    }
}

template<unsigned DIM>
double CellPopulationMigrationRule<DIM>::GetOccupyingVolumeFraction(boost::shared_ptr<AbstractCellMutationState> mutation_state)
{
    typedef std::map<boost::shared_ptr<AbstractCellMutationState> , double>::iterator it_type; it_type iterator;
    for(iterator = mVolumeFractionMap.begin(); iterator != mVolumeFractionMap.end(); iterator++)
    {
        if (iterator->first->IsSame(mutation_state))
        {
            return iterator->second;
        }
    }

    // if a map is not provided or if the prescribed mutation state is not in the map then the
    // occupying volume fraction is 1.
    return 1;
}

template<unsigned DIM>
std::vector<double> CellPopulationMigrationRule<DIM>::GetNeighbourMovementProbabilities(boost::shared_ptr<VesselNode<DIM> > pNode,
                                                       std::vector<unsigned> neighbourIndices, unsigned gridIndex)
{
    std::vector<double> probability_of_moving(neighbourIndices.size(), 0.0);

    for(unsigned idx=0; idx<neighbourIndices.size(); idx++)
    {
        // Check for cell occupancy, if it is occupied don;t go anywhere
        double total_occupancy = 0.0;
        for(unsigned jdx=0; jdx<mPointCellMap[idx].size(); jdx++)
        {
            total_occupancy += GetOccupyingVolumeFraction(mPointCellMap[idx][jdx]->GetMutationState());
        }

        if(total_occupancy>=1.0)
        {
            continue;
        }

        // Make sure that tip cell does not try to move into a location already occupied by the vessel that it comes from
        DimensionalChastePoint<DIM> neighbour_location = this->mpGrid->GetLocationOf1dIndex(neighbourIndices[idx]);

        bool already_attached = false;
        for (unsigned seg_index = 0; seg_index < pNode->GetNumberOfSegments(); seg_index++)
        {
            if(pNode->GetSegment(seg_index)->GetOppositeNode(pNode)->IsCoincident(neighbour_location))
            {
                already_attached = true;
                break;
            }
        }

        // Also ensure that the new location would not try to cross a vessel which is oriented diagonally
        // TODO: Very slow, bottleneck
//        if(already_attached or this->mpVesselNetwork->VesselCrossesLineSegment(neighbour_location, pNode->rGetLocation()))
//        {
//            continue;
//        }

        if(already_attached)
        {
            continue;
        }

        // Simple rule, equal probability for all directions
        probability_of_moving[idx] = this->mMovementProbability * SimulationTime::Instance()->GetTimeStep();
    }
    return probability_of_moving;
}

template<unsigned DIM>
std::vector<int> CellPopulationMigrationRule<DIM>::GetIndices(const std::vector<boost::shared_ptr<VesselNode<DIM> > >& rNodes)
{
    if(!this->mpGrid)
    {
        EXCEPTION("A regular grid is required for this type of migration rule.");
    }

    if(!this->mpVesselNetwork)
    {
        EXCEPTION("A vessel network is required for this type of migration rule.");
    }

    if(!this->mpCellPopulation)
    {
        EXCEPTION("A cell population is required for this type of migration rule.");
    }

    mPointCellMap = this->mpGrid->GetPointCellMap();

    // Set up the output indices vector
    std::vector<int> indices(rNodes.size(), -1);

    // Get the point-node map from the regular grid
    std::vector<std::vector<boost::shared_ptr<VesselNode<DIM> > > > point_node_map = this->mpGrid->GetPointNodeMap();

    // Get the neighbour data from the regular grid
    std::vector<std::vector<unsigned> > neighbour_indices = this->mpGrid->GetNeighbourData();

    // Loop over all nodes, if they can move set the index
    for(unsigned idx = 0; idx < rNodes.size(); idx++)
    {
        // Get the grid index of the node
        unsigned grid_index = this->mpGrid->GetNearestGridIndex(rNodes[idx]->rGetLocation());

        // Get the probability of moving into each of the neighbour sites
        std::vector<double> probability_of_moving = GetNeighbourMovementProbabilities(rNodes[idx], neighbour_indices[grid_index], grid_index);

        // Get the index of the neighbour to move into
        double sum = std::fabs(std::accumulate(probability_of_moving.begin(), probability_of_moving.end(), 0.0));
        if(sum > 0.0)
        {
            indices[idx] = LatticeBasedMigrationRule<DIM>::GetNeighbourMovementIndex(probability_of_moving, neighbour_indices[grid_index]);
        }
    }
    return indices;
}

// Explicit instantiation
template class CellPopulationMigrationRule<2> ;
template class CellPopulationMigrationRule<3> ;