LatticeBasedMigrationRule.cpp

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#include "GeometryTools.hpp"
#include "LatticeBasedMigrationRule.hpp"
#include "RandomNumberGenerator.hpp"

template<unsigned DIM>
LatticeBasedMigrationRule<DIM>::LatticeBasedMigrationRule()
    : AbstractMigrationRule<DIM>(),
      mMovementProbability(0.01)
{

}

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

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

}

template<unsigned DIM>
std::vector<double> LatticeBasedMigrationRule<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++)
    {
        // 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;
            }
        }

        if(already_attached)
        {
            continue;
        }

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

template<unsigned DIM>
int LatticeBasedMigrationRule<DIM>::GetNeighbourMovementIndex(std::vector<double> movementProbabilities,
                                                                   std::vector<unsigned> neighbourIndices)
{
    int location_index = -1;

    // Check that the cumulative movement probability is less than one, otherwise our time-step is too large
    std::vector<double> cumulativeProbabilityVector(movementProbabilities.size());
    std::partial_sum(movementProbabilities.begin(), movementProbabilities.end(), cumulativeProbabilityVector.begin());

    if (cumulativeProbabilityVector.back() > 1.0)
    {
        EXCEPTION("Cumulative probability of tip cell moving is greater than one");
    }

    // Use roulette-wheel style selection to select which location the tip will move into
    double cumulativeProbability = cumulativeProbabilityVector.back();
    double random_number = RandomNumberGenerator::Instance()->ranf();

    // If we move, choose a node to go to
    if(random_number < cumulativeProbability)
    {
        for (unsigned ind = 0; ind < cumulativeProbabilityVector.size(); ind++)
        {
            if (random_number <= cumulativeProbabilityVector[ind])
            {
                location_index = neighbourIndices[ind];
                break;
            }
        }
    }
    return location_index;
}

template<unsigned DIM>
void LatticeBasedMigrationRule<DIM>::SetMovementProbability(double movementProbability)
{
    mMovementProbability = movementProbability;
}

template<unsigned DIM>
std::vector<int> LatticeBasedMigrationRule<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.");
    }

    // 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] = GetNeighbourMovementIndex(probability_of_moving, neighbour_indices[grid_index]);
        }
    }
    return indices;
}

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