Owen2011MigrationRule.cpp

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#include "RandomNumberGenerator.hpp"
#include "VesselSegment.hpp"
#include "Vessel.hpp"
#include "Owen2011MigrationRule.hpp"
#include "AbstractRegularGridDiscreteContinuumSolver.hpp"
#include "BaseUnits.hpp"
#include "Owen11Parameters.hpp"

template<unsigned DIM>
Owen2011MigrationRule<DIM>::Owen2011MigrationRule()
    : LatticeBasedMigrationRule<DIM>(),
      mCellMotility(Owen11Parameters::mpCellMotilityEndothelial->GetValue("Owen2011MigrationRule")),
      mCellChemotacticParameter(0.05*Owen11Parameters::mpChemotacticSensitivity->GetValue("Owen2011MigrationRule")),
      mVegfField()
{

}

template <unsigned DIM>
boost::shared_ptr<Owen2011MigrationRule<DIM> > Owen2011MigrationRule<DIM>::Create()
{
    MAKE_PTR(Owen2011MigrationRule<DIM>, pSelf);
    return pSelf;
}

template<unsigned DIM>
Owen2011MigrationRule<DIM>::~Owen2011MigrationRule()
{

}

template<unsigned DIM>
void Owen2011MigrationRule<DIM>::SetCellChemotacticParameter(units::quantity<unit::diffusivity_per_concentration> cellChemotacticParameter)
{
    mCellChemotacticParameter = cellChemotacticParameter;
}

template<unsigned DIM>
void Owen2011MigrationRule<DIM>::SetCellMotilityParameter(units::quantity<unit::diffusivity> cellMotility)
{
    mCellMotility = cellMotility;
}

template<unsigned DIM>
std::vector<int> Owen2011MigrationRule<DIM>::GetIndices(const std::vector<boost::shared_ptr<VesselNode<DIM> > >& rNodes)
{
    if(!this->mpSolver)
    {
        EXCEPTION("A DiscreteContinuum solver is required for this type of sprouting rule.");
    }

    mVegfField = this->mpSolver->GetConcentrations(this->mpGrid);

    // Use the base class for the rest
    return LatticeBasedMigrationRule<DIM>::GetIndices(rNodes);
}

template<unsigned DIM>
std::vector<double> Owen2011MigrationRule<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 jdx=0; jdx<neighbourIndices.size(); jdx++)
    {
        // make sure that tip cell does not try to move into a location already occupied by the vessel that it comes from
        // i.e. that it doesn't loop back around
        DimensionalChastePoint<DIM> neighbour_location = this->mpGrid->GetLocationOf1dIndex(neighbourIndices[jdx]);

        bool sprout_already_attached_to_vessel_at_location = false;

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

        //ensure that the new sprout would not try to cross a vessel which is oriented diagonally.
        // todo bottleneck, dont think it is even needed for current neighbourhood
//        bool vessel_crosses_line_segment = this->mpVesselNetwork->VesselCrossesLineSegment(neighbour_location, pNode->rGetLocation());
        bool vessel_crosses_line_segment = false;

        if (!vessel_crosses_line_segment && !sprout_already_attached_to_vessel_at_location)
        {
            units::quantity<unit::concentration> VEGF_diff = mVegfField[neighbourIndices[jdx]] - mVegfField[gridIndex];
            units::quantity<unit::time> dt = SimulationTime::Instance()->GetTimeStep() * BaseUnits::Instance()->GetReferenceTimeScale();
            units::quantity<unit::length> dij = pNode->rGetLocation().GetDistance(neighbour_location);
            probability_of_moving[jdx] = ((mCellMotility * dt)/(2.0*dij*dij))*(1.0 + mCellChemotacticParameter*VEGF_diff/(2.0*mCellMotility));
            if (probability_of_moving[jdx] < 0.0)
            {
                probability_of_moving[jdx] = 0.0;
            }
        }
    }
    return probability_of_moving;
}

// Explicit instantiation
template class Owen2011MigrationRule<2> ;
template class Owen2011MigrationRule<3> ;