Owen11CaUpdateRule.cpp

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#include "Owen11CaUpdateRule.hpp"
#include "Owen11Parameters.hpp"
#include "BaseUnits.hpp"
#include "CancerCellMutationState.hpp"
#include "QuiescentCancerCellMutationState.hpp"

template<unsigned DIM>
Owen11CaUpdateRule<DIM>::Owen11CaUpdateRule()
    : AbstractCaUpdateRule<DIM>(),
      mDiffusionParameter(Owen11Parameters::mpCellMotilityCancer->GetValue("Owen11CaUpdateRule")),
      mpVesselNetwork(),
      mpRegularGrid(),
      mReferenceLengthScale(BaseUnits::Instance()->GetReferenceLengthScale()),
      mCancerCellCarryingCapacity(2)

{
}

template<unsigned DIM>
Owen11CaUpdateRule<DIM>::~Owen11CaUpdateRule()
{
}

template<unsigned DIM>
double Owen11CaUpdateRule<DIM>::EvaluateProbability(unsigned currentNodeIndex,
                                                               unsigned targetNodeIndex,
                                                               CaBasedCellPopulation<DIM>& rCellPopulation,
                                                               double dt,
                                                               double deltaX,
                                                               CellPtr pCell)
{
   if(pCell->GetMutationState()->IsType<CancerCellMutationState>() || pCell->GetMutationState()->IsType<QuiescentCancerCellMutationState>())
   {
       // Check if the carrying capacity is sufficient
       unsigned num_cells_at_site = 0;

       if(mpVesselNetwork and DIM>1)
       {
           if(!mpRegularGrid)
           {
               EXCEPTION("A regular grid is required for determining vessel based lattice occupancy");
           }
           if(mpRegularGrid->IsSegmentAtLatticeSite(targetNodeIndex, false))
           {
               num_cells_at_site = 1;
           }
       }

       num_cells_at_site += rCellPopulation.GetCellsUsingLocationIndex(targetNodeIndex).size();

       // Get the sprouting probability
       c_vector<double, DIM> node_index_location = rCellPopulation.GetNode(currentNodeIndex)->rGetLocation();
       c_vector<double, DIM> node_neighbour_location = rCellPopulation.GetNode(targetNodeIndex)->rGetLocation();
       units::quantity<unit::length> grid_distance = norm_2(rCellPopulation.rGetMesh().GetVectorFromAtoB(node_index_location,
                                                                                                         node_neighbour_location))*mReferenceLengthScale;

       units::quantity<unit::time> time_increment = dt*BaseUnits::Instance()->GetReferenceTimeScale();
       double carrying_capacity_factor = (double(mCancerCellCarryingCapacity)-double(num_cells_at_site))/double(mCancerCellCarryingCapacity);
       return mDiffusionParameter*time_increment*carrying_capacity_factor/(2.0* units::pow<2>(grid_distance));
   }
   else
   {
       return 0.0;
   }
}

template<>
double Owen11CaUpdateRule<1>::EvaluateProbability(unsigned currentNodeIndex,
                                                               unsigned targetNodeIndex,
                                                               CaBasedCellPopulation<1>& rCellPopulation,
                                                               double dt,
                                                               double deltaX,
                                                               CellPtr pCell)
{
    EXCEPTION("This update rule is not supported in 1D");
}

template<unsigned DIM>
void Owen11CaUpdateRule<DIM>::SetVesselNetwork(boost::shared_ptr<VesselNetwork<DIM> > pVesselNetwork)
{
    mpVesselNetwork = pVesselNetwork;
}

template<unsigned DIM>
void Owen11CaUpdateRule<DIM>::SetReferenceLengthScale(units::quantity<unit::length> referenceLengthScale)
{
    mReferenceLengthScale = referenceLengthScale;
}

template<unsigned DIM>
void Owen11CaUpdateRule<DIM>::SetRegularGrid(boost::shared_ptr<RegularGrid<DIM> > pRegularGrid)
{
    mpRegularGrid = pRegularGrid;
}

template<unsigned DIM>
units::quantity<unit::diffusivity> Owen11CaUpdateRule<DIM>::GetDiffusionParameter()
{
    return mDiffusionParameter;
}

template<unsigned DIM>
void Owen11CaUpdateRule<DIM>::SetDiffusionParameter(units::quantity<unit::diffusivity> diffusionParameter)
{
    mDiffusionParameter = diffusionParameter;
}

template<unsigned DIM>
void Owen11CaUpdateRule<DIM>::OutputUpdateRuleParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t\t<DiffusionParameter>" << mDiffusionParameter << "</DiffusionParameter>\n";

    // Call method on direct parent class
    AbstractCaUpdateRule<DIM>::OutputUpdateRuleParameters(rParamsFile);
}

// Explicit instantiation
template class Owen11CaUpdateRule<2u>;
template class Owen11CaUpdateRule<3u>;

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(Owen11CaUpdateRule)