OffLatticeSproutingRule.cpp

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#include "OffLatticeSproutingRule.hpp"
#include "RandomNumberGenerator.hpp"
#include "GeometryTools.hpp"
#include "UblasIncludes.hpp"
#include "UblasCustomFunctions.hpp"
#include "BaseUnits.hpp"
#include "Owen11Parameters.hpp"

template<unsigned DIM>
OffLatticeSproutingRule<DIM>::OffLatticeSproutingRule()
    : AbstractSproutingRule<DIM>(),
      mTipExclusionRadius(80.0 * 1.e-6 * unit::metres),
      mHalfMaxVegf(Owen11Parameters::mpVegfConventrationAtHalfMaxProbSprouting->GetValue("Owen2011SproutingRule")),
      mVegfField()
{
    // Owen11 equation is dimensionally inconsistent as it includes an extra vessel surface area term. In order to
    // have a similar magnitude multiply this value by a typical vessel surface area = 2*pi*R*L
    // = 2*pi*15*40
    this->mSproutingProbability = Owen11Parameters::mpMaximumSproutingRate->GetValue("Owen2011SproutingRule")*2.0*M_PI*15.0*40.0;
    this->mTipExclusionRadius = 80.0*1.e-6*unit::metres;
}

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

}

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

template<unsigned DIM>
std::vector<boost::shared_ptr<VesselNode<DIM> > > OffLatticeSproutingRule<DIM>::GetSprouts(const std::vector<boost::shared_ptr<VesselNode<DIM> > >& rNodes)
{
    if(!this->mpVesselNetwork)
    {
        EXCEPTION("A vessel network is required for this type of sprouting rule.");
    }

    std::vector<units::quantity<unit::concentration> > probed_solutions(rNodes.size(), 0.0*unit::mole_per_metre_cubed);
    std::vector<DimensionalChastePoint<DIM> > probe_locations(rNodes.size(), DimensionalChastePoint<DIM>(0.0, 0.0, 0.0, 1.e-6*unit::metres));

    if(this->mpSolver)
    {
        for(unsigned idx=0; idx<rNodes.size(); idx++)
        {
            probe_locations[idx] = rNodes[idx]->rGetLocation();
        }
        if(probe_locations.size()>0)
        {
            probed_solutions = this->mpSolver->GetConcentrations(probe_locations);
        }
    }

    // Set up the output sprouts vector
    std::vector<boost::shared_ptr<VesselNode<DIM> > > sprouts;

    // Loop over all nodes and randomly select sprouts
    for(unsigned idx = 0; idx < rNodes.size(); idx++)
    {
        // Check we are not too close to the end of the vessel
        if(rNodes[idx]->GetNumberOfSegments() != 2)
        {
            continue;
        }

        if(this->mVesselEndCutoff > 0.0 * unit::metres)
        {
            if(rNodes[idx]->GetSegment(0)->GetVessel()->GetClosestEndNodeDistance(rNodes[idx]->rGetLocation())< this->mVesselEndCutoff)
            {
                continue;
            }
            if(rNodes[idx]->GetSegment(1)->GetVessel()->GetClosestEndNodeDistance(rNodes[idx]->rGetLocation())< this->mVesselEndCutoff)
            {
                continue;
            }
        }

        // Check we are not too close to an existing candidate
        if(mTipExclusionRadius>0.0 * unit::metres)
        {
            bool too_close = false;
            for(unsigned jdx=0; jdx<sprouts.size(); jdx++)
            {
                if(rNodes[idx]->GetDistance(sprouts[jdx]->rGetLocation()) < mTipExclusionRadius)
                {
                    too_close = true;
                }
            }
            if(too_close)
            {
                continue;
            }
        }
        units::quantity<unit::concentration> vegf_conc = 0.0*unit::mole_per_metre_cubed;
        if(this->mpSolver)
        {
            vegf_conc = probed_solutions[idx];
        }

        double vegf_fraction = vegf_conc/(vegf_conc + mHalfMaxVegf);
        double max_prob_per_time_step = this->mSproutingProbability*SimulationTime::Instance()->GetTimeStep()*BaseUnits::Instance()->GetReferenceTimeScale();
        double prob_tip_selection = max_prob_per_time_step*vegf_fraction;

        if (RandomNumberGenerator::Instance()->ranf() < prob_tip_selection)
        {
            sprouts.push_back(rNodes[idx]);
        }
    }
    return sprouts;
}

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