LQRadiotherapyCellKiller.cpp

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#include "LQRadiotherapyCellKiller.hpp"
#include "CancerCellMutationState.hpp"
#include "StalkCellMutationState.hpp"
#include "BaseUnits.hpp"

template<unsigned DIM>
LQRadiotherapyCellKiller<DIM>::LQRadiotherapyCellKiller(AbstractCellPopulation<DIM>* pCellPopulation) :
        AbstractCellKiller<DIM>(pCellPopulation),
        cancerousLinearRadiosensitivity(0.3 * unit::per_gray),
        cancerousQuadraticRadiosensitivity(0.03 * unit::per_gray_squared),
        normalLinearRadiosensitivity(0.15 * unit::per_gray),
        normalQuadraticRadiosensitivity(0.05 * unit::per_gray_squared),
        mDose(2.0 * unit::gray),
        mRadiationTimes(),
        mOerAlphaMax(1.75),
        mOerAlphaMin(1.0),
        mOerBetaMax(3.25),
        mOerBetaMin(1.0),
        mKOer(3.28),
        mAlphaMax(0.3 * unit::per_gray),
        mBetaMax(0.03 * unit::per_gray_squared),
        mUseOer(false)
{

}

template<unsigned DIM>
void LQRadiotherapyCellKiller<DIM>::SetDoseInjected(units::quantity<unit::absorbed_dose> d)
{
    mDose = d;
}

template<unsigned DIM>
void LQRadiotherapyCellKiller<DIM>::SetTimeOfRadiation(std::vector<units::quantity<unit::time> > t)
{
    mRadiationTimes = t;
}

template<unsigned DIM>
void LQRadiotherapyCellKiller<DIM>::SetOerAlphaMax(double value)
{
    mOerAlphaMax = value;
}

template<unsigned DIM>
void LQRadiotherapyCellKiller<DIM>::SetOerAlphaMin(double value)
{
    mOerAlphaMin = value;
}

template<unsigned DIM>
void LQRadiotherapyCellKiller<DIM>::SetOerBetaMax(double value)
{
    mOerBetaMax = value;
}

template<unsigned DIM>
void LQRadiotherapyCellKiller<DIM>::SetOerBetaMin(double value)
{
    mOerBetaMin = value;
}

template<unsigned DIM>
void LQRadiotherapyCellKiller<DIM>::SetOerConstant(double value)
{
    mKOer = value;
}

template<unsigned DIM>
void LQRadiotherapyCellKiller<DIM>::SetAlphaMax(units::quantity<unit::per_absorbed_dose> value)
{
    mAlphaMax = value;
}

template<unsigned DIM>
void LQRadiotherapyCellKiller<DIM>::SetBetaMax(units::quantity<unit::per_absorbed_dose_squared> value)
{
    mBetaMax = value;
}

template<unsigned DIM>
void LQRadiotherapyCellKiller<DIM>::UseOer(bool useOer)
{
    mUseOer = useOer;
}

template<unsigned DIM>
void LQRadiotherapyCellKiller<DIM>::SetCancerousRadiosensitivity(units::quantity<unit::per_absorbed_dose> alpha,
                                                                 units::quantity<unit::per_absorbed_dose_squared> beta)
{
    cancerousLinearRadiosensitivity = alpha;
    cancerousQuadraticRadiosensitivity = beta;
}

template<unsigned DIM>
void LQRadiotherapyCellKiller<DIM>::SetNormalRadiosensitivity(units::quantity<unit::per_absorbed_dose> alpha,
                                                              units::quantity<unit::per_absorbed_dose_squared> beta)
{
    normalLinearRadiosensitivity = alpha;
    normalQuadraticRadiosensitivity = beta;
}

template<unsigned DIM>
void LQRadiotherapyCellKiller<DIM>::CheckAndLabelSingleCellForApoptosis(CellPtr pCell)
{
    if (!pCell->GetMutationState()->IsType<StalkCellMutationState>())
    {
        for (unsigned idx = 0; idx < mRadiationTimes.size(); idx++)
        {
            if (SimulationTime::Instance()->GetTime()*BaseUnits::Instance()->GetReferenceTimeScale() == mRadiationTimes[idx])
            {
                // Model radiation hit
                if (mUseOer)
                {
                    double oxygen = pCell->GetCellData()->GetItem("oxygen");
                    double oer_alpha = (mOerAlphaMax - mOerAlphaMin) * mKOer / (oxygen + mKOer) + mOerAlphaMin;
                    double oer_beta = (mOerBetaMax - mOerBetaMin) * mKOer / (oxygen + mKOer) + mOerBetaMin;
                    units::quantity<unit::per_absorbed_dose> alpha = mAlphaMax / oer_alpha;
                    units::quantity<unit::per_absorbed_dose_squared> beta = mBetaMax / (oer_beta * oer_beta);
                    double death_prob = (1.0 - exp(-alpha * mDose - beta * mDose * mDose));

                    if (!pCell->HasApoptosisBegun() && RandomNumberGenerator::Instance()->ranf() < death_prob)
                    {
                        pCell->StartApoptosis();
                    }
                }
                else
                {
                    double death_prob = (1.0
                            - exp(-cancerousLinearRadiosensitivity * mDose
                                    - cancerousQuadraticRadiosensitivity * mDose * mDose));

                    if (!pCell->HasApoptosisBegun() && RandomNumberGenerator::Instance()->ranf() < death_prob)
                    {
                        pCell->StartApoptosis();
                    }
                }
            }
        }
    }

}

template<unsigned DIM>
void LQRadiotherapyCellKiller<DIM>::CheckAndLabelCellsForApoptosisOrDeath()
{
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->mpCellPopulation->Begin();
            cell_iter != this->mpCellPopulation->End(); ++cell_iter)
    {
        CheckAndLabelSingleCellForApoptosis(*cell_iter);
    }
}

template<unsigned DIM>
void LQRadiotherapyCellKiller<DIM>::OutputCellKillerParameters(out_stream& rParamsFile)
{
    *rParamsFile;

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

// Explicit instantiation

template class LQRadiotherapyCellKiller<1> ;
template class LQRadiotherapyCellKiller<2> ;
template class LQRadiotherapyCellKiller<3> ;

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