CellStateDependentDiscreteSource.cpp

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#include "CellStateDependentDiscreteSource.hpp"
#include "AbstractCellPopulation.hpp"
#include "VesselNetwork.hpp"

template<unsigned DIM>
CellStateDependentDiscreteSource<DIM>::CellStateDependentDiscreteSource()
    :   DiscreteSource<DIM>(),
        mStateRateMap(),
        mStateRateThresholdMap(),
        mConsumptionRatePerUnitConcentration(1.0*unit::metre_cubed_per_second)
{

}

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

}

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

template<unsigned DIM>
std::vector<units::quantity<unit::concentration_flow_rate> > CellStateDependentDiscreteSource<DIM>::GetConstantInUMeshValues()
{
    EXCEPTION("This source does not yet support meshes.");
}

template<unsigned DIM>
std::vector<units::quantity<unit::rate> > CellStateDependentDiscreteSource<DIM>::GetLinearInUMeshValues()
{
    EXCEPTION("This source does not yet support meshes.");
}

template<unsigned DIM>
std::vector<units::quantity<unit::concentration_flow_rate> > CellStateDependentDiscreteSource<DIM>::GetConstantInURegularGridValues()
{
    if(!this->mpRegularGrid)
    {
        EXCEPTION("A regular grid is required for this type of source");
    }

//    units::quantity<unit::length> grid_spacing = this->mpRegularGrid->GetSpacing();
//    units::quantity<unit::volume> grid_volume = units::pow<3>(grid_spacing);
    std::vector<units::quantity<unit::concentration_flow_rate> > values(this->mpRegularGrid->GetNumberOfPoints(), 0.0*unit::mole_per_metre_cubed_per_second);

    boost::shared_ptr<ApoptoticCellProperty> apoptotic_property(new ApoptoticCellProperty);
    unsigned apoptotic_label = apoptotic_property->GetColour();

    // Loop through all points
    std::vector<std::vector<CellPtr> > point_cell_map = this->mpRegularGrid->GetPointCellMap();
    for(unsigned idx=0; idx<point_cell_map.size(); idx++)
    {
        for(unsigned jdx=0; jdx<point_cell_map[idx].size(); jdx++)
        {
            // If a mutation specific consumption rate has been specified
            if(mStateRateMap.size()>0)
            {
                std::map<unsigned, units::quantity<unit::concentration_flow_rate> >::iterator it;
                // If the cell is apoptotic
                if (point_cell_map[idx][jdx]->template HasCellProperty<ApoptoticCellProperty>())
                {
                    it = mStateRateMap.find(apoptotic_label);
                    if (it != mStateRateMap.end())
                    {
                        values[idx] += it->second;
                    }
                }
                else
                {
                    it = mStateRateMap.find(point_cell_map[idx][jdx]->GetMutationState()->GetColour());
                    if (it != mStateRateMap.end())
                    {
                        if(!this->mLabel.empty())
                        {
                            // Get a threshold value if it has been set, use the label to determine the field from which the label
                            // value is obtained.
                            units::quantity<unit::concentration> threshold = 0.0 * unit::mole_per_metre_cubed;
                            if(mStateRateThresholdMap.size()>0)
                            {
                                std::map<unsigned, units::quantity<unit::concentration> >::iterator it_threshold;
                                it_threshold = mStateRateThresholdMap.find(point_cell_map[idx][jdx]->GetMutationState()->GetColour());
                                if (it_threshold != mStateRateThresholdMap.end())
                                {
                                    threshold = it_threshold->second;
                                }
                            }
//                            units::quantity<unit::concentration_flow_rate> conversion_factor = mConsumptionRatePerUnitConcentration*unit::mole_per_metre_cubed/grid_volume;

                            if(threshold>0.0* unit::mole_per_metre_cubed)
                            {
                                if(point_cell_map[idx][jdx]->GetCellData()->GetItem(this->mLabel)>threshold.value())
                                {
                                    values[idx] += it->second;
                                }
                            }
                            else
                            {
                                values[idx] += it->second;
                            }
                        }
                        else
                        {
                            values[idx] += it->second;
                        }
                    }
                }
            }
            else
            {
                values[idx] += this->mConstantInUValue;
            }
        }
    }
    return values;
}

template<unsigned DIM>
std::vector<units::quantity<unit::rate> > CellStateDependentDiscreteSource<DIM>::GetLinearInURegularGridValues()
{
    // This map is only for constant values
    return std::vector<units::quantity<unit::rate> >(this->mpRegularGrid->GetNumberOfPoints(), 0.0*unit::per_second);
}

template<unsigned DIM>
void CellStateDependentDiscreteSource<DIM>::SetStateRateMap(std::map<unsigned, units::quantity<unit::concentration_flow_rate> > stateRateMap)
{
    mStateRateMap = stateRateMap;
}

template<unsigned DIM>
void CellStateDependentDiscreteSource<DIM>::SetStateRateThresholdMap(std::map<unsigned, units::quantity<unit::concentration> > stateThresholdMap)
{
    mStateRateThresholdMap = stateThresholdMap;
}

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