DivisionBiasTrackingModifier.cpp

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*/
 
#include "DivisionBiasTrackingModifier.hpp"
#include "MeshBasedCellPopulation.hpp"
 
template<unsigned DIM>
DivisionBiasTrackingModifier<DIM>::DivisionBiasTrackingModifier(c_vector<double, DIM> divisionBiasVector)
    : AbstractCellBasedSimulationModifier<DIM>(),
      mDivisionBiasVector(divisionBiasVector)
{
    // mDivisionBiasVector must be a unit vector
    assert(fabs(norm_2(mDivisionBiasVector) - 1.0) < 1e-6);
}
 
template<unsigned DIM>
DivisionBiasTrackingModifier<DIM>::~DivisionBiasTrackingModifier()
{
}
 
template<unsigned DIM>
const c_vector<double, DIM>& DivisionBiasTrackingModifier<DIM>::rGetDivisionBiasVector() const
{
    return mDivisionBiasVector;
}
 
template<unsigned DIM>
void DivisionBiasTrackingModifier<DIM>::UpdateAtEndOfTimeStep(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    UpdateCellData(rCellPopulation);
}
 
template<unsigned DIM>
void DivisionBiasTrackingModifier<DIM>::SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory)
{
    /*
     * We must update CellData in SetupSolve(), otherwise it will not have been
     * fully initialised by the time we enter the main time loop.
     */
    UpdateCellData(rCellPopulation);
}
 
template<unsigned DIM>
void DivisionBiasTrackingModifier<DIM>::UpdateCellData(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    // Make sure the cell population is updated
    rCellPopulation.Update();
 
    if (bool(dynamic_cast<MeshBasedCellPopulation<DIM>*>(&rCellPopulation)))
    {
        static_cast<MeshBasedCellPopulation<DIM>*>(&(rCellPopulation))->CreateVoronoiTessellation();
    }
 
    // Find centroid of cell population
    c_vector<double, DIM> centroid = rCellPopulation.GetCentroidOfCellPopulation();
 
    std::vector<double> biases;
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
         cell_iter != rCellPopulation.End();
         ++cell_iter)
    {
        double distance = inner_prod(rCellPopulation.GetLocationOfCellCentre(*cell_iter) - centroid, mDivisionBiasVector);
        biases.push_back(distance);
    }
 
    // Map signed distances into [0,1]
    double min_distance = *std::min_element(biases.begin(), biases.end());
    double max_distance = *std::max_element(biases.begin(), biases.end());
    for (unsigned i = 0; i < biases.size(); i++)
    {
        biases[i] = (biases[i] - min_distance) / (max_distance - min_distance);
    }
 
    // Iterate over cell population
    unsigned i = 0;
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
         cell_iter != rCellPopulation.End();
         ++cell_iter)
    {
        // Store the cell's volume in CellData
        cell_iter->GetCellData()->SetItem("bias", biases[i]);
        i++;
    }
}
 
template<unsigned DIM>
void DivisionBiasTrackingModifier<DIM>::OutputSimulationModifierParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t\t<DivisionBiasVector>";
    for (unsigned index=0; index != DIM-1U; index++) // Note: inequality avoids testing index < 0U when DIM=1
    {
        *rParamsFile << mDivisionBiasVector[index] << ",";
    }
    *rParamsFile << mDivisionBiasVector[DIM-1] << "</DivisionBiasVector>\n";
 
    // Call method on direct parent class
    AbstractCellBasedSimulationModifier<DIM>::OutputSimulationModifierParameters(rParamsFile);
}
 
// Explicit instantiation
template class DivisionBiasTrackingModifier<1>;
template class DivisionBiasTrackingModifier<2>;
template class DivisionBiasTrackingModifier<3>;
 
// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(DivisionBiasTrackingModifier)