CellsGenerator.hpp

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*/

#ifndef CELLSGENERATOR_HPP_
#define CELLSGENERATOR_HPP_

#include <vector>
#include "Cell.hpp"
#include "WildTypeCellMutationState.hpp"
#include "StemCellProliferativeType.hpp"
#include "TransitCellProliferativeType.hpp"
#include "RandomNumberGenerator.hpp"

template<class CELL_CYCLE_MODEL, unsigned DIM>
class CellsGenerator
{
public:

    void GenerateBasic(std::vector<CellPtr>& rCells,
                       unsigned numCells,
                       const std::vector<unsigned> locationIndices=std::vector<unsigned>(),
                       boost::shared_ptr<AbstractCellProperty> pCellProliferativeType=boost::shared_ptr<AbstractCellProperty>());

    void GenerateBasicRandom(std::vector<CellPtr>& rCells,
                             unsigned numCells,
                             boost::shared_ptr<AbstractCellProperty> pCellProliferativeType=boost::shared_ptr<AbstractCellProperty>());

    void GenerateGivenLocationIndices(std::vector<CellPtr>& rCells,
                                      const std::vector<unsigned> locationIndices,
                                      boost::shared_ptr<AbstractCellProperty> pCellProliferativeType=boost::shared_ptr<AbstractCellProperty>());
};

template<class CELL_CYCLE_MODEL, unsigned DIM>
void CellsGenerator<CELL_CYCLE_MODEL,DIM>::GenerateBasic(std::vector<CellPtr>& rCells,
                                                         unsigned numCells,
                                                         const std::vector<unsigned> locationIndices,
                                                         boost::shared_ptr<AbstractCellProperty> pCellProliferativeType)
{
    rCells.clear();

    if (!locationIndices.empty())
    {
        // If location indices is given, then it needs to match the number of output cells
        if (numCells != locationIndices.size())
        {
            EXCEPTION("The size of the locationIndices vector must match the required number of output cells");
        }
    }
    rCells.reserve(numCells);

    // Create cells
    for (unsigned i=0; i<numCells; i++)
    {
        CELL_CYCLE_MODEL* p_cell_cycle_model = new CELL_CYCLE_MODEL;
        p_cell_cycle_model->SetDimension(DIM);

        boost::shared_ptr<AbstractCellProperty> p_state(CellPropertyRegistry::Instance()->Get<WildTypeCellMutationState>());
        CellPtr p_cell(new Cell(p_state, p_cell_cycle_model));

        if (!pCellProliferativeType)
        {
            p_cell->SetCellProliferativeType(CellPropertyRegistry::Instance()->Get<StemCellProliferativeType>());
        }
        else
        {
            p_cell->SetCellProliferativeType(pCellProliferativeType);
        }

        double birth_time;
        if (!locationIndices.empty())
        {
            birth_time = 0.0 - locationIndices[i];
        }
        else
        {
            birth_time = 0.0 - i;
        }

        p_cell->SetBirthTime(birth_time);
        rCells.push_back(p_cell);
    }
}

template<class CELL_CYCLE_MODEL, unsigned DIM>
void CellsGenerator<CELL_CYCLE_MODEL,DIM>::GenerateBasicRandom(std::vector<CellPtr>& rCells,
                                                               unsigned numCells,
                                                               boost::shared_ptr<AbstractCellProperty> pCellProliferativeType)
{
    rCells.clear();

    rCells.reserve(numCells);

    // Create cells
    for (unsigned i=0; i<numCells; i++)
    {
        CELL_CYCLE_MODEL* p_cell_cycle_model = new CELL_CYCLE_MODEL;
        p_cell_cycle_model->SetDimension(DIM);

        boost::shared_ptr<AbstractCellProperty> p_state(CellPropertyRegistry::Instance()->Get<WildTypeCellMutationState>());
        CellPtr p_cell(new Cell(p_state, p_cell_cycle_model));

        if (!pCellProliferativeType)
        {
            p_cell->SetCellProliferativeType(CellPropertyRegistry::Instance()->Get<StemCellProliferativeType>());
        }
        else
        {
            p_cell->SetCellProliferativeType(pCellProliferativeType);
        }

        double birth_time = -p_cell_cycle_model->GetAverageStemCellCycleTime()*RandomNumberGenerator::Instance()->ranf();

        if (p_cell->GetCellProliferativeType()->IsType<TransitCellProliferativeType>())
        {
            birth_time = -p_cell_cycle_model->GetAverageTransitCellCycleTime()*RandomNumberGenerator::Instance()->ranf();
        }

        p_cell->SetBirthTime(birth_time);
        rCells.push_back(p_cell);
    }
}

template<class CELL_CYCLE_MODEL, unsigned DIM>
void CellsGenerator<CELL_CYCLE_MODEL,DIM>::GenerateGivenLocationIndices(std::vector<CellPtr>& rCells,
                                                                        const std::vector<unsigned> locationIndices,
                                                                        boost::shared_ptr<AbstractCellProperty> pCellProliferativeType)
{
    assert(!locationIndices.empty());

    unsigned num_cells = locationIndices.size();

    rCells.clear();
    rCells.reserve(num_cells);
    CellPropertyRegistry::Instance()->Clear();

    for (unsigned i=0; i<num_cells; i++)
    {
        CELL_CYCLE_MODEL* p_cell_cycle_model = new CELL_CYCLE_MODEL;
        p_cell_cycle_model->SetDimension(DIM);

        boost::shared_ptr<AbstractCellProperty> p_state(CellPropertyRegistry::Instance()->Get<WildTypeCellMutationState>());

        CellPtr p_cell(new Cell(p_state, p_cell_cycle_model));

        if (!pCellProliferativeType)
        {
            p_cell->SetCellProliferativeType(CellPropertyRegistry::Instance()->Get<StemCellProliferativeType>());
        }
        else
        {
            p_cell->SetCellProliferativeType(pCellProliferativeType);
        }

        double birth_time = 0.0 - locationIndices[i];
        p_cell->SetBirthTime(birth_time);
        rCells.push_back(p_cell);
    }
}

#endif /* CELLSGENERATOR_HPP_ */