AbstractCentreBasedCellPopulation.cpp

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*/

#include "AbstractCentreBasedCellPopulation.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::AbstractCentreBasedCellPopulation( AbstractMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
                                                                    std::vector<CellPtr>& rCells,
                                                                  const std::vector<unsigned> locationIndices)
    : AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>(rMesh, rCells, locationIndices),
      mMeinekeDivisionSeparation(0.3) // educated guess
{
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::AbstractCentreBasedCellPopulation(AbstractMesh<ELEMENT_DIM, SPACE_DIM>& rMesh)
    : AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>(rMesh),
      mMeinekeDivisionSeparation(0.3) // educated guess

{
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_vector<double, SPACE_DIM> AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::GetLocationOfCellCentre(CellPtr pCell)
{
    return GetNodeCorrespondingToCell(pCell)->rGetLocation();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Node<SPACE_DIM>* AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::GetNodeCorrespondingToCell(CellPtr pCell)
{
    unsigned index = this->GetLocationIndexUsingCell(pCell);
    return this->GetNode(index);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
CellPtr AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::AddCell(CellPtr pNewCell, const c_vector<double,SPACE_DIM>& rCellDivisionVector, CellPtr pParentCell)
{
    // Create a new node
    Node<SPACE_DIM>* p_new_node = new Node<SPACE_DIM>(this->GetNumNodes(), rCellDivisionVector, false);   // never on boundary
    unsigned new_node_index = this->AddNode(p_new_node); // use copy constructor so it doesn't matter that new_node goes out of scope

    // Update cells vector
    this->mCells.push_back(pNewCell);

    // Update mappings between cells and location indices
    this->SetCellUsingLocationIndex(new_node_index,pNewCell);
    this->mCellLocationMap[pNewCell.get()] = new_node_index;

    return pNewCell;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::pair<CellPtr,CellPtr> AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::CreateCellPair(CellPtr pCell1, CellPtr pCell2)
{
    assert(pCell1);
    assert(pCell2);

    std::pair<CellPtr,CellPtr> cell_pair;

    if (pCell1->GetCellId() < pCell2->GetCellId())
    {
        cell_pair.first = pCell1;
        cell_pair.second = pCell2;
    }
    else
    {
        cell_pair.first = pCell2;
        cell_pair.second = pCell1;
    }
    return cell_pair;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::IsMarkedSpring(const std::pair<CellPtr,CellPtr>& rCellPair)
{
    // the pair should be ordered like this (CreateCellPair will ensure this)
    assert(rCellPair.first->GetCellId() < rCellPair.second->GetCellId());

    return mMarkedSprings.find(rCellPair) != mMarkedSprings.end();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::MarkSpring(std::pair<CellPtr,CellPtr>& rCellPair)
{
    // the pair should be ordered like this (CreateCellPair will ensure this)
    assert(rCellPair.first->GetCellId() < rCellPair.second->GetCellId());

    mMarkedSprings.insert(rCellPair);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::UnmarkSpring(std::pair<CellPtr,CellPtr>& rCellPair)
{
    // the pair should be ordered like this (CreateCellPair will ensure this)
    assert(rCellPair.first->GetCellId() < rCellPair.second->GetCellId());

    mMarkedSprings.erase(rCellPair);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::IsCellAssociatedWithADeletedLocation(CellPtr pCell)
{
    return GetNodeCorrespondingToCell(pCell)->IsDeleted();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::UpdateNodeLocations(const std::vector< c_vector<double, SPACE_DIM> >& rNodeForces, double dt)
{
    // Iterate over all nodes associated with real cells to update their positions
    for (typename AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::Iterator cell_iter = this->Begin();
         cell_iter != this->End();
         ++cell_iter)
    {
        // Get index of node associated with cell
        unsigned node_index = this->GetLocationIndexUsingCell((*cell_iter));

        // Get damping constant for node
        double damping_const = this->GetDampingConstant(node_index);

        // Get displacement
        c_vector<double,SPACE_DIM> displacement=dt*rNodeForces[node_index]/damping_const;

        // Throws an exception if the cell movement goes beyond mAbsoluteMovementThreshold
        if (norm_2(displacement) > this->mAbsoluteMovementThreshold)
        {
            EXCEPTION("Cells are moving by: " << norm_2(displacement) <<
                    ", which is more than the AbsoluteMovementThreshold: "
                    << this->mAbsoluteMovementThreshold <<
                    ". Use a smaller timestep to avoid this exception.");
        }

        // Get new node location
        c_vector<double, SPACE_DIM> new_node_location = this->GetNode(node_index)->rGetLocation() + displacement;

        // Create ChastePoint for new node location
        ChastePoint<SPACE_DIM> new_point(new_node_location);

        // Move the node
        this->SetNode(node_index, new_point);
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::GetDampingConstant(unsigned nodeIndex)
{
    CellPtr p_cell = this->GetCellUsingLocationIndex(nodeIndex);
    if (p_cell->GetMutationState()->IsType<WildTypeCellMutationState>() && !p_cell->HasCellProperty<CellLabel>())
    {
        return this->GetDampingConstantNormal();
    }
    else
    {
        return this->GetDampingConstantMutant();
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::IsGhostNode(unsigned index)
{
    return false;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::IsParticle(unsigned index)
{
    return false;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::GenerateCellResultsAndWriteToFiles()
{

    // Set up cell type counter
    unsigned num_cell_types = this->mCellProliferativeTypeCount.size();
    std::vector<unsigned> cell_type_counter(num_cell_types);
    for (unsigned i=0; i<num_cell_types; i++)
    {
        cell_type_counter[i] = 0;
    }

    // Set up cell cycle phase counter
    unsigned num_cell_cycle_phases = this->mCellCyclePhaseCount.size();
    std::vector<unsigned> cell_cycle_phase_counter(num_cell_cycle_phases);
    for (unsigned i=0; i<num_cell_cycle_phases; i++)
    {
        cell_cycle_phase_counter[i] = 0;
    }

    // Write cell data to file
    for (unsigned node_index=0; node_index<this->GetNumNodes(); node_index++)
    {
        // Hack that covers the case where the node is associated with a cell that has just been killed (#1129)
        bool node_corresponds_to_dead_cell = false;
        if (this->IsCellAttachedToLocationIndex(node_index))
        {
            node_corresponds_to_dead_cell = this->GetCellUsingLocationIndex(node_index)->IsDead();
        }

        // Write cell data to file
        if (!(this->GetNode(node_index)->IsDeleted())
                && !node_corresponds_to_dead_cell
                && !(this->IsParticle(node_index)))
        {

            if (IsGhostNode(node_index) == true)
            {
                *(this->mpVizCellProliferativeTypesFile) << INVISIBLE_COLOUR << " ";
            }
            else
            {
                this->GenerateCellResults(this->GetCellUsingLocationIndex(node_index),cell_type_counter,cell_cycle_phase_counter);
            }
        }
    }

    this->WriteCellResultsToFiles(cell_type_counter, cell_cycle_phase_counter);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::WriteTimeAndNodeResultsToFiles()
{
    OutputFileHandler output_file_handler(this->mDirPath, false);

    PetscTools::BeginRoundRobin();
    {
        if (!PetscTools::AmMaster() || SimulationTime::Instance()->GetTimeStepsElapsed()!=0)
        {
            this->mpVizNodesFile = output_file_handler.OpenOutputFile("results.viznodes", std::ios::app);
            this->mpVizBoundaryNodesFile = output_file_handler.OpenOutputFile("results.vizboundarynodes", std::ios::app);
        }
        if (PetscTools::AmMaster())
        {
            double time = SimulationTime::Instance()->GetTime();

            *this->mpVizNodesFile << time << "\t";
            *this->mpVizBoundaryNodesFile << time << "\t";
        }


        // Write node data to file
        for (typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator node_iter = this->mrMesh.GetNodeIteratorBegin();
                node_iter != this->mrMesh.GetNodeIteratorEnd();
                ++node_iter)
        {

            /*
             * Hack that covers the case where the node in an AbstractCentreBasedCellPopulation
             * is associated with a cell that has just been killed (#1129). This breaks the
             * vertex visualizer when apoptotic cells are involved.
             */
            bool node_corresponds_to_dead_cell = false;
            if (this->IsCellAttachedToLocationIndex(node_iter->GetIndex()))
            {
                node_corresponds_to_dead_cell = this->GetCellUsingLocationIndex(node_iter->GetIndex())->IsDead();
            }

            // Write node data to file
            if (!(node_iter->IsDeleted()) && !node_corresponds_to_dead_cell)
            {
                const c_vector<double,SPACE_DIM>& position = node_iter->rGetLocation();

                for (unsigned i=0; i<SPACE_DIM; i++)
                {
                    *this->mpVizNodesFile << position[i] << " ";
                }
                *this->mpVizBoundaryNodesFile << node_iter->IsBoundaryNode() << " ";
            }
        }

        if (PetscTools::AmTopMost())
        {
            *this->mpVizNodesFile << "\n";
            *this->mpVizBoundaryNodesFile << "\n";
        }

        this->mpVizNodesFile->close();
        this->mpVizBoundaryNodesFile->close();
    }
    PetscTools::EndRoundRobin();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::GetMeinekeDivisionSeparation()
{
    return mMeinekeDivisionSeparation;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::SetMeinekeDivisionSeparation(double divisionSeparation)
{
    assert(divisionSeparation <= 1.0);
    assert(divisionSeparation >= 0.0);
    mMeinekeDivisionSeparation = divisionSeparation;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::OutputCellPopulationParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t<MeinekeDivisionSeparation>" << mMeinekeDivisionSeparation << "</MeinekeDivisionSeparation>\n";

    // Call method on direct parent class
    AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::OutputCellPopulationParameters(rParamsFile);
}

// Explicit instantiation

template class AbstractCentreBasedCellPopulation<1,1>;
template class AbstractCentreBasedCellPopulation<1,2>;
template class AbstractCentreBasedCellPopulation<2,2>;
template class AbstractCentreBasedCellPopulation<1,3>;
template class AbstractCentreBasedCellPopulation<2,3>;
template class AbstractCentreBasedCellPopulation<3,3>;