PottsBasedCellPopulation.cpp

/*

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*/

#include "PottsBasedCellPopulation.hpp"
#include "RandomNumberGenerator.hpp"
#include "Warnings.hpp"

// Needed to convert mesh in order to write nodes to VTK (visualize as glyphs)
#include "VtkMeshWriter.hpp"
#include "NodesOnlyMesh.hpp"
#include "Exception.hpp"

template<unsigned DIM>
void PottsBasedCellPopulation<DIM>::Validate()
{
    // Check each element has only one cell associated with it
    std::vector<unsigned> validated_element = std::vector<unsigned>(this->GetNumElements(), 0);

    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->Begin();
         cell_iter != this->End();
         ++cell_iter)
    {
        unsigned elem_index = this->GetLocationIndexUsingCell(*cell_iter);
        validated_element[elem_index]++;
    }

    for (unsigned i=0; i<validated_element.size(); i++)
    {
        if (validated_element[i] == 0)
        {
            EXCEPTION("Element " << i << " does not appear to have a cell associated with it");
        }

        if (validated_element[i] > 1)
        {
            EXCEPTION("Element " << i << " appears to have " << validated_element[i] << " cells associated with it");
        }
    }
}

template<unsigned DIM>
PottsBasedCellPopulation<DIM>::PottsBasedCellPopulation(PottsMesh<DIM>& rMesh,
                                                        std::vector<CellPtr>& rCells,
                                                        bool deleteMesh,
                                                        bool validate,
                                                        const std::vector<unsigned> locationIndices)
    : AbstractOnLatticeCellPopulation<DIM>(rMesh, rCells, locationIndices, deleteMesh),
      mpElementTessellation(NULL),
      mpMutableMesh(NULL),
      mTemperature(0.1),
      mNumSweepsPerTimestep(1)
{
    mpPottsMesh = static_cast<PottsMesh<DIM>* >(&(this->mrMesh));
    // Check each element has only one cell associated with it
    if (validate)
    {
        Validate();
    }
}

template<unsigned DIM>
PottsBasedCellPopulation<DIM>::PottsBasedCellPopulation(PottsMesh<DIM>& rMesh)
    : AbstractOnLatticeCellPopulation<DIM>(rMesh),
      mpElementTessellation(NULL),
      mpMutableMesh(NULL),
      mTemperature(0.1),
      mNumSweepsPerTimestep(1)
{
    mpPottsMesh = static_cast<PottsMesh<DIM>* >(&(this->mrMesh));
}

template<unsigned DIM>
PottsBasedCellPopulation<DIM>::~PottsBasedCellPopulation()
{
    delete mpElementTessellation;

    delete mpMutableMesh;

    if (this->mDeleteMesh)
    {
        delete &this->mrMesh;
    }
}

template<unsigned DIM>
PottsMesh<DIM>& PottsBasedCellPopulation<DIM>::rGetMesh()
{
    return *mpPottsMesh;
}

template<unsigned DIM>
const PottsMesh<DIM>& PottsBasedCellPopulation<DIM>::rGetMesh() const
{
    return *mpPottsMesh;
}

template<unsigned DIM>
PottsElement<DIM>* PottsBasedCellPopulation<DIM>::GetElement(unsigned elementIndex)
{
    return mpPottsMesh->GetElement(elementIndex);
}

template<unsigned DIM>
unsigned PottsBasedCellPopulation<DIM>::GetNumElements()
{
    return mpPottsMesh->GetNumElements();
}

template<unsigned DIM>
Node<DIM>* PottsBasedCellPopulation<DIM>::GetNode(unsigned index)
{
    return this->mrMesh.GetNode(index);
}

template<unsigned DIM>
unsigned PottsBasedCellPopulation<DIM>::GetNumNodes()
{
    return this->mrMesh.GetNumNodes();
}

template<unsigned DIM>
c_vector<double, DIM> PottsBasedCellPopulation<DIM>::GetLocationOfCellCentre(CellPtr pCell)
{
    return mpPottsMesh->GetCentroidOfElement(this->GetLocationIndexUsingCell(pCell));
}

template<unsigned DIM>
PottsElement<DIM>* PottsBasedCellPopulation<DIM>::GetElementCorrespondingToCell(CellPtr pCell)
{
    return mpPottsMesh->GetElement(this->GetLocationIndexUsingCell(pCell));
}

template<unsigned DIM>
CellPtr PottsBasedCellPopulation<DIM>::AddCell(CellPtr pNewCell, const c_vector<double,DIM>& rCellDivisionVector, CellPtr pParentCell)
{
    // Get the element associated with this cell
    PottsElement<DIM>* p_element = GetElementCorrespondingToCell(pParentCell);

    // Divide the element
    unsigned new_element_index = mpPottsMesh->DivideElement(p_element, true); // new element will be below the existing element

    // Associate the new cell with the element
    this->mCells.push_back(pNewCell);

    // Update location cell map
    CellPtr p_created_cell = this->mCells.back();
    this->SetCellUsingLocationIndex(new_element_index,p_created_cell);
    return p_created_cell;
}

template<unsigned DIM>
unsigned PottsBasedCellPopulation<DIM>::RemoveDeadCells()
{
    unsigned num_removed = 0;

    for (std::list<CellPtr>::iterator it = this->mCells.begin();
         it != this->mCells.end();
         ++it)
    {
        if ((*it)->IsDead())
        {
            // Remove the element from the mesh
            num_removed++;
            mpPottsMesh->DeleteElement(this->GetLocationIndexUsingCell((*it)));
            it = this->mCells.erase(it);
            --it;
        }
    }
    return num_removed;
}
template<unsigned DIM>
void PottsBasedCellPopulation<DIM>::UpdateCellLocations(double dt)
{
    /*
     * This method implements a Monte Carlo method to update the cell population.
     * We sample randomly from all nodes in the mesh. Once we have selected a target
     * node we randomly select a neighbour. The Hamiltonian is evaluated in the
     * current configuration (H_0) and with the target node added to the same
     * element as the neighbour (H_1). Based on the vale of deltaH = H_1 - H_0,
     * the switch is either made or not.
     *
     * For each time step (i.e. each time this method is called) we sample
     * mrMesh.GetNumNodes() nodes. This is known as a Monte Carlo Step (MCS).
     */

    RandomNumberGenerator* p_gen = RandomNumberGenerator::Instance();
    unsigned num_nodes = this->mrMesh.GetNumNodes();

    // Randomly permute mUpdateRuleCollection if specified
    if (this->mIterateRandomlyOverUpdateRuleCollection)
    {
        // Randomly permute mUpdateRuleCollection
        p_gen->Shuffle(mUpdateRuleCollection);
    }

    for (unsigned i=0; i<num_nodes*mNumSweepsPerTimestep; i++)
    {
        unsigned node_index;

        if (this->mUpdateNodesInRandomOrder)
        {
            node_index = p_gen->randMod(num_nodes);
        }
        else
        {
            // Loop over nodes in index order.
            node_index = i%num_nodes;
        }

        Node<DIM>* p_node = this->mrMesh.GetNode(node_index);

        // Each node in the mesh must be in at most one element
        assert(p_node->GetNumContainingElements() <= 1);

        // Find a random available neighbouring node to overwrite current site
        std::set<unsigned> neighbouring_node_indices = mpPottsMesh->GetMooreNeighbouringNodeIndices(node_index);
        unsigned neighbour_location_index;

        if (!neighbouring_node_indices.empty())
        {
            unsigned num_neighbours = neighbouring_node_indices.size();
            unsigned chosen_neighbour = p_gen->randMod(num_neighbours);

            std::set<unsigned>::iterator neighbour_iter = neighbouring_node_indices.begin();
            for (unsigned j=0; j<chosen_neighbour; j++)
            {
                neighbour_iter++;
            }

            neighbour_location_index = *neighbour_iter;
        }
        else
        {
            // Each node in the mesh must have at least one neighbour
            NEVER_REACHED;
        }

        std::set<unsigned> containing_elements = p_node->rGetContainingElementIndices();
        std::set<unsigned> neighbour_containing_elements = GetNode(neighbour_location_index)->rGetContainingElementIndices();
        // Only calculate Hamiltonian and update elements if the nodes are from different elements, or one is from the medium
        if (  (  *containing_elements.begin() != *neighbour_containing_elements.begin() && !containing_elements.empty() && !neighbour_containing_elements.empty() )
                || ( !containing_elements.empty() && neighbour_containing_elements.empty() )
                || ( containing_elements.empty() && !neighbour_containing_elements.empty() ) )
        {
            double delta_H = 0.0; // This is H_1-H_0.

            // Now add contributions to the Hamiltonian from each AbstractPottsUpdateRule
            for (typename std::vector<boost::shared_ptr<AbstractPottsUpdateRule<DIM> > >::iterator iter = mUpdateRuleCollection.begin();
                 iter != mUpdateRuleCollection.end();
                 ++iter)
            {
                delta_H += (*iter)->EvaluateHamiltonianContribution(neighbour_location_index, p_node->GetIndex(), *this);
            }

            // Generate a uniform random number to do the random motion
            double random_number = p_gen->ranf();
            double p = exp(-delta_H/mTemperature);
            if (delta_H <= 0 || random_number < p)
            {
                // Do swap

                // Remove the current node from any elements containing it (there should be at most one such element)
                for (std::set<unsigned>::iterator iter = containing_elements.begin();
                     iter != containing_elements.end();
                     ++iter)
                {
                    GetElement(*iter)->DeleteNode(GetElement(*iter)->GetNodeLocalIndex(node_index));

                }

                // Next add the current node to any elements containing the neighbouring node (there should be at most one such element)
                for (std::set<unsigned>::iterator iter = neighbour_containing_elements.begin();
                     iter != neighbour_containing_elements.end();
                     ++iter)
                {
                    GetElement(*iter)->AddNode(this->mrMesh.GetNode(node_index));
                }
            }
        }
    }
}

template<unsigned DIM>
bool PottsBasedCellPopulation<DIM>::IsCellAssociatedWithADeletedLocation(CellPtr pCell)
{
    return GetElementCorrespondingToCell(pCell)->IsDeleted();
}

template<unsigned DIM>
void PottsBasedCellPopulation<DIM>::Update(bool hasHadBirthsOrDeaths)
{
}

template<unsigned DIM>
void PottsBasedCellPopulation<DIM>::CreateOutputFiles(const std::string& rDirectory, bool cleanOutputDirectory)
{
    AbstractCellPopulation<DIM>::CreateOutputFiles(rDirectory, cleanOutputDirectory);

    OutputFileHandler output_file_handler(rDirectory, cleanOutputDirectory);
    mpVizElementsFile = output_file_handler.OpenOutputFile("results.vizelements");
}

template<unsigned DIM>
void PottsBasedCellPopulation<DIM>::CloseOutputFiles()
{
    AbstractCellPopulation<DIM>::CloseOutputFiles();
    mpVizElementsFile->close();
}

template<unsigned DIM>
void PottsBasedCellPopulation<DIM>::WriteResultsToFiles()
{
    AbstractCellPopulation<DIM>::WriteResultsToFiles();

    CreateElementTessellation(); // To be used to output to the visualizer

    SimulationTime* p_time = SimulationTime::Instance();

    // Write element data to file
    *mpVizElementsFile << p_time->GetTime() << "\t";

    // Loop over cells and find associated elements so in the same order as the cells in output files
    for (std::list<CellPtr>::iterator cell_iter = this->mCells.begin();
         cell_iter != this->mCells.end();
         ++cell_iter)
    {
        unsigned elem_index = this->GetLocationIndexUsingCell(*cell_iter);

        // Hack that covers the case where the element is associated with a cell that has just been killed (#1129)
        bool elem_corresponds_to_dead_cell = false;

        if (this->IsCellAttachedToLocationIndex(elem_index))
        {
            elem_corresponds_to_dead_cell = this->GetCellUsingLocationIndex(elem_index)->IsDead();
        }

        // Write node data to file
        if (!(GetElement(elem_index)->IsDeleted()) && !elem_corresponds_to_dead_cell)
        {
            PottsElement<DIM>* p_element = mpPottsMesh->GetElement(elem_index);

            unsigned num_nodes_in_element = p_element->GetNumNodes();

            // First write the number of Nodes belonging to this PottsElement
            *mpVizElementsFile << num_nodes_in_element << " ";

            // Then write the global index of each Node in this element
            for (unsigned i=0; i<num_nodes_in_element; i++)
            {
                *mpVizElementsFile << p_element->GetNodeGlobalIndex(i) << " ";
            }
        }
    }
    *mpVizElementsFile << "\n";
}

template<unsigned DIM>
double PottsBasedCellPopulation<DIM>::GetVolumeOfCell(CellPtr pCell)
{
    // Get element index corresponding to this cell
    unsigned elem_index = this->GetLocationIndexUsingCell(pCell);

    // Get volume of this element in the Potts mesh
    double cell_volume = mpPottsMesh->GetVolumeOfElement(elem_index);

    return cell_volume;
}

template<unsigned DIM>
void PottsBasedCellPopulation<DIM>::WriteCellVolumeResultsToFile()
{
    // Write time to file
    *(this->mpCellVolumesFile) << SimulationTime::Instance()->GetTime() << " ";

    // Loop over cells and find associated elements so in the same order as the cells in output files
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->Begin();
         cell_iter != this->End();
         ++cell_iter)
    {
        unsigned elem_index = this->GetLocationIndexUsingCell(*cell_iter);

        // Hack that covers the case where the element is associated with a cell that has just been killed (#1129)
        bool elem_corresponds_to_dead_cell = false;

        if (this->IsCellAttachedToLocationIndex(elem_index))
        {
            elem_corresponds_to_dead_cell = this->GetCellUsingLocationIndex(elem_index)->IsDead();
        }

        // Write node data to file
        if (!(GetElement(elem_index)->IsDeleted()) && !elem_corresponds_to_dead_cell)
        {
           // Write element index to file
            *(this->mpCellVolumesFile) << elem_index << " ";

            // Write cell ID to file
            unsigned cell_index = cell_iter->GetCellId();
            *(this->mpCellVolumesFile) << cell_index << " ";

            // Write centroid location to file
            c_vector<double, DIM> centroid_location = mpPottsMesh->GetCentroidOfElement(elem_index);

            *(this->mpCellVolumesFile) << centroid_location[0] << " ";
            *(this->mpCellVolumesFile) << centroid_location[1] << " ";

            // Write cell volume (in 3D) or area (in 2D) to file
            double cell_volume = this->GetVolumeOfCell(*cell_iter);
            *(this->mpCellVolumesFile) << cell_volume << " ";
        }
    }
    *(this->mpCellVolumesFile) << "\n";
}

template<unsigned DIM>
void PottsBasedCellPopulation<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;
    }

    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->Begin();
         cell_iter != this->End();
         ++cell_iter)
    {
        this->GenerateCellResults(*cell_iter, cell_type_counter, cell_cycle_phase_counter);
    }

    this->WriteCellResultsToFiles(cell_type_counter, cell_cycle_phase_counter);
}

template<unsigned DIM>
double PottsBasedCellPopulation<DIM>::GetWidth(const unsigned& rDimension)
{
    // Call GetWidth() on the mesh
    double width = this->mrMesh.GetWidth(rDimension);

    return width;
}

template<unsigned DIM>
void PottsBasedCellPopulation<DIM>::AddUpdateRule(boost::shared_ptr<AbstractPottsUpdateRule<DIM> > pUpdateRule)
{
    mUpdateRuleCollection.push_back(pUpdateRule);
}

template<unsigned DIM>
void PottsBasedCellPopulation<DIM>::RemoveAllUpdateRules()
{
    mUpdateRuleCollection.clear();
}

template<unsigned DIM>
const std::vector<boost::shared_ptr<AbstractPottsUpdateRule<DIM> > >& PottsBasedCellPopulation<DIM>::rGetUpdateRuleCollection() const
{
    return mUpdateRuleCollection;
}

template<unsigned DIM>
void PottsBasedCellPopulation<DIM>::CreateElementTessellation()
{
//  delete mpElementTessellation;
//
//    ///\todo this code would need to be extended if the domain were required to be periodic
//
//  std::vector<Node<2>*> nodes;
//  for (unsigned node_index=0; node_index<mrMesh.GetNumNodes(); node_index++)
//  {
//      Node<2>* p_temp_node = mrMesh.GetNode(node_index);
//      nodes.push_back(p_temp_node);
//  }
//  MutableMesh<2,2> mesh(nodes);
//    mpElementTessellation = new VertexMesh<2,2>(mesh);
}

template<unsigned DIM>
VertexMesh<DIM,DIM>* PottsBasedCellPopulation<DIM>::GetElementTessellation()
{
//    assert(mpElementTessellation != NULL);
    return mpElementTessellation;
}

template<unsigned DIM>
void PottsBasedCellPopulation<DIM>::CreateMutableMesh()
{
    delete mpMutableMesh;

    // Get the nodes of the PottsMesh
    std::vector<Node<DIM>*> nodes;
    for (unsigned node_index=0; node_index<this->mrMesh.GetNumNodes(); node_index++)
    {
      c_vector<double, DIM> location = this->mrMesh.GetNode(node_index)->rGetLocation();
      nodes.push_back(new Node<DIM>(node_index, location));
    }

    mpMutableMesh = new MutableMesh<DIM,DIM>(nodes);
}

template<unsigned DIM>
MutableMesh<DIM,DIM>* PottsBasedCellPopulation<DIM>::GetMutableMesh()
{
    assert(mpMutableMesh);
    return mpMutableMesh;
}

template<unsigned DIM>
void PottsBasedCellPopulation<DIM>::OutputCellPopulationParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t<Temperature>" << mTemperature << "</Temperature>\n";
    *rParamsFile << "\t\t<NumSweepsPerTimestep>" << mNumSweepsPerTimestep << "</NumSweepsPerTimestep>\n";

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

template<unsigned DIM>
std::set<unsigned> PottsBasedCellPopulation<DIM>::GetNeighbouringNodeIndices(unsigned index)
{
    EXCEPTION("Cannot call GetNeighbouringNodeIndices() on a PottsBasedCellPopulation, need to go through the PottsMesh instead");
    std::set<unsigned> neighbouring_node_indices;
    return neighbouring_node_indices;
}

template<unsigned DIM>
void PottsBasedCellPopulation<DIM>::SetTemperature(double temperature)
{
    mTemperature = temperature;
}

template<unsigned DIM>
double PottsBasedCellPopulation<DIM>::GetTemperature()
{
    return mTemperature;
}

template<unsigned DIM>
void PottsBasedCellPopulation<DIM>::SetNumSweepsPerTimestep(unsigned numSweepsPerTimestep)
{
    mNumSweepsPerTimestep = numSweepsPerTimestep;
}

template<unsigned DIM>
unsigned PottsBasedCellPopulation<DIM>::GetNumSweepsPerTimestep()
{
    return mNumSweepsPerTimestep;
}

template<unsigned DIM>
void PottsBasedCellPopulation<DIM>::WriteVtkResultsToFile()
{
#ifdef CHASTE_VTK
    std::stringstream time;
    time << SimulationTime::Instance()->GetTimeStepsElapsed();
    VtkMeshWriter<DIM, DIM> mesh_writer(this->mDirPath, "results_"+time.str(), false);

    unsigned num_nodes = GetNumNodes();
    std::vector<double> cell_types;
    std::vector<double> cell_mutation_states;
    std::vector<double> cell_labels;
    std::vector<double> elem_ids;
    cell_types.reserve(num_nodes);
    cell_mutation_states.reserve(num_nodes);
    cell_labels.reserve(num_nodes);
    elem_ids.reserve(num_nodes);
    std::vector<std::vector<double> > cellwise_data;

    unsigned num_cell_data_items = 0;
    std::vector<std::string> cell_data_names;
    //We assume that the first cell is representative of all cells
    num_cell_data_items = this->Begin()->GetCellData()->GetNumItems();
    cell_data_names = this->Begin()->GetCellData()->GetKeys();

    for (unsigned var=0; var<num_cell_data_items; var++)
    {
        std::vector<double> cellwise_data_var(num_nodes);
        cellwise_data.push_back(cellwise_data_var);
    }
    for (typename AbstractMesh<DIM,DIM>::NodeIterator iter = mpPottsMesh->GetNodeIteratorBegin();
         iter != mpPottsMesh->GetNodeIteratorEnd();
         ++iter)
    {
        std::set<unsigned> element_indices = iter->rGetContainingElementIndices();

        if (element_indices.empty())
        {
            // No elements associated with this gridpoint
            cell_types.push_back(-1.0);
            elem_ids.push_back(-1.0);
            if (this->mOutputCellMutationStates)
            {
                cell_mutation_states.push_back(-1.0);
                cell_labels.push_back(-1.0);
            }
        }
        else
        {
            // The number of elements should be zero or one
            assert(element_indices.size() == 1);

            unsigned element_index = *(element_indices.begin());
            elem_ids.push_back((double)element_index);

            CellPtr p_cell = this->GetCellUsingLocationIndex(element_index);
            double cell_type = p_cell->GetCellProliferativeType();
            cell_types.push_back(cell_type);

            if (this->mOutputCellMutationStates)
            {
                double cell_mutation_state = p_cell->GetMutationState()->GetColour();
                cell_mutation_states.push_back(cell_mutation_state);

                double cell_label = 0.0;
                if (p_cell->HasCellProperty<CellLabel>())
                {
                    CellPropertyCollection collection = p_cell->rGetCellPropertyCollection().GetProperties<CellLabel>();
                    boost::shared_ptr<CellLabel> p_label = boost::static_pointer_cast<CellLabel>(collection.GetProperty());
                    cell_label = p_label->GetColour();
                }
                cell_labels.push_back(cell_label);
            }
            for (unsigned var=0; var<num_cell_data_items; var++)
            {
                cellwise_data[var][iter->GetIndex()] = p_cell->GetCellData()->GetItem(cell_data_names[var]);
            }
        }
    }

    assert(cell_types.size() == num_nodes);
    assert(elem_ids.size() == num_nodes);

    mesh_writer.AddPointData("Element index", elem_ids);
    mesh_writer.AddPointData("Cell types", cell_types);

    if (this->mOutputCellMutationStates)
    {
        assert(cell_mutation_states.size() == num_nodes);
        mesh_writer.AddPointData("Mutation states", cell_mutation_states);
        assert(cell_labels.size() == num_nodes);
        mesh_writer.AddPointData("Cell labels", cell_labels);
    }

    if (num_cell_data_items > 0)
    {
        for (unsigned var=0; var<cellwise_data.size(); var++)
        {
            mesh_writer.AddPointData(cell_data_names[var], cellwise_data[var]);
        }
    }

    /*
     * The current VTK writer can only write things which inherit from AbstractTetrahedralMeshWriter.
     * For now, we do an explicit conversion to NodesOnlyMesh. This can be written to VTK then visualized as glyphs.
     */
    NodesOnlyMesh<DIM> temp_mesh;
    temp_mesh.ConstructNodesWithoutMesh(*mpPottsMesh);
    mesh_writer.WriteFilesUsingMesh(temp_mesh);

    *(this->mpVtkMetaFile) << "        <DataSet timestep=\"";
    *(this->mpVtkMetaFile) << time.str();
    *(this->mpVtkMetaFile) << "\" group=\"\" part=\"0\" file=\"results_";
    *(this->mpVtkMetaFile) << time.str();
    *(this->mpVtkMetaFile) << ".vtu\"/>\n";
#endif //CHASTE_VTK
}

// Explicit instantiation

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

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