NodeBasedCellPopulation.hpp

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/
#ifndef NODEBASEDCELLPOPULATION_HPP_
#define NODEBASEDCELLPOPULATION_HPP_

#include "AbstractCentreBasedCellPopulation.hpp"
#include "AbstractTetrahedralMesh.hpp" // for constructor which takes in a mesh
#include "BoxCollection.hpp"

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/set.hpp>
#include <boost/serialization/vector.hpp>

template<unsigned DIM>
class NodeBasedCellPopulation : public AbstractCentreBasedCellPopulation<DIM>
{
    friend class TestNodeBasedCellPopulation;
    friend class TestBoxCollection;

protected:

    std::vector<Node<DIM>* > mNodes;

    std::vector<unsigned> mDeletedNodeIndices;

    bool mAddedNodes;

private:

    BoxCollection<DIM>* mpBoxCollection;

    c_vector<double, DIM> mMinSpatialPositions;

    c_vector<double, DIM> mMaxSpatialPositions;

    std::set< std::pair<Node<DIM>*, Node<DIM>* > > mNodePairs;

    bool mDeleteNodes;

    double mMechanicsCutOffLength;

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCentreBasedCellPopulation<DIM> >(*this);

        Validate(); // paranoia
    }

    unsigned AddNode(Node<DIM>* pNewNode);

    void SetNode(unsigned nodeIndex, ChastePoint<DIM>& rNewLocation);

    void Validate();

    void SplitUpIntoBoxes(double cutOffLength, c_vector<double, 2*DIM> domainSize);

    void FindMaxAndMin();

    void WriteVtkResultsToFile();

public:

    NodeBasedCellPopulation(const std::vector<Node<DIM>* > nodes,
                    std::vector<CellPtr>& rCells,
                    const std::vector<unsigned> locationIndices=std::vector<unsigned>(),
                    bool deleteNodes=true);

    NodeBasedCellPopulation(const std::vector<Node<DIM>* > nodes, double mechanicsCutOffLength, bool deleteNodes=true);

    NodeBasedCellPopulation(const AbstractMesh<DIM,DIM>& rMesh,
                    std::vector<CellPtr>& rCells);

    ~NodeBasedCellPopulation();

    unsigned GetNumNodes();

    Node<DIM>* GetNode(unsigned index);

    unsigned RemoveDeadCells();

    void Clear();

    void Update(bool hasHadBirthsOrDeaths=true);

    std::vector<Node<DIM>* >& rGetNodes();

    const std::vector<Node<DIM>* >& rGetNodes() const;

    BoxCollection<DIM>* GetBoxCollection();

    std::set< std::pair<Node<DIM>*, Node<DIM>* > >& rGetNodePairs();

    void OutputCellPopulationParameters(out_stream& rParamsFile);

    double GetMechanicsCutOffLength();

    void SetMechanicsCutOffLength(double mechanicsCutOffLength);

    double GetWidth(const unsigned& rDimension);

    void SetOutputCellVolumes(bool outputCellVolumes);
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(NodeBasedCellPopulation)

namespace boost {
namespace serialization {

template<class Archive, unsigned SPACE_DIM>
inline void save(
    Archive & ar,
    const Node<SPACE_DIM>& rNode,
    const unsigned int /* file_version */)
{
    // Save deleted flag
    const bool is_deleted = rNode.IsDeleted();
    ar << is_deleted;
}

template<class Archive, unsigned SPACE_DIM>
inline void load(
    Archive & ar,
    Node<SPACE_DIM>& rNode,
    const unsigned int /* file_version */)
{
    // Load deleted flag
    bool is_deleted;
    ar >> is_deleted;
    #define COVERAGE_IGNORE
    if (is_deleted)
    {
        rNode.MarkAsDeleted();
    }
    #undef COVERAGE_IGNORE
}

template<class Archive, unsigned SPACE_DIM>
inline void serialize(
    Archive & ar,
    Node<SPACE_DIM>& rNode,
    const unsigned int file_version)
{
    boost::serialization::split_free(ar, rNode, file_version);
}

template<class Archive, unsigned DIM>
inline void save_construct_data(
    Archive & ar, const Node<DIM> * t, const BOOST_PFTO unsigned int file_version)
{
    // Save the global index of the node
    const unsigned index = t->GetIndex();
    ar << index;

    // Save whether the node is a boundary node
    const bool is_boundary = t->IsBoundaryNode();
    ar << is_boundary;

    // Save the location of the node
    const c_vector<double, DIM>& r_loc = t->rGetLocation();
    for (unsigned i=0; i<DIM; i++)
    {
        ar << r_loc[i];
    }
}

template<class Archive, unsigned DIM>
inline void load_construct_data(
    Archive & ar, Node<DIM> * t, const unsigned int file_version)
{
    // Load the global index of the node
    unsigned index;
    ar >> index;

    // Load whether the node is a boundary node
    bool is_boundary;
    ar >> is_boundary;

    // Load the location of the node
    c_vector<double, DIM> loc;
    for (unsigned i=0; i<DIM; i++)
    {
        ar >> loc[i];
    }

    // Invoke inplace constructor to initialise instance
    ::new(t)Node<DIM>(index, loc, is_boundary);
}

template<class Archive, unsigned DIM>
inline void save_construct_data(
    Archive & ar, const NodeBasedCellPopulation<DIM> * t, const BOOST_PFTO unsigned int file_version)
{
    ar & t->rGetNodes();
//    const double cut_off_length = t->GetMechanicsCutOffLength();
//    ar << cut_off_length;

}

template<class Archive, unsigned DIM>
inline void load_construct_data(
    Archive & ar, NodeBasedCellPopulation<DIM> * t, const unsigned int file_version)
{
    // Load the nodes
    std::vector<Node<DIM>* > nodes;
    ar >> nodes;

    // load the cut of distance
    double cut_off_length = 1.0; //\todo this is temporary till we fix archiving
//    ar >> cut_off_length;

    // Invoke inplace constructor to initialize instance
    ::new(t)NodeBasedCellPopulation<DIM>(nodes, cut_off_length);
}

}} // close namespaces

#endif /*NODEBASEDCELLPOPULATION_HPP_*/

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