AbstractCardiacTissue.hpp

/*

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*/
#ifndef ABSTRACTCARDIACTISSUE_HPP_
#define ABSTRACTCARDIACTISSUE_HPP_

#include <set>
#include <vector>
#include <boost/shared_ptr.hpp>

#include "UblasMatrixInclude.hpp"

#include "ChasteSerialization.hpp"
#include "ClassIsAbstract.hpp"
#include "ChasteSerializationVersion.hpp"
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/shared_ptr.hpp>
#include <boost/serialization/vector.hpp>
#include <boost/serialization/string.hpp>
#include <boost/serialization/split_member.hpp>

#include "AbstractCardiacCellInterface.hpp"
#include "FakeBathCell.hpp"
#include "AbstractCardiacCellFactory.hpp"
#include "AbstractConductivityTensors.hpp"
#include "AbstractPurkinjeCellFactory.hpp"
#include "ReplicatableVector.hpp"
#include "HeartConfig.hpp"
#include "ArchiveLocationInfo.hpp"
#include "AbstractDynamicallyLoadableEntity.hpp"
#include "DynamicModelLoaderRegistry.hpp"
#include "AbstractConductivityModifier.hpp"

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
class AbstractCardiacTissue : private boost::noncopyable
{
private:

    friend class boost::serialization::access;
    friend class TestMonodomainTissue;

    template<class Archive>
    void save(Archive & archive, const unsigned int version) const
    {
        if (version >= 3)
        {
            archive & mHasPurkinje;
        }
        if (version >= 2)
        {
            archive & mExchangeHalos;
        }
        // Don't use the std::vector serialization for cardiac cells, so that we can load them
        // more cleverly when migrating checkpoints.
        SaveCardiacCells(*ProcessSpecificArchive<Archive>::Get(), version);

        // archive & mpMesh; Archived in save/load_constructs at the bottom of Mono/BidomainTissue.hpp
        // archive & mpIntracellularConductivityTensors; Loaded from HeartConfig every time constructor is called
        if (HeartConfig::Instance()->IsMeshProvided() && HeartConfig::Instance()->GetLoadMesh())
        {
            switch (HeartConfig::Instance()->GetConductivityMedia())
            {
                case cp::media_type::Orthotropic:
                {
                    FileFinder source_file(mFibreFilePathNoExtension + ".ortho", RelativeTo::AbsoluteOrCwd);
                    assert(source_file.Exists());
                    FileFinder dest_file(ArchiveLocationInfo::GetArchiveRelativePath() + ArchiveLocationInfo::GetMeshFilename() + ".ortho", RelativeTo::ChasteTestOutput);

                    TRY_IF_MASTER(source_file.CopyTo(dest_file));
                    break;
                }

                case cp::media_type::Axisymmetric:
                {
                    FileFinder source_file(mFibreFilePathNoExtension + ".axi", RelativeTo::AbsoluteOrCwd);
                    assert(source_file.Exists());
                    FileFinder dest_file(ArchiveLocationInfo::GetArchiveRelativePath()
                                       + ArchiveLocationInfo::GetMeshFilename() + ".axi", RelativeTo::ChasteTestOutput);

                    TRY_IF_MASTER(source_file.CopyTo(dest_file));
                    break;
                }

                case cp::media_type::NoFibreOrientation:
                    break;

                default :
                    NEVER_REACHED;
            }
        }

        // archive & mIionicCacheReplicated; // will be regenerated
        // archive & mIntracellularStimulusCacheReplicated; // will be regenerated
        archive & mDoCacheReplication;
        // archive & mMeshUnarchived; Not archived since set to true when archiving constructor is called.

        (*ProcessSpecificArchive<Archive>::Get()) & mpDistributedVectorFactory;

        // Paranoia: check we agree with the mesh on who owns what
        assert(mpDistributedVectorFactory == mpMesh->GetDistributedVectorFactory());
        assert(mpDistributedVectorFactory->GetLow()==mpMesh->GetDistributedVectorFactory()->GetLow());
        assert(mpDistributedVectorFactory->GetLocalOwnership()==mpMesh->GetDistributedVectorFactory()->GetLocalOwnership());
    }

    template<class Archive>
    void load(Archive & archive, const unsigned int version)
    {
        // archive & mpMesh; Archived in save/load_constructs at the bottom of Mono/BidomainTissue.hpp
        // archive & mpIntracellularConductivityTensors; Loaded from HeartConfig every time constructor is called

        if (version >= 3)
        {
            archive & mHasPurkinje;
            if (mHasPurkinje)
            {
                mPurkinjeIionicCacheReplicated.Resize(mpDistributedVectorFactory->GetProblemSize());
            }
        }
        if (version >= 2)
        {
            archive & mExchangeHalos;
            if (mExchangeHalos)
            {
                mpMesh->CalculateNodeExchange(mNodesToSendPerProcess, mNodesToReceivePerProcess);
                CalculateHaloNodesFromNodeExchange();
                unsigned num_halo_nodes = mHaloNodes.size();
                mHaloCellsDistributed.resize( num_halo_nodes );
                for (unsigned local_index = 0; local_index < num_halo_nodes; local_index++)
                {
                    unsigned global_index = mHaloNodes[local_index];
                    mHaloGlobalToLocalIndexMap[global_index] = local_index;
                }
            }
        }

        // mCellsDistributed & mHaloCellsDistributed:
        LoadCardiacCells(*ProcessSpecificArchive<Archive>::Get(), version);

        // archive & mIionicCacheReplicated; // will be regenerated
        // archive & mIntracellularStimulusCacheReplicated; // will be regenerated
        archive & mDoCacheReplication;

        // we no longer have a bool mDoOneCacheReplication, but to maintain backwards compatibility
        // we archive something if version==0
        if (version==0)
        {
            bool do_one_cache_replication = true;
            archive & do_one_cache_replication;
        }

        (*ProcessSpecificArchive<Archive>::Get()) & mpDistributedVectorFactory;

        // Paranoia: check we agree with the mesh on who owns what
        assert(mpDistributedVectorFactory == mpMesh->GetDistributedVectorFactory());
        assert(mpDistributedVectorFactory->GetLow()==mpMesh->GetDistributedVectorFactory()->GetLow());
        assert(mpDistributedVectorFactory->GetLocalOwnership()==mpMesh->GetDistributedVectorFactory()->GetLocalOwnership());
        // archive & mMeshUnarchived; Not archived since set to true when archiving constructor is called.

        // not archiving mpConductivityModifier for the time being (mechanics simulations are only use-case at the moment, and they
        // do not get archived...). mpConductivityModifier has to be reset to NULL upon load.
        mpConductivityModifier = NULL;
    }
    BOOST_SERIALIZATION_SPLIT_MEMBER()

    
    void CreateIntracellularConductivityTensor();

protected:

    AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* mpMesh;

    AbstractConductivityTensors<ELEMENT_DIM,SPACE_DIM>* mpIntracellularConductivityTensors;

    std::vector< AbstractCardiacCellInterface* > mCellsDistributed;

    std::vector< AbstractCardiacCellInterface* > mPurkinjeCellsDistributed;

    ReplicatableVector mIionicCacheReplicated;

    ReplicatableVector mPurkinjeIionicCacheReplicated;

    ReplicatableVector mIntracellularStimulusCacheReplicated;

    ReplicatableVector mPurkinjeIntracellularStimulusCacheReplicated;

    HeartConfig* mpConfig;

    DistributedVectorFactory* mpDistributedVectorFactory;

    std::string mFibreFilePathNoExtension;

    AbstractConductivityModifier<ELEMENT_DIM,SPACE_DIM>* mpConductivityModifier;

    bool mHasPurkinje;

    bool mDoCacheReplication;

    bool mMeshUnarchived;

    bool mExchangeHalos;

    std::vector<unsigned> mHaloNodes;

    std::vector< AbstractCardiacCellInterface* > mHaloCellsDistributed;

    std::map<unsigned, unsigned> mHaloGlobalToLocalIndexMap;

    std::vector<std::vector<unsigned> > mNodesToSendPerProcess;

    std::vector<std::vector<unsigned> > mNodesToReceivePerProcess;

    void CalculateHaloNodesFromNodeExchange();

    void SetUpHaloCells(AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>* pCellFactory);

public:
    AbstractCardiacTissue(AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>* pCellFactory, bool exchangeHalos=false);

    AbstractCardiacTissue(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh);

    virtual ~AbstractCardiacTissue();

    bool HasPurkinje();

    void SetCacheReplication(bool doCacheReplication);

    bool GetDoCacheReplication();

    const c_matrix<double, SPACE_DIM, SPACE_DIM>& rGetIntracellularConductivityTensor(unsigned elementIndex);

    virtual const c_matrix<double, SPACE_DIM, SPACE_DIM>& rGetExtracellularConductivityTensor(unsigned elementIndex);

    AbstractCardiacCellInterface* GetCardiacCell( unsigned globalIndex );

    AbstractCardiacCellInterface* GetPurkinjeCell( unsigned globalIndex );

    AbstractCardiacCellInterface* GetCardiacCellOrHaloCell( unsigned globalIndex );

    virtual void SolveCellSystems(Vec existingSolution, double time, double nextTime, bool updateVoltage=false);

    ReplicatableVector& rGetIionicCacheReplicated();

    ReplicatableVector& rGetIntracellularStimulusCacheReplicated();

    ReplicatableVector& rGetPurkinjeIionicCacheReplicated();

    ReplicatableVector& rGetPurkinjeIntracellularStimulusCacheReplicated();


    void UpdateCaches(unsigned globalIndex, unsigned localIndex, double nextTime);

    void UpdatePurkinjeCaches(unsigned globalIndex, unsigned localIndex, double nextTime);

    void ReplicateCaches();

    const std::vector<AbstractCardiacCellInterface*>& rGetCellsDistributed() const;

    const std::vector<AbstractCardiacCellInterface*>& rGetPurkinjeCellsDistributed() const;

    const AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pGetMesh() const;

    void SetConductivityModifier(AbstractConductivityModifier<ELEMENT_DIM,SPACE_DIM>* pModifier);

    template<class Archive>
    void SaveCardiacCells(Archive & archive, const unsigned int version) const
    {
        const std::vector<AbstractCardiacCellInterface*> & r_cells_distributed = rGetCellsDistributed();
        assert(mpDistributedVectorFactory == this->mpMesh->GetDistributedVectorFactory());
        archive & mpDistributedVectorFactory; // Needed when loading
        const unsigned num_cells = r_cells_distributed.size();
        archive & num_cells;
        for (unsigned i=0; i<num_cells; i++)
        {
            AbstractDynamicallyLoadableEntity* p_entity = dynamic_cast<AbstractDynamicallyLoadableEntity*>(r_cells_distributed[i]);
            bool is_dynamic = (p_entity != NULL);
            archive & is_dynamic;
            if (is_dynamic)
            {
#ifdef CHASTE_CAN_CHECKPOINT_DLLS
                archive & p_entity->GetLoader()->GetLoadableModulePath();
#else
                // We should have thrown an exception before this point
                NEVER_REACHED;
#endif // CHASTE_CAN_CHECKPOINT_DLLS
            }
            archive & r_cells_distributed[i];
            if (mHasPurkinje)
            {
                archive & rGetPurkinjeCellsDistributed()[i];
            }
        }
    }

    template<class Archive>
    void LoadCardiacCells(Archive & archive, const unsigned int version)
    {
        // Note that p_factory loaded from this archive might not be the same as our mesh's factory,
        // since we're loading a process-specific archive that could have been written by any process.
        // We therefore need to use p_mesh_factory to determine the partitioning in use for the resumed
        // simulation, and p_factory to determine what the original partitioning was when the simulation
        // was saved.
        DistributedVectorFactory* p_factory;
        DistributedVectorFactory* p_mesh_factory = this->mpMesh->GetDistributedVectorFactory();
        archive & p_factory;
        unsigned num_cells;
        archive & num_cells;
        if (mCellsDistributed.empty())
        {
            mCellsDistributed.resize(p_mesh_factory->GetLocalOwnership());
#ifndef NDEBUG
            // Paranoia
            for (unsigned i=0; i<mCellsDistributed.size(); i++)
            {
                assert(mCellsDistributed[i] == NULL);
            }
#endif
        }
        else
        {
            assert(mCellsDistributed.size() == p_mesh_factory->GetLocalOwnership());
        }
        if (mHasPurkinje)
        {
            if (mPurkinjeCellsDistributed.empty())
            {
                mPurkinjeCellsDistributed.resize(p_mesh_factory->GetLocalOwnership());
            }
            else
            {
                assert(mPurkinjeCellsDistributed.size() == p_mesh_factory->GetLocalOwnership());
            }
        }

        // We don't store a cell index in the archive, so need to work out what global index this tissue starts at.
        // If we have an original factory we use the original low index; otherwise we use the current low index.
        unsigned index_low = p_factory->GetOriginalFactory() ? p_factory->GetOriginalFactory()->GetLow() : p_mesh_factory->GetLow();

        // Track fake cells (which might have multiple pointers to the same object) to make sure we only delete non-local ones
        std::set<FakeBathCell*> fake_cells_non_local, fake_cells_local;

        /*
         * Historical note:
         *
         * We always do a dumb partition when we unarchive.
         *
         * When unarchive was first implemented in parallel (migration #1199) it was thought that we might want to repartition the mesh. This would be feasible and would give
         * better partitions when we move to different numbers of processes.  However it would require us to apply a new permutation to entire data structure.
         *
         * In the case where the original mesh was permuted and *copied* into the archive, we need to apply the stored permutation to the mesh but not to the archive (cells).  That
         * is, any permutation stored with the mesh can be safely ignored.  (If we also had to repartition/permute the archive, then we would be applying a double permutation to the
         * mesh and a single permutation to archive.)
         *
         */
        for (unsigned local_index=0; local_index<num_cells; local_index++)
        {
            // Figure out where this cell goes
            unsigned global_index = index_low + local_index;
            bool local = p_mesh_factory->IsGlobalIndexLocal(global_index);

            // Check if this will be a halo cell
            std::map<unsigned, unsigned>::const_iterator halo_position;
            bool halo = ((halo_position=mHaloGlobalToLocalIndexMap.find(global_index)) != mHaloGlobalToLocalIndexMap.end());
            // halo_position->second is local halo index

            bool is_dynamic;
            archive & is_dynamic;
            if (is_dynamic)
            {
#ifdef CHASTE_CAN_CHECKPOINT_DLLS
                // Ensure the shared object file for this cell model is loaded.
                // We need to do this here, rather than in the class' serialization code,
                // because that code won't be available until this is done...
                std::string shared_object_path;
                archive & shared_object_path;
                DynamicModelLoaderRegistry::Instance()->GetLoader(shared_object_path);
#else
                // Since checkpoints with dynamically loadable cells can only be
                // created on Boost>=1.37, trying to load such a checkpoint on an
                // earlier Boost would give an error when first opening the archive.
                NEVER_REACHED;
#endif // CHASTE_CAN_CHECKPOINT_DLLS
            }
            AbstractCardiacCellInterface* p_cell;
            archive & p_cell;
            AbstractCardiacCellInterface* p_purkinje_cell = NULL;
            if (mHasPurkinje)
            {
                archive & p_purkinje_cell;
            }
            // Check if it's a fake cell
            FakeBathCell* p_fake = dynamic_cast<FakeBathCell*>(p_cell);
            if (p_fake)
            {
                if (halo || local)
                {
                    fake_cells_local.insert(p_fake);
                }
                else
                {
                    fake_cells_non_local.insert(p_fake);
                }
            }
            FakeBathCell* p_fake_purkinje = dynamic_cast<FakeBathCell*>(p_purkinje_cell);
            if (p_fake_purkinje)
            {
                if (halo || local)
                {
                    fake_cells_local.insert(p_fake_purkinje);
                }
                else
                {
                    fake_cells_non_local.insert(p_fake_purkinje);
                }
            }
            // Add real cells to the local or halo vectors
            if (local)
            {
                // Note that the original local_index was relative to the archived partition (distributed vector)
                // The new_local_index is local relative to the new partition in memory
                unsigned new_local_index = global_index - p_mesh_factory->GetLow();
                assert(mCellsDistributed[new_local_index] == NULL);
                mCellsDistributed[new_local_index] = p_cell;
                if (mHasPurkinje)
                {
                    assert(mPurkinjeCellsDistributed[new_local_index] == NULL);
                    mPurkinjeCellsDistributed[new_local_index] = p_purkinje_cell;
                }
            }
            else if (halo)
            {
                assert(mHaloCellsDistributed[halo_position->second] == NULL);
                mHaloCellsDistributed[halo_position->second] = p_cell;
            }
            else
            {
                if (!p_fake)
                {
                    // Non-local real cell, so free the memory.
                    delete p_cell;
                }
                if (!p_fake_purkinje)
                {
                    // This will be NULL if there's no Purkinje, so a delete is OK.
                    delete p_purkinje_cell;
                }
            }
        }

        // Delete any unused fake cells
        for (std::set<FakeBathCell*>::iterator it = fake_cells_non_local.begin();
             it != fake_cells_non_local.end();
             ++it)
        {
            if (fake_cells_local.find(*it) == fake_cells_local.end())
            {
                delete (*it);
            }
        }
    }
};

TEMPLATED_CLASS_IS_ABSTRACT_2_UNSIGNED(AbstractCardiacTissue)

namespace boost {
namespace serialization {
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
struct version<AbstractCardiacTissue<ELEMENT_DIM, SPACE_DIM> >
{
    CHASTE_VERSION_CONTENT(3);
};
} // namespace serialization
} // namespace boost

#endif /*ABSTRACTCARDIACTISSUE_HPP_*/