AbstractCardiacTissue.hpp

/*

Copyright (c) 2005-2015, University of Oxford.
All rights reserved.

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.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*/
#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_*/