ExtendedBidomainTissue.hpp

/*

Copyright (c) 2005-2012, 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 EXTENDEDBIDOMAINTISSUE_HPP_
#define EXTENDEDBIDOMAINTISSUE_HPP_

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

#include <vector>
#include <boost/numeric/ublas/matrix.hpp>

#include "AbstractStimulusFunction.hpp"
#include "AbstractStimulusFactory.hpp"
#include "AbstractConductivityTensors.hpp"

#include "AbstractCardiacTissue.hpp"

template <unsigned SPACE_DIM>
class ExtendedBidomainTissue : public virtual AbstractCardiacTissue<SPACE_DIM>
{
private:
    friend class TestExtendedBidomainTissue; // for testing.

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCardiacTissue<SPACE_DIM> >(*this);
        // Conductivity tensors are dealt with by HeartConfig, and the caches get regenerated.

        archive & mAmFirstCell;
        archive & mAmSecondCell;
        archive & mAmGap;
        archive & mCmFirstCell;
        archive & mCmSecondCell;
        archive & mGGap;
        archive & mUserSuppliedExtracellularStimulus;
    }

    AbstractConductivityTensors<SPACE_DIM, SPACE_DIM> *mpIntracellularConductivityTensorsSecondCell;

    c_vector<double, SPACE_DIM>  mIntracellularConductivitiesSecondCell;


    AbstractConductivityTensors<SPACE_DIM, SPACE_DIM> *mpExtracellularConductivityTensors;

    ReplicatableVector mExtracellularStimulusCacheReplicated;

    ReplicatableVector mGgapCacheReplicated;

    ReplicatableVector mIionicCacheReplicatedSecondCell;

    ReplicatableVector mIntracellularStimulusCacheReplicatedSecondCell;

    std::vector< AbstractCardiacCellInterface* > mCellsDistributedSecondCell;

    std::vector<boost::shared_ptr<AbstractStimulusFunction> > mExtracellularStimuliDistributed;

    std::vector<double> mGgapDistributed;

    double mAmFirstCell;
    double mAmSecondCell;
    double mAmGap;
    double mCmFirstCell;
    double mCmSecondCell;
    double mGGap;

    bool mUserSuppliedExtracellularStimulus;

    void CreateExtracellularConductivityTensors();

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

    void ReplicateAdditionalCaches();

    std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > mGgapHeterogeneityRegions;
    std::vector<double> mGgapValues;

public:

    ExtendedBidomainTissue(AbstractCardiacCellFactory<SPACE_DIM>* pCellFactory, AbstractCardiacCellFactory<SPACE_DIM>* pCellFactorySecondCell, AbstractStimulusFactory<SPACE_DIM>* pExtracellularStimulusFactory);

    ExtendedBidomainTissue(std::vector<AbstractCardiacCellInterface*> & rCellsDistributed, std::vector<AbstractCardiacCellInterface*> & rSecondCellsDistributed, std::vector<boost::shared_ptr<AbstractStimulusFunction> > & rExtraStimuliDistributed, std::vector<double>& rGgapsDistributed, AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* pMesh, c_vector<double, SPACE_DIM>  intracellularConductivitiesSecondCell);

    ~ExtendedBidomainTissue();

    void SetIntracellularConductivitiesSecondCell(c_vector<double, SPACE_DIM> conductivities);

    AbstractCardiacCellInterface* GetCardiacSecondCell( unsigned globalIndex );


    boost::shared_ptr<AbstractStimulusFunction> GetExtracellularStimulus( unsigned globalIndex );

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

    const std::vector<double>& rGetGapsDistributed() const;


    const std::vector<boost::shared_ptr<AbstractStimulusFunction> >& rGetExtracellularStimulusDistributed() const;


    c_vector<double, SPACE_DIM> GetIntracellularConductivitiesSecondCell() const;

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

    void CreateIntracellularConductivityTensorSecondCell();

    void SetGgapHeterogeneities ( std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > & rGgapHeterogeneityRegions, std::vector<double> rGgapValues);

    void CreateGGapConductivities();

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

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


     ReplicatableVector& rGetIionicCacheReplicatedSecondCell();

     ReplicatableVector& rGetIntracellularStimulusCacheReplicatedSecondCell();

     ReplicatableVector& rGetExtracellularStimulusCacheReplicated();

     ReplicatableVector& rGetGgapCacheReplicated();

     double GetAmFirstCell();

     double GetAmSecondCell();

     double GetAmGap();

     double GetCmFirstCell();

     double GetCmSecondCell();

     double GetGGap();

     void SetAmFirstCell(double value);

     void SetAmSecondCell(double value);

     void SetAmGap(double value);

     void SetCmFirstCell(double value);

     void SetCmSecondCell(double value);

     void SetGGap(double value);

     bool HasTheUserSuppliedExtracellularStimulus();

     void SetUserSuppliedExtracellularStimulus(bool flag);


     template<class Archive>
     void SaveExtendedBidomainCells(Archive & archive, const unsigned int version) const
     {
         Archive& r_archive = *ProcessSpecificArchive<Archive>::Get();
         const std::vector<AbstractCardiacCellInterface*> & r_cells_distributed = this->rGetCellsDistributed();
         const std::vector<AbstractCardiacCellInterface*> & r_cells_distributed_second_cell = rGetSecondCellsDistributed();
         const std::vector<double> & r_ggaps_distributed = rGetGapsDistributed();

         r_archive & this->mpDistributedVectorFactory; // Needed when loading
         const unsigned num_cells = r_cells_distributed.size();
         r_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);
             r_archive & is_dynamic;
             if (is_dynamic)
             {
 #ifdef CHASTE_CAN_CHECKPOINT_DLLS
                 r_archive & p_entity->GetLoader()->GetLoadableModulePath();
 #else
                 // We should have thrown an exception before this point
                 NEVER_REACHED;
 #endif // CHASTE_CAN_CHECKPOINT_DLLS
             }
             r_archive & r_cells_distributed[i];
             r_archive & r_cells_distributed_second_cell[i];
             r_archive & r_ggaps_distributed[i];
         }
     }

     template<class Archive>
     static void LoadExtendedBidomainCells(Archive & archive, const unsigned int version,
                                  std::vector<AbstractCardiacCellInterface*>& rCells,
                                  std::vector<AbstractCardiacCellInterface*>& rSecondCells,
                                  std::vector<double>& rGgaps,
                                  AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* pMesh)
     {
         assert(pMesh!=NULL);
         DistributedVectorFactory* p_factory;
         archive & p_factory;
         unsigned num_cells;
         archive & num_cells;
         rCells.resize(p_factory->GetLocalOwnership());
         rSecondCells.resize(p_factory->GetLocalOwnership());
         rGgaps.resize(p_factory->GetLocalOwnership());
 #ifndef NDEBUG
         // Paranoia
         assert(rCells.size() == rSecondCells.size());
         for (unsigned i=0; i<rCells.size(); i++)
         {
             assert(rCells[i] == NULL);
             assert(rSecondCells[i] == NULL);
         }
 #endif

         // We don't store a cell index in the archive, so need to work out what global
         // index this tissue starts up.  If we're migrating (so 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_factory->GetLow();

         for (unsigned local_index=0; local_index<num_cells; local_index++)
         {
             unsigned global_index = index_low + local_index;
             unsigned new_local_index = global_index - p_factory->GetLow();
             bool local = p_factory->IsGlobalIndexLocal(global_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;
             AbstractCardiacCellInterface* p_second_cell;
             double g_gap;
             archive & p_cell;
             archive & p_second_cell;
             archive & g_gap;
             if (local)
             {
                 rCells[new_local_index] = p_cell; // Add to local cells
                 rSecondCells[new_local_index] = p_second_cell;
                 rGgaps[new_local_index] = g_gap;
             }
             else
             {
                 //not sure how to cover this, we are already looping over local cells...
                 NEVER_REACHED;
                // Non-local real cell, so free the memory.
                // delete p_cell;
                // delete p_second_cell;
             }
         }
     }

     template<class Archive>
     void SaveExtracellularStimulus(Archive & archive, const unsigned int version) const
     {
         Archive& r_archive = *ProcessSpecificArchive<Archive>::Get();
         const std::vector<boost::shared_ptr<AbstractStimulusFunction> > & r_stimulus_distributed = rGetExtracellularStimulusDistributed();
         r_archive & this->mpDistributedVectorFactory; // Needed when loading
         const unsigned num_cells = r_stimulus_distributed.size();
         r_archive & num_cells;
         for (unsigned i=0; i<num_cells; i++)
         {
             r_archive & r_stimulus_distributed[i];
         }
     }

     template<class Archive>
     void LoadExtracellularStimulus(Archive & archive, const unsigned int version,
                                               std::vector<boost::shared_ptr<AbstractStimulusFunction> >& rStimuli,
                                               AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* pMesh)
     {

        DistributedVectorFactory* p_factory;
        archive & p_factory;
        unsigned num_cells;
        archive & num_cells;
        rStimuli.resize(p_factory->GetLocalOwnership());
#ifndef NDEBUG
          // Paranoia
          for (unsigned i=0; i<rStimuli.size(); i++)
          {
              assert(rStimuli[i] == NULL);
          }
#endif

        // We don't store a cell index in the archive, so need to work out what global
        // index this tissue starts up.  If we're migrating (so 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_factory->GetLow();

        assert(pMesh!=NULL);
        //unsigned num_cells = pMesh->GetNumNodes();
        for (unsigned local_index=0; local_index<num_cells; local_index++)
        {
          unsigned global_index = index_low + local_index;

          unsigned new_local_index = global_index - p_factory->GetLow();
          bool local = p_factory->IsGlobalIndexLocal(global_index);

          boost::shared_ptr<AbstractStimulusFunction> p_stim;
          archive & p_stim;//get from archive

          if (local)
          {
              rStimuli[new_local_index] = p_stim; // Add stimulus to local cells
          }
          //otherwise we should delete, but I think shared pointers delete themselves?
        }
    }
};

 // Declare identifier for the serializer
 #include "SerializationExportWrapper.hpp"
 EXPORT_TEMPLATE_CLASS_SAME_DIMS(ExtendedBidomainTissue)

 namespace boost
 {
 namespace serialization
 {

 template<class Archive, unsigned SPACE_DIM>
 inline void save_construct_data(
     Archive & ar, const ExtendedBidomainTissue<SPACE_DIM> * t, const unsigned int file_version)
 {
     //archive the conductivity tensor of the second cell (which may not be dealt with by heartconfig)
     c_vector<double, SPACE_DIM>  intracellular_conductivities_second_cell = t->GetIntracellularConductivitiesSecondCell();
     //note that simple: ar & intracellular_conductivities_second_cell may not be liked by some boost versions
     for (unsigned i = 0; i < SPACE_DIM; i++)
     {
         ar & intracellular_conductivities_second_cell(i);
     }

     const AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* p_mesh = t->pGetMesh();
     ar & p_mesh;

     // Don't use the std::vector serialization for cardiac cells, so that we can load them
     // more cleverly when migrating checkpoints.
     t->SaveExtendedBidomainCells(ar, file_version);
     t->SaveExtracellularStimulus(ar, file_version);

     // Creation of conductivity tensors are called by constructor and uses HeartConfig. So make sure that it is
     // archived too (needs doing before construction so appears here instead of usual archive location).
     HeartConfig* p_config = HeartConfig::Instance();
     ar & *p_config;
     ar & p_config;
 }

 template<class Archive, unsigned SPACE_DIM>
 inline void load_construct_data(
     Archive & ar, ExtendedBidomainTissue<SPACE_DIM> * t, const unsigned int file_version)
 {
     //Load conductivities of the conductivity of the second cell.
     c_vector<double, SPACE_DIM>  intra_cond_second_cell;
     //note that simple: ar & intra_cond_second_cell may not be liked by some boost versions
     for (unsigned i = 0; i < SPACE_DIM; i++)
     {
         double cond;
         ar & cond;
         intra_cond_second_cell(i) = cond;
     }


     std::vector<AbstractCardiacCellInterface*> cells_distributed;
     std::vector<AbstractCardiacCellInterface*> cells_distributed_second_cell;
     std::vector<boost::shared_ptr<AbstractStimulusFunction> > extra_stim;
     std::vector<double> g_gaps;
     AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* p_mesh;
     ar & p_mesh;

     // Load only the cells we actually own
     t->LoadExtendedBidomainCells(
             *ProcessSpecificArchive<Archive>::Get(), file_version, cells_distributed, cells_distributed_second_cell, g_gaps, p_mesh);

     t->LoadExtracellularStimulus(
             *ProcessSpecificArchive<Archive>::Get(), file_version, extra_stim, p_mesh);

     // CreateIntracellularConductivityTensor() is called by AbstractCardiacTissue constructor and uses HeartConfig.
     // (as does CreateExtracellularConductivityTensor). So make sure that it is
     // archived too (needs doing before construction so appears here instead of usual archive location).
     HeartConfig* p_config = HeartConfig::Instance();
     ar & *p_config;
     ar & p_config;

     ::new(t)ExtendedBidomainTissue<SPACE_DIM>(cells_distributed, cells_distributed_second_cell, extra_stim, g_gaps, p_mesh, intra_cond_second_cell);
 }
 }
 } // namespace ...



#endif /*EXTENDEDBIDOMAINTISSUE_HPP_*/