예제 #1
0
void ExtendedBidomainTissue<SPACE_DIM>::CreateExtracellularConductivityTensors()
{
    if (this->mpConfig->IsMeshProvided() && this->mpConfig->GetLoadMesh())
    {
        assert(this->mFibreFilePathNoExtension != "");
        switch (this->mpConfig->GetConductivityMedia())
        {
            case cp::media_type::Orthotropic:
            {
                mpExtracellularConductivityTensors =  new OrthotropicConductivityTensors<SPACE_DIM,SPACE_DIM>;
                FileFinder ortho_file(this->mFibreFilePathNoExtension + ".ortho", RelativeTo::AbsoluteOrCwd);
                assert(ortho_file.Exists());
                mpExtracellularConductivityTensors->SetFibreOrientationFile(ortho_file);
                break;
            }

            case cp::media_type::Axisymmetric:
            {
                mpExtracellularConductivityTensors =  new AxisymmetricConductivityTensors<SPACE_DIM,SPACE_DIM>;
                FileFinder axi_file(this->mFibreFilePathNoExtension + ".axi", RelativeTo::AbsoluteOrCwd);
                assert(axi_file.Exists());
                mpExtracellularConductivityTensors->SetFibreOrientationFile(axi_file);
                break;
            }

            case cp::media_type::NoFibreOrientation:
                mpExtracellularConductivityTensors =  new OrthotropicConductivityTensors<SPACE_DIM,SPACE_DIM>;
                break;

            default :
                NEVER_REACHED;
        }
    }
    else // no fibre orientation assumed
    {
        mpExtracellularConductivityTensors =  new OrthotropicConductivityTensors<SPACE_DIM,SPACE_DIM>;
    }

    c_vector<double, SPACE_DIM> extra_conductivities;
    this->mpConfig->GetExtracellularConductivities(extra_conductivities);

    // this definition must be here (and not inside the if statement) because SetNonConstantConductivities() will keep
    // a pointer to it and we don't want it to go out of scope before Init() is called
    unsigned num_elements = this->mpMesh->GetNumElements();
    std::vector<c_vector<double, SPACE_DIM> > hetero_extra_conductivities;

    if (this->mpConfig->GetConductivityHeterogeneitiesProvided())
    {
        try
        {
            assert(hetero_extra_conductivities.size()==0);
            //initialise with the values of teh default conductivity tensor
            hetero_extra_conductivities.resize(num_elements, extra_conductivities);
        }
        catch(std::bad_alloc &badAlloc)
        {
#define COVERAGE_IGNORE
            std::cout << "Failed to allocate std::vector of size " << num_elements << std::endl;
            PetscTools::ReplicateException(true);
            throw badAlloc;
#undef COVERAGE_IGNORE
        }
        PetscTools::ReplicateException(false);

        std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > conductivities_heterogeneity_areas;
        std::vector< c_vector<double,3> > intra_h_conductivities;
        std::vector< c_vector<double,3> > extra_h_conductivities;
        HeartConfig::Instance()->GetConductivityHeterogeneities(conductivities_heterogeneity_areas,
                                                                intra_h_conductivities,
                                                                extra_h_conductivities);
        unsigned local_element_index = 0;
        for (typename AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>::ElementIterator iter = (this->mpMesh)->GetElementIteratorBegin();
             iter != (this->mpMesh)->GetElementIteratorEnd();
             ++iter)
        {
            //unsigned element_index = iter->GetIndex();
            // if element centroid is contained in the region
            ChastePoint<SPACE_DIM> element_centroid(iter->CalculateCentroid());
            for (unsigned region_index=0; region_index< conductivities_heterogeneity_areas.size(); region_index++)
            {
                // if element centroid is contained in the region
                if ( conductivities_heterogeneity_areas[region_index]->DoesContain( element_centroid ) )
                {
                    //We don't use ublas vector assignment here, because we might be getting a subvector of a 3-vector
                    for (unsigned i=0; i<SPACE_DIM; i++)
                    {
                        hetero_extra_conductivities[local_element_index][i] = extra_h_conductivities[region_index][i];
                    }
                }
            }
            local_element_index++;
        }

        mpExtracellularConductivityTensors->SetNonConstantConductivities(&hetero_extra_conductivities);
    }
    else
    {
        mpExtracellularConductivityTensors->SetConstantConductivities(extra_conductivities);
    }
    mpExtracellularConductivityTensors->Init(this->mpMesh);
}
예제 #2
0
void ExtendedBidomainTissue<SPACE_DIM>::CreateIntracellularConductivityTensorSecondCell()
{
    HeartEventHandler::BeginEvent(HeartEventHandler::READ_MESH);
    this->mpConfig = HeartConfig::Instance();
    mpIntracellularConductivityTensorsSecondCell = new OrthotropicConductivityTensors<SPACE_DIM,SPACE_DIM>;

    // this definition must be here (and not inside the if statement) because SetNonConstantConductivities() will keep
    // a pointer to it and we don't want it to go out of scope before Init() is called
    unsigned num_elements = this->mpMesh->GetNumElements();
    std::vector<c_vector<double, SPACE_DIM> > hetero_intra_conductivities;

    c_vector<double, SPACE_DIM> intra_conductivities;
    this->mpConfig->GetIntracellularConductivities(intra_conductivities);//this one is used just for resizing

    if (this->mpConfig->GetConductivityHeterogeneitiesProvided())
    {
        try
        {
            assert(hetero_intra_conductivities.size()==0);
            hetero_intra_conductivities.resize(num_elements, intra_conductivities);
        }
        catch(std::bad_alloc &badAlloc)
        {
#define COVERAGE_IGNORE
            std::cout << "Failed to allocate std::vector of size " << num_elements << std::endl;
            PetscTools::ReplicateException(true);
            throw badAlloc;
#undef COVERAGE_IGNORE
        }
        PetscTools::ReplicateException(false);

        std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > conductivities_heterogeneity_areas;
        std::vector< c_vector<double,3> > intra_h_conductivities;
        std::vector< c_vector<double,3> > extra_h_conductivities;
        HeartConfig::Instance()->GetConductivityHeterogeneities(conductivities_heterogeneity_areas,
                                                                intra_h_conductivities,
                                                                extra_h_conductivities);
        unsigned local_element_index = 0;
        for (typename AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>::ElementIterator it = this->mpMesh->GetElementIteratorBegin();
             it != this->mpMesh->GetElementIteratorEnd();
             ++it)
        {
            //unsigned element_index = it->GetIndex();
            // if element centroid is contained in the region
            ChastePoint<SPACE_DIM> element_centroid(it->CalculateCentroid());
            for (unsigned region_index=0; region_index< conductivities_heterogeneity_areas.size(); region_index++)
            {
                if ( conductivities_heterogeneity_areas[region_index]->DoesContain(element_centroid) )
                {
                    //We don't use ublas vector assignment here, because we might be getting a subvector of a 3-vector
                    for (unsigned i=0; i<SPACE_DIM; i++)
                    {
                        hetero_intra_conductivities[local_element_index][i] = intra_h_conductivities[region_index][i];
                    }
                }
            }
            local_element_index++;
        }

        mpIntracellularConductivityTensorsSecondCell->SetNonConstantConductivities(&hetero_intra_conductivities);
    }
    else
    {
        mpIntracellularConductivityTensorsSecondCell->SetConstantConductivities(mIntracellularConductivitiesSecondCell);
    }

    mpIntracellularConductivityTensorsSecondCell->Init(this->mpMesh);
    HeartEventHandler::EndEvent(HeartEventHandler::READ_MESH);
}