void TestExtendedTissueHeterogeneousGgap3D() throw (Exception)
{
HeartConfig::Instance()->Reset();
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/cube_2mm_12_elements");
TetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
std::vector<boost::shared_ptr<AbstractChasteRegion<3> > > heterogeneity_areas;
std::vector<double> Ggap_values;
//first cuboid include node 0
ChastePoint<3> cornerA(-1, -1, 0);
ChastePoint<3> cornerB(0.001, 0.001, 0.001);
boost::shared_ptr<ChasteCuboid<3> > p_cuboid_1(new ChasteCuboid<3>(cornerA, cornerB));
heterogeneity_areas.push_back(p_cuboid_1);
//second cuboid include node 6
ChastePoint<3> cornerC(0.199, 0.199, 0.199);
ChastePoint<3> cornerD(0.25, 0.25, 0.25);
boost::shared_ptr<ChasteCuboid<3> > p_cuboid_2(new ChasteCuboid<3>(cornerC, cornerD));
ChasteCuboid<3> cuboid_2(cornerC, cornerD);
heterogeneity_areas.push_back(p_cuboid_2);
//within the first area
Ggap_values.push_back(143.0);
//within the second area
Ggap_values.push_back(9143.0);
//elsewhere
double isotropic_ggap=586.0;
StimulatedCellFactory stimulated_cell_factory;
UnStimulatedCellFactory unstimulated_cell_factory;
ExtracellularStimulusFactory extracellular_stimulus_factory;
stimulated_cell_factory.SetMesh(&mesh);
unstimulated_cell_factory.SetMesh(&mesh);
extracellular_stimulus_factory.SetMesh(&mesh);
ExtendedBidomainTissue<3> extended_bidomain_tissue( &stimulated_cell_factory, &unstimulated_cell_factory, &extracellular_stimulus_factory);
extended_bidomain_tissue.SetGGap(isotropic_ggap);//this is what the problem class does first
extended_bidomain_tissue.SetGgapHeterogeneities(heterogeneity_areas, Ggap_values);
extended_bidomain_tissue.CreateGGapConductivities();
unsigned probe_node_1 = 0u;
unsigned probe_node_2 = 6u;
unsigned probe_node_3 = 5u;
const std::vector<unsigned>& r_permutation = mesh.rGetNodePermutation();
if (!r_permutation.empty())
{
probe_node_1 = r_permutation[0u];//within first cuboid
probe_node_2 = r_permutation[6u];//within second cuboid
probe_node_3 = r_permutation[5u];//elsewhere
}
Vec vector = mesh.GetDistributedVectorFactory()->CreateVec();
DistributedVector dist_solution = mesh.GetDistributedVectorFactory()->CreateDistributedVector(vector);
for (DistributedVector::Iterator index = dist_solution.Begin();
index != dist_solution.End();
++index)
{
extended_bidomain_tissue.UpdateAdditionalCaches(index.Global, index.Local, 2.0);
}
extended_bidomain_tissue.ReplicateAdditionalCaches();
//Ggap
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetGgapCacheReplicated()[probe_node_1],143.0);//within first cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetGgapCacheReplicated()[probe_node_2],9143.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetGgapCacheReplicated()[probe_node_3],586.0);//elsewhere
PetscTools::Destroy(vector);
}
/**This test checks heterogeneous conductivities*/
void TestExtendedTissueHeterogeneous3D() throw (Exception)
{
HeartConfig::Instance()->Reset();
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/cube_2mm_12_elements");
TetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
std::vector<ChasteCuboid<3> > heterogeneity_area;
std::vector< c_vector<double,3> > intra_conductivities;
std::vector< c_vector<double,3> > extra_conductivities;
//first cuboid include element 0
ChastePoint<3> cornerA(-1, -1, 0);
ChastePoint<3> cornerB(0.1, 0.2, 0.2);
ChasteCuboid<3> cuboid_1(cornerA, cornerB);
heterogeneity_area.push_back(cuboid_1);
//second cuboid include element 4
ChastePoint<3> cornerC(0.11, 0.0, 0);
ChastePoint<3> cornerD(0.2, 0.11, 0.2);
ChasteCuboid<3> cuboid_2(cornerC, cornerD);
heterogeneity_area.push_back(cuboid_2);
//within the first area
intra_conductivities.push_back( Create_c_vector(1.0, 2.0, 3.0) );
extra_conductivities.push_back( Create_c_vector(51.0, 52.0, 53.0) );
//within the second area
intra_conductivities.push_back( Create_c_vector(11.0, 22.0, 33.0) );
extra_conductivities.push_back( Create_c_vector(151.0, 152.0, 153.0) );
HeartConfig::Instance()->SetConductivityHeterogeneities(heterogeneity_area, intra_conductivities, extra_conductivities);
//elsewhere
double isotropic_intra_conductivity=15.0;
double isotropic_extra_conductivity=65.0;
HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(isotropic_intra_conductivity, isotropic_intra_conductivity, isotropic_intra_conductivity));
HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(isotropic_extra_conductivity, isotropic_extra_conductivity, isotropic_extra_conductivity));
StimulatedCellFactory stimulated_cell_factory;
UnStimulatedCellFactory unstimulated_cell_factory;
ExtracellularStimulusFactory extracellular_stimulus_factory;
stimulated_cell_factory.SetMesh(&mesh);
unstimulated_cell_factory.SetMesh(&mesh);
extracellular_stimulus_factory.SetMesh(&mesh);
ExtendedBidomainTissue<3> extended_bidomain_tissue( &stimulated_cell_factory, &unstimulated_cell_factory, &extracellular_stimulus_factory);
extended_bidomain_tissue.SetIntracellularConductivitiesSecondCell(Create_c_vector(isotropic_intra_conductivity, isotropic_intra_conductivity, isotropic_intra_conductivity));
extended_bidomain_tissue.CreateIntracellularConductivityTensorSecondCell();
//first cell
// TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensor(0u)(0,0),1.0);//within first cuboid
//Line above commented due to curious problem with IntelProduction interprocedural optimisation
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensor(4u)(0,0),11.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensor(4u)(1,1),22.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensor(8u)(0,0),15.0);//elsewhere, e.g. element 8
//second cell, should be the same as first cell
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensorSecondCell(0u)(0,0),1.0);//within first cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensorSecondCell(4u)(0,0),11.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensorSecondCell(4u)(1,1),22.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensorSecondCell(8u)(0,0),15.0);//elsewhere, e.g. element 8
//sigma_e
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetExtracellularConductivityTensor(0u)(0,0),51.0);//within first cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetExtracellularConductivityTensor(4u)(0,0),151.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetExtracellularConductivityTensor(4u)(1,1),152.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetExtracellularConductivityTensor(8u)(0,0),65.0);//elsewhere, e.g. element 8
}
void TestExtendedTissueHeterogeneousConductivities2D() throw (Exception)
{
HeartConfig::Instance()->Reset();
TrianglesMeshReader<2,2> mesh_reader("mesh/test/data/square_4_elements");
TetrahedralMesh<2,2> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
//HeartConfig setup needs to be in 3D anyway (hardcoded in HeartConfig).
std::vector<ChasteCuboid<3> > heterogeneity_area;
std::vector< c_vector<double,3> > intra_conductivities;
std::vector< c_vector<double,3> > extra_conductivities;
//first cuboid includes element 0
ChastePoint<3> cornerA(-1, -1,-1);
ChastePoint<3> cornerB(0.48, 2.0, 0.48);
ChasteCuboid<3> cuboid_1(cornerA, cornerB);
heterogeneity_area.push_back(cuboid_1);
//second cuboid includes element 2
ChastePoint<3> cornerC(0.52, -1, 0.52);
ChastePoint<3> cornerD(2, 2, 2);
ChasteCuboid<3> cuboid_2(cornerC, cornerD);
heterogeneity_area.push_back(cuboid_2);
//within the first area
intra_conductivities.push_back( Create_c_vector(1.0, 2.0, 3.0) );
extra_conductivities.push_back( Create_c_vector(51.0, 52.0, 53.0) );
//within the second area
intra_conductivities.push_back( Create_c_vector(11.0, 22.0, 33.0) );
extra_conductivities.push_back( Create_c_vector(151.0, 152.0, 153.0) );
HeartConfig::Instance()->SetConductivityHeterogeneities(heterogeneity_area, intra_conductivities, extra_conductivities);
//elsewhere
double isotropic_intra_conductivity=15.0;
double isotropic_extra_conductivity=65.0;
HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(isotropic_intra_conductivity, isotropic_intra_conductivity, isotropic_intra_conductivity));
HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(isotropic_extra_conductivity, isotropic_extra_conductivity, isotropic_extra_conductivity));
PlaneStimulusCellFactory<CellLuoRudy1991FromCellML, 2> cell_factory_1;
PlaneStimulusCellFactory<CellLuoRudy1991FromCellML, 2> cell_factory_2;
StimulusFactory2D extracellular_stimulus_factory;
cell_factory_1.SetMesh(&mesh);
cell_factory_2.SetMesh(&mesh);
extracellular_stimulus_factory.SetMesh(&mesh);
//2D tissue
ExtendedBidomainTissue<2> extended_bidomain_tissue( &cell_factory_1, &cell_factory_2, &extracellular_stimulus_factory);
// Do conductivity modifier here too (for coverage)
SimpleConductivityModifier conductivity_modifier;
extended_bidomain_tissue.SetConductivityModifier( &conductivity_modifier );
extended_bidomain_tissue.SetIntracellularConductivitiesSecondCell(Create_c_vector(isotropic_intra_conductivity, isotropic_intra_conductivity));
extended_bidomain_tissue.CreateIntracellularConductivityTensorSecondCell();
//first cell
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensor(0u)(0,0),1.0);//within first cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensor(1u)(0,0),30.0);//within no cuboid (modified from 15 to 30!)
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensor(2u)(1,1),22.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensor(3u)(0,0),15.0);//within no cuboid
//second cell, should be the same as first cell
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensorSecondCell(0u)(0,0),1.0);//within first cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensorSecondCell(1u)(0,0),30.0);//within no cuboid (modified from 15 to 30!)
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensorSecondCell(2u)(1,1),22.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetIntracellularConductivityTensorSecondCell(3u)(0,0),15.0);//within no cuboid
//sigma_e
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetExtracellularConductivityTensor(0u)(0,0),51.0);//within first cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetExtracellularConductivityTensor(1u)(0,0),130.0);//within no cuboid (modified from 65 to 130!)
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetExtracellularConductivityTensor(2u)(1,1),152.0);//within second cuboid
TS_ASSERT_EQUALS(extended_bidomain_tissue.rGetExtracellularConductivityTensor(3u)(0,0),65.0);//within no cuboid
}
void TestBidomainTissueWithHeterogeneousConductivitiesDistributed() throw (Exception)
{
HeartConfig::Instance()->Reset();
// This call is required to set the appropriate conductivity media and to make sure that
// HeartConfig knows the mesh filename despite we use our own mesh reader.
HeartConfig::Instance()->SetMeshFileName("mesh/test/data/cube_2mm_12_elements", cp::media_type::NoFibreOrientation);
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/cube_2mm_12_elements");
// METIS_LIBRARY partition ensures that we have never own all the elements (even when there are as few as 2 processes)
// DUMB and PARMETIS_LIBRARY may allow single process to see all the elements because it's a very small mesh
DistributedTetrahedralMesh<3,3> mesh(DistributedTetrahedralMeshPartitionType::METIS_LIBRARY);
mesh.ConstructFromMeshReader(mesh_reader);
// Check that if we're in parallel no single process owns every element (to ensure that the conductivities
// really are distributed).
if (PetscTools::IsParallel())
{
TS_ASSERT_DIFFERS( mesh.GetNumElements(), mesh.GetNumLocalElements() );
}
std::vector<ChasteCuboid<3> > heterogeneity_area;
std::vector< c_vector<double,3> > intra_conductivities;
std::vector< c_vector<double,3> > extra_conductivities;
//first cuboid include element 0
ChastePoint<3> cornerA(-1, -1, 0);
ChastePoint<3> cornerB(0.1, 0.2, 0.2);
ChasteCuboid<3> cuboid_1(cornerA, cornerB);
heterogeneity_area.push_back(cuboid_1);
//second cuboid include element 4
ChastePoint<3> cornerC(0.11, 0.0, 0);
ChastePoint<3> cornerD(0.2, 0.11, 0.2);
ChasteCuboid<3> cuboid_2(cornerC, cornerD);
heterogeneity_area.push_back(cuboid_2);
//within the first area
intra_conductivities.push_back( Create_c_vector(1.0, 2.0, 3.0) );
extra_conductivities.push_back( Create_c_vector(51.0, 52.0, 53.0) );
//within the second area
intra_conductivities.push_back( Create_c_vector(11.0, 22.0, 33.0) );
extra_conductivities.push_back( Create_c_vector(151.0, 152.0, 153.0) );
HeartConfig::Instance()->SetConductivityHeterogeneities(heterogeneity_area, intra_conductivities, extra_conductivities);
//elsewhere
double isotropic_intra_conductivity=15.0;
double isotropic_extra_conductivity=65.0;
HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(isotropic_intra_conductivity, isotropic_intra_conductivity, isotropic_intra_conductivity));
HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(isotropic_extra_conductivity, isotropic_extra_conductivity, isotropic_extra_conductivity));
PlaneStimulusCellFactory<CellLuoRudy1991FromCellML,3> cell_factory_for_het;
cell_factory_for_het.SetMesh(&mesh);
//CreateIntracellularConductivityTensor called in the constructor
BidomainTissue<3> bidomain_tissue( &cell_factory_for_het );
if (mesh.CalculateDesignatedOwnershipOfElement(0u))
{
TS_ASSERT_EQUALS(bidomain_tissue.rGetIntracellularConductivityTensor(0u)(0,0),1.0);//within first cuboid
TS_ASSERT_EQUALS(bidomain_tissue.rGetExtracellularConductivityTensor(0u)(0,0),51.0);//within first cuboid
}
if (mesh.CalculateDesignatedOwnershipOfElement(4u))
{
TS_ASSERT_EQUALS(bidomain_tissue.rGetIntracellularConductivityTensor(4u)(0,0),11.0);//within second cuboid
TS_ASSERT_EQUALS(bidomain_tissue.rGetIntracellularConductivityTensor(4u)(1,1),22.0);//within second cuboid
TS_ASSERT_EQUALS(bidomain_tissue.rGetExtracellularConductivityTensor(4u)(0,0),151.0);//within second cuboid
TS_ASSERT_EQUALS(bidomain_tissue.rGetExtracellularConductivityTensor(4u)(1,1),152.0);//within second cuboid
}
if (mesh.CalculateDesignatedOwnershipOfElement(8u))
{
TS_ASSERT_EQUALS(bidomain_tissue.rGetIntracellularConductivityTensor(8u)(0,0),15.0);//elsewhere, e.g. element 8
TS_ASSERT_EQUALS(bidomain_tissue.rGetExtracellularConductivityTensor(8u)(0,0),65.0);//elsewhere, e.g. element 8
}
}
