/*
* Cellular birth has been tested in TestCaSingleCellWithBirth for one cell per lattice site.
* This test adds to the above by further testing cellular birth considering multiple cells per lattice site.
* A two-lattice mesh was created and only one lattice had free space to add one daughter cell.
*/
void TestMultipleCellsPerLatticeSiteWithBirth() throw (Exception)
{
EXIT_IF_PARALLEL;
// Create a simple 2D PottsMesh
PottsMeshGenerator<2> generator(2, 0, 0, 1, 0, 0);
PottsMesh<2>* p_mesh = generator.GetMesh();
// Create cells
std::vector<CellPtr> cells;
MAKE_PTR(StemCellProliferativeType, p_stem_type);
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 2> cells_generator;
cells_generator.GenerateBasicRandom(cells, 3, p_stem_type);
// Specify where cells lie
std::vector<unsigned> location_indices;
location_indices.push_back(0);
location_indices.push_back(0);
location_indices.push_back(1);
// Create cell population
CaBasedCellPopulation<2> cell_population(*p_mesh, cells, location_indices, 2);
// Set up cell-based simulation
OnLatticeSimulation<2> simulator(cell_population);
std::string output_directory = "TestMultipleCellsPerLatticeSiteWithBirth";
simulator.SetOutputDirectory(output_directory);
simulator.SetDt(0.1);
simulator.SetEndTime(40);
// Add update rule
MAKE_PTR(DiffusionCaUpdateRule<2u>, p_diffusion_update_rule);
p_diffusion_update_rule->SetDiffusionParameter(0.5);
simulator.AddCaUpdateRule(p_diffusion_update_rule);
// Run simulation
simulator.Solve();
// Check the number of cells
TS_ASSERT_EQUALS(simulator.rGetCellPopulation().GetNumRealCells(), 4u);
// Test no deaths and some births
TS_ASSERT_EQUALS(simulator.GetNumBirths(), 1u);
TS_ASSERT_EQUALS(simulator.GetNumDeaths(), 0u);
#ifdef CHASTE_VTK
// Test that VTK writer has produced a file
OutputFileHandler output_file_handler(output_directory, false);
std::string results_dir = output_file_handler.GetOutputDirectoryFullPath();
// Initial condition file
FileFinder vtk_file(results_dir + "results_from_time_0/results_0.vtu", RelativeTo::Absolute);
TS_ASSERT(vtk_file.Exists());
// Final file
FileFinder vtk_file2(results_dir + "results_from_time_0/results_400.vtu", RelativeTo::Absolute);
TS_ASSERT(vtk_file2.Exists());
#endif //CHASTE_VTK
}
void TestPottsSpheroidCellSorting() throw (Exception)
{
EXIT_IF_PARALLEL; // Potts simulations don't work in parallel because they depend on NodesOnlyMesh for writing.
// Create a simple 3D PottsMesh
unsigned domain_size = 10;
unsigned element_number = 4;
unsigned element_size = 2;
PottsMeshGenerator<3> generator(domain_size, element_number, element_size, domain_size, element_number, element_size, domain_size, element_number, element_size);
PottsMesh<3>* p_mesh = generator.GetMesh();
// Create cells
std::vector<CellPtr> cells;
MAKE_PTR(DifferentiatedCellProliferativeType, p_diff_type);
CellsGenerator<FixedDurationGenerationBasedCellCycleModel, 3> cells_generator;
cells_generator.GenerateBasicRandom(cells, p_mesh->GetNumElements(), p_diff_type);
// Randomly label some cells
boost::shared_ptr<AbstractCellProperty> p_label(CellPropertyRegistry::Instance()->Get<CellLabel>());
RandomlyLabelCells(cells, p_label, 0.5);
// Create cell population
PottsBasedCellPopulation<3> cell_population(*p_mesh, cells);
cell_population.AddCellPopulationCountWriter<CellMutationStatesCountWriter>(); // So outputs the labelled cells
// Set up cell-based simulation
OnLatticeSimulation<3> simulator(cell_population);
simulator.SetOutputDirectory("TestPotts3DCellSorting");
simulator.SetDt(0.1);
simulator.SetEndTime(1.0);
// Create update rules and pass to the simulation
MAKE_PTR(VolumeConstraintPottsUpdateRule<3>, p_volume_constraint_update_rule);
p_volume_constraint_update_rule->SetMatureCellTargetVolume(element_size*element_size*element_size);
p_volume_constraint_update_rule->SetDeformationEnergyParameter(0.2);
simulator.AddPottsUpdateRule(p_volume_constraint_update_rule);
MAKE_PTR(DifferentialAdhesionPottsUpdateRule<3>, p_differential_adhesion_update_rule);
p_differential_adhesion_update_rule->SetLabelledCellLabelledCellAdhesionEnergyParameter(0.16);
p_differential_adhesion_update_rule->SetLabelledCellCellAdhesionEnergyParameter(0.11);
p_differential_adhesion_update_rule->SetCellCellAdhesionEnergyParameter(0.02);
p_differential_adhesion_update_rule->SetLabelledCellBoundaryAdhesionEnergyParameter(0.16);
p_differential_adhesion_update_rule->SetCellBoundaryAdhesionEnergyParameter(0.16);
simulator.AddPottsUpdateRule(p_differential_adhesion_update_rule);
// Run simulation
simulator.Solve();
// Check that the same number of cells
TS_ASSERT_EQUALS(simulator.rGetCellPopulation().GetNumRealCells(), 64u);
// Test no births or deaths
TS_ASSERT_EQUALS(simulator.GetNumBirths(), 0u);
TS_ASSERT_EQUALS(simulator.GetNumDeaths(), 0u);
#ifdef CHASTE_VTK
// Test that VTK writer has produced some files
OutputFileHandler handler("TestPotts3DCellSorting", false);
std::string results_dir = handler.GetOutputDirectoryFullPath();
// Initial condition file
FileFinder vtk_file(results_dir + "results_from_time_0/results_0.vtu", RelativeTo::Absolute);
TS_ASSERT(vtk_file.Exists());
// Final file
FileFinder vtk_file2(results_dir + "results_from_time_0/results_10.vtu", RelativeTo::Absolute);
TS_ASSERT(vtk_file2.Exists());
// Check that the second VTK file for Potts specific data (element IDs)
VtkMeshReader<3,3> vtk_reader(results_dir + "results_from_time_0/results_10.vtu");
std::vector<double> cell_types;
vtk_reader.GetPointData("Cell types", cell_types);
TS_ASSERT_EQUALS(cell_types.size(), 1000u);
// The cell types are between -1 and 5. Check the maximum
TS_ASSERT_DELTA(*max_element(cell_types.begin(), cell_types.end()), 5.0, 1e-12);
std::vector<double> cell_ids;
vtk_reader.GetPointData("Cell IDs", cell_ids);
// Prior to release 3.2 this was called "Element index".
// It is changed to cell_id as this is preferable for VTK output.
TS_ASSERT_EQUALS(cell_ids.size(), 1000u);
TS_ASSERT_DELTA(*max_element(cell_ids.begin(), cell_ids.end()), 63.0, 1e-12);
#endif //CHASTE_VTK
}
