// This test covers the case when the hdf5 file contains 3 variables (e.g., after solving a problem with PROBLEM_DIM=3)
void TestMeshalyzerConversion3Variables() throw(Exception)
{
/*
* Firstly, copy the .h5 file to CHASTE_TEST_OUTPUT/TestHdf5ToMeshalyzerConverter,
* as that is where the reader reads from.
*/
std::string output_folder("TestHdf5Converters_TestMeshalyzerConversion3Variables");
CopyToTestOutputDirectory("heart/test/data/three_variables/3_vars.h5", output_folder);
TrianglesMeshReader<1,1> mesh_reader("mesh/test/data/1D_0_to_1_100_elements");
TetrahedralMesh<1,1> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
// Convert
Hdf5ToMeshalyzerConverter<1,1> converter(FileFinder(output_folder, RelativeTo::ChasteTestOutput),
"3_vars", &mesh, true);
// Compare the first voltage file
std::string test_output_directory = OutputFileHandler::GetChasteTestOutputDirectory();
NumericFileComparison(test_output_directory + output_folder + "/output/3_vars_Vm_1.dat",
"heart/test/data/three_variables/extended_bidomain_Vm_1.dat").CompareFiles();
// Compare the second voltage file
NumericFileComparison(test_output_directory + output_folder +"/output/3_vars_Vm_2.dat",
"heart/test/data/three_variables/extended_bidomain_Vm_2.dat").CompareFiles();
// Compare the Phi_e file
NumericFileComparison(test_output_directory + output_folder + "/output/3_vars_Phi_e.dat",
"heart/test/data/three_variables/extended_bidomain_Phi_e.dat").CompareFiles();
// Compare the time information file
FileComparison(test_output_directory + output_folder + "/output/3_vars_times.info",
"heart/test/data/three_variables/extended_bidomain_times.info").CompareFiles();
}
void TestMakeMeinekeGraphs() throw (Exception)
{
// Specify output directory
std::string output_directory = "MakeMeinekeGraphs";
// Create mesh
double crypt_length = 22.0;
unsigned cells_across = 13;
unsigned cells_up = 25;
double crypt_width = 12.1;
unsigned thickness_of_ghost_layer = 3;
CylindricalHoneycombMeshGenerator generator(cells_across, cells_up, thickness_of_ghost_layer, crypt_width/cells_across);
Cylindrical2dMesh* p_mesh = generator.GetCylindricalMesh();
// Get location indices corresponding to real cells
std::vector<unsigned> location_indices = generator.GetCellLocationIndices();
// Set up cells
std::vector<CellPtr> temp_cells;
CryptCellsGenerator<StochasticDurationGenerationBasedCellCycleModel> cells_generator;
cells_generator.Generate(temp_cells, p_mesh, std::vector<unsigned>(), true, 0.3, 2.0, 3.0, 4.0, true);
// This awkward way of setting up the cells is a result of #430
std::vector<CellPtr> cells;
for (unsigned i=0; i<location_indices.size(); i++)
{
cells.push_back(temp_cells[location_indices[i]]);
}
// Create cell population
MeshBasedCellPopulationWithGhostNodes<2> crypt(*p_mesh, cells, location_indices, false, 30.0); // Last parameter adjusts Ghost spring stiffness in line with the linear_force later on
// Set cell population to output cell types
crypt.AddPopulationWriter<CellMutationStatesCountWriter>();
// Create and configure simulation
CryptSimulation2d simulator(crypt, false, false);
simulator.SetOutputDirectory(output_directory);
double time_of_each_run = simulator.GetDt(); // for each run
simulator.SetEndTime(time_of_each_run);
// Create a force law and cell killer and pass then to the simulation
MAKE_PTR(GeneralisedLinearSpringForce<2>, p_linear_force);
p_linear_force->SetMeinekeSpringStiffness(30.0); // normally 15.0;
simulator.AddForce(p_linear_force);
MAKE_PTR_ARGS(SloughingCellKiller<2>, p_killer, (&simulator.rGetCellPopulation(), crypt_length));
simulator.AddCellKiller(p_killer);
// Specify unusual set up
simulator.UseJiggledBottomCells();
// Test CryptStatistics::GetCryptSectionPeriodic() by labelling a column of cells...
CryptStatistics crypt_statistics(crypt);
std::vector<CellPtr> test_section = crypt_statistics.GetCryptSectionPeriodic(crypt_length + 2.0, 8.0, 8.0);
for (unsigned i=0; i<test_section.size(); i++)
{
test_section[i]->AddCellProperty(crypt.GetCellPropertyRegistry()->Get<CellLabel>());
}
simulator.Solve();
CellBasedSimulationArchiver<2, CryptSimulation2d>::Save(&simulator);
// ... and checking visualization of labelled cells against previous run
OutputFileHandler handler(output_directory, false);
std::string results_file = handler.GetOutputDirectoryFullPath() + "results_from_time_0/results.viznodes";
TS_ASSERT(NumericFileComparison( results_file, "crypt/test/data/MakeMeinekeGraphs/results.viznodes").CompareFiles());
std::string results_file2 = handler.GetOutputDirectoryFullPath() + "results_from_time_0/results.vizcelltypes";
FileComparison( results_file2, "crypt/test/data/MakeMeinekeGraphs/results.vizcelltypes").CompareFiles();
// Next, test LabelSPhaseCells()
for (AbstractCellPopulation<2>::Iterator cell_iter = crypt.Begin();
cell_iter != crypt.End();
++cell_iter)
{
cell_iter->RemoveCellProperty<CellLabel>();
}
crypt_statistics.LabelSPhaseCells();
// Iterate over cells checking for correct labels
unsigned counter = 0;
for (AbstractCellPopulation<2>::Iterator cell_iter = crypt.Begin();
cell_iter != crypt.End();
++cell_iter)
{
bool is_labelled = cell_iter->HasCellProperty<CellLabel>();
bool in_s_phase = (cell_iter->GetCellCycleModel()->GetCurrentCellCyclePhase() == S_PHASE);
TS_ASSERT_EQUALS(is_labelled, in_s_phase);
if (in_s_phase)
{
counter++;
}
}
TS_ASSERT_EQUALS(counter, 28u);
// Test that LabelAllCellsAsHealthy sets all cells back to be UNLABELLED wild type cells
crypt_statistics.LabelAllCellsAsHealthy();
// Iterate over cells checking for correct labels
counter = 0;
for (AbstractCellPopulation<2>::Iterator cell_iter = crypt.Begin();
cell_iter != crypt.End();
++cell_iter)
{
TS_ASSERT_EQUALS(cell_iter->GetMutationState()->IsType<WildTypeCellMutationState>(), true);
TS_ASSERT_EQUALS(cell_iter->HasCellProperty<CellLabel>(), false);
counter++;
}
TS_ASSERT_EQUALS(counter, simulator.rGetCellPopulation().GetNumRealCells());
crypt_statistics.LabelSPhaseCells();
simulator.SetEndTime(2*time_of_each_run);
simulator.Solve();
// TEST CryptStatistics::AreCryptSectionCellsLabelled
// Set cells which are not in the crypt section to be in state APC +/-, so that we can
// see the section
test_section = crypt_statistics.GetCryptSectionPeriodic(crypt_length + 2.0, 8.0, 8.0);
MAKE_PTR(ApcOneHitCellMutationState, p_apc1);
for (AbstractCellPopulation<2>::Iterator cell_iter = crypt.Begin();
cell_iter != crypt.End();
++cell_iter)
{
bool in_section = false;
for (unsigned vector_index=0; vector_index<test_section.size(); vector_index++)
{
if (test_section[vector_index] == *cell_iter)
{
in_section = true;
}
}
if (!in_section)
{
cell_iter->SetMutationState(p_apc1);
}
}
simulator.SetEndTime(3*time_of_each_run);
simulator.Solve();
std::vector<CellPtr> crypt_section = crypt_statistics.GetCryptSection(crypt_length + 2.0, 8.0, 8.0);
std::vector<bool> labelled = crypt_statistics.AreCryptSectionCellsLabelled(crypt_section);
// Test that the vector of booleans corresponds with a visualisation of the data -
// only the first few cells at the base of the crypt have been labelled
for (unsigned vector_index=0; vector_index<labelled.size(); vector_index++)
{
if (vector_index == 2u || vector_index == 3u || vector_index == 4u)
{
TS_ASSERT_EQUALS(labelled[vector_index], true);
}
else
{
TS_ASSERT_EQUALS(labelled[vector_index], false);
}
}
RandomNumberGenerator::Destroy();
}
