/**
* This tests the HDF5 to .txt converter using a 3D example
* taken from a bidomain simulation.
*/
void TestBidomainTxtConversion3D() throw(Exception)
{
std::string working_directory = "TestHdf5ToTxtConverter_bidomain";
/*
* Firstly, copy the .h5 file to CHASTE_TEST_OUTPUT/TestHdf5ToTxtConverter_bidomain,
* as that is where the reader reads from.
*/
CopyToTestOutputDirectory("pde/test/data/cube_2mm_12_elements.h5",
working_directory);
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/cube_2mm_12_elements");
TetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
// Convert
Hdf5ToTxtConverter<3,3> converter(FileFinder(working_directory, RelativeTo::ChasteTestOutput),
"cube_2mm_12_elements", &mesh);
std::vector<std::string> files_to_compare;
files_to_compare.push_back("cube_2mm_12_elements_V_0.txt");
files_to_compare.push_back("cube_2mm_12_elements_V_1.txt");
files_to_compare.push_back("cube_2mm_12_elements_Phi_e_0.txt");
files_to_compare.push_back("cube_2mm_12_elements_Phi_e_1.txt");
for (unsigned i=0; i<files_to_compare.size(); i++)
{
std::cout << "Comparing generated and reference " << files_to_compare[i] << std::endl;
FileFinder generated_file(working_directory +"/txt_output/" + files_to_compare[i], RelativeTo::ChasteTestOutput);
FileFinder reference_file("pde/test/data/" + files_to_compare[i], RelativeTo::ChasteSourceRoot);
NumericFileComparison comparer(generated_file, reference_file);
TS_ASSERT(comparer.CompareFiles());
}
}
/**
* This tests the HDF5 to XDMF converter
*/
void TestHdf5ToXdmfConverter() throw(Exception)
{
#ifndef _MSC_VER
std::string working_directory = "TestHdf5Converters_TestHdf5ToXdmfConverter";
CopyToTestOutputDirectory("pde/test/data/cube_2mm_12_elements.h5",
working_directory);
TrianglesMeshReader<3,3> mesh_reader("mesh/test/data/cube_2mm_12_elements");
TetrahedralMesh<3,3> mesh;
mesh.ConstructFromMeshReader(mesh_reader);
// Convert
Hdf5ToXdmfConverter<3,3> converter(FileFinder(working_directory, RelativeTo::ChasteTestOutput),
"cube_2mm_12_elements",
&mesh);
std::vector<std::string> files_to_compare;
files_to_compare.push_back("cube_2mm_12_elements.xdmf");
files_to_compare.push_back("cube_2mm_12_elements_geometry_0.xml");
files_to_compare.push_back("cube_2mm_12_elements_topology_0.xml");
for (unsigned i=0; i<files_to_compare.size(); i++)
{
std::cout << "Comparing generated and reference " << files_to_compare[i] << std::endl;
FileFinder generated_file(working_directory +"/xdmf_output/" + files_to_compare[i], RelativeTo::ChasteTestOutput);
FileFinder reference_file("pde/test/data/xdmf_output/" + files_to_compare[i], RelativeTo::ChasteSourceRoot);
FileComparison comparer(generated_file, reference_file);
TS_ASSERT(comparer.CompareFiles());
}
#endif // _MSC_VER
}
void TestCellCycleModelOutputParameters()
{
std::string output_directory = "TestCellCycleModelOutputParameters";
OutputFileHandler output_file_handler(output_directory, false);
// Test with Alarcon2004OxygenBasedCellCycleModel
Alarcon2004OxygenBasedCellCycleModel alarcon_oxygen_based_cell_cycle_model;
TS_ASSERT_EQUALS(alarcon_oxygen_based_cell_cycle_model.GetIdentifier(), "Alarcon2004OxygenBasedCellCycleModel");
out_stream alarcon_oxygen_based_parameter_file = output_file_handler.OpenOutputFile("alarcon_oxygen_based_results.parameters");
alarcon_oxygen_based_cell_cycle_model.OutputCellCycleModelParameters(alarcon_oxygen_based_parameter_file);
alarcon_oxygen_based_parameter_file->close();
{
FileFinder generated_file = output_file_handler.FindFile("alarcon_oxygen_based_results.parameters");
FileFinder reference_file("cell_based/test/data/TestCellCycleModels/alarcon_oxygen_based_results.parameters",
RelativeTo::ChasteSourceRoot);
FileComparison comparer(generated_file,reference_file);
TS_ASSERT(comparer.CompareFiles());
}
// Test with TysonNovakCellCycleModel
TysonNovakCellCycleModel tyson_novak_based_cell_cycle_model;
TS_ASSERT_EQUALS(tyson_novak_based_cell_cycle_model.GetIdentifier(), "TysonNovakCellCycleModel");
out_stream tyson_novak_based_parameter_file = output_file_handler.OpenOutputFile("tyson_novak_based_results.parameters");
tyson_novak_based_cell_cycle_model.OutputCellCycleModelParameters(tyson_novak_based_parameter_file);
tyson_novak_based_parameter_file->close();
{
FileFinder generated_file = output_file_handler.FindFile("tyson_novak_based_results.parameters");
FileFinder reference_file("cell_based/test/data/TestCellCycleModels/tyson_novak_based_results.parameters",
RelativeTo::ChasteSourceRoot);
FileComparison comparer(generated_file,reference_file);
TS_ASSERT(comparer.CompareFiles());
}
}
