public void CreateAndSerializeScenario()
{
var config = new SimConfigurator(filename);
var sim_config = config.SimConfig;
// Experiment
sim_config.experiment_name = "Test experiment for XML serialization";
sim_config.scenario.time_config.duration = 100;
sim_config.scenario.time_config.timestep = 3;
// Global Paramters
sim_config.LoadDefaultGlobalParameters();
// Entity Repository
EntityRepository repository = new EntityRepository();
// Possible solfac types
SolfacType st = new SolfacType();
st.solfac_type_name = "ccr7";
repository.solfac_types.Add(st);
st = new SolfacType();
st.solfac_type_name = "cxcl13";
repository.solfac_types.Add(st);
// Possible cell types
CellType ct = new CellType();
ct.cell_type_name = "bcell";
ct.LoadDefaultMotileCellParams();
repository.cell_types.Add(ct);
ct = new CellType();
ct.cell_type_name = "tcell";
ct.LoadDefaultMotileCellParams();
repository.cell_types.Add(ct);
sim_config.entity_repository = repository;
// Gaussian Gradients
GaussianSpecification gg = new GaussianSpecification();
gg.gaussian_spec_name = "Default on-center gradient";
sim_config.entity_repository.gaussian_gradients.Add(gg);
// Regions (not part of repository right now...)
sim_config.scenario.regions.Add(new Region("Sphere", RegionShape.Ellipsoid));
sim_config.scenario.regions.Add(new Region("Cube", RegionShape.Rectangular));
// Cells
CellSet cs = new CellSet();
cs.cell_name = "Generic motile bcell";
cs.cell_type_ref = sim_config.entity_repository.cell_types[0].cell_type_name;
cs.number = 200;
cs.cells_constrained_to_region = true;
cs.region_name_ref = sim_config.scenario.regions[0].region_name;
cs.wrt_region = RelativePosition.Inside;
sim_config.scenario.cellsets.Add(cs);
cs = new CellSet();
cs.cell_name = "Generic motile tcell";
cs.cell_type_ref = sim_config.entity_repository.cell_types[1].cell_type_name;
cs.number = 200;
cs.cells_constrained_to_region = true;
cs.region_name_ref = sim_config.scenario.regions[1].region_name;
cs.wrt_region = RelativePosition.Outside;
sim_config.scenario.cellsets.Add(cs);
// Solfacs
Solfac solfac = new Solfac();
solfac.solfac_name = "Gauss";
solfac.solfac_type_ref = sim_config.entity_repository.solfac_types[0].solfac_type_name;
SolfacGaussianGradient sgg = new SolfacGaussianGradient();
sgg.gaussian_spec_name_ref = sim_config.entity_repository.gaussian_gradients[0].gaussian_spec_name;
solfac.solfac_distribution = sgg;
sim_config.scenario.solfacs.Add(solfac);
solfac = new Solfac();
solfac.solfac_name = "Lin";
SolfacLinearGradient sll = new SolfacLinearGradient();
sll.min_concentration = 20;
sll.max_concentration = 150;
solfac.solfac_distribution = sll;
solfac.solfac_type_ref = sim_config.entity_repository.solfac_types[1].solfac_type_name;
solfac.solfac_is_time_varying = false;
sim_config.scenario.solfacs.Add(solfac);
solfac = new Solfac();
solfac.solfac_name = "Homog";
solfac.solfac_type_ref = sim_config.entity_repository.solfac_types[1].solfac_type_name;
solfac.solfac_is_time_varying = true;
solfac.solfac_amplitude_keyframes.Add(new TimeAmpPair(0, 1));
sim_config.scenario.solfacs.Add(solfac);
// Write out XML file
config.SerializeSimConfigToFile();
}
public void CreateAndSerializeScenario()
{
var config = new SimConfigurator(filename);
var sim_config = config.SimConfig;
// Experiment
sim_config.experiment_name = "Test experiment for XML serialization";
sim_config.scenario.time_config.duration = 100;
sim_config.scenario.time_config.timestep = 3;
// Global Paramters
sim_config.LoadDefaultGlobalParameters();
// Entity Repository
EntityRepository repository = new EntityRepository();
// Possible solfac types
SolfacType st = new SolfacType();
st.solfac_type_name = "ccr7";
repository.solfac_types.Add(st);
st = new SolfacType();
st.solfac_type_name = "cxcl13";
repository.solfac_types.Add(st);
// Possible cell types
CellType ct = new CellType();
ct.cell_type_name = "bcell";
ct.LoadDefaultMotileCellParams();
repository.cell_types.Add(ct);
ct = new CellType();
ct.cell_type_name = "tcell";
ct.LoadDefaultMotileCellParams();
repository.cell_types.Add(ct);
sim_config.entity_repository = repository;
// Gaussian Gradients
GaussianSpecification gg = new GaussianSpecification();
gg.gaussian_spec_name = "Default on-center gradient";
sim_config.entity_repository.gaussian_gradients.Add(gg);
// Regions (not part of repository right now...)
sim_config.scenario.regions.Add(new Region("Sphere", RegionShape.Ellipsoid));
sim_config.scenario.regions.Add(new Region("Cube", RegionShape.Rectangular));
// Cells
CellSet cs = new CellSet();
cs.cell_name = "Generic motile bcell";
cs.cell_type_ref = sim_config.entity_repository.cell_types[0].cell_type_name;
cs.number = 200;
cs.cells_constrained_to_region = true;
cs.region_name_ref = sim_config.scenario.regions[0].region_name;
cs.wrt_region = RelativePosition.Inside;
sim_config.scenario.cellsets.Add(cs);
cs = new CellSet();
cs.cell_name = "Generic motile tcell";
cs.cell_type_ref = sim_config.entity_repository.cell_types[1].cell_type_name;
cs.number = 200;
cs.cells_constrained_to_region = true;
cs.region_name_ref = sim_config.scenario.regions[1].region_name;
cs.wrt_region = RelativePosition.Outside;
sim_config.scenario.cellsets.Add(cs);
// Solfacs
Solfac solfac = new Solfac();
solfac.solfac_name = "Gauss";
solfac.solfac_type_ref = sim_config.entity_repository.solfac_types[0].solfac_type_name;
SolfacGaussianGradient sgg = new SolfacGaussianGradient();
sgg.gaussian_spec_name_ref = sim_config.entity_repository.gaussian_gradients[0].gaussian_spec_name;
solfac.solfac_distribution = sgg;
sim_config.scenario.solfacs.Add(solfac);
solfac = new Solfac();
solfac.solfac_name = "Lin";
SolfacLinearGradient sll = new SolfacLinearGradient();
sll.min_concentration = 20;
sll.max_concentration = 150;
solfac.solfac_distribution = sll;
solfac.solfac_type_ref = sim_config.entity_repository.solfac_types[1].solfac_type_name;
solfac.solfac_is_time_varying = false;
sim_config.scenario.solfacs.Add(solfac);
solfac = new Solfac();
solfac.solfac_name = "Homog";
solfac.solfac_type_ref = sim_config.entity_repository.solfac_types[1].solfac_type_name;
solfac.solfac_is_time_varying = true;
solfac.solfac_amplitude_keyframes.Add(new TimeAmpPair(0, 1));
sim_config.scenario.solfacs.Add(solfac);
// Write out XML file
config.SerializeSimConfigToFile();
}