/// <summary>
/// Creates a new cell definition, choosing an appropriate name
/// </summary>
public void createNewCellDefinition()
{
Experiment parentExperiment = null;
String namePrefix = "CellDef ";
int highestID = 1;
for (int attempt = 0; attempt < 1000; attempt++)
{
if (isCellDefinitionNameTaken(namePrefix + highestID))
{
highestID++;
}
else
{
break;
}
}
foreach (Experiment experiment in openExperiments)
{
if (experiment.Id == currentExperimentID)
{
parentExperiment = experiment;
break;
}
}
if (parentExperiment != null)
{
CellDefinition cell = new CellDefinition(namePrefix + highestID);
cell.addSBMLModel(System.AppDomain.CurrentDomain.BaseDirectory+"/Models/blank.xml");
parentExperiment.addCellDefinition(cell);
experimentTreePanelController.refreshTreeElements(getExperiments());
experimentTreePanelController.setSelectedCellDefinition(cell.Name);
}
}
/// <summary>
/// Constructor for creating a cell instance with a cell definition
/// </summary>
/// <param name="cellDefinition">
/// A <see cref="CellDefinition"/>
/// </param>
public CellInstance(CellDefinition cellDefinition)
{
this.cellInstanceDefinition = cellDefinition;
SBML.Model model = cellDefinition.getModel();
if (model != null)
{
this.species = cellDefinition.getModel().listOfSpecies;
}
// Initialize the specials Dictionary
this.speciesVariables = new Dictionary<string, double>();
this.localSpeciesVariables = new Dictionary<string, double>();
this.localSpeciesDelta = new Dictionary<string, double>();
this.speciesToIndexMap = new Dictionary<string, int>();
this.indexToSpeciesMap = new Dictionary<int, string>();
// set up the list
this.convertSpeciesListToVariables();
this.components = new List<MuCell.Model.SBML.ExtracellularComponents.ComponentWorldStateBase>();
this.flaggy = new MuCell.Model.SBML.ExtracellularComponents.FlagellaComponent();
cellInstanceSpatialContext = new SpatialContext();
}
/// <summary>
/// Base constructor
/// </summary>
public AggregateReferenceNode(Experiment experiment, Simulation simulation)
{
this.cellDefinition = null;
this.group = null;
this.species = null;
this.experiment = experiment;
this.simulation = simulation;
}
public static void setupExperiment(MuCell.Model.SBML.Model model, MuCell.Model.Experiment experiment, MuCell.Model.Simulation simulation)
{
MuCell.Model.SBML.Species species1 = new MuCell.Model.SBML.Species();
MuCell.Model.SBML.Species species2 = new MuCell.Model.SBML.Species();
model.listOfSpecies = new List<MuCell.Model.SBML.Species>();
model.listOfSpecies.Add(species1);
model.listOfSpecies.Add(species2);
// Set some values for species1
species1.ID = "s1";
species1.InitialAmount = 4.0d;
// Set some values for species2
species2.ID = "s2";
species2.InitialAmount = 0.1d;
model.AddId("s1", species1);
model.AddId("s2", species2);
// set up the cell definition
MuCell.Model.CellDefinition celldef1 = new MuCell.Model.CellDefinition("celldef1");
celldef1.addSBMLModel(model);
MuCell.Model.CellDefinition celldef2 = new MuCell.Model.CellDefinition("celldef2");
celldef2.addSBMLModel(model);
MuCell.Model.CellInstance cell1 = celldef1.createCell();
MuCell.Model.CellInstance cell2 = celldef2.createCell();
List<MuCell.Model.CellInstance> cells = new List<CellInstance>();
cells.Add(cell1);
cells.Add(cell2);
// StateSnapshot for intial state
MuCell.Model.StateSnapshot initialState = new MuCell.Model.StateSnapshot(cells);
MuCell.Model.Vector3 size = new MuCell.Model.Vector3(1, 1, 1);
initialState.SimulationEnvironment = new MuCell.Model.Environment(size);
// Create two groups with one cell of each type in each
initialState.SimulationEnvironment.AddCellToGroup(1, celldef1.createCell());
initialState.SimulationEnvironment.AddCellToGroup(2, celldef2.createCell());
// Parameters
MuCell.Model.SimulationParameters parameters = new MuCell.Model.SimulationParameters();
parameters.InitialState = initialState;
// Simulation
simulation.Parameters = parameters;
// Experiment
experiment.addCellDefinition(celldef1);
experiment.addCellDefinition(celldef2);
experiment.addSimulation(simulation);
}
public void TestGroupOperators()
{
//create an environemnt, and an array of 100 cells
MuCell.Model.Environment env = new MuCell.Model.Environment(new Vector3(1, 1, 1));
CellInstance[] cells = new CellInstance[100];
CellDefinition celDef = new CellDefinition("testCellDef");
for (int i = 0; i < 100; i++)
{
CellInstance cell = new CellInstance(celDef);
cells[i] = cell;
}
//assert that there are no groups yet formed in the env
Assert.That( env.GetGroups().Count == 0 );
//obtain an unused group index, and create a group with 25 cells in it
int newGroupIndex1 = env.GetUnusedGroupIndex();
for (int i = 0; i < 25; i++)
{
env.AddCellToGroup(newGroupIndex1, cells[i]);
}
//assert that there is now one group
Assert.That(env.GetGroups().Count == 1);
//assert that it is the correct group
Assert.That(env.ContainsGroup(newGroupIndex1));
//assert that there are 25 cells in the group
Assert.That(env.CellsFromGroup(newGroupIndex1).Count == 25);
//obtain another unused group index
int newGroupIndex2 = env.GetUnusedGroupIndex();
//group indexes should differ
Assert.That(newGroupIndex1 != newGroupIndex2);
//add some cells to the new group index
for (int i = 25; i < 50; i++)
{
env.AddCellToGroup(newGroupIndex2, cells[i]);
}
//assert that there is now one group
Assert.That(env.GetGroups().Count == 2);
}
public void setCellDefinitions(CellDefinition[] cellDefs)
{
CellTypeComboBox.Items.Clear();
foreach (CellDefinition cellDef in cellDefs)
{
CellTypeComboBox.Items.Add(cellDef);
}
if (CellTypeComboBox.Items.Count > 0)
{
CellTypeComboBox.SelectedIndex = 0;
}
}
public bool exptEquals(CellDefinition other)
{
if (this.Name != other.Name)
{
Console.Write("CellDefinition objects not equal: ");
Console.WriteLine("this.Name='" + this.Name + "'; other.Name='" + other.Name);
return false;
}
return true;
}
public void TestSerializationEquality()
{
String filename = "../../UnitTests/expt1.serialized.xml";
MuCell.Model.Experiment experiment = new MuCell.Model.Experiment("experiment1");
Simulation simulation1 = new Simulation("simulation1");
Results results = new Results();
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
CellDefinition cellDef1 = new CellDefinition("cellDef1");
cellDef1.addSBMLModel(model);
for (int i = 0; i < 5; i++)
{
StateSnapshot snapshot = new StateSnapshot();
for (int j = 0; j < 10; j++)
{
CellInstance cell = new CellInstance(cellDef1);
cell.GroupID = j;
cell.CellInstanceSpatialContext.Position = new Vector3(1*j, 1+i, 2+j);
cell.CellInstanceSpatialContext.Velocity = new Vector3(4*i, 5+j, 3+i);
cell.CellInstanceSpatialContext.Volume = new Vector3(10+j, 14*i, 15*i);
cell.CellInstanceSpatialContext.Orientation = new Vector3(2+i, 3*j, 4*j);
snapshot.Cells.Add(cell);
}
MuCell.Model.Environment environment = new MuCell.Model.Environment(new Vector3(10 * i, 14 * i, 15 * i));
SerializableDictionary<int, MuCell.Model.SBML.Group> dict = new SerializableDictionary<int, MuCell.Model.SBML.Group>();
// create new groups x3
MuCell.Model.SBML.Group group1 = new MuCell.Model.SBML.Group(1);
group1.Col = System.Drawing.Color.Beige;
MuCell.Model.SBML.Group group2 = new MuCell.Model.SBML.Group(2);
group2.Col = System.Drawing.Color.Brown;
MuCell.Model.SBML.Group group3 = new MuCell.Model.SBML.Group(3);
group3.Col = System.Drawing.Color.Green;
dict.Add(1, group1); dict.Add(2, group2); dict.Add(3, group3);
environment.Groups = dict;
//SerializableDictionary<int, MuCell.Model.NutrientField> nutDict = new SerializableDictionary<int, MuCell.Model.NutrientField>();
//// create new nutrients x2
//MuCell.Model.NutrientField nut1 = new MuCell.Model.NutrientField(1);
//MuCell.Model.NutrientField nut2 = new MuCell.Model.NutrientField(2);
//nut2.Col = System.Drawing.Color.Fuchsia;
//nutDict.Add(1,nut1); nutDict.Add(2,nut2);
//environment.Nutrients = nutDict;
snapshot.SimulationEnvironment = environment;
results.StateSnapshots.Add(snapshot);
}
results.CurrentState = results.StateSnapshots[4];
for (int i = 0; i < 3; i++)
{
TimeSeries timeSeries = new TimeSeries("Function" + i, 1.2 * i);
for (int j = 0; j < 20; j++)
{
timeSeries.Series.Add(0.43+i*j+0.031*j);
}
results.TimeSeries.Add(timeSeries);
}
results.FilePath = "some-file-path";
simulation1.SimulationResults = results;
SimulationParameters simulationParams1 = new SimulationParameters();
simulationParams1.TimeSeries = results.TimeSeries;
simulationParams1.InitialState = results.StateSnapshots[0];
// add to simulation
simulation1.Parameters = simulationParams1;
// expt.addSimulation
experiment.addSimulation(simulation1);
XmlSerializer s = new XmlSerializer(typeof(MuCell.Model.Experiment));
TextWriter w = new StreamWriter(filename);
s.Serialize(w, experiment);
w.Close();
TextReader tr = new StreamReader(filename);
Experiment deserializedExpt = (Experiment)s.Deserialize(tr);
tr.Close();
Assert.IsTrue(experiment.exptEquals(deserializedExpt));
}
public void Setup(Experiment experiment, Simulation simulation, string speciesName)
{
// ********* INITIAL SETUP
// Hopf model
MuCell.Model.SBML.Reader.SBMLReader s = new MuCell.Model.SBML.Reader.SBMLReader("../../UnitTests/smallest.Hopf.xml");
// Cell definition 1
MuCell.Model.CellDefinition celldef1 = new MuCell.Model.CellDefinition("celldef1");
celldef1.addSBMLModel(s.model);
// Create a NEW model
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
MuCell.Model.SBML.Species species1 = new MuCell.Model.SBML.Species();
MuCell.Model.SBML.Species species2 = new MuCell.Model.SBML.Species();
model.listOfSpecies = new List<MuCell.Model.SBML.Species>();
model.listOfSpecies.Add(species1);
model.listOfSpecies.Add(species2);
// Set some values for species1
species1.ID = speciesName;
species1.InitialAmount = 4.0d;
// Set some values for species2
species2.ID = "Y";
species2.InitialAmount = 0.1d;
model.AddId(speciesName, species1);
model.AddId("Y", species2);
// Set up the reaction
MuCell.Model.SBML.Reaction reaction1 = new MuCell.Model.SBML.Reaction("reaction1");
model.listOfReactions = new List<MuCell.Model.SBML.Reaction>();
model.listOfReactions.Add(reaction1);
// Set up the kinetic law
reaction1.KineticLaw = new MuCell.Model.SBML.KineticLaw(model);
reaction1.KineticLaw.Formula = speciesName.Replace(' ', '_')+"*2";
// set up the species reference for the reactants
MuCell.Model.SBML.SpeciesReference ref1 = new MuCell.Model.SBML.SpeciesReference(species1, 1);
// set up the species references for the products
MuCell.Model.SBML.SpeciesReference ref2 = new MuCell.Model.SBML.SpeciesReference(species1, 0.75);
MuCell.Model.SBML.SpeciesReference ref3 = new MuCell.Model.SBML.SpeciesReference(species2, 2);
// Add the references
reaction1.Reactants.Add(ref1);
reaction1.Products.Add(ref2);
reaction1.Products.Add(ref3);
// set up the cell definition
MuCell.Model.CellDefinition celldef2 = new MuCell.Model.CellDefinition("celldef2");
celldef2.addSBMLModel(model);
// instantiat the environment
MuCell.Model.Vector3 size = new MuCell.Model.Vector3(1, 1, 1);
MuCell.Model.Environment environment = new MuCell.Model.Environment(size);
// Cells
List<MuCell.Model.CellInstance> cells = new List<MuCell.Model.CellInstance>();
// Create 10 cells of celldef1 and 20 cells of celldef2
for(int i=0;i<10;i++){
int a = ((i+2)%3)+1;
int b = (i%3)+1;
int c = ((i+1)%3)+1;
CellInstance cell11 = celldef1.createCell();
cells.Add(cell11);
environment.AddCellToGroup(a, cell11);
CellInstance cell21 = celldef2.createCell();
CellInstance cell22 = celldef2.createCell();
cells.Add(cell21);
cells.Add(cell22);
environment.AddCellToGroup(b, cell21);
environment.AddCellToGroup(c, cell22);
}
// StateSnapshot for intial state
MuCell.Model.StateSnapshot initialState = new MuCell.Model.StateSnapshot(cells);
initialState.SimulationEnvironment = environment;
// Parameters
MuCell.Model.SimulationParameters parameters = new MuCell.Model.SimulationParameters();
parameters.InitialState = initialState;
parameters.SimulationLength = 0.01001d;
parameters.SnapshotInterval = 1;
parameters.StepTime = 0.01001d;
parameters.SolverMethod = MuCell.Model.Solver.SolverMethods.RungeKutta;
// Simulation
simulation.Parameters = parameters;
// Experiment
experiment.addCellDefinition(celldef1);
experiment.addCellDefinition(celldef2);
experiment.addSimulation(simulation);
// Start simulation
simulation.StartSimulation();
this.models = new List<MuCell.Model.SBML.Model>();
this.models.Add(s.model);
this.models.Add(model);
}
private List<Experiment> generateHardcodedExperiment()
{
List<Experiment> exps = new List<Experiment>();
Simulation sim1 = new Simulation("sim 1");
Simulation sim2 = new Simulation("sim 2");
Simulation sim3 = new Simulation("sim 3");
Simulation sim4 = new Simulation("sim 4");
Simulation sim5 = new Simulation("sim 5");
Simulation sim6 = new Simulation("sim 6");
sim1.Parameters.StepTime = 5.3d;
sim5.Parameters.StepTime = -6.3d;
CellDefinition cellDef1 = new CellDefinition("CellDef 1");
cellDef1.addSBMLModel("Models/smallest.Hopf.xml");
//CellDefinition cellDef2 = new CellDefinition("CellDef 2");
//CellDefinition cellDef3 = new CellDefinition("CellDef 3");
//CellDefinition cellDef4 = new CellDefinition("CellDef 4");
//CellDefinition cellDef5 = new CellDefinition("CellDef 5");
//CellDefinition cellDef6 = new CellDefinition("CellDef 6");
//CellDefinition cellDef7 = new CellDefinition("CellDef 7");
Experiment exp1 = new Experiment("Experiment 1");
Experiment exp2 = new Experiment("Experiment 2");
Experiment exp3 = new Experiment("Experiment 3");
exp1.Id = 1;
exp2.Id = 2;
exp3.Id = 3;
exp1.addCellDefinition(cellDef1);
exp1.addSimulation(sim1);
exp1.addSimulation(sim2);
exp1.addSimulation(sim3);
/*exp2.addCellDefinition(cellDef2);
exp2.addCellDefinition(cellDef3);
exp2.addCellDefinition(cellDef4);
exp2.addCellDefinition(cellDef5);*/
exp2.addSimulation(sim4);
//exp3.addCellDefinition(cellDef6);
//exp3.addCellDefinition(cellDef7);
exp3.addSimulation(sim5);
exp3.addSimulation(sim6);
exps.Add(exp1);
exps.Add(exp2);
exps.Add(exp3);
return exps;
}
/// <summary>
/// Removes a cell definition from the experiment
/// </summary>
/// <param name="cellDefinition">
/// A <see cref="CellDefinition"/>
/// </param>
public void removeCellDefinition(CellDefinition cellDefinition)
{
this.cellDefinitions.Remove(cellDefinition);
}
/// <summary>
/// Add a cell definition to the experiment
/// </summary>
/// <param name="cellDefinition">
/// A <see cref="CellDefinition"/>
/// </param>
public void addCellDefinition(CellDefinition cellDefinition)
{
this.cellDefinitions.Add(cellDefinition);
}
/// <summary>
/// Secondary constructor that takes a cell definition,
/// a spatial context, a list of species and a species variables dictionary
/// </summary>
/// <param name="cellDefinition">
/// A <see cref="CellDefinition"/>
/// </param>
/// <param name="spatialContext">
/// A <see cref="SpatialContext"/>
/// </param>
/// <param name="species">
/// A <see cref="List`1"/>
/// </param>
/// <param name="speciesVariables">
/// A <see cref="Dictionary`2"/>
/// </param>
public CellInstance(CellDefinition cellDefinition, SpatialContext spatialContext,
List<SBML.Species> species, Dictionary<string, double> speciesVariables,
Dictionary<int, string> indexToSpeciesMap, Dictionary<string, int> speciesToIndexMap,
Solver.SolverBase solver, List<SBML.ExtracellularComponents.ComponentWorldStateBase> components,
System.Random random)
{
this.cellInstanceDefinition = cellDefinition;
this.species = species;
this.speciesVariables = speciesVariables;
this.cellInstanceSpatialContext = spatialContext;
this.indexToSpeciesMap = indexToSpeciesMap;
this.speciesToIndexMap = speciesToIndexMap;
this.solver = solver;
this.components = components;
this.randomObject = random;
this.localSpeciesVariables = new Dictionary<string, double>();
this.localSpeciesDelta = new Dictionary<string, double>();
}