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);
}
/// <summary>
/// Constructs a cell instance object using this as the cell definition
/// </summary>
/// <returns>
/// A newly instantiated <see cref="CellInstance" />
/// </returns>
public CellInstance createCell()
{
// Create a new instance
CellInstance newInstance = new CellInstance(this);
if (this.sbmlModel.listOfReactions != null)
{
// Fold all relevant reactions into a list of functions
List<EffectReactionEvaluationFunction> reactions = new List<EffectReactionEvaluationFunction>();
foreach (SBML.Reaction reaction in this.sbmlModel.listOfReactions)
{
reactions.Add(reaction.ToEffectReactionEvaluationFunction());
}
// Add the reaction function list
newInstance.setReactions(reactions);
}
// Add the compnents from the model
if (this.sbmlModel.listOfComponents != null)
{
foreach (SBML.ExtracellularComponents.ComponentBase component in this.sbmlModel.listOfComponents)
{
newInstance.Components.Add(component.CreateWorldStateObject());
}
}
return newInstance;
}
public void testWithVariables()
{
// create a formula
MuCell.Model.SBML.Reader.SBMLReader reader = new MuCell.Model.SBML.Reader.SBMLReader();
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
Species s = new Species("X");
s.BoundaryCondition = false;
model.AddId(s.ID, s); // else FormulaParser can't find what X is
reader.model = model;
FormulaParser fp = new FormulaParser(reader, "10+sin(X)", model);
MathTree formulaTree = fp.getFormulaTree();
// fold the function
CellEvaluationFunction fun = formulaTree.ToCellEvaluationFunction();
// create a new CellInstance with a variable X
CellInstance cell = new CellInstance(new CellDefinition());
cell.setSpeciesAmount("X", 2.3d);
// evaluate and test that this gets the right result
Assert.AreEqual(10+Math.Sin(2.3), fun(new StateSnapshot(), cell));
}
/// <summary>
/// Private method for performing the spatial simulation.
/// </summary>
/// <param name="cell"></param>
/// <param name="currentState"></param>
/// <param name="time"></param>
/// <param name="StepTime"></param>
private void SpatialSimulator(CellInstance cell, StateSnapshot currentState, double time, double StepTime)
{
Vector3 p = cell.CellInstanceSpatialContext.Position;
Vector3 v = cell.CellInstanceSpatialContext.Velocity;
Vector3 ang = cell.CellInstanceSpatialContext.Orientation;
float visc = currentState.SimulationEnvironment.Viscosity;
float h = (float)StepTime;
//viscous drag (Stokes's drag)
v.x += -visc * h * v.x * 1.5f;
v.y += -visc * h * v.y * 1.5f;
v.z += -visc * h * v.z * 1.5f;
//cell collisions
if (currentState.SimulationEnvironment.EnableCellCollisions)
{
foreach (CellInstance cellB in currentState.Cells)
{
if (cell != cellB) //avoid collision with self
{
//the vector from the centre of this cell to cellB
Vector3 dist = new Vector3(p.x - cellB.CellInstanceSpatialContext.Position.x,
p.y - cellB.CellInstanceSpatialContext.Position.y,
p.z - cellB.CellInstanceSpatialContext.Position.z);
float distMag = dist.magnitude();
if (distMag < cell.CellInstanceSpatialContext.Radius*0.001 + cellB.CellInstanceSpatialContext.Radius*0.001)
{
/*
* Collision occured: accelerate this cell away from the centre of the cell it is colliding with:
*/
dist.unitVect(); //normalize
dist.x *= -h*0.1f;
dist.y *= -h*0.1f;
dist.z *= -h*0.1f;
//accelerate this cell and the one it collided with in oppose directions:
v.x -= dist.x;
v.y -= dist.y;
v.z -= dist.z;
cellB.CellInstanceSpatialContext.Accelerate(dist);
}
}
}
}
//positional change
p.x += v.x * h;
p.y += v.y * h;
p.z += v.z * h;
//check that boundary conditions are maintained (most of the time this will be true, and will be the only test needed)
if (!currentState.SimulationEnvironment.Boundary.InsideBoundary(p))
{
/*
* If the cell is not inside the environment boundary, we move it back
* and attempt to move the cell by individual components (this allows
* the cell to "slide" along the edges of the boundary without
* breaking the boundary conditions). In most cases these three boundary
* checks should not be necessary
*/
//begin by checking x component, so move back y and z components
p.y -= v.y * h;
p.z -= v.z * h;
if (!currentState.SimulationEnvironment.Boundary.InsideBoundary(p))
{
//x failed, so move back x
p.x -= v.x * h;
}
//check y component
p.y += v.y * h;
if (!currentState.SimulationEnvironment.Boundary.InsideBoundary(p))
{
//y failed
p.y -= v.y * h;
}
//check z component
p.z += v.z * h;
if (!currentState.SimulationEnvironment.Boundary.InsideBoundary(p))
{
//z failed
p.z -= v.z * h;
}
}
cell.CellInstanceSpatialContext.Position = p;
cell.CellInstanceSpatialContext.Velocity = v;
cell.CellInstanceSpatialContext.Orientation = ang;
}
public static void SpatialSimulatorZZZ(CellInstance cell, StateSnapshot currentState, double time, double StepTime)
{
}
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));
}
/// <summary>
/// Private method for performing the spatial simulation.
/// </summary>
/// <param name="cell"></param>
/// <param name="currentState"></param>
/// <param name="time"></param>
/// <param name="StepTime"></param>
private void SpatialSimulator(CellInstance cell, StateSnapshot currentState, double time, double StepTime)
{
Vector3 p = cell.CellInstanceSpatialContext.Position;
Vector3 v = cell.CellInstanceSpatialContext.Velocity;
Vector3 ang = cell.CellInstanceSpatialContext.Orientation;
float visc = currentState.SimulationEnvironment.Viscosity;
float h = (float)StepTime;
//viscous drag (Stokes's drag)
v.x += -visc * h * v.x * 1.5f;
v.y += -visc * h * v.y * 1.5f;
v.z += -visc * h * v.z * 1.5f;
//positional change
p.x += v.x * h;
p.y += v.y * h;
p.z += v.z * h;
//check that boundary conditions are maintained (most of the time this will be true, and will be the only test needed)
if (!currentState.SimulationEnvironment.Boundary.InsideBoundary(p))
{
/*
* If the cell is not inside the environment boundary, we move it back
* and attempt to move the cell by individual components (this allows
* the cell to "slide" along the edges of the boundary without
* breaking the boundary conditions). In most cases these three boundary
* checks should not be necessary
*/
//begin by checking x component, so move back y and z components
p.y -= v.y * h;
p.z -= v.z * h;
if (!currentState.SimulationEnvironment.Boundary.InsideBoundary(p))
{
//x failed, so move back x
p.x -= v.x * h;
}
//check y component
p.y += v.y * h;
if (!currentState.SimulationEnvironment.Boundary.InsideBoundary(p))
{
//y failed
p.y -= v.y * h;
}
//check z component
p.z += v.z * h;
if (!currentState.SimulationEnvironment.Boundary.InsideBoundary(p))
{
//z failed
p.z -= v.z * h;
}
}
cell.CellInstanceSpatialContext.Position = p;
cell.CellInstanceSpatialContext.Velocity = v;
cell.CellInstanceSpatialContext.Orientation = ang;
}
public CellToSort(CellInstance cell,float depth)
{
this.cell = cell;
this.depth = depth;
}
public bool exptEquals(CellInstance other)
{
if (this.GroupID != other.GroupID)
{
Console.Write("CellInstance objects not equal: ");
Console.WriteLine("this.GroupID='" + this.GroupID + "'; other.GroupID='" + other.GroupID);
return false;
}
if (this.CellInstanceDefinition.exptEquals(other.CellInstanceDefinition) == false)
{
Console.Write("CellInstance objects not equal: ");
Console.Write("this.CellInstanceDefinition.Name='" + this.CellInstanceDefinition.Name);
Console.WriteLine("'; other.CellInstanceDefinition.Name'" + other.CellInstanceDefinition.Name);
return false;
}
if (this.CellInstanceSpatialContext.exptEquals(other.CellInstanceSpatialContext) == false)
{
Console.Write("CellInstance objects not equal: ");
Console.WriteLine("this.CellInstanceSpatialContext != other.CellInstanceSpatialContext");
return false;
}
return true;
}
/// <summary>
/// Clones a CellInstance
/// </summary>
/// <returns>
/// A <see cref="Object"/>
/// </returns>
public Object Clone()
{
// Clone the component world states
List<SBML.ExtracellularComponents.ComponentWorldStateBase> clonedComponents = new List<SBML.ExtracellularComponents.ComponentWorldStateBase>();
foreach (SBML.ExtracellularComponents.ComponentWorldStateBase componentWorldState in this.components)
{
clonedComponents.Add((SBML.ExtracellularComponents.ComponentWorldStateBase)componentWorldState.Clone());
}
// create the objects
CellInstance cloned = new CellInstance(this.cellInstanceDefinition, (SpatialContext)this.cellInstanceSpatialContext.Clone(),
this.species, this.speciesVariables, this.indexToSpeciesMap, this.speciesToIndexMap,
this.solver, clonedComponents, this.randomObject);
// Set reactions
cloned.GroupID = this.GroupID;
cloned.reactions = this.reactions;
return cloned;
}
