public void setSimulationParameters(MuCell.Model.SimulationParameters simulationParameters)
{
simParameters = simulationParameters;
if (simParameters.StepTime > 0)
{
foreach (Model.TimeSeries ts in listOfTimeSeries.Items)
{
decimal currentTimeInterval = (decimal)ts.Parameters.TimeInterval;
decimal currentSimStep = (decimal)simParameters.StepTime;
ts.Parameters.TimeInterval = (double)(Math.Ceiling(currentTimeInterval / currentSimStep) * currentSimStep);
if (ts == listOfTimeSeries.SelectedItem)
{
numericUpDown1.Value = Math.Ceiling(currentTimeInterval / currentSimStep);
setTimeIntervalHelperLabel(ts);
}
}
}
else
{
foreach (Model.TimeSeries ts in listOfTimeSeries.Items)
{
}
}
}
public double evaluate(string formula, MuCell.Model.Experiment experiment, MuCell.Model.Simulation simulation)
{
MuCell.Model.SBML.Reader.SBMLReader reader = new MuCell.Model.SBML.Reader.SBMLReader();
FormulaParser fp = new FormulaParser(reader, formula, this.models, experiment, simulation);
MathTree formulaTree = fp.getFormulaTree();
MuCell.Model.AggregateEvaluationFunction fun1 = formulaTree.ToAggregateEvaluationFunction();
return fun1(simulation.GetCurrentState());
}
public void RunHopfParseAndReactions(MuCell.Model.SBML.Reader.SBMLReader s)
{
Assert.AreEqual(5, s.model.listOfReactions.Count);
MuCell.Model.SBML.Reaction[] reactions = s.model.listOfReactions.ToArray();
// Reaction 1
Assert.AreEqual(2, reactions[0].Reactants.Count);
Assert.AreEqual(1, reactions[0].Reactants.ToArray()[0].Stoichiometry);
Assert.AreEqual(1, reactions[0].Reactants.ToArray()[1].Stoichiometry);
Assert.AreEqual("X", reactions[0].Reactants.ToArray()[0].SpeciesID);
Assert.AreEqual("A", reactions[0].Reactants.ToArray()[1].SpeciesID);
Assert.AreEqual(1, reactions[0].Products.Count);
Assert.AreEqual(2, reactions[0].Products.ToArray()[0].Stoichiometry);
Assert.AreEqual("X", reactions[0].Products.ToArray()[0].SpeciesID);
// Reaction 2
Assert.AreEqual(2, reactions[1].Reactants.Count);
Assert.AreEqual(1, reactions[1].Reactants.ToArray()[0].Stoichiometry);
Assert.AreEqual(1, reactions[1].Reactants.ToArray()[1].Stoichiometry);
Assert.AreEqual("X", reactions[1].Reactants.ToArray()[0].SpeciesID);
Assert.AreEqual("Y", reactions[1].Reactants.ToArray()[1].SpeciesID);
Assert.AreEqual(2, reactions[1].Products.Count);
Assert.AreEqual(1, reactions[1].Products.ToArray()[0].Stoichiometry);
Assert.AreEqual(1, reactions[1].Products.ToArray()[1].Stoichiometry);
Assert.AreEqual("A", reactions[1].Products.ToArray()[0].SpeciesID);
Assert.AreEqual("Y", reactions[1].Products.ToArray()[1].SpeciesID);
// Reaction 3
Assert.AreEqual(1, reactions[2].Reactants.Count);
Assert.AreEqual(1, reactions[2].Reactants.ToArray()[0].Stoichiometry);
Assert.AreEqual("X", reactions[2].Reactants.ToArray()[0].SpeciesID);
Assert.AreEqual(1, reactions[2].Products.Count);
Assert.AreEqual(1, reactions[2].Products.ToArray()[0].Stoichiometry);
Assert.AreEqual("Z", reactions[2].Products.ToArray()[0].SpeciesID);
// Reaction 4
Assert.AreEqual(1, reactions[3].Reactants.Count);
Assert.AreEqual(1, reactions[3].Reactants.ToArray()[0].Stoichiometry);
Assert.AreEqual("Z", reactions[3].Reactants.ToArray()[0].SpeciesID);
Assert.AreEqual(1, reactions[3].Products.Count);
Assert.AreEqual(1, reactions[3].Products.ToArray()[0].Stoichiometry);
Assert.AreEqual("Y", reactions[3].Products.ToArray()[0].SpeciesID);
// Reaction 5
Assert.AreEqual(1, reactions[4].Reactants.Count);
Assert.AreEqual(1, reactions[4].Reactants.ToArray()[0].Stoichiometry);
Assert.AreEqual("Y", reactions[4].Reactants.ToArray()[0].SpeciesID);
Assert.AreEqual(1, reactions[4].Products.Count);
Assert.AreEqual(1, reactions[4].Products.ToArray()[0].Stoichiometry);
Assert.AreEqual("_void_", reactions[4].Products.ToArray()[0].SpeciesID);
}
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);
}
/// <summary>
/// Sets which nutrient is selected in the nutrient list box
/// </summary>
/// <param name="nutrient"></param>
public void setSelectedNutrient(MuCell.Model.NutrientField nutrient)
{
if (nutrientFieldListBox.Items.Contains(nutrient))
{
nutrientFieldListBox.SelectedItem = nutrient;
}
}
/// <summary>
/// Sets which group is selected in the group list box.
/// </summary>
/// <param name="group"></param>
public void setSelectedGroup(MuCell.Model.SBML.Group group)
{
if (groupListBox.Items.Contains(group))
{
groupListBox.SelectedItem = group;
}
}
public void RunHopfSimulationRK(MuCell.Model.SBML.Reader.SBMLReader s)
{
// Cell definition
MuCell.Model.CellDefinition celldef1 = new MuCell.Model.CellDefinition("celldef1");
celldef1.addSBMLModel(s.model);
// Cells
List<MuCell.Model.CellInstance> cells = new List<MuCell.Model.CellInstance>();
MuCell.Model.CellInstance cell1 = celldef1.createCell();
cells.Add(cell1);
// 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);
// Parameters
MuCell.Model.SimulationParameters parameters = new MuCell.Model.SimulationParameters();
parameters.InitialState = initialState;
parameters.SimulationLength = 0.01001d;
parameters.SnapshotInterval = 2;
parameters.StepTime = 0.01001d;
parameters.SolverMethod = MuCell.Model.Solver.SolverMethods.RungeKutta;
// Simulation
MuCell.Model.Simulation simulation = new MuCell.Model.Simulation("simulation1");
simulation.Parameters = parameters;
// Assert that is not complete at all
Assert.AreEqual(0.0d, simulation.SimulationProgress());
// Test the initial conditions
Assert.AreEqual(1.0d, cell1.getSpeciesAmount("A"));
Assert.AreEqual(2.5d, cell1.getSpeciesAmount("X"));
Assert.AreEqual(2.5d, cell1.getSpeciesAmount("Y"));
Assert.AreEqual(2.5d, cell1.getSpeciesAmount("Z"));
Assert.AreEqual(0.0d, cell1.getSpeciesAmount("_void_"));
// Start simulation
simulation.StartSimulation();
// Assert that is complete
Assert.AreEqual(1.0d, simulation.SimulationProgress());
// Test the results (test generated from the Python model)
AssertDouble.AreEqual(1.0d, cell1.getSpeciesAmount("A"));
AssertDouble.AreEqual(rk_x_t1, cell1.getSpeciesAmount("X"));
AssertDouble.AreEqual(rk_y_t1, cell1.getSpeciesAmount("Y"));
AssertDouble.AreEqual(rk_z_t1, cell1.getSpeciesAmount("Z"));
Assert.AreEqual(0.0d, cell1.getSpeciesAmount("_void_"));
// Make the simulation run a bit longer
parameters.SimulationLength = 0.02002;
simulation.UnPauseSimulation();
AssertDouble.AreEqual(1.0d, cell1.getSpeciesAmount("A"));
AssertDouble.AreEqual(rk_x_t2, cell1.getSpeciesAmount("X"));
AssertDouble.AreEqual(rk_y_t2, cell1.getSpeciesAmount("Y"));
AssertDouble.AreEqual(rk_z_t2, cell1.getSpeciesAmount("Z"));
Assert.AreEqual(0.0d, cell1.getSpeciesAmount("_void_"));
// Make the simulation run a bit longer
parameters.SimulationLength = 0.03003;
simulation.UnPauseSimulation();
AssertDouble.AreEqual(1.0d, cell1.getSpeciesAmount("A"));
AssertDouble.AreEqual(rk_x_t3, cell1.getSpeciesAmount("X"));
AssertDouble.AreEqual(rk_y_t3, cell1.getSpeciesAmount("Y"));
AssertDouble.AreEqual(rk_z_t3, cell1.getSpeciesAmount("Z"));
Assert.AreEqual(0.0d, cell1.getSpeciesAmount("_void_"));
}
protected override MacroCommand resolveGraph(GraphNode[] nodes, GraphLink[] links, MuCell.View.IDrawingInterface drawable)
{
Vector2 topLeft = drawable.getScreenTopLeftInWorldCoordinates();
Vector2 bottomRight = drawable.getScreenBottomRightInWorldCoordinates();
float screenWidth = bottomRight.x - topLeft.x;
float screenHeight = bottomRight.y - topLeft.y;
float G = 60f;
float sideForce = 30f;
running = true;
long iterationCount = 0;
long renderTime = 1000;// (long)(1000.0 * (10.0 / nodes.Length));
while (running)
{
for (int l = 0; l < links.Length; l++)
{
GraphLink link = links[l];
link.step();
}
//push all nodes away from each other
for (int a = 0; a < nodes.Length-1; a++)
{
GraphNode nodeA = nodes[a];
for (int b = a + 1; b < nodes.Length; b++)
{
GraphNode nodeB = nodes[b];
Vector2 aToB = nodeB.getComponent().getPosition() - nodeA.getComponent().getPosition();
float distSqrd = aToB.getSqrdLength();
if (distSqrd < 1)
{
distSqrd = 1;
}
aToB.normalise();
Vector2 force = (aToB*G*(nodeA.getMass() * nodeB.getMass())) / distSqrd;
nodeA.push(-force);
nodeB.push(force);
}
}
//push all nodes in from the sides
for (int a = 0; a < nodes.Length; a++)
{
GraphNode nodeA = nodes[a];
Vector2 pos=nodeA.getComponent().getPosition();
float leftDistance = pos.x - topLeft.x;
if (leftDistance < 1f)
{
leftDistance = 1f;
}
float topDistance = pos.y - topLeft.y;
if (topDistance < 1f)
{
topDistance = 1f;
}
float rightDistance =bottomRight.x-pos.x;
if (rightDistance < 1f)
{
rightDistance = 1f;
}
float bottomDistance = bottomRight.y-pos.y;
if (bottomDistance < 1f)
{
bottomDistance = 1f;
}
Vector2 force = new Vector2((sideForce / leftDistance) - (sideForce / rightDistance), (sideForce / topDistance) - (sideForce / bottomDistance));
nodeA.push(force);
}
for (int n = 0; n < nodes.Length; n++)
{
GraphNode node = nodes[n];
node.step();
}
iterationCount++;
if (iterationCount % renderTime == 0)
{
drawable.redrawGraphPanel();
}
//Thread.Sleep(100);
}
drawable.redrawGraphPanel();
MacroCommand rearrangeCommand = new MacroCommand();
for (int n = 0; n < nodes.Length; n++)
{
GraphNode node = nodes[n];
MoveComponentCommand moveCommand = new MoveComponentCommand(node.getComponent(), node.getStartPosition(), node.getComponent().getPosition());
rearrangeCommand.addCommand(moveCommand);
}
return rearrangeCommand;
}
public MuCell.Model.Vector2 getClosestPoint(MuCell.Model.Vector2 otherPosition)
{
return mousePos;
}
