public void simpleTest()
{
MuCell.Model.SBML.Reader.SBMLReader reader = new MuCell.Model.SBML.Reader.SBMLReader();
FormulaParser fp = new FormulaParser(reader, "3.4+4/(abs(2-4))");
MathTree formulaTree = fp.getFormulaTree();
MuCell.Model.SBML.InnerNode root = (InnerNode)formulaTree.root;
Assert.AreEqual(BinaryMathOperators.Plus, root.data);
/// Assert that the left node is 3.4
Assert.AreEqual(3.4, ((NumberLeafNode)(root.subtree.ToArray())[0]).data);
// Assert that the right is divide
MuCell.Model.SBML.InnerNode right = (InnerNode)(root.subtree.ToArray())[1];
Assert.AreEqual(BinaryMathOperators.Divide, right.data);
// Assert that the right's child is 4 and abs
Assert.AreEqual(4, ((NumberLeafNode)right.subtree[0]).data);
Assert.AreEqual(UnaryMathOperators.Abs, ((InnerNode)right.subtree[1]).data);
// assert that this is a minus
InnerNode minus_child = (InnerNode)((InnerNode)(right.subtree[1])).subtree[0];
Assert.AreEqual(BinaryMathOperators.Minus, minus_child.data);
Assert.AreEqual(2, ((NumberLeafNode)minus_child.subtree[0]).data);
Assert.AreEqual(4, ((NumberLeafNode)minus_child.subtree[1]).data);
// Finally evaluate and check the result
// Fold the tree into a cell function
CellEvaluationFunction fun = formulaTree.ToCellEvaluationFunction();
Assert.AreEqual(5.4, fun(new StateSnapshot(), new CellInstance(new CellDefinition())));
}
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 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));
}
public void testWithSpecies()
{
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
MuCell.Model.Experiment experiment = new MuCell.Model.Experiment("experimen1");
MuCell.Model.Simulation simulation = new MuCell.Model.Simulation("simulation1");
setupExperiment(model, experiment, simulation);
// Test parsing cell def references, group references etc.
MuCell.Model.SBML.Reader.SBMLReader reader = new MuCell.Model.SBML.Reader.SBMLReader();
FormulaParser fp = new FormulaParser(reader, "5.2+s2", model, experiment, simulation);
MathTree formulaTree = fp.getFormulaTree();
MuCell.Model.SBML.InnerNode root = (InnerNode)formulaTree.root;
Assert.AreEqual(BinaryMathOperators.Plus, root.data);
Assert.AreEqual(5.2, ((MuCell.Model.SBML.NumberLeafNode)(root.subtree.ToArray()[0])).data);
Assert.AreEqual("5.2+s2", root.ToString());
MuCell.Model.SBML.AggregateReferenceNode right = (MuCell.Model.SBML.AggregateReferenceNode)(root.subtree.ToArray()[1]);
Assert.AreEqual("s2", right.ToString());
Assert.AreEqual(null, right.CellDefinition);
Assert.AreEqual(null, right.Group);
Assert.AreEqual("s2", right.Species.ID);
}
public void testWithGroup()
{
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
MuCell.Model.Experiment experiment = new MuCell.Model.Experiment("experimen1");
MuCell.Model.Simulation simulation = new MuCell.Model.Simulation("simulation1");
setupExperiment(model, experiment, simulation);
// Test parsing cell def references, group references etc.
MuCell.Model.SBML.Reader.SBMLReader reader = new MuCell.Model.SBML.Reader.SBMLReader();
FormulaParser fp = new FormulaParser(reader, "group1", model, experiment, simulation);
MathTree formulaTree = fp.getFormulaTree();
MuCell.Model.SBML.AggregateReferenceNode root = (MuCell.Model.SBML.AggregateReferenceNode)formulaTree.root;
Assert.AreEqual("group1", root.ToString());
Assert.AreEqual(null, root.CellDefinition);
Assert.AreEqual("1", root.Group.ID);
Assert.AreEqual(null, root.Species);
}
public void testWithCellDefWithSpaces()
{
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
MuCell.Model.Experiment experiment = new MuCell.Model.Experiment("experimen1");
MuCell.Model.Simulation simulation = new MuCell.Model.Simulation("simulation1");
setupExperiment(model, experiment, simulation);
experiment.GetCellDefinition("celldef1").Name = "cell def1";
Assert.That(experiment.ContainsCellDefinition("cell_def1"));
// Test parsing cell def references, group references etc.
MuCell.Model.SBML.Reader.SBMLReader reader = new MuCell.Model.SBML.Reader.SBMLReader();
FormulaParser fp = new FormulaParser(reader, "cell_def1", model, experiment, simulation);
MathTree formulaTree = fp.getFormulaTree();
MuCell.Model.SBML.AggregateReferenceNode root = (MuCell.Model.SBML.AggregateReferenceNode)formulaTree.root;
Assert.AreEqual("cell def1", root.ToString());
Assert.AreEqual(experiment.getCellDefinitions()[0], root.CellDefinition);
Assert.AreEqual(null, root.Group);
Assert.AreEqual(null, root.Species);
}
public void testIdentifiersLists()
{
MuCell.Model.SBML.Reader.SBMLReader s = new MuCell.Model.SBML.Reader.SBMLReader("../../UnitTests/smallest.Hopf.xml");
MuCell.Model.SBML.Reader.SBMLReader reader = new MuCell.Model.SBML.Reader.SBMLReader();
FormulaParser fp = new FormulaParser(reader, "X*A+k_1*B_A", s.model);
MathTree formulaTree = fp.getFormulaTree();
List<Species> formulaSpecies = fp.SpeciesFromFormula();
Assert.AreEqual(2, formulaSpecies.Count);
Assert.AreEqual("X", formulaSpecies.ToArray()[0].ID);
Assert.AreEqual("A", formulaSpecies.ToArray()[1].ID);
List<Parameter> parameters = fp.ParametersFromFormula();
Assert.AreEqual(1, parameters.Count);
Assert.AreEqual("k_1", parameters.ToArray()[0].ID);
List<UnknownEntity> identifiers = fp.UnknownEntitiesFromFormula();
Assert.AreEqual(1, identifiers.Count);
Assert.AreEqual("B_A", identifiers.ToArray()[0].ID);
}
public void testApproximateUnits()
{
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
MuCell.Model.Experiment experiment = new MuCell.Model.Experiment("experimen1");
MuCell.Model.Simulation simulation = new MuCell.Model.Simulation("simulation1");
setupExperiment(model, experiment, simulation);
// Test parsing cell def references, group references etc.
MuCell.Model.SBML.Reader.SBMLReader reader = new MuCell.Model.SBML.Reader.SBMLReader();
FormulaParser fp = new FormulaParser(reader, "5.2", model, experiment, simulation);
MathTree formulaTree = fp.getFormulaTree();
Assert.AreEqual("No units", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "5.2+10", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("No units", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "5.2-10", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("No units", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "5.2*10", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("No units", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "5.2/10", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("No units", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1+celldef2", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1-celldef1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1*celldef2", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells*Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1/celldef2", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells/Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1*celldef2*celldef1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells*Cells*Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1+10", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1*10", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1 / 34.2", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "4/celldef1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("1/Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "24/(celldef1*celldef1)", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("1/Cells*Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1.group1/(celldef1*celldef1)", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells/Cells*Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1/celldef1+10", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells/Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1.group1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1.group2 + celldef1.group1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1.group1/celldef1.group2", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells/Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "143/celldef1.group1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("1/Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s1*4", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s1*s2", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Concentration*Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s1*s2*celldef1.s1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Concentration*Concentration*Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s1*celldef1.group1.s1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Concentration*Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "group2.s2*celldef1.group1.s1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Concentration*Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s1/s2", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Concentration/Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "4.345/s1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("1/Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s1+celldef1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("No units", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "4.345/s1+celldef1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("No units", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1*celldef1.group1.s1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells*Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s2/celldef1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Concentration/Cells", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s2/celldef1+s1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("No units", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "s2/celldef1+celldef2", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("No units", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "celldef1/celldef1.group1.s1", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Cells/Concentration", formulaTree.ApproximateUnits());
fp = new FormulaParser(reader, "Abs(s1)", model, experiment, simulation);
formulaTree = fp.getFormulaTree();
Assert.AreEqual("Concentration", formulaTree.ApproximateUnits());
}
public void evaluateFormula()
{
if (this.formula != null)
{
this.formulaParser = new FormulaParser(new Reader.SBMLReader(), this.formula, this.model);
this.math = formulaParser.getFormulaTree();
}
else
{
// Likely a MathML rate law => therefore set any SBase references
this.math.SetSBaseReferences(this.model);
}
}
/// <summary>
/// Initalizes the time series function - must be called after setting the function string
/// </summary>
/// <param name="models">
/// A <see cref="List`1"/>
/// </param>
/// <param name="experiment">
/// A <see cref="Experiment"/>
/// </param>
/// <param name="simulation">
/// A <see cref="Simulation"/>
/// </param>
public void InitializeTimeSeriesFunction(List<Model.SBML.Model> models, Experiment experiment, Simulation simulation)
{
if (this.functionString!=null)
{
// create a reader
MuCell.Model.SBML.Reader.SBMLReader reader = new MuCell.Model.SBML.Reader.SBMLReader();
// parse the formular
SBML.FormulaParser fp = new SBML.FormulaParser(reader, this.functionString, models, experiment, simulation);
// Get the formula tree
SBML.MathTree formulaTree = fp.getFormulaTree();
// Convert to a function
this.function = formulaTree.ToAggregateEvaluationFunction();
units = formulaTree.ApproximateUnits();
}
}
