public static SampleValue MassCompileSample(Symbol outSymbol, SampleValue inSample, Netlist netlist, Style style)
{
//inSample.Consume(null, 0, null, netlist, style); // this prevents simulating a sample and its massaction version in succession
List <ReactionValue> inReactions = inSample.RelevantReactions(netlist, style);
CRN inCrn = new CRN(inSample, inReactions);
Gui.Log(Environment.NewLine + inCrn.FormatNice(style));
(Lst <Polynomize.ODE> odes, Lst <Polynomize.Equation> eqs) = Polynomize.FromCRN(inCrn);
(Lst <Polynomize.PolyODE> polyOdes, Lst <Polynomize.Equation> polyEqs) = Polynomize.PolynomizeODEs(odes, eqs.Reverse(), style);
Gui.Log("Polynomize:" + Environment.NewLine + Polynomize.PolyODE.Format(polyOdes, style)
+ "Initial:" + Environment.NewLine + Polynomize.Equation.Format(polyEqs, style));
(Lst <Polynomize.PolyODE> posOdes, Lst <Polynomize.Equation> posEqs, Dictionary <Symbol, SpeciesFlow> dict, Lst <Positivize.Subst> substs) = Positivize.PositivizeODEs(polyOdes, polyEqs, style);
Gui.Log("Positivize:" + Environment.NewLine + Polynomize.PolyODE.Format(posOdes, style)
+ "Initial:" + Environment.NewLine + Polynomize.Equation.Format(posEqs, style));
Lst <ReactionValue> outReactions = Hungarize.ToReactions(posOdes, style);
Gui.Log("Hungarize:" + Environment.NewLine + outReactions.FoldR((r, s) => { return(r.FormatNormal(style) + Environment.NewLine + s); }, "")
+ "Initial:" + Environment.NewLine + Polynomize.Equation.Format(posEqs, style));
SampleValue outSample = new SampleValue(outSymbol, new StateMap(outSymbol, new List <SpeciesValue> {
}, new State(0, lna: inSample.stateMap.state.lna)), new NumberValue(inSample.Volume()), new NumberValue(inSample.Temperature()), produced: true);
netlist.Emit(new SampleEntry(outSample));
posOdes.Each(ode => {
Flow initFlow = Polynomize.Equation.ToFlow(ode.var, posEqs, style).Normalize(style);
double init; if (initFlow is NumberFlow num)
{
init = num.value;
}
else
{
throw new Error("Cannot generate a simulatable sample because initial values contain constants (but the symbolic version has been generated assuming constants are nonnegative).");
}
if (init < 0)
{
throw new Error("Negative initial value of Polynomized ODE for: " + Polynomize.Lookup(ode.var, eqs, style).Format(style) + " = " + init + Environment.NewLine + Polynomize.Equation.Format(eqs, style));
}
outSample.stateMap.AddDimensionedSpecies(new SpeciesValue(ode.var.species, -1.0), init, 0.0, "M", outSample.Volume(), style);
});
outReactions.Each(reaction => { netlist.Emit(new ReactionEntry(reaction)); });
substs.Each(subst => { ReportEntry report = new ReportEntry(null, OpFlow.Op(subst.plus, "-", subst.minus), null, outSample); outSample.AddReport(report); });
foreach (KeyValuePair <Symbol, SpeciesFlow> keypair in dict)
{
ReportEntry report = new ReportEntry(null, keypair.Value, null, outSample); outSample.AddReport(report);
}
;
return(outSample);
}
public ValueEnv(string name, Type type, Value value, Netlist netlist, Env next) : this(new Symbol(name), type, value, next)
{
if (netlist != null)
{
netlist.Emit(new ValueEntry(this.symbol, type, value)); // also emit the new binding to netlist
}
}
private static void Execute_Worker(bool doParse, bool doAST, bool doScope, bool autoContinue, bool chartOutput)
{
KGui.gui.GuiBeginningExecution();
lastExecution = null;
KGui.gui.GuiSaveInput();
KGui.gui.GuiOutputClear();
DateTime startTime = DateTime.Now;
if (TheParser.Parser().Parse(KGui.gui.GuiInputGetText(), out IReduction root))
{
if (doParse)
{
root.DrawReductionTree();
}
else
{
Netlist netlist = new Netlist(autoContinue);
try
{
Statements statements = Parser.ParseTop(root);
if (doAST)
{
KGui.gui.GuiOutputAppendText(statements.Format());
}
else
{
SampleValue vessel = Vessel(KControls.SelectNoiseSelectedItem != Noise.None);
Env initialEnv = new ValueEnv("vessel", Type.Sample, vessel, new BuiltinEnv(new NullEnv()));
Scope initialScope = initialEnv.ToScope();
Scope scope = statements.Scope(initialScope);
if (doScope)
{
KGui.gui.GuiOutputAppendText(scope.Format());
}
else
{
Style style = new Style(varchar: scopeVariants ? defaultVarchar : null, new SwapMap(),
map: remapVariants ? new AlphaMap() : null, numberFormat: "G4", dataFormat: "full", // we want it full for samples, but maybe only headers for functions/networks?
exportTarget: ExportTarget.Standard, traceFull: false, chartOutput: chartOutput);
KChartHandler.ChartClear("", "s", "M", style);
KChartHandler.LegendUpdate(style);
KScoreHandler.ScoreClear();
KControls.ParametersClear(style);
KDeviceHandler.Clear(style);
KDeviceHandler.Sample(vessel, style);
netlist.Emit(new SampleEntry(vessel));
DateTime evalTime = DateTime.Now;
lastExecution = new ExecutionInstance(vessel, netlist, style, startTime, evalTime);
lastExecution.environment = statements.EvalReject(initialEnv, netlist, style, 0);
if (lastExecution.environment == null)
{
throw new Error("Top level reject");
}
lastExecution.EndTime();
if (style.chartOutput)
{
foreach (ParameterEntry parameter in netlist.Parameters())
{
KControls.AddParameter(parameter.symbol.Format(style), (parameter.value as NumberValue).value, parameter.distribution, style);
}
KGui.gui.GuiParametersUpdate(); // calls back KControls.ParametersUpdate, but only on Win/Mac
}
KGui.gui.GuiProcessOutput();
}
}
}
catch (ExecutionEnded) { lastExecution.EndTime(); KGui.gui.GuiOutputAppendText(lastExecution.ElapsedTime()); }
catch (ConstantEvaluation ex) { string cat = "Does not have a value: "; netlist.Emit(new CommentEntry(cat + ": " + ex.Message)); KGui.gui.GuiInputSetErrorSelection(-1, -1, 0, cat, ex.Message); }
catch (Error ex) { netlist.Emit(new CommentEntry(ex.Message)); KGui.gui.GuiInputSetErrorSelection(-1, -1, 0, "Error", ex.Message); try { KGui.gui.GuiProcessOutput(); } catch { }; }
catch (StackOverflowException ex) { netlist.Emit(new CommentEntry(ex.Message)); KGui.gui.GuiInputSetErrorSelection(-1, -1, 0, "Stack Overflow", ex.Message); }
catch (Exception ex) { string cat = "Something happened"; netlist.Emit(new CommentEntry(cat + ": " + ex.Message)); KGui.gui.GuiInputSetErrorSelection(-1, -1, 0, cat, ex.Message); }
}
}
else
{
KGui.gui.GuiInputSetErrorSelection(TheParser.Parser().FailLineNumber(), TheParser.Parser().FailColumnNumber(), TheParser.Parser().FailLength(), TheParser.Parser().FailCategory(), TheParser.Parser().FailMessage());
}
EndingExecution();
}