Examples with Variable cbit.vcell.math.Variable used on opensource projects

Example 1 with Variable

use of cbit.vcell.math.Variable in project vcell by virtualcell.

the class MatlabOdeFileCoder method write_V6_MFile.

/**
 * Insert the method's description here.
 * Creation date: (3/8/00 10:31:52 PM)
 */
public void write_V6_MFile(java.io.PrintWriter pw, String functionName) throws MathException, ExpressionException {
    MathDescription mathDesc = simulation.getMathDescription();
    if (!mathDesc.isValid()) {
        throw new MathException("invalid math description\n" + mathDesc.getWarning());
    }
    if (mathDesc.isSpatial()) {
        throw new MathException("spatial math description, cannot create ode file");
    }
    if (mathDesc.hasFastSystems()) {
        throw new MathException("math description contains algebraic constraints, cannot create .m file");
    }
    // 
    // print function declaration
    // 
    pw.println("function [T,Y,yinit,param, allNames, allValues] = " + functionName + "(argTimeSpan,argYinit,argParam)");
    pw.println("% [T,Y,yinit,param] = " + functionName + "(argTimeSpan,argYinit,argParam)");
    pw.println("%");
    pw.println("% input:");
    pw.println("%     argTimeSpan is a vector of start and stop times (e.g. timeSpan = [0 10.0])");
    pw.println("%     argYinit is a vector of initial conditions for the state variables (optional)");
    pw.println("%     argParam is a vector of values for the parameters (optional)");
    pw.println("%");
    pw.println("% output:");
    pw.println("%     T is the vector of times");
    pw.println("%     Y is the vector of state variables");
    pw.println("%     yinit is the initial conditions that were used");
    pw.println("%     param is the parameter vector that was used");
    pw.println("%     allNames is the output solution variable names");
    pw.println("%     allValues is the output solution variable values corresponding to the names");
    pw.println("%");
    pw.println("%     example of running this file: [T,Y,yinit,param,allNames,allValues] = myMatlabFunc; <-(your main function name)");
    pw.println("%");
    VariableHash varHash = new VariableHash();
    for (Variable var : simulationSymbolTable.getVariables()) {
        varHash.addVariable(var);
    }
    Variable[] variables = varHash.getTopologicallyReorderedVariables();
    CompartmentSubDomain subDomain = (CompartmentSubDomain) mathDesc.getSubDomains().nextElement();
    // 
    // collect "true" constants (Constants without identifiers)
    // 
    // 
    // collect "variables" (VolVariables only)
    // 
    // 
    // collect "functions" (Functions and Constants with identifiers)
    // 
    Vector<Constant> constantList = new Vector<Constant>();
    Vector<VolVariable> volVarList = new Vector<VolVariable>();
    Vector<Variable> functionList = new Vector<Variable>();
    for (int i = 0; i < variables.length; i++) {
        if (variables[i] instanceof Constant) {
            Constant constant = (Constant) variables[i];
            String[] symbols = constant.getExpression().getSymbols();
            if (symbols == null || symbols.length == 0) {
                constantList.addElement(constant);
            } else {
                functionList.add(constant);
            }
        } else if (variables[i] instanceof VolVariable) {
            volVarList.addElement((VolVariable) variables[i]);
        } else if (variables[i] instanceof Function) {
            functionList.addElement(variables[i]);
        }
    }
    Constant[] constants = (Constant[]) BeanUtils.getArray(constantList, Constant.class);
    VolVariable[] volVars = (VolVariable[]) BeanUtils.getArray(volVarList, VolVariable.class);
    Variable[] functions = (Variable[]) BeanUtils.getArray(functionList, Variable.class);
    int numVars = volVarList.size() + functionList.size();
    String varNamesForStringArray = "";
    String varNamesForValueArray = "";
    for (Variable var : volVarList) {
        varNamesForStringArray = varNamesForStringArray + "'" + var.getName() + "';";
        varNamesForValueArray = varNamesForValueArray + var.getName() + " ";
    }
    for (Variable func : functionList) {
        varNamesForStringArray = varNamesForStringArray + "'" + func.getName() + "';";
        varNamesForValueArray = varNamesForValueArray + func.getName() + " ";
    }
    pw.println("");
    pw.println("%");
    pw.println("% Default time span");
    pw.println("%");
    double beginTime = 0.0;
    double endTime = simulation.getSolverTaskDescription().getTimeBounds().getEndingTime();
    pw.println("timeSpan = [" + beginTime + " " + endTime + "];");
    pw.println("");
    pw.println("% output variable lengh and names");
    pw.println("numVars = " + numVars + ";");
    pw.println("allNames = {" + varNamesForStringArray + "};");
    pw.println("");
    pw.println("if nargin >= 1");
    pw.println("\tif length(argTimeSpan) > 0");
    pw.println("\t\t%");
    pw.println("\t\t% TimeSpan overridden by function arguments");
    pw.println("\t\t%");
    pw.println("\t\ttimeSpan = argTimeSpan;");
    pw.println("\tend");
    pw.println("end");
    pw.println("%");
    pw.println("% Default Initial Conditions");
    pw.println("%");
    pw.println("yinit = [");
    for (int j = 0; j < volVars.length; j++) {
        Expression initial = subDomain.getEquation(volVars[j]).getInitialExpression();
        double defaultInitialCondition = 0;
        try {
            initial.bindExpression(mathDesc);
            defaultInitialCondition = initial.evaluateConstant();
            pw.println("\t" + defaultInitialCondition + ";\t\t% yinit(" + (j + 1) + ") is the initial condition for '" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[j].getName()) + "'");
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            pw.println("\t" + initial.infix_Matlab() + ";\t\t% yinit(" + (j + 1) + ") is the initial condition for '" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[j].getName()) + "'");
        // throw new RuntimeException("error evaluating initial condition for variable "+volVars[j].getName());
        }
    }
    pw.println("];");
    pw.println("if nargin >= 2");
    pw.println("\tif length(argYinit) > 0");
    pw.println("\t\t%");
    pw.println("\t\t% initial conditions overridden by function arguments");
    pw.println("\t\t%");
    pw.println("\t\tyinit = argYinit;");
    pw.println("\tend");
    pw.println("end");
    pw.println("%");
    pw.println("% Default Parameters");
    pw.println("%   constants are only those \"Constants\" from the Math Description that are just floating point numbers (no identifiers)");
    pw.println("%   note: constants of the form \"A_init\" are really initial conditions and are treated in \"yinit\"");
    pw.println("%");
    pw.println("param = [");
    int paramIndex = 0;
    for (int i = 0; i < constants.length; i++) {
        pw.println("\t" + constants[i].getExpression().infix_Matlab() + ";\t\t% param(" + (paramIndex + 1) + ") is '" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(constants[i].getName()) + "'");
        paramIndex++;
    }
    pw.println("];");
    pw.println("if nargin >= 3");
    pw.println("\tif length(argParam) > 0");
    pw.println("\t\t%");
    pw.println("\t\t% parameter values overridden by function arguments");
    pw.println("\t\t%");
    pw.println("\t\tparam = argParam;");
    pw.println("\tend");
    pw.println("end");
    pw.println("%");
    pw.println("% invoke the integrator");
    pw.println("%");
    pw.println("[T,Y] = ode15s(@f,timeSpan,yinit,odeset('OutputFcn',@odeplot),param,yinit);");
    pw.println("");
    pw.println("% get the solution");
    pw.println("all = zeros(size(T), numVars);");
    pw.println("for i = 1:size(T)");
    pw.println("\tall(i,:) = getRow(T(i), Y(i,:), yinit, param);");
    pw.println("end");
    pw.println("");
    pw.println("allValues = all;");
    pw.println("end");
    // get row data for solution
    pw.println("");
    pw.println("% -------------------------------------------------------");
    pw.println("% get row data");
    pw.println("function rowValue = getRow(t,y,y0,p)");
    // 
    // print volVariables (in order and assign to var vector)
    // 
    pw.println("\t% State Variables");
    for (int i = 0; i < volVars.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[i].getName()) + " = y(" + (i + 1) + ");");
    }
    // 
    // print constants
    // 
    pw.println("\t% Constants");
    paramIndex = 0;
    for (int i = 0; i < constants.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(constants[i].getName()) + " = p(" + (paramIndex + 1) + ");");
        paramIndex++;
    }
    // 
    // print variables
    // 
    pw.println("\t% Functions");
    for (int i = 0; i < functions.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(functions[i].getName()) + " = " + functions[i].getExpression().infix_Matlab() + ";");
    }
    pw.println("");
    pw.println("\trowValue = [" + varNamesForValueArray + "];");
    pw.println("end");
    // 
    // print ode-rate
    // 
    pw.println("");
    pw.println("% -------------------------------------------------------");
    pw.println("% ode rate");
    pw.println("function dydt = f(t,y,p,y0)");
    // 
    // print volVariables (in order and assign to var vector)
    // 
    pw.println("\t% State Variables");
    for (int i = 0; i < volVars.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[i].getName()) + " = y(" + (i + 1) + ");");
    }
    // 
    // print constants
    // 
    pw.println("\t% Constants");
    paramIndex = 0;
    for (int i = 0; i < constants.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(constants[i].getName()) + " = p(" + (paramIndex + 1) + ");");
        paramIndex++;
    }
    // 
    // print variables
    // 
    pw.println("\t% Functions");
    for (int i = 0; i < functions.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(functions[i].getName()) + " = " + functions[i].getExpression().infix_Matlab() + ";");
    }
    pw.println("\t% Rates");
    pw.println("\tdydt = [");
    for (int i = 0; i < volVars.length; i++) {
        pw.println("\t\t" + subDomain.getEquation(volVars[i]).getRateExpression().infix_Matlab() + ";    % rate for " + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[i].getName()));
    }
    pw.println("\t];");
    pw.println("end");
}

Example 2 with Variable

use of cbit.vcell.math.Variable in project vcell by virtualcell.

the class TestingFrameworkWindowManager method getVariableNamesToCompare.

// /**
// * Insert the method's description here.
// * Creation date: (11/23/2004 1:53:11 PM)
// * @return java.lang.String[]
// * @param sim1 cbit.vcell.solver.Simulation
// * @param sim2 cbit.vcell.solver.Simulation
// */
// private VariablePair[] getVariableNamesToCompare(BioModel testBioModel,SimulationSymbolTable testSymboltable, SimulationSymbolTable refSymbolTable){
// Vector<VariablePair> variablePairs = new Vector<VariablePair>();
// 
// //
// // get Variables from Simulation 1
// //
// Variable refVars[] = refSymbolTable.getVariables();
// for (int i = 0;refVars!=null && i < refVars.length; i++){
// if (refVars[i] instanceof VolVariable ||
// refVars[i] instanceof StochVolVariable ||
// refVars[i] instanceof MemVariable ||
// refVars[i] instanceof VolumeRegionVariable ||
// refVars[i] instanceof MembraneRegionVariable ||
// refVars[i] instanceof FilamentVariable ||
// refVars[i] instanceof FilamentRegionVariable){
// 
// VariablePair varPair = new VariablePair();
// varPair.refVariable = refVars[i];
// varPair.domain = refVars[i].getDomain();
// varPair.testVariable = null;
// variablePairs.add(varPair);
// }
// //		Constant sensitivityParameter = simSymbolTable1.getSimulation().getSolverTaskDescription().getSensitivityParameter();
// //		if (sensitivityParameter != null) {
// //			if (simVars[i] instanceof VolVariable) {
// //				hashSet.add(SensVariable.getSensName((VolVariable)simVars[i], sensitivityParameter));
// //			}
// //		}
// }
// 
// //
// // add Variables from Simulation 2
// //
// Variable[] testVars = testSymboltable.getVariables();
// for (int i = 0;testVars!=null && i < testVars.length; i++){
// if (testVars[i] instanceof VolVariable ||
// testVars[i] instanceof MemVariable ||
// testVars[i] instanceof VolumeRegionVariable ||
// testVars[i] instanceof MembraneRegionVariable ||
// testVars[i] instanceof FilamentVariable ||
// testVars[i] instanceof FilamentRegionVariable){
// 
// if(testVars[i].getDomain() == null){
// boolean BFoundMatchingName = false;
// for (int j = 0; j < variablePairs.size(); j++) {
// VariablePair varPair = variablePairs.elementAt(j);
// if(varPair.refVariable.getName().equals(testVars[i].getName())){
// varPair.testVariable = testVars[i];
// BFoundMatchingName = true;
// break;
// }
// }
// if(!BFoundMatchingName){
// //Try to find other matching variable types (e.g. functions)
// Variable dataSet1Match = refSymbolTable.getVariable(testVars[i].getName());
// if(dataSet1Match != null){
// VariablePair varPair = new VariablePair();
// varPair.refVariable = dataSet1Match;
// varPair.testVariable = testVars[i];
// varPair.domain = varPair.refVariable.getDomain();
// variablePairs.add(varPair);
// }else{
// SpeciesContext testSpeciescontext0 = testBioModel.getModel().getSpeciesContext(testVars[i].getName());
// if(testSpeciescontext0 != null){
// Species refspecies = testSpeciescontext0.getSpecies();
// Variable refVariable = refSymbolTable.getVariable(refspecies.getCommonName());
// if(refVariable != null){
// VariablePair varPair = new VariablePair();
// varPair.refVariable = refVariable;
// varPair.testVariable = testVars[i];
// varPair.domain = varPair.refVariable.getDomain();
// variablePairs.add(varPair);
// }
// }else{
// Species testSpecies = testBioModel.getModel().getSpecies(testVars[i].getName());
// if(testSpecies != null){
// for (int j = 0; j < testBioModel.getModel().getSpeciesContexts().length; j++) {
// if(testBioModel.getModel().getSpeciesContexts()[j].getSpecies() == testSpecies){
// Variable refVar = refSymbolTable.getVariable(testBioModel.getModel().getSpeciesContexts()[j].getName());
// if(refVar != null){
// VariablePair varPair = new VariablePair();
// varPair.refVariable = refVar;
// varPair.testVariable = testVars[i];
// varPair.domain = varPair.refVariable.getDomain();
// variablePairs.add(varPair);
// }
// }
// }
// }
// }
// }
// }
// }else{
// 
// }
// hashSet.add(simVars[i].getName());
// }
// Constant sensitivityParameter = refSymbolTable.getSimulation().getSolverTaskDescription().getSensitivityParameter();
// if (sensitivityParameter != null) {
// if (simVars[i] instanceof VolVariable) {
// hashSet.add(SensVariable.getSensName((VolVariable)simVars[i], sensitivityParameter));
// }
// }
// }
// 
// return (String[])hashSet.toArray(new String[hashSet.size()]);
// }
/**
 * Insert the method's description here.
 * Creation date: (11/23/2004 1:53:11 PM)
 * @return java.lang.String[]
 * @param sim1 cbit.vcell.solver.Simulation
 * @param sim2 cbit.vcell.solver.Simulation
 */
private String[] getVariableNamesToCompare(SimulationSymbolTable simSymbolTable1, SimulationSymbolTable simSymbolTable2) {
    java.util.HashSet<String> hashSet = new java.util.HashSet<String>();
    // 
    // get Variables from Simulation 1
    // 
    Variable[] simVars = simSymbolTable1.getVariables();
    for (int i = 0; simVars != null && i < simVars.length; i++) {
        if (simVars[i] instanceof VolVariable || simVars[i] instanceof StochVolVariable || simVars[i] instanceof MemVariable || simVars[i] instanceof VolumeRegionVariable || simVars[i] instanceof MembraneRegionVariable || simVars[i] instanceof FilamentVariable || simVars[i] instanceof FilamentRegionVariable) {
            hashSet.add(simVars[i].getName());
        }
        Constant sensitivityParameter = simSymbolTable1.getSimulation().getSolverTaskDescription().getSensitivityParameter();
        if (sensitivityParameter != null) {
            if (simVars[i] instanceof VolVariable) {
                hashSet.add(SensVariable.getSensName((VolVariable) simVars[i], sensitivityParameter));
            }
        }
    }
    // 
    // add Variables from Simulation 2
    // 
    simVars = simSymbolTable2.getVariables();
    for (int i = 0; simVars != null && i < simVars.length; i++) {
        if (simVars[i] instanceof VolVariable || simVars[i] instanceof MemVariable || simVars[i] instanceof VolumeRegionVariable || simVars[i] instanceof MembraneRegionVariable || simVars[i] instanceof FilamentVariable || simVars[i] instanceof FilamentRegionVariable) {
            hashSet.add(simVars[i].getName());
        }
        Constant sensitivityParameter = simSymbolTable2.getSimulation().getSolverTaskDescription().getSensitivityParameter();
        if (sensitivityParameter != null) {
            if (simVars[i] instanceof VolVariable) {
                hashSet.add(SensVariable.getSensName((VolVariable) simVars[i], sensitivityParameter));
            }
        }
    }
    return (String[]) hashSet.toArray(new String[hashSet.size()]);
}

Example 3 with Variable

use of cbit.vcell.math.Variable in project vcell by virtualcell.

the class SimulationWorkspace method getExpectedSizeBytes.

/**
 * Insert the method's description here.
 * Creation date: (6/12/2001 10:09:25 AM)
 * @return boolean
 * @param simulation cbit.vcell.solver.Simulation
 */
private static long getExpectedSizeBytes(SimulationSymbolTable simSymbolTable) {
    Simulation simulation = simSymbolTable.getSimulation();
    long numTimepoints;
    if (simulation.getMathDescription().isNonSpatialStoch()) {
        numTimepoints = getEstimatedNumTimePointsForStoch(simSymbolTable);
    } else {
        numTimepoints = getExpectedNumTimePoints(simulation);
    }
    int x, y, z;
    int numVariables = 0;
    if (simulation.isSpatial()) {
        x = simulation.getMeshSpecification().getSamplingSize().getX();
        y = simulation.getMeshSpecification().getSamplingSize().getY();
        z = simulation.getMeshSpecification().getSamplingSize().getZ();
        // 
        // compute number of volume variables only (they are multiplied by x*y*z)
        // 
        numVariables = 0;
        Enumeration<Variable> variables = simulation.getMathDescription().getVariables();
        while (variables.hasMoreElements()) {
            Variable var = variables.nextElement();
            if (var instanceof VolVariable) {
                numVariables++;
            }
        }
    } else {
        x = 1;
        y = 1;
        z = 1;
        numVariables = 0;
        Enumeration<Variable> variables = simulation.getMathDescription().getVariables();
        while (variables.hasMoreElements()) {
            Variable var = variables.nextElement();
            if ((var instanceof VolVariable) || (var instanceof Function)) {
                numVariables++;
            }
        }
    }
    // approximate, don't compute header size since it's negligible whenever we approach quota size anyway...
    // values are actually written as longs
    long expectedSize = numTimepoints * numVariables * x * y * z * 8;
    return expectedSize;
}

Example 4 with Variable

use of cbit.vcell.math.Variable in project vcell by virtualcell.

the class OutputFunctionsPanel method getPossibleGeometryClassesAndVariableTypes.

private ArrayList<Object> getPossibleGeometryClassesAndVariableTypes(Expression expr) throws ExpressionException, InconsistentDomainException {
    SimulationOwner simulationOwner = getSimulationWorkspace().getSimulationOwner();
    MathDescription mathDescription = simulationOwner.getMathDescription();
    boolean bSpatial = simulationOwner.getGeometry().getDimension() > 0;
    if (!bSpatial) {
        return null;
    }
    // making sure that output function is not direct function of constant.
    expr.bindExpression(outputFunctionContext);
    // new expression itself to be function of constant.
    try {
        expr = MathUtilities.substituteFunctions(expr, outputFunctionContext).flatten();
    } catch (ExpressionBindingException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
        expr = MathUtilities.substituteFunctions(expr, outputFunctionContext, true).flatten();
    }
    String[] symbols = expr.getSymbols();
    // using bit operation to determine whether geometry classes for symbols in expression are vol, membrane or both. 01 => vol; 10 => membrane; 11 => both
    int gatherFlag = 0;
    Set<GeometryClass> geomClassSet = new HashSet<GeometryClass>();
    ArrayList<Object> objectsList = new ArrayList<Object>();
    boolean bHasVariable = false;
    VariableType[] varTypes = null;
    if (symbols != null && symbols.length > 0) {
        // making sure that new expression is defined in the same domain
        varTypes = new VariableType[symbols.length];
        for (int i = 0; i < symbols.length; i++) {
            if (ReservedMathSymbolEntries.getReservedVariableEntry(symbols[i]) != null) {
                varTypes[i] = VariableType.VOLUME;
            } else {
                Variable var = mathDescription.getVariable(symbols[i]);
                if (var == null) {
                    var = mathDescription.getPostProcessingBlock().getDataGenerator(symbols[i]);
                }
                varTypes[i] = VariableType.getVariableType(var);
                bHasVariable = true;
                if (var.getDomain() != null) {
                    GeometryClass varGeoClass = simulationOwner.getGeometry().getGeometryClass(var.getDomain().getName());
                    geomClassSet.add(varGeoClass);
                    if (varGeoClass instanceof SubVolume) {
                        gatherFlag |= 1;
                    } else if (varGeoClass instanceof SurfaceClass) {
                        gatherFlag |= 2;
                    }
                }
                if (varTypes[i].equals(VariableType.POSTPROCESSING)) {
                    gatherFlag |= 4;
                }
            }
        }
    }
    if (gatherFlag > 4) {
        throw new RuntimeException("cannot mix post processing variables with membrane or volume variables");
    }
    int numGeomClasses = geomClassSet.size();
    if (numGeomClasses == 0) {
        if (bHasVariable) {
            // if there are no variables (like built in function, vcRegionArea), check with flattened expression to find out the variable type of the new expression
            Function flattenedFunction = new Function(getFunctionNameTextField().getText(), expr, null);
            flattenedFunction.bind(outputFunctionContext);
            VariableType newVarType = SimulationSymbolTable.getFunctionVariableType(flattenedFunction, simulationOwner.getMathDescription(), symbols, varTypes, bSpatial);
            objectsList.add(newVarType);
        } else {
            objectsList.add(VariableType.VOLUME);
            objectsList.add(VariableType.MEMBRANE);
        }
    } else if (numGeomClasses == 1) {
        objectsList.add(geomClassSet.iterator().next());
        if (gatherFlag == 1) {
            objectsList.add(VariableType.MEMBRANE);
        }
    } else if (gatherFlag == 1) {
        // all volumes
        if (numGeomClasses == 2) {
            // all subvolumes, if there are only 2, check for adjacency.
            GeometryClass[] geomClassesArray = geomClassSet.toArray(new GeometryClass[0]);
            SurfaceClass sc = simulationOwner.getGeometry().getGeometrySurfaceDescription().getSurfaceClass((SubVolume) geomClassesArray[0], (SubVolume) geomClassesArray[1]);
            if (sc != null) {
                objectsList.add(sc);
            }
        }
        objectsList.add(VariableType.VOLUME);
    } else if (gatherFlag == 2) {
        // all membranes
        objectsList.add(VariableType.MEMBRANE);
    } else if (gatherFlag == 3) {
        // mixed - both vols and membranes
        // add only membranes?
        objectsList.add(VariableType.MEMBRANE);
    }
    return objectsList;
}

Example 5 with Variable

use of cbit.vcell.math.Variable in project vcell by virtualcell.

the class ParameterEstimationRunTaskPanel method plot.

private void plot() {
    try {
        java.util.Vector<DataSource> dataSourceList = new java.util.Vector<DataSource>();
        java.util.Vector<String> nameVector = new java.util.Vector<String>();
        ModelOptimizationSpec modelOptimizationSpec = parameterEstimationTask.getModelOptimizationSpec();
        final ReferenceDataMappingSpec[] mappingSpecs = modelOptimizationSpec.getReferenceDataMappingSpecs();
        int timeIndex = modelOptimizationSpec.getReferenceDataTimeColumnIndex();
        ReferenceData referenceData = modelOptimizationSpec.getReferenceData();
        if (referenceData != null) {
            dataSourceList.add(new DataSource.DataSourceReferenceData("EXPT", timeIndex, referenceData));
            String[] refColumnNames = referenceData.getColumnNames();
            for (int i = 0; i < refColumnNames.length; i++) {
                if (i == timeIndex) {
                    continue;
                }
                nameVector.add(refColumnNames[i]);
                break;
            }
        }
        ParameterEstimationTaskSimulatorIDA parestSimulator = new ParameterEstimationTaskSimulatorIDA();
        ODESolverResultSet odeSolverResultSet = parestSimulator.getOdeSolverResultSet(parameterEstimationTask);
        if (odeSolverResultSet != null) {
            dataSourceList.add(new DataSource.DataSourceRowColumnResultSet("EST", odeSolverResultSet));
            if (mappingSpecs != null) {
                for (int i = 0; i < mappingSpecs.length; i++) {
                    if (i == timeIndex) {
                        continue;
                    }
                    Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(mappingSpecs[i].getModelObject());
                    nameVector.add(var.getName());
                    break;
                }
            }
        }
        DataSource[] dataSources = (DataSource[]) BeanUtils.getArray(dataSourceList, DataSource.class);
        MultisourcePlotPane multisourcePlotPane = new MultisourcePlotPane();
        multisourcePlotPane.setGroupingListSorter(new Comparator<SortDataReferenceHelper>() {

            @Override
            public int compare(SortDataReferenceHelper o1, SortDataReferenceHelper o2) {
                DataSource ds01 = o1.dataReference.getDataSource();
                DataSource ds02 = o2.dataReference.getDataSource();
                // System.out.println(ds01.getClass().getSimpleName()+" "+o1.dataReference.getIdentifier()+" "+ds02.getClass().getSimpleName()+" "+o2.dataReference.getIdentifier());
                if (ds01 instanceof DataSource.DataSourceReferenceData) {
                    if (ds02 instanceof DataSource.DataSourceReferenceData) {
                        // both reference data, sort names
                        ReferenceDataMappingSpec mspec01 = null;
                        ReferenceDataMappingSpec mspec02 = null;
                        for (ReferenceDataMappingSpec rdMappingSpec : mappingSpecs) {
                            // Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(rdMappingSpec.getModelObject());
                            if (rdMappingSpec.getModelObject() instanceof ReservedSymbol) {
                                continue;
                            }
                            if (o1.dataReference.getIdentifier().equals(rdMappingSpec.getReferenceDataColumnName())) {
                                mspec01 = rdMappingSpec;
                                o1.setReferenceDataMappingSpec(rdMappingSpec);
                            } else if (o2.dataReference.getIdentifier().equals(rdMappingSpec.getReferenceDataColumnName())) {
                                mspec02 = rdMappingSpec;
                                o2.setReferenceDataMappingSpec(rdMappingSpec);
                            }
                        }
                        if (mspec01 == null && mspec02 == null) {
                            return o1.dataReference.getIdentifier().compareToIgnoreCase(o2.dataReference.getIdentifier());
                        } else if (mspec01 != null && mspec02 != null) {
                            return mspec01.getReferenceDataColumnName().compareToIgnoreCase(mspec02.getReferenceDataColumnName());
                        } else if (mspec01 != null && mspec02 == null) {
                            return -1;
                        } else {
                            return 1;
                        }
                    } else {
                        // compare ref to ode
                        ReferenceDataMappingSpec mspec01 = null;
                        ReferenceDataMappingSpec mspec02 = null;
                        for (ReferenceDataMappingSpec rdMappingSpec : mappingSpecs) {
                            Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(rdMappingSpec.getModelObject());
                            if (rdMappingSpec.getModelObject() instanceof ReservedSymbol) {
                                continue;
                            }
                            if (o1.dataReference.getIdentifier().equals(rdMappingSpec.getReferenceDataColumnName())) {
                                mspec01 = rdMappingSpec;
                                o1.setReferenceDataMappingSpec(rdMappingSpec);
                            } else if (o2.dataReference.getIdentifier().equals(var.getName())) {
                                mspec02 = rdMappingSpec;
                                o2.setReferenceDataMappingSpec(rdMappingSpec);
                            }
                        }
                        if (mspec01 == null && mspec02 == null) {
                            return -1;
                        } else if (mspec01 != null && mspec02 == null) {
                            return -1;
                        } else if (mspec02 != null && mspec01 == null) {
                            return 1;
                        } else {
                            // BeanUtils.forceStringSize(mspec02.getReferenceDataColumnName(), 25, " ", true));
                            return mspec01.getReferenceDataColumnName().compareToIgnoreCase(mspec02.getReferenceDataColumnName());
                        }
                    }
                } else {
                    if (ds02 instanceof DataSource.DataSourceRowColumnResultSet) {
                        // both OdeSolverResultSet data, sort names
                        ReferenceDataMappingSpec mspec01 = null;
                        ReferenceDataMappingSpec mspec02 = null;
                        for (ReferenceDataMappingSpec rdMappingSpec : mappingSpecs) {
                            Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(rdMappingSpec.getModelObject());
                            if (rdMappingSpec.getModelObject() instanceof ReservedSymbol) {
                                continue;
                            }
                            if (o1.dataReference.getIdentifier().equals(var.getName())) {
                                mspec01 = rdMappingSpec;
                                o1.setReferenceDataMappingSpec(rdMappingSpec);
                            } else if (o2.dataReference.getIdentifier().equals(var.getName())) {
                                mspec02 = rdMappingSpec;
                                o2.setReferenceDataMappingSpec(rdMappingSpec);
                            }
                        }
                        if (mspec01 == null && mspec02 == null) {
                            return o1.dataReference.getIdentifier().compareToIgnoreCase(o2.dataReference.getIdentifier());
                        } else if (mspec01 != null && mspec02 != null) {
                            return mspec01.getReferenceDataColumnName().compareToIgnoreCase(mspec02.getReferenceDataColumnName());
                        } else if (mspec01 != null && mspec02 == null) {
                            return -1;
                        } else {
                            return 1;
                        }
                    } else {
                        // compare ode to ref
                        ReferenceDataMappingSpec mspec01 = null;
                        ReferenceDataMappingSpec mspec02 = null;
                        for (ReferenceDataMappingSpec rdMappingSpec : mappingSpecs) {
                            Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(rdMappingSpec.getModelObject());
                            if (rdMappingSpec.getModelObject() instanceof ReservedSymbol) {
                                continue;
                            }
                            if (o2.dataReference.getIdentifier().equals(rdMappingSpec.getReferenceDataColumnName())) {
                                mspec02 = rdMappingSpec;
                                o2.setReferenceDataMappingSpec(rdMappingSpec);
                            } else if (o1.dataReference.getIdentifier().equals(var.getName())) {
                                mspec01 = rdMappingSpec;
                                o1.setReferenceDataMappingSpec(rdMappingSpec);
                            }
                        }
                        if (mspec01 == null && mspec02 == null) {
                            return 1;
                        } else if (mspec01 != null && mspec02 == null) {
                            return -1;
                        } else if (mspec02 != null && mspec01 == null) {
                            return 1;
                        } else {
                            // BeanUtils.forceStringSize(mspec02.getReferenceDataColumnName(), 25, " ", true));
                            return mspec01.getReferenceDataColumnName().compareToIgnoreCase(mspec02.getReferenceDataColumnName());
                        }
                    }
                }
            }
        });
        multisourcePlotPane.setDataSources(dataSources);
        String[] nameArray = new String[nameVector.size()];
        nameArray = (String[]) BeanUtils.getArray(nameVector, String.class);
        multisourcePlotPane.select(nameArray);
        DialogUtils.showComponentCloseDialog(JOptionPane.getFrameForComponent(this), multisourcePlotPane, "Data Plot");
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}