Examples with ExpressionException cbit.vcell.parser.ExpressionException used on opensource projects

Example 81 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class OutputFunctionContext method computeFunctionTypeWRTExpression.

// check if the new expression is valid for outputFunction of functionType
public VariableType computeFunctionTypeWRTExpression(AnnotatedFunction outputFunction, Expression exp) throws ExpressionException, InconsistentDomainException {
    MathDescription mathDescription = getSimulationOwner().getMathDescription();
    boolean bSpatial = getSimulationOwner().getGeometry().getDimension() > 0;
    if (!bSpatial) {
        return VariableType.NONSPATIAL;
    }
    Expression newexp = new Expression(exp);
    // making sure that output function is not direct function of constant.
    newexp.bindExpression(this);
    // here use math description as symbol table because we allow
    // new expression itself to be function of constant.
    newexp = MathUtilities.substituteFunctions(newexp, this).flatten();
    String[] symbols = newexp.getSymbols();
    VariableType functionType = outputFunction.getFunctionType();
    String funcName = outputFunction.getName();
    Domain funcDomain = outputFunction.getDomain();
    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] = functionType;
            } else {
                Variable var = mathDescription.getVariable(symbols[i]);
                if (var == null) {
                    var = mathDescription.getPostProcessingBlock().getDataGenerator(symbols[i]);
                }
                varTypes[i] = VariableType.getVariableType(var);
                if (funcDomain != null) {
                    if (var.getDomain() == null) {
                        // OK
                        continue;
                    }
                    GeometryClass funcGeoClass = simulationOwner.getGeometry().getGeometryClass(funcDomain.getName());
                    GeometryClass varGeoClass = simulationOwner.getGeometry().getGeometryClass(var.getDomain().getName());
                    if (varGeoClass instanceof SubVolume && funcGeoClass instanceof SurfaceClass) {
                        // seems ok if membrane refereces volume
                        if (!((SurfaceClass) funcGeoClass).isAdjacentTo((SubVolume) varGeoClass)) {
                            // but has to be adjacent
                            String errMsg = "'" + funcName + "' defined on Membrane '" + funcDomain.getName() + "' directly or indirectly references " + " variable '" + symbols[i] + "' defined on Volume '" + var.getDomain().getName() + " which is not adjacent to Membrane '" + funcDomain.getName() + "'.";
                            throw new ExpressionException(errMsg);
                        }
                    } else if (!var.getDomain().compareEqual(funcDomain)) {
                        String errMsg = "'" + funcName + "' defined on '" + funcDomain.getName() + "' directly or indirectly references " + " variable '" + symbols[i] + "' defined on '" + var.getDomain().getName() + ".";
                        throw new ExpressionException(errMsg);
                    }
                }
            }
        }
    }
    // if there are no variables (like built in function, vcRegionArea), check with flattened expression to find out the variable type of the new expression
    VariableDomain functionVariableDomain = functionType.getVariableDomain();
    Function flattenedFunction = new Function(funcName, newexp, funcDomain);
    flattenedFunction.bind(this);
    VariableType newVarType = SimulationSymbolTable.getFunctionVariableType(flattenedFunction, getSimulationOwner().getMathDescription(), symbols, varTypes, bSpatial);
    if (!newVarType.getVariableDomain().equals(functionVariableDomain)) {
        String errMsg = "The expression for '" + funcName + "' includes at least one " + newVarType.getVariableDomain().getName() + " variable. Please make sure that only " + functionVariableDomain.getName() + " variables are " + "referenced in " + functionVariableDomain.getName() + " output functions.";
        throw new ExpressionException(errMsg);
    }
    return newVarType;
}

Example 82 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class NetCDFWriter method getReactionRateLaws.

/**
 * @param reacs
 * @return ReactionRateLaw[]
 */
private ReactionRateLaw[] getReactionRateLaws(Expression[] probs) throws ExpressionException, MathException {
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    ReactionRateLaw[] results = new ReactionRateLaw[probs.length];
    varInProbOrderHash = new Hashtable[probs.length];
    for (int i = 0; i < probs.length; i++) {
        varInProbOrderHash[i] = new Hashtable<String, Integer>();
        results[i] = new ReactionRateLaw();
        Expression prob = probs[i];
        String[] symbols = prob.getSymbols();
        // get stoch variables involved in the reaction
        String[] varSymbols = getVariableSymbols(symbols);
        // max allowed order for each variable(species)
        int maxOrder = 5;
        // order of the reaction
        int totalOrder = 0;
        // the expression of the rate constant
        Expression coefExp = null;
        if (symbols != null) {
            if ((varSymbols != null && !Compare.isEqual(symbols, varSymbols)) || varSymbols == null) {
                throw new MathException("Unrecognized symbols in propensity function " + prob + ". Propensity function should contain stochastic variable symbols only.");
            }
            if (symbols != null && varSymbols != null) {
                PropensitySolver.PropensityFunction pf = PropensitySolver.solvePropensity(prob, varSymbols, maxOrder);
                // get total order and save each var's order according to each reaction.
                for (int j = 0; j < pf.getSpeciesOrders().length; j++) {
                    varInProbOrderHash[i].put(pf.getSpeceisNames()[j], pf.getSpeciesOrders()[j]);
                    totalOrder = totalOrder + pf.getSpeciesOrders()[j];
                }
                // get rate constant
                coefExp = new Expression(pf.getRateExpression());
            }
        } else {
            coefExp = new Expression(prob);
        }
        if (totalOrder == 0) {
            results[i].setLawType(ReactionRateLaw.order_0);
            coefExp = new Expression(coefExp.flatten().infix() + "/6.02e23");
            try {
                coefExp.bindExpression(simSymbolTable);
                coefExp = simSymbolTable.substituteFunctions(coefExp).flatten();
                double val = coefExp.evaluateConstant();
                results[i].setRateConstant(val);
            } catch (Exception e) {
                e.printStackTrace(System.err);
                throw new ExpressionException(e.getMessage());
            }
        } else if (totalOrder == 1) {
            results[i].setLawType(ReactionRateLaw.order_1);
            coefExp = coefExp.flatten();
            try {
                coefExp.bindExpression(simSymbolTable);
                coefExp = simSymbolTable.substituteFunctions(coefExp).flatten();
                double val = coefExp.evaluateConstant();
                results[i].setRateConstant(val);
            } catch (Exception e) {
                e.printStackTrace(System.err);
                throw new ExpressionException(e.getMessage());
            }
        } else if (totalOrder == 2) {
            if (// second order, two same molecules
            varSymbols.length == 1) {
                // k= c*6.02e23/2, since in VCell, "/2" is already incorporated into c, so we don'y need to take care of this item from the conversion.
                coefExp = new Expression(coefExp.flatten().infix() + "*6.02e23");
                results[i].setLawType(ReactionRateLaw.order_2_1substrate);
                try {
                    coefExp.bindExpression(simSymbolTable);
                    coefExp = simSymbolTable.substituteFunctions(coefExp).flatten();
                    double val = coefExp.evaluateConstant();
                    results[i].setRateConstant(val);
                } catch (Exception e) {
                    e.printStackTrace(System.err);
                    throw new ExpressionException(e.getMessage());
                }
            } else if (// second order, two different molecules
            varSymbols.length == 2) {
                coefExp = new Expression(coefExp.flatten().infix() + "*6.02e23");
                results[i].setLawType(ReactionRateLaw.order_2_2substrate);
                try {
                    coefExp.bindExpression(simSymbolTable);
                    coefExp = simSymbolTable.substituteFunctions(coefExp).flatten();
                    double val = coefExp.evaluateConstant();
                    results[i].setRateConstant(val);
                } catch (Exception e) {
                    e.printStackTrace(System.err);
                    throw new ExpressionException(e.getMessage());
                }
            }
        } else if (totalOrder == 3) {
            if (// third order, three same molecules
            varSymbols.length == 1) {
                results[i].setLawType(ReactionRateLaw.order_3_1substrate);
                // use c directly.  "/3!" is already incorporated into c, so we compensate this item from the conversion.
                coefExp = new Expression(coefExp.flatten().infix() + "*6");
            } else if (// third order, three different molecules
            varSymbols.length == 3) {
                results[i].setLawType(ReactionRateLaw.order_3_3substrate);
            } else if (// third order, two different molecules
            varSymbols.length == 2) {
                results[i].setLawType(ReactionRateLaw.order_3_2substrate);
                // use c directly.  "/(2!*1!)" is already incorporated into c, so we compensate this item from the conversion.
                coefExp = new Expression(coefExp.flatten().infix() + "*2");
            }
            coefExp = coefExp.flatten();
            try {
                coefExp.bindExpression(simSymbolTable);
                coefExp = simSymbolTable.substituteFunctions(coefExp).flatten();
                double val = coefExp.evaluateConstant();
                results[i].setRateConstant(val);
            } catch (Exception e) {
                e.printStackTrace(System.err);
                throw new ExpressionException(e.getMessage());
            }
        } else // order more than 3, throw exception
        {
            throw new RuntimeException("Reaction order is more than 3, we couldn't solve it by Hybrid simulation.");
        }
    }
    return results;
}

Example 83 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class StochFileWriter method write.

/**
 * Write the model to a text file which serves as an input for Stochastic simulation engine.
 * Creation date: (6/22/2006 5:37:26 PM)
 */
public void write(String[] parameterNames) throws Exception, ExpressionException {
    Simulation simulation = simTask.getSimulation();
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    initialize();
    if (bUseMessaging) {
        writeJMSParamters();
    }
    // Write control information
    printWriter.println("<control>");
    cbit.vcell.solver.SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
    cbit.vcell.solver.TimeBounds timeBounds = solverTaskDescription.getTimeBounds();
    cbit.vcell.solver.OutputTimeSpec outputTimeSpec = solverTaskDescription.getOutputTimeSpec();
    ErrorTolerance errorTolerance = solverTaskDescription.getErrorTolerance();
    NonspatialStochSimOptions stochOpt = solverTaskDescription.getStochOpt();
    printWriter.println("STARTING_TIME" + "\t" + timeBounds.getStartingTime());
    printWriter.println("ENDING_TIME " + "\t" + timeBounds.getEndingTime());
    // pw.println("MAX_ITERATION"+"\t"+outputTimeSpec.getKeepAtMost());
    printWriter.println("TOLERANCE " + "\t" + errorTolerance.getAbsoluteErrorTolerance());
    if (outputTimeSpec.isDefault()) {
        printWriter.println("SAMPLE_INTERVAL" + "\t" + ((DefaultOutputTimeSpec) outputTimeSpec).getKeepEvery());
        printWriter.println("MAX_SAVE_POINTS" + "\t" + ((DefaultOutputTimeSpec) outputTimeSpec).getKeepAtMost());
    } else if (outputTimeSpec.isUniform()) {
        printWriter.println("SAVE_PERIOD" + "\t" + ((UniformOutputTimeSpec) outputTimeSpec).getOutputTimeStep());
    }
    printWriter.println("NUM_TRIAL" + "\t" + solverTaskDescription.getStochOpt().getNumOfTrials());
    if (stochOpt.isUseCustomSeed()) {
        printWriter.println("SEED" + "\t" + stochOpt.getCustomSeed());
    } else {
        // we generate our own random seed
        RandomDataGenerator rdg = new RandomDataGenerator();
        int randomSeed = rdg.nextInt(1, Integer.MAX_VALUE);
        printWriter.println("SEED" + "\t" + randomSeed);
    }
    printWriter.println("</control>");
    printWriter.println();
    // write model information
    // Model info. will be extracted from subDomain of mathDescription
    Enumeration<SubDomain> e = simulation.getMathDescription().getSubDomains();
    SubDomain subDomain = null;
    if (e.hasMoreElements()) {
        subDomain = e.nextElement();
    }
    if (subDomain != null) {
        printWriter.println("<model>");
        // variables
        printWriter.println("<discreteVariables>");
        // Species iniCondition (if in concentration) is sampled from a poisson distribution(which has a mean of the current iniExp value)
        // There is only one subDomain for compartmental model
        List<VarIniCondition> varInis = subDomain.getVarIniConditions();
        if ((varInis != null) && (varInis.size() > 0)) {
            RandomDataGenerator dist = new RandomDataGenerator();
            if (simulation.getSolverTaskDescription().getStochOpt().isUseCustomSeed()) {
                Integer randomSeed = simulation.getSolverTaskDescription().getStochOpt().getCustomSeed();
                if (randomSeed != null) {
                    dist.reSeed(randomSeed);
                }
            }
            printWriter.println("TotalVars" + "\t" + varInis.size());
            for (VarIniCondition varIniCondition : varInis) {
                try {
                    Expression iniExp = varIniCondition.getIniVal();
                    iniExp.bindExpression(simSymbolTable);
                    iniExp = simSymbolTable.substituteFunctions(iniExp).flatten();
                    double expectedCount = iniExp.evaluateConstant();
                    // 1000 mill
                    final Integer limit = 1000000000;
                    if (limit < expectedCount) {
                        String eMessage = "The Initial count for Species '" + varIniCondition.getVar().getName() + "' is " + BigDecimal.valueOf(expectedCount).toBigInteger() + "\n";
                        eMessage += "which is higher than the internal vCell limit of " + limit + ".\n";
                        eMessage += "Please reduce the Initial Condition value for this Species or reduce the compartment size.";
                        throw new MathFormatException(eMessage);
                    }
                    long varCount = 0;
                    if (varIniCondition instanceof VarIniCount) {
                        varCount = (long) expectedCount;
                    } else {
                        if (expectedCount > 0) {
                            varCount = dist.nextPoisson(expectedCount);
                        }
                    }
                    // System.out.println("expectedCount: " + expectedCount + ", varCount: " + varCount);
                    printWriter.println(varIniCondition.getVar().getName() + "\t" + varCount);
                } catch (ExpressionException ex) {
                    ex.printStackTrace();
                    throw new MathFormatException("variable " + varIniCondition.getVar().getName() + "'s initial condition is required to be a constant.");
                }
            }
        } else
            printWriter.println("TotalVars" + "\t" + "0");
        printWriter.println("</discreteVariables>");
        printWriter.println();
        // jump processes
        printWriter.println("<jumpProcesses>");
        List<JumpProcess> jumpProcesses = subDomain.getJumpProcesses();
        if ((jumpProcesses != null) && (jumpProcesses.size() > 0)) {
            printWriter.println("TotalProcesses" + "\t" + jumpProcesses.size());
            for (int i = 0; i < jumpProcesses.size(); i++) {
                printWriter.println(jumpProcesses.get(i).getName());
            }
        } else
            printWriter.println("TotalProcesses" + "\t" + "0");
        printWriter.println("</jumpProcesses>");
        printWriter.println();
        // process description
        printWriter.println("<processDesc>");
        if ((jumpProcesses != null) && (jumpProcesses.size() > 0)) {
            printWriter.println("TotalDescriptions" + "\t" + jumpProcesses.size());
            for (int i = 0; i < jumpProcesses.size(); i++) {
                JumpProcess temProc = (JumpProcess) jumpProcesses.get(i);
                // jump process name
                printWriter.println("JumpProcess" + "\t" + temProc.getName());
                Expression probExp = temProc.getProbabilityRate();
                try {
                    probExp.bindExpression(simSymbolTable);
                    probExp = simSymbolTable.substituteFunctions(probExp).flatten();
                    if (!isValidProbabilityExpression(probExp)) {
                        throw new MathFormatException("probability rate in jump process " + temProc.getName() + " has illegal symbols(should only contain variable names).");
                    }
                } catch (cbit.vcell.parser.ExpressionException ex) {
                    ex.printStackTrace();
                    throw new cbit.vcell.parser.ExpressionException("Binding math description error in probability rate in jump process " + temProc.getName() + ". Some symbols can not be resolved.");
                }
                // Expression temp = replaceVarIniInProbability(probExp);
                // Propensity
                printWriter.println("\t" + "Propensity" + "\t" + probExp.infix());
                // effects
                printWriter.println("\t" + "Effect" + "\t" + temProc.getActions().size());
                for (int j = 0; j < temProc.getActions().size(); j++) {
                    printWriter.print("\t\t" + ((Action) temProc.getActions().get(j)).getVar().getName() + "\t" + ((Action) temProc.getActions().get(j)).getOperation());
                    printWriter.println("\t" + ((Action) temProc.getActions().get(j)).evaluateOperand());
                    printWriter.println();
                }
                // dependencies
                Vector<String> dependencies = getDependencies(temProc, jumpProcesses);
                if ((dependencies != null) && (dependencies.size() > 0)) {
                    printWriter.println("\t" + "DependentProcesses" + "\t" + dependencies.size());
                    for (int j = 0; j < dependencies.size(); j++) printWriter.println("\t\t" + dependencies.elementAt(j));
                } else
                    printWriter.println("\t" + "DependentProcesses" + "\t" + "0");
                printWriter.println();
            }
        } else
            printWriter.println("TotalDescriptions" + "\t" + "0");
        printWriter.println("</processDesc>");
        printWriter.println("</model>");
    }
// if (subDomain != null)
}

Example 84 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class AugmentedObjectiveFunctionTest method getExample1.

/**
 * Insert the method's description here.
 * Creation date: (5/3/2002 2:49:06 PM)
 * @return opt.AugmentedObjectiveFunction
 */
public static AugmentedObjectiveFunction getExample1() {
    try {
        Expression scalarFn_exp = new Expression("pow(x1-2,4)+pow(x1-2*x2,2)");
        Expression[] eqConstraints_exps = { new Expression("pow(x1,2)-x2") };
        Expression[] ineqConstraints_exps = { new Expression("pow(x1,2)-x2") };
        ;
        String[] ids = { "x1", "x2" };
        ScalarFunction scalarFn = new DynamicScalarFunction(scalarFn_exp, ids);
        VectorFunction eqConstraints = new DynamicVectorFunction(eqConstraints_exps, ids);
        VectorFunction ineqConstraints = new DynamicVectorFunction(ineqConstraints_exps, ids);
        AugmentedObjectiveFunction aof = new AugmentedObjectiveFunction(scalarFn, eqConstraints, ineqConstraints, 2.0, 0.1, new DefaultOptSolverCallbacks());
        return aof;
    } catch (ExpressionException e) {
        e.printStackTrace();
        throw new RuntimeException(e.getMessage());
    }
}

Example 85 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class ExpressionCanvas method getMinimumSize.

/**
 * Insert the method's description here.
 * Creation date: (11/19/2002 11:26:26 AM)
 * @return java.awt.Dimension
 */
public Dimension getMinimumSize() {
    Graphics2D g = (Graphics2D) getGraphics();
    if (g != null) {
        g.setClip(0, 0, getSize().width, getSize().height);
        Font canvasFont = new Font("SansSerif", Font.ITALIC, 11);
        g.setFont(canvasFont);
        FontMetrics fontMetrics = g.getFontMetrics();
        try {
            Dimension minSize = new Dimension(10, 10);
            if (fieldExpressions != null) {
                for (int i = 0; i < fieldExpressions.length; i++) {
                    ExpressionPrintFormatter expPrintFormatter = new ExpressionPrintFormatter(fieldExpressions[i]);
                    Dimension expressionDim = expPrintFormatter.getSize(g);
                    int labelWidth = 0;
                    if (fieldPrefixLabels != null) {
                        labelWidth += g.getFontMetrics().stringWidth(fieldPrefixLabels[i]) + 20;
                    }
                    if (fieldSuffixLabels != null) {
                        labelWidth += g.getFontMetrics().stringWidth(fieldSuffixLabels[i]) + 20;
                    }
                    minSize.width = Math.max(minSize.width, expressionDim.width + 20 + labelWidth);
                    minSize.height += expressionDim.height + 20;
                }
            } else {
                for (String expString : fieldStrings) {
                    int stringWidth = fontMetrics.stringWidth(expString);
                    int stringHeight = fontMetrics.getHeight();
                    minSize.width = Math.max(minSize.width, stringWidth);
                    minSize.height += stringHeight + 20;
                }
            }
            return minSize;
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            return super.getMinimumSize();
        }
    } else {
        return super.getMinimumSize();
    }
}