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

Example 6 with MathFormatException

use of cbit.vcell.math.MathFormatException 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 7 with MathFormatException

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

the class CartesianMesh method readMembraneMeshMetrics.

/**
 * Insert the method's description here.
 * Creation date: (2/15/2006 2:06:21 PM)
 */
public MembraneMeshMetrics readMembraneMeshMetrics(CommentStringTokenizer tokens) throws MathException {
    MembraneMeshMetrics membraneMeshMetrics = new MembraneMeshMetrics();
    String token = null;
    token = tokens.nextToken();
    if (token.equalsIgnoreCase(VCML.MembraneElements)) {
        token = tokens.nextToken();
    } else {
        throw new MathFormatException("unexpected token " + token + " expecting " + VCML.CartesianMesh);
    }
    if (!token.equalsIgnoreCase(VCML.BeginBlock)) {
        throw new MathFormatException("unexpected token " + token + " expecting " + VCML.BeginBlock);
    }
    token = tokens.nextToken();
    int numMembraneElements = 0;
    try {
        numMembraneElements = Integer.valueOf(token).intValue();
    } catch (NumberFormatException e) {
        throw new MathFormatException("unexpected token " + token + " expecting MembraneElement count");
    }
    short[] regionIndex = new short[numMembraneElements];
    float[] areas = new float[numMembraneElements];
    float[][] normals = new float[numMembraneElements][3];
    float[][] centroids = new float[numMembraneElements][3];
    if (!(token = tokens.nextToken()).equals("Index") || !(token = tokens.nextToken()).equals("RegionIndex") || !(token = tokens.nextToken()).equals("X") || !(token = tokens.nextToken()).equals("Y") || !(token = tokens.nextToken()).equals("Z") || !(token = tokens.nextToken()).equals("Area") || !(token = tokens.nextToken()).equals("Nx") || !(token = tokens.nextToken()).equals("Ny") || !(token = tokens.nextToken()).equals("Nz")) {
        throw new MathFormatException("unexpected MeshMetrics column description = " + token);
    }
    int counter = 0;
    while (tokens.hasMoreTokens()) {
        token = tokens.nextToken();
        if (token.equalsIgnoreCase(VCML.EndBlock)) {
            break;
        }
        if (counter >= numMembraneElements) {
            throw new MathFormatException("Error parsing MembraneMeshMetrics values index=" + counter + ".  Expecting only " + numMembraneElements + " MembraneElements");
        }
        try {
            int index = Integer.valueOf(token).intValue();
            if (index != counter) {
                throw new MathFormatException("unexpected token " + token + " expecting " + counter);
            }
            regionIndex[counter] = Short.parseShort(tokens.nextToken());
            // centroids
            centroids[counter][0] = Float.parseFloat(tokens.nextToken());
            centroids[counter][1] = Float.parseFloat(tokens.nextToken());
            centroids[counter][2] = Float.parseFloat(tokens.nextToken());
            // area
            areas[counter] = Float.parseFloat(tokens.nextToken());
            // normals
            normals[counter][0] = Float.parseFloat(tokens.nextToken());
            normals[counter][1] = Float.parseFloat(tokens.nextToken());
            normals[counter][2] = Float.parseFloat(tokens.nextToken());
        } catch (NumberFormatException e) {
            throw new MathFormatException("Error parsing MembraneMeshMetrics values index=" + counter + "  " + e.getMessage());
        }
        counter += 1;
    }
    membraneMeshMetrics.regionIndexes = regionIndex;
    membraneMeshMetrics.areas = areas;
    membraneMeshMetrics.normals = normals;
    membraneMeshMetrics.centroids = centroids;
    return membraneMeshMetrics;
}

Example 8 with MathFormatException

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

the class XmlReader method getVarIniPoissonExpectedCount.

private VarIniCondition getVarIniPoissonExpectedCount(Element param, MathDescription md) throws XmlParseException, MathException, ExpressionException {
    // retrieve values
    Expression exp = unMangleExpression(param.getText());
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    Variable var = md.getVariable(name);
    if (var == null) {
        throw new MathFormatException("variable " + name + " not defined");
    }
    if (!(var instanceof StochVolVariable)) {
        throw new MathFormatException("variable " + name + " not a Stochastic Volume Variable");
    }
    try {
        VarIniCondition varIni = new VarIniPoissonExpectedCount(var, exp);
        return varIni;
    } catch (Exception e) {
        e.printStackTrace();
    }
    return null;
}