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

Example 46 with ExpressionException

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

the class ConvFunctionDefinition method differentiate.

public Expression differentiate(Expression[] args, String variable) throws ExpressionException {
    if (variable == null) {
        throw new RuntimeException("cannot differentiate with respect to a null variable");
    }
    if (args.length != 2) {
        throw new IllegalArgumentException("expecting 2 arguments for vcConv()");
    }
    if (variable.equals(ReservedVariable.X.getName()) || variable.equals(ReservedVariable.Y.getName()) || variable.equals(ReservedVariable.Z.getName())) {
        throw new ExpressionException("differentiation with respect to x,y,z not supported for vcConv() function");
    }
    // 
    // TODO: take advantage of commutative property of differential operators: d/dvar(conv(u,v)) = conv(du/dvar,dv/dvar) ????? (check this).
    // so, if du/dvar=constant then grad(du/dvar) = 0, since grad(constant)=0
    // 
    Expression exp0 = args[0].differentiate(variable).flatten();
    Expression exp1 = args[1].differentiate(variable).flatten();
    if (exp0.isNumeric() || exp1.isNumeric()) {
        // conv(0,f) = 0
        return new Expression(0.0);
    } else {
        return new Expression(Expression.function(FUNCTION_name, exp0, exp1));
    }
}

Example 47 with ExpressionException

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

the class FieldFunctionDefinition method differentiate.

public Expression differentiate(Expression[] args, String variable) throws ExpressionException {
    if (variable == null) {
        throw new RuntimeException("cannot differentiate with respect to a null variable");
    }
    if (args.length != 4) {
        throw new IllegalArgumentException("expecting 4 arguments for vcField()");
    }
    if (variable.equals(ReservedVariable.X.getName()) || variable.equals(ReservedVariable.Y.getName()) || variable.equals(ReservedVariable.Z.getName())) {
        throw new ExpressionException("differentiation with respect to x,y,z not supported for fields");
    }
    Expression timeArgument = args[2];
    Expression exp = timeArgument.differentiate(variable);
    if (exp.isZero()) {
        return new Expression(0.0);
    } else {
        throw new ExpressionException("differentiation with respect to '" + variable + "' not supported for function vcField() with time argument '" + timeArgument.infix() + "'");
    }
}

Example 48 with ExpressionException

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

the class GradientFunctionDefinition method differentiate.

public Expression differentiate(Expression[] args, String variable) throws ExpressionException {
    if (variable == null) {
        throw new RuntimeException("cannot differentiate with respect to a null variable");
    }
    if (args.length != 2) {
        throw new IllegalArgumentException("expecting 2 arguments for vcGrad()");
    }
    if (variable.equals(ReservedVariable.X.getName()) || variable.equals(ReservedVariable.Y.getName()) || variable.equals(ReservedVariable.Z.getName())) {
        throw new ExpressionException("differentiation with respect to x,y,z not supported for vcGrad() function");
    }
    // 
    // take advantage of commutative property of differential operators: d/dvar(grad(u)) = grad(du/dvar)
    // so, if du/dvar=constant then grad(du/dvar) = 0, since grad(constant)=0
    // 
    Expression variableArgument = args[0];
    Expression exp = variableArgument.differentiate(variable).flatten();
    if (exp.isNumeric()) {
        return new Expression(0.0);
    } else {
        throw new ExpressionException("differentiation with respect to '" + variable + "' not supported for function vcField() with time argument '" + variableArgument.infix() + "'");
    }
}

Example 49 with ExpressionException

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

the class FRAPEstimationPanel_NotUsed method initialize.

private void initialize() {
    initTable();
    for (int i = 0; i < FrapDataAnalysisResults.DiffusionOnlyAnalysisRestults.BLEACH_TYPE_NAMES.length; i++) {
        bleachEstimationComboBox.addItem(FrapDataAnalysisResults.DiffusionOnlyAnalysisRestults.BLEACH_TYPE_NAMES[i]);
    // bleachEstimationComboBox.insertItemAt(/*"Estimation method '"+*/"'"+FrapDataAnalysisResults.BLEACH_TYPE_NAMES[i]+"'", i);
    }
    bleachEstimationComboBox.addActionListener(new ActionListener() {

        public void actionPerformed(final ActionEvent e) {
            // }else
            if (bleachEstimationComboBox.getSelectedItem().equals(FrapDataAnalysisResults.DiffusionOnlyAnalysisRestults.BLEACH_TYPE_NAMES[FrapDataAnalysisResults.DiffusionOnlyAnalysisRestults.BleachType_GaussianSpot])) {
                // expression on canvas
                try {
                    String[] prefixes = new String[] { "I(t) = ", "u(t)= ", "D = " };
                    Expression[] expressions = new Expression[] { new Expression(FRAPDataAnalysis.gaussianSpot_IntensityFunc), new Expression(FRAPDataAnalysis.gaussianSpot_MuFunc), new Expression(FRAPDataAnalysis.gaussianSpot_DiffFunc) };
                    String[] suffixes = new String[] { "", "", "[um2.s-1]" };
                    expressionCanvas.setExpressions(expressions, prefixes, suffixes);
                } catch (ExpressionException e2) {
                    e2.printStackTrace(System.out);
                }
            } else if (bleachEstimationComboBox.getSelectedItem().equals(FrapDataAnalysisResults.DiffusionOnlyAnalysisRestults.BLEACH_TYPE_NAMES[FrapDataAnalysisResults.DiffusionOnlyAnalysisRestults.BleachType_HalfCell])) {
                // expression on canvas
                try {
                    String[] prefixes = new String[] { "I(t) = ", "u(t)= ", "D = " };
                    Expression[] expressions = new Expression[] { new Expression(FRAPDataAnalysis.halfCell_IntensityFunc), new Expression(FRAPDataAnalysis.halfCell_MuFunc), new Expression(FRAPDataAnalysis.halfCell_DiffFunc) };
                    String[] suffixes = new String[] { "", "", "[um2.s-1]" };
                    expressionCanvas.setExpressions(expressions, prefixes, suffixes);
                } catch (ExpressionException e2) {
                    e2.printStackTrace(System.out);
                }
            }
            frapModelParameterLabel.setText(PARAM_EST_EQUATION_STRING + "  ('" + bleachEstimationComboBox.getSelectedItem() + "')");
            // FrapDataAnalysisResults.BLEACH_TYPE_NAMES[bleachEstimationComboBox.getSelectedIndex()]+"')");
            try {
                refreshFRAPModelParameterEstimates(initFRAPData, FRAPDataAnalysis.calculateRecoveryIndex(initFRAPData));
            } catch (Exception e2) {
                e2.printStackTrace();
                DialogUtils.showErrorDialog(FRAPEstimationPanel_NotUsed.this, "Error setting estimation method " + FrapDataAnalysisResults.DiffusionOnlyAnalysisRestults.BLEACH_TYPE_NAMES[bleachEstimationComboBox.getSelectedIndex()] + "\n" + e2.getMessage());
            }
        }
    });
    bleachEstimationComboBox.setSelectedItem(FrapDataAnalysisResults.DiffusionOnlyAnalysisRestults.BLEACH_TYPE_NAMES[FrapDataAnalysisResults.DiffusionOnlyAnalysisRestults.BleachType_GaussianSpot]);
}

Example 50 with ExpressionException

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

the class BNGOutputFileParser method createBngSpeciesOutputSpec.

public static List<BNGSpecies> createBngSpeciesOutputSpec(String inputString) {
    String newLineDelimiters = "\n\r";
    StringTokenizer lineTokenizer = new StringTokenizer(inputString, newLineDelimiters);
    String token1 = new String("");
    String token2 = new String("");
    String blankDelimiters = " \t";
    List<BNGSpecies> speciesVector = new ArrayList<>();
    while (lineTokenizer.hasMoreTokens()) {
        token1 = lineTokenizer.nextToken();
        StringTokenizer nextLine = null;
        // Fill in list of species ONLY
        nextLine = new StringTokenizer(token1, blankDelimiters);
        int i = 0;
        int speciesNtwkFileIndx = 0;
        String speciesName = null;
        Expression speciesConcExpr = null;
        // 'nextLine' is the line with a species and its concentration; the index is necessary to build the reactions.
        while (nextLine.hasMoreTokens()) {
            token2 = nextLine.nextToken();
            if (token2 != null) {
                token2 = token2.trim();
            }
            // First token is index number, second is the name, last token is the concentration.
            if (i == 0) {
                speciesNtwkFileIndx = Integer.parseInt(token2);
            } else if (i == 1) {
                speciesName = token2;
            } else if (i == 2) {
                try {
                    speciesConcExpr = new Expression(token2);
                } catch (ExpressionException e) {
                    throw new RuntimeException("Error in reading expression for species concentration \"" + speciesName + "\"");
                }
            }
            i++;
        }
        // After parsing species from the line, create a new BNGSpecies and add it to speciesVector.
        if (speciesName != null && speciesConcExpr != null && speciesNtwkFileIndx > 0) {
            BNGSpecies newSpecies = null;
            if (speciesName.indexOf(".") >= 0) {
                newSpecies = new BNGComplexSpecies(speciesName, speciesConcExpr, speciesNtwkFileIndx);
            } else if ((speciesName.indexOf("(") > 0) && (speciesName.indexOf(".") < 0)) {
                newSpecies = new BNGMultiStateSpecies(speciesName, speciesConcExpr, speciesNtwkFileIndx);
            } else {
                newSpecies = new BNGSingleStateSpecies(speciesName, speciesConcExpr, speciesNtwkFileIndx);
            }
            speciesVector.add(newSpecies);
        }
    }
    return speciesVector;
}