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

Example 96 with ExpressionException

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

the class SpatialProcessParameterTableModel method setValueAt.

public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
    Parameter parameter = getValueAt(rowIndex);
    switch(columnIndex) {
        case COLUMN_NAME:
            {
                try {
                    if (aValue instanceof String) {
                        String newName = (String) aValue;
                        if (!parameter.getName().equals(newName)) {
                            parameter.setName(newName);
                        }
                    }
                } catch (java.beans.PropertyVetoException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "error changing parameter name\n" + e.getMessage());
                }
                break;
            }
        case COLUMN_VALUE:
            {
                try {
                    if (aValue instanceof String) {
                        String newExpressionString = (String) aValue;
                        Expression newExp = null;
                        if (newExpressionString == null || newExpressionString.trim().length() == 0) {
                            newExp = new Expression(0.0);
                        } else {
                            newExp = new Expression(newExpressionString);
                        }
                        parameter.setExpression(newExp);
                    }
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "expression error\n" + e.getMessage());
                }
                break;
            }
    }
}

Example 97 with ExpressionException

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

the class SpeciesContextSpecParameterTableModel method setValueAt.

public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
    Parameter parameter = getValueAt(rowIndex);
    switch(columnIndex) {
        case COLUMN_NAME:
            {
                try {
                    if (aValue instanceof String) {
                        String newName = (String) aValue;
                        if (!parameter.getName().equals(newName)) {
                            if (parameter instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
                                SpeciesContextSpec.SpeciesContextSpecParameter scsParm = (SpeciesContextSpec.SpeciesContextSpecParameter) parameter;
                                scsParm.setName(newName);
                            }
                        }
                    }
                } catch (java.beans.PropertyVetoException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "error changing parameter name\n" + e.getMessage());
                }
                break;
            }
        case COLUMN_VALUE:
            {
                try {
                    if (aValue instanceof String) {
                        String newExpressionString = (String) aValue;
                        if (parameter instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
                            SpeciesContextSpec.SpeciesContextSpecParameter scsParm = (SpeciesContextSpec.SpeciesContextSpecParameter) parameter;
                            Expression newExp = null;
                            if (newExpressionString == null || newExpressionString.trim().length() == 0) {
                                if (scsParm.getRole() == SpeciesContextSpec.ROLE_InitialConcentration || scsParm.getRole() == SpeciesContextSpec.ROLE_DiffusionRate || scsParm.getRole() == SpeciesContextSpec.ROLE_InitialCount) {
                                    newExp = new Expression(0.0);
                                }
                            } else {
                                newExp = new Expression(newExpressionString);
                            }
                            scsParm.setExpression(newExp);
                        }
                    }
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "expression error\n" + e.getMessage());
                }
                break;
            }
    }
}

Example 98 with ExpressionException

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

the class StructureMappingTableModel method setValueAt.

public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
    if (rowIndex < 0 || rowIndex >= getRowCount()) {
        throw new RuntimeException("StructureMappingTableModel.setValueAt(), row = " + rowIndex + " out of range [" + 0 + "," + (getRowCount() - 1) + "]");
    }
    if (columnIndex < 0 || columnIndex >= getColumnCount()) {
        throw new RuntimeException("StructureMappingTableModel.setValueAt(), column = " + columnIndex + " out of range [" + 0 + "," + (getColumnCount() - 1) + "]");
    }
    StructureMapping structureMapping = getValueAt(rowIndex);
    Structure structure = structureMapping.getStructure();
    if (bNonSpatial) {
        switch(columnIndex) {
            case NONSPATIAL_COLUMN_SIZE:
                {
                    try {
                        Expression exp = null;
                        if (aValue instanceof String) {
                            exp = new Expression((String) aValue);
                        } else if (aValue instanceof Double) {
                            exp = new Expression(((Double) aValue).doubleValue());
                        }
                        // if the input volumn is null, leave it as it was.
                        if (exp != null) {
                            // for old ode model, once one size is input, solve the rest.                                                                                                          if it is unnamed compartment(the only one), we don't need to solve anything
                            if (!getGeometryContext().getSimulationContext().isStoch() && getGeometryContext().isAllSizeSpecifiedNull() && getGeometryContext().isAllVolFracAndSurfVolSpecified() && getGeometryContext().getStructureMappings().length > 1) {
                                structureMapping.getSizeParameter().setExpression(exp);
                                double size;
                                try {
                                    size = exp.evaluateConstant();
                                    VCUnitDefinition volumeUnit = getGeometryContext().getSimulationContext().getModel().getUnitSystem().getVolumeUnit();
                                    StructureSizeSolver.updateAbsoluteStructureSizes(getGeometryContext().getSimulationContext(), structure, size, volumeUnit);
                                    fireTableRowsUpdated(0, getRowCount());
                                } catch (ExpressionException ex) {
                                    ex.printStackTrace(System.out);
                                    PopupGenerator.showErrorDialog(ownerTable, "Size of Feature " + structure.getName() + " can not be solved as constant!");
                                } catch (Exception ex) {
                                    ex.printStackTrace(System.out);
                                    PopupGenerator.showErrorDialog(ownerTable, ex.getMessage());
                                }
                            } else {
                                structureMapping.getSizeParameter().setExpression(exp);
                                // set fraction in stoch math description, because these might be used when copy from stoch app to ode app.
                                if (getGeometryContext().isAllSizeSpecifiedPositive()) /*&& !getGeometryContext().getSimulationContext().isStoch()*/
                                {
                                    try {
                                        StructureSizeSolver.updateRelativeStructureSizes(getGeometryContext().getSimulationContext());
                                    } catch (Exception ex) {
                                        ex.printStackTrace(System.out);
                                        PopupGenerator.showErrorDialog(ownerTable, ex.getMessage());
                                    }
                                }
                            }
                        }
                    } catch (ExpressionException e) {
                        e.printStackTrace(System.out);
                        PopupGenerator.showErrorDialog(ownerTable, "expression error\n" + e.getMessage());
                    }
                    break;
                }
        }
    } else {
        switch(columnIndex) {
            case SPATIAL_COLUMN_SUBDOMAIN:
                {
                    GeometryClass geometryClass = null;
                    if (aValue instanceof String) {
                        String svname = (String) aValue;
                        geometryClass = getGeometryContext().getGeometry().getGeometryClass(svname);
                    } else if (aValue instanceof GeometryClass) {
                        geometryClass = (GeometryClass) aValue;
                    }
                    if (geometryClass != null) {
                        try {
                            getGeometryContext().assignStructure(structure, geometryClass);
                        } catch (PropertyVetoException e) {
                            e.printStackTrace(System.out);
                            PopupGenerator.showErrorDialog(ownerTable, e.getMessage());
                        } catch (IllegalMappingException e) {
                            e.printStackTrace(System.out);
                            PopupGenerator.showErrorDialog(ownerTable, e.getMessage());
                        } catch (MappingException e) {
                            e.printStackTrace(System.out);
                            PopupGenerator.showErrorDialog(ownerTable, e.getMessage());
                        }
                    }
                    break;
                }
            case SPATIAL_COLUMN_SIZERATIO:
                try {
                    Expression exp = null;
                    if (aValue instanceof String) {
                        exp = new Expression((String) aValue);
                    } else if (aValue instanceof Double) {
                        exp = new Expression(((Double) aValue).doubleValue());
                    }
                    if (exp != null) {
                        structureMapping.getUnitSizeParameter().setExpression(exp);
                        StructureSizeSolver.updateUnitStructureSizes(getGeometryContext().getSimulationContext(), structureMapping.getGeometryClass());
                    }
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "expression error\n" + e.getMessage());
                }
                break;
            case SPATIAL_COLUMN_X_MINUS:
                {
                    if (aValue != null) {
                        structureMapping.setBoundaryConditionTypeXm(new BoundaryConditionType((String) aValue));
                    }
                    break;
                }
            case SPATIAL_COLUMN_X_PLUS:
                {
                    if (aValue != null) {
                        structureMapping.setBoundaryConditionTypeXp(new BoundaryConditionType((String) aValue));
                    }
                    break;
                }
            case SPATIAL_COLUMN_Y_MINUS:
                {
                    if (aValue != null) {
                        structureMapping.setBoundaryConditionTypeYm(new BoundaryConditionType((String) aValue));
                    }
                    break;
                }
            case SPATIAL_COLUMN_Y_PLUS:
                {
                    if (aValue != null) {
                        structureMapping.setBoundaryConditionTypeYp(new BoundaryConditionType((String) aValue));
                    }
                    break;
                }
            case SPATIAL_COLUMN_Z_MINUS:
                {
                    if (aValue != null) {
                        structureMapping.setBoundaryConditionTypeZm(new BoundaryConditionType((String) aValue));
                    }
                    break;
                }
            case SPATIAL_COLUMN_Z_PLUS:
                {
                    if (aValue != null) {
                        structureMapping.setBoundaryConditionTypeZp(new BoundaryConditionType((String) aValue));
                    }
                    break;
                }
        }
    }
}

Example 99 with ExpressionException

use of cbit.vcell.parser.ExpressionException 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 100 with ExpressionException

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

the class ElectricalMembraneMappingTableModel method setValueAt.

public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
    MembraneMapping membraneMapping = getValueAt(rowIndex);
    switch(columnIndex) {
        case COLUMN_CALCULATE_POTENTIAL:
            {
                boolean bCalculatePotential = ((Boolean) aValue).booleanValue();
                membraneMapping.setCalculateVoltage(bCalculatePotential);
                fireTableRowsUpdated(rowIndex, rowIndex);
                break;
            }
        case COLUMN_INITIAL_POTENTIAL:
            {
                Expression newExpression = null;
                try {
                    if (aValue instanceof String) {
                        String newExpressionString = (String) aValue;
                        newExpression = new Expression(newExpressionString);
                    }
                    membraneMapping.getInitialVoltageParameter().setExpression(newExpression);
                    fireTableRowsUpdated(rowIndex, rowIndex);
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "expression error\n" + e.getMessage());
                }
                break;
            }
        case COLUMN_SPECIFIC_CAPACITANCE:
            {
                Expression newExpression = null;
                try {
                    if (aValue instanceof String) {
                        String newExpressionString = (String) aValue;
                        newExpression = new Expression(newExpressionString);
                    } else if (aValue instanceof ScopedExpression) {
                        // newExpression = ((ScopedExpression)aValue).getExpression();
                        throw new RuntimeException("unexpected value type ScopedExpression");
                    }
                    membraneMapping.getSpecificCapacitanceParameter().setExpression(newExpression);
                    fireTableRowsUpdated(rowIndex, rowIndex);
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "expression error\n" + e.getMessage());
                }
                break;
            }
    }
}