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

Example 21 with ExpressionException

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

the class XmlReader method getAction.

/**
 * This method returns a Action object from a XML element.
 * Creation date: (7/24/2006 5:56:36 PM)
 * @return cbit.vcell.math.Action
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private Action getAction(Element param, MathDescription md) throws XmlParseException, MathException, ExpressionException {
    // retrieve values
    String operation = unMangle(param.getAttributeValue(XMLTags.OperationAttrTag));
    String operand = param.getText();
    Expression exp = null;
    if (operand != null && operand.length() != 0) {
        exp = unMangleExpression(operand);
    }
    String name = unMangle(param.getAttributeValue(XMLTags.VarNameAttrTag));
    Variable var = md.getVariable(name);
    if (var == null) {
        throw new MathFormatException("variable " + name + " not defined");
    }
    if (!(var instanceof StochVolVariable) && !(var instanceof ParticleVariable)) {
        throw new MathFormatException("variable " + name + " not a Stochastic Volume Variable");
    }
    try {
        Action action = new Action(var, operation, exp);
        return action;
    } catch (Exception e) {
        e.printStackTrace();
    }
    return null;
}

Example 22 with ExpressionException

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

the class XmlReader method getElectricalStimulus.

/**
 * This method process Electrical Stimulus, also called Clamps.
 * Creation date: (6/6/2002 4:46:18 PM)
 * @return cbit.vcell.mapping.ElectricalStimulus
 * @param param org.jdom.Element
 */
private ElectricalStimulus getElectricalStimulus(Element param, SimulationContext currentSimulationContext) throws XmlParseException {
    ElectricalStimulus clampStimulus = null;
    // get name
    // String name = unMangle( param.getAttributeValue(XMLTags.NameAttrTag) );
    // get Electrode
    Electrode electrode = getElectrode(param.getChild(XMLTags.ElectrodeTag, vcNamespace), currentSimulationContext);
    if (param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.VoltageClampTag)) {
        // is a voltage clamp
        clampStimulus = new VoltageClampStimulus(electrode, "voltClampElectrode", new Expression(0.0), currentSimulationContext);
    } else if (param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.CurrentDensityClampTag) || param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.CurrentDensityClampTag_oldName)) {
        // is a current density clamp
        clampStimulus = new CurrentDensityClampStimulus(electrode, "currDensityClampElectrode", new Expression(0.0), currentSimulationContext);
    } else if (param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.TotalCurrentClampTag)) {
        // is a "total" current clamp
        clampStimulus = new TotalCurrentClampStimulus(electrode, "totalCurrClampElectrode", new Expression(0.0), currentSimulationContext);
    }
    try {
        // transaction begin flag ... yeah, this is a hack
        clampStimulus.reading(true);
        // Read all of the parameters
        List<Element> list = param.getChildren(XMLTags.ParameterTag, vcNamespace);
        // add constants that may be used in the electrical stimulus.
        VariableHash varHash = new VariableHash();
        Model model = currentSimulationContext.getModel();
        addResevedSymbols(varHash, model);
        // 
        for (Element xmlParam : list) {
            String paramName = unMangle(xmlParam.getAttributeValue(XMLTags.NameAttrTag));
            String role = xmlParam.getAttributeValue(XMLTags.ParamRoleAttrTag);
            String paramExpStr = xmlParam.getText();
            Expression paramExp = unMangleExpression(paramExpStr);
            try {
                if (varHash.getVariable(paramName) == null) {
                    Domain domain = null;
                    varHash.addVariable(new Function(paramName, paramExp, domain));
                } else {
                    if (model.getReservedSymbolByName(paramName) != null) {
                        varHash.removeVariable(paramName);
                        Domain domain = null;
                        varHash.addVariable(new Function(paramName, paramExp, domain));
                    }
                }
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException("error reordering parameters according to dependencies:", e);
            }
            LocalParameter tempParam = null;
            if (!role.equals(XMLTags.ParamRoleUserDefinedTag)) {
                if (role.equals(XMLTags.ParamRoleTotalCurrentTag)) {
                    if (clampStimulus instanceof TotalCurrentClampStimulus) {
                        tempParam = ((TotalCurrentClampStimulus) clampStimulus).getCurrentParameter();
                    } else {
                        varHash.removeVariable(paramName);
                        continue;
                    }
                } else if (role.equals(XMLTags.ParamRoleTotalCurrentDensityTag) || role.equals(XMLTags.ParamRoleTotalCurrentDensityOldNameTag)) {
                    if (clampStimulus instanceof CurrentDensityClampStimulus) {
                        tempParam = ((CurrentDensityClampStimulus) clampStimulus).getCurrentDensityParameter();
                    } else {
                        varHash.removeVariable(paramName);
                        continue;
                    }
                } else if (role.equals(XMLTags.ParamRolePotentialDifferenceTag)) {
                    if (clampStimulus instanceof VoltageClampStimulus) {
                        tempParam = ((VoltageClampStimulus) clampStimulus).getVoltageParameter();
                    } else {
                        varHash.removeVariable(paramName);
                        continue;
                    }
                }
            } else {
                continue;
            }
            if (tempParam == null) {
                throw new XmlParseException("parameter with role '" + role + "' not found in electricalstimulus");
            }
            // 
            if (!tempParam.getName().equals(paramName)) {
                LocalParameter multNameParam = clampStimulus.getLocalParameter(paramName);
                int n = 0;
                while (multNameParam != null) {
                    String tempName = paramName + "_" + n++;
                    clampStimulus.renameParameter(paramName, tempName);
                    multNameParam = clampStimulus.getLocalParameter(tempName);
                }
                clampStimulus.renameParameter(tempParam.getName(), paramName);
            }
        }
        // 
        // create unresolved parameters for all unresolved symbols
        // 
        String unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
        while (unresolvedSymbol != null) {
            try {
                Domain domain = null;
                // will turn into an UnresolvedParameter.
                varHash.addVariable(new Function(unresolvedSymbol, new Expression(0.0), domain));
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e.getMessage());
            }
            clampStimulus.addUnresolvedParameter(unresolvedSymbol);
            unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
        }
        Variable[] sortedVariables = varHash.getTopologicallyReorderedVariables();
        ModelUnitSystem modelUnitSystem = model.getUnitSystem();
        for (int i = sortedVariables.length - 1; i >= 0; i--) {
            if (sortedVariables[i] instanceof Function) {
                Function paramFunction = (Function) sortedVariables[i];
                Element xmlParam = null;
                for (int j = 0; j < list.size(); j++) {
                    Element tempParam = (Element) list.get(j);
                    if (paramFunction.getName().equals(unMangle(tempParam.getAttributeValue(XMLTags.NameAttrTag)))) {
                        xmlParam = tempParam;
                        break;
                    }
                }
                if (xmlParam == null) {
                    // must have been an unresolved parameter
                    continue;
                }
                String symbol = xmlParam.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
                VCUnitDefinition unit = null;
                if (symbol != null) {
                    unit = modelUnitSystem.getInstance(symbol);
                }
                LocalParameter tempParam = clampStimulus.getLocalParameter(paramFunction.getName());
                if (tempParam == null) {
                    clampStimulus.addUserDefinedParameter(paramFunction.getName(), paramFunction.getExpression(), unit);
                } else {
                    if (tempParam.getExpression() != null) {
                        // if the expression is null, it should remain null.
                        clampStimulus.setParameterValue(tempParam, paramFunction.getExpression());
                    }
                    tempParam.setUnitDefinition(unit);
                }
            }
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("Exception while setting parameters for simContext : " + currentSimulationContext.getName(), e);
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("Exception while settings parameters for simContext : " + currentSimulationContext.getName(), e);
    } finally {
        clampStimulus.reading(false);
    }
    return clampStimulus;
}

Example 23 with ExpressionException

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

the class XmlReader method getAnalyticSubVolume.

/**
 * This method returns an AnalyticSubVolume object from a XML representation.
 * Creation date: (5/1/2001 5:26:17 PM)
 * @return cbit.vcell.geometry.AnalyticSubVolume
 * @param param org.jdom.Element
 */
private AnalyticSubVolume getAnalyticSubVolume(Element param) throws XmlParseException {
    // retrieve the attributes
    String name = param.getAttributeValue(XMLTags.NameAttrTag);
    int handle = Integer.parseInt(param.getAttributeValue(XMLTags.HandleAttrTag));
    // process the key
    KeyValue key = null;
    String temp = param.getAttributeValue(XMLTags.KeyValueAttrTag);
    if (temp != null && temp.length() > 0 && this.readKeysFlag) {
        key = new KeyValue(temp);
    }
    // Retrieve the expression
    temp = param.getChildText(XMLTags.AnalyticExpressionTag, vcNamespace);
    if (temp == null) {
        throw new XmlParseException("A Problem occured while retrieving the analytic expression of the AnalyticSubvolume " + name);
    }
    Expression newexpression = unMangleExpression(temp);
    // Create the AnalyticCompartment
    AnalyticSubVolume newsubvolume = null;
    try {
        newsubvolume = new AnalyticSubVolume(key, name, newexpression, handle);
    } catch (ExpressionException e) {
        e.printStackTrace();
        throw new XmlParseException("An ExpressionException occured when creating the new AnalyticSubvolume " + name, e);
    }
    return newsubvolume;
}

Example 24 with ExpressionException

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

the class LocalOptimizationService method solve.

/**
 * solve method comment.
 */
public OptimizationResultSet solve(OptimizationSpec optSpec, OptimizationSolverSpec optSolverSpec, OptSolverCallbacks optSolverCallbacks) {
    OptimizationSolver optSolver = null;
    if (optSolverSpec.getSolverType().equals(OptimizationSolverSpec.SOLVERTYPE_POWELL)) {
        optSolver = new PowellOptimizationSolver();
    // }else if (optSolverSpec.getSolverType().equals(OptimizationSolverSpec.SOLVERTYPE_CONJUGATE_GRADIENT)){
    // optSolver = new ConjugateGradientOptimizationSolver();
    } else {
        throw new RuntimeException("unsupported solver type '" + optSolverSpec.getSolverType() + "'");
    }
    OptimizationResultSet optResultSet = null;
    try {
        optResultSet = optSolver.solve(optSpec, optSolverSpec, optSolverCallbacks);
    } catch (IOException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException(e.getMessage());
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException(e.getMessage());
    } catch (OptimizationException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException(e.getMessage());
    }
    return optResultSet;
}

Example 25 with ExpressionException

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

the class XmlReader method getGeometry.

/**
 * This method returns a Geometry object from a XML representation.
 * Creation date: (4/26/2001 12:12:18 PM)
 * @return cbit.vcell.geometry.Geometry
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
public Geometry getGeometry(Element param) throws XmlParseException {
    // Get the Extent object
    Extent newextent = getExtent(param.getChild(XMLTags.ExtentTag, vcNamespace));
    // Get VCimage information
    VCImage newimage = null;
    if (param.getChild(XMLTags.ImageTag, vcNamespace) != null) {
        try {
            newimage = getVCImage(param.getChild(XMLTags.ImageTag, vcNamespace), newextent);
        } catch (Throwable e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Get attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    int newdimension = Integer.parseInt(param.getAttributeValue(XMLTags.DimensionAttrTag));
    // Get Version
    Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    // Try to construct the geometry upon four different cases
    Geometry newgeometry = null;
    if (version != null && newimage != null) {
        newgeometry = new Geometry(version, newimage);
    } else if (version != null) {
        newgeometry = new Geometry(version, newdimension);
    } else if (newimage != null) {
        newgeometry = new Geometry(name, newimage);
    } else {
        newgeometry = new Geometry(name, newdimension);
    }
    // set attributes
    try {
        if (!newgeometry.getName().equalsIgnoreCase(name)) {
            newgeometry.setName(name);
        }
        // String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag);
        // if (annotation!=null) {
        // newgeometry.setDescription( unMangle(annotation) );
        // }
        // Add annotation
        String annotation = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotation != null && annotation.length() > 0) {
            newgeometry.setDescription(unMangle(annotation));
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException occurred when setting the name " + name + " to a Geometry object!", e);
    }
    // Add the Extent
    try {
        newgeometry.getGeometrySpec().setExtent(newextent);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException occurred while trying to set the Extent for the Geometry " + name, e);
    }
    // Add the Origin
    newgeometry.getGeometrySpec().setOrigin(getOrigin(param.getChild(XMLTags.OriginTag, vcNamespace)));
    // Add the SubVolumes
    List<Element> children = param.getChildren(XMLTags.SubVolumeTag, vcNamespace);
    SubVolume[] newsubvolumes = new SubVolume[children.size()];
    int subvolumeCounter = 0;
    for (Element child : children) {
        newsubvolumes[subvolumeCounter] = getSubVolume(child);
        subvolumeCounter++;
    }
    try {
        newgeometry.getGeometrySpec().setSubVolumes(newsubvolumes);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException was generated when ading the subvolumes to the Geometry " + name, e);
    }
    if (newgeometry.getDimension() > 0) {
        // Add SurfaceClasses
        List<Element> surfaceClassChildren = param.getChildren(XMLTags.SurfaceClassTag, vcNamespace);
        SurfaceClass[] newSurfaceClassArr = new SurfaceClass[surfaceClassChildren.size()];
        int surfClassCounter = 0;
        for (Element surfClassChild : surfaceClassChildren) {
            newSurfaceClassArr[surfClassCounter] = getSurfaceClass(surfClassChild, newgeometry);
            surfClassCounter++;
        }
        try {
            newgeometry.getGeometrySurfaceDescription().setSurfaceClasses(newSurfaceClassArr);
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace();
            throw new XmlParseException("A PropertyVetoException was generated when ading the subvolumes to the Geometry " + name, e);
        }
    }
    // read Filaments (if any)
    Iterator<Element> iterator = param.getChildren(XMLTags.FilamentTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempElement = iterator.next();
        String filname = unMangle(tempElement.getAttributeValue(XMLTags.NameAttrTag));
        Iterator<Element> curveiterator = tempElement.getChildren().iterator();
        while (curveiterator.hasNext()) {
            ControlPointCurve curve = getControlPointCurve(curveiterator.next());
            newgeometry.getGeometrySpec().getFilamentGroup().addCurve(filname, curve);
        }
    }
    // read Surface description (if any)
    Element sd = param.getChild(XMLTags.SurfaceDescriptionTag, vcNamespace);
    if (sd != null) {
        GeometrySurfaceDescription dummy = getGeometrySurfaceDescription(sd, newgeometry);
    }
    try {
        newgeometry.precomputeAll(new GeometryThumbnailImageFactoryAWT(), false, false);
    } catch (GeometryException e) {
        e.printStackTrace(System.out);
    } catch (ImageException e) {
        e.printStackTrace(System.out);
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
    }
    return newgeometry;
}