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Example 1 with FilamentRegionVariable

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

the class Xmlproducer method getXML.

/**
 * This method returns a XML representation of a MathDescription object.
 * Creation date: (3/2/2001 10:57:25 AM)
 * @return Element
 * @param mathdes cbit.vcell.math.MathDescription
 */
Element getXML(MathDescription mathdes) throws XmlParseException {
    Element math = new Element(XMLTags.MathDescriptionTag);
    // Add attributes
    math.setAttribute(XMLTags.NameAttrTag, mangle(mathdes.getName()));
    // Add annotation
    if (mathdes.getDescription() != null && mathdes.getDescription().length() > 0) {
        Element annotationElem = new Element(XMLTags.AnnotationTag);
        annotationElem.setText(mangle(mathdes.getDescription()));
        math.addContent(annotationElem);
    }
    List<ParticleMolecularType> particleMolecularTypes = mathdes.getParticleMolecularTypes();
    for (ParticleMolecularType particleMolecularType : particleMolecularTypes) {
        math.addContent(getXML(particleMolecularType));
    }
    // Add Constant subelements
    Enumeration<Variable> enum1 = mathdes.getVariables();
    /*java.util.Iterator k;
    try {
    	VariableHash varHash = new VariableHash();
    	while (enum1.hasMoreElements()) 
    	 	varHash.addVariable((Variable)enum1.nextElement());
    	Variable vars [] = varHash.getReorderedVariables();
    	k = new ArrayList(java.util.Arrays.asList(vars)).iterator();
    } catch (cbit.vcell.mapping.MappingException e) {
		e.printStackTrace();
		return null;
    }*/
    while (enum1.hasMoreElements()) {
        Variable var = enum1.nextElement();
        Element element = null;
        if (var instanceof Constant) {
            element = getXML((Constant) var);
        } else if (var instanceof FilamentRegionVariable) {
            element = getXML((FilamentRegionVariable) var);
        } else if (var instanceof FilamentVariable) {
            element = getXML((FilamentVariable) var);
        } else if (var instanceof PointVariable) {
            element = getXML((PointVariable) var);
        } else if (var instanceof Function) {
            element = getXML((Function) var);
        } else if (var instanceof RandomVariable) {
            element = getXML((RandomVariable) var);
        } else if (var instanceof InsideVariable) {
            // *** for internal use! Ignore it ***
            continue;
        } else if (var instanceof MembraneRegionVariable) {
            element = getXML((MembraneRegionVariable) var);
        } else if (var instanceof MemVariable) {
            element = getXML((MemVariable) var);
        } else if (var instanceof OutsideVariable) {
            // *** for internal use! Ignore it ****
            continue;
        } else if (var instanceof VolumeRegionVariable) {
            element = getXML((VolumeRegionVariable) var);
        } else if (var instanceof VolVariable) {
            element = getXML((VolVariable) var);
        } else if (var instanceof StochVolVariable) {
            // added for stochastic volumn variables
            element = getXML((StochVolVariable) var);
        } else if (var instanceof ParticleVariable) {
            element = getXML((ParticleVariable) var);
        } else if (var instanceof ParticleObservable) {
            element = getXML((ParticleObservable) var);
        } else {
            throw new XmlParseException("An unknown variable type " + var.getClass().getName() + " was found when parsing the mathdescription " + mathdes.getName() + "!");
        }
        transcribeComments(var, element);
        math.addContent(element);
    }
    // this was moved to the simspec!
    /*	buffer.append("\n");
    	if (geometry != null){
    		buffer.append(geometry.getXML());
    	}	
    	buffer.append("\n");*/
    // Add subdomains
    Enumeration<SubDomain> enum2 = mathdes.getSubDomains();
    while (enum2.hasMoreElements()) {
        SubDomain subDomain = enum2.nextElement();
        math.addContent(getXML(subDomain));
    }
    // Add Metadata (Version) if there is!
    if (mathdes.getVersion() != null) {
        math.addContent(getXML(mathdes.getVersion(), mathdes));
    }
    Iterator<Event> iter = mathdes.getEvents();
    while (iter.hasNext()) {
        math.addContent(getXML(iter.next()));
    }
    PostProcessingBlock postProcessingBlock = mathdes.getPostProcessingBlock();
    if (postProcessingBlock.getNumDataGenerators() > 0) {
        math.addContent(getXML(postProcessingBlock));
    }
    return math;
}
Also used : FilamentVariable(cbit.vcell.math.FilamentVariable) OutsideVariable(cbit.vcell.math.OutsideVariable) StochVolVariable(cbit.vcell.math.StochVolVariable) RandomVariable(cbit.vcell.math.RandomVariable) VolumeRandomVariable(cbit.vcell.math.VolumeRandomVariable) VolumeParticleVariable(cbit.vcell.math.VolumeParticleVariable) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) InsideVariable(cbit.vcell.math.InsideVariable) VolVariable(cbit.vcell.math.VolVariable) MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) PointVariable(cbit.vcell.math.PointVariable) MembraneParticleVariable(cbit.vcell.math.MembraneParticleVariable) ParticleVariable(cbit.vcell.math.ParticleVariable) MemVariable(cbit.vcell.math.MemVariable) FilamentRegionVariable(cbit.vcell.math.FilamentRegionVariable) Variable(cbit.vcell.math.Variable) MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) MacroscopicRateConstant(cbit.vcell.math.MacroscopicRateConstant) Constant(cbit.vcell.math.Constant) VolumeParticleVariable(cbit.vcell.math.VolumeParticleVariable) MembraneParticleVariable(cbit.vcell.math.MembraneParticleVariable) ParticleVariable(cbit.vcell.math.ParticleVariable) Element(org.jdom.Element) RandomVariable(cbit.vcell.math.RandomVariable) VolumeRandomVariable(cbit.vcell.math.VolumeRandomVariable) InsideVariable(cbit.vcell.math.InsideVariable) PostProcessingBlock(cbit.vcell.math.PostProcessingBlock) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) SubDomain(cbit.vcell.math.SubDomain) MembraneSubDomain(cbit.vcell.math.MembraneSubDomain) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) FilamentSubDomain(cbit.vcell.math.FilamentSubDomain) PointSubDomain(cbit.vcell.math.PointSubDomain) AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction) Function(cbit.vcell.math.Function) MemVariable(cbit.vcell.math.MemVariable) ParticleMolecularType(cbit.vcell.math.ParticleMolecularType) StochVolVariable(cbit.vcell.math.StochVolVariable) StochVolVariable(cbit.vcell.math.StochVolVariable) VolVariable(cbit.vcell.math.VolVariable) FilamentRegionVariable(cbit.vcell.math.FilamentRegionVariable) FilamentVariable(cbit.vcell.math.FilamentVariable) Event(cbit.vcell.math.Event) BioEvent(cbit.vcell.mapping.BioEvent) PointVariable(cbit.vcell.math.PointVariable) OutsideVariable(cbit.vcell.math.OutsideVariable) VolumeParticleObservable(cbit.vcell.math.VolumeParticleObservable) ParticleObservable(cbit.vcell.math.ParticleObservable)

Example 2 with FilamentRegionVariable

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

the class TestingFrameworkWindowManager method getVariableNamesToCompare.

// /**
// * Insert the method's description here.
// * Creation date: (11/23/2004 1:53:11 PM)
// * @return java.lang.String[]
// * @param sim1 cbit.vcell.solver.Simulation
// * @param sim2 cbit.vcell.solver.Simulation
// */
// private VariablePair[] getVariableNamesToCompare(BioModel testBioModel,SimulationSymbolTable testSymboltable, SimulationSymbolTable refSymbolTable){
// Vector<VariablePair> variablePairs = new Vector<VariablePair>();
// 
// //
// // get Variables from Simulation 1
// //
// Variable refVars[] = refSymbolTable.getVariables();
// for (int i = 0;refVars!=null && i < refVars.length; i++){
// if (refVars[i] instanceof VolVariable ||
// refVars[i] instanceof StochVolVariable ||
// refVars[i] instanceof MemVariable ||
// refVars[i] instanceof VolumeRegionVariable ||
// refVars[i] instanceof MembraneRegionVariable ||
// refVars[i] instanceof FilamentVariable ||
// refVars[i] instanceof FilamentRegionVariable){
// 
// VariablePair varPair = new VariablePair();
// varPair.refVariable = refVars[i];
// varPair.domain = refVars[i].getDomain();
// varPair.testVariable = null;
// variablePairs.add(varPair);
// }
// //		Constant sensitivityParameter = simSymbolTable1.getSimulation().getSolverTaskDescription().getSensitivityParameter();
// //		if (sensitivityParameter != null) {
// //			if (simVars[i] instanceof VolVariable) {
// //				hashSet.add(SensVariable.getSensName((VolVariable)simVars[i], sensitivityParameter));
// //			}
// //		}
// }
// 
// //
// // add Variables from Simulation 2
// //
// Variable[] testVars = testSymboltable.getVariables();
// for (int i = 0;testVars!=null && i < testVars.length; i++){
// if (testVars[i] instanceof VolVariable ||
// testVars[i] instanceof MemVariable ||
// testVars[i] instanceof VolumeRegionVariable ||
// testVars[i] instanceof MembraneRegionVariable ||
// testVars[i] instanceof FilamentVariable ||
// testVars[i] instanceof FilamentRegionVariable){
// 
// if(testVars[i].getDomain() == null){
// boolean BFoundMatchingName = false;
// for (int j = 0; j < variablePairs.size(); j++) {
// VariablePair varPair = variablePairs.elementAt(j);
// if(varPair.refVariable.getName().equals(testVars[i].getName())){
// varPair.testVariable = testVars[i];
// BFoundMatchingName = true;
// break;
// }
// }
// if(!BFoundMatchingName){
// //Try to find other matching variable types (e.g. functions)
// Variable dataSet1Match = refSymbolTable.getVariable(testVars[i].getName());
// if(dataSet1Match != null){
// VariablePair varPair = new VariablePair();
// varPair.refVariable = dataSet1Match;
// varPair.testVariable = testVars[i];
// varPair.domain = varPair.refVariable.getDomain();
// variablePairs.add(varPair);
// }else{
// SpeciesContext testSpeciescontext0 = testBioModel.getModel().getSpeciesContext(testVars[i].getName());
// if(testSpeciescontext0 != null){
// Species refspecies = testSpeciescontext0.getSpecies();
// Variable refVariable = refSymbolTable.getVariable(refspecies.getCommonName());
// if(refVariable != null){
// VariablePair varPair = new VariablePair();
// varPair.refVariable = refVariable;
// varPair.testVariable = testVars[i];
// varPair.domain = varPair.refVariable.getDomain();
// variablePairs.add(varPair);
// }
// }else{
// Species testSpecies = testBioModel.getModel().getSpecies(testVars[i].getName());
// if(testSpecies != null){
// for (int j = 0; j < testBioModel.getModel().getSpeciesContexts().length; j++) {
// if(testBioModel.getModel().getSpeciesContexts()[j].getSpecies() == testSpecies){
// Variable refVar = refSymbolTable.getVariable(testBioModel.getModel().getSpeciesContexts()[j].getName());
// if(refVar != null){
// VariablePair varPair = new VariablePair();
// varPair.refVariable = refVar;
// varPair.testVariable = testVars[i];
// varPair.domain = varPair.refVariable.getDomain();
// variablePairs.add(varPair);
// }
// }
// }
// }
// }
// }
// }
// }else{
// 
// }
// hashSet.add(simVars[i].getName());
// }
// Constant sensitivityParameter = refSymbolTable.getSimulation().getSolverTaskDescription().getSensitivityParameter();
// if (sensitivityParameter != null) {
// if (simVars[i] instanceof VolVariable) {
// hashSet.add(SensVariable.getSensName((VolVariable)simVars[i], sensitivityParameter));
// }
// }
// }
// 
// return (String[])hashSet.toArray(new String[hashSet.size()]);
// }
/**
 * Insert the method's description here.
 * Creation date: (11/23/2004 1:53:11 PM)
 * @return java.lang.String[]
 * @param sim1 cbit.vcell.solver.Simulation
 * @param sim2 cbit.vcell.solver.Simulation
 */
private String[] getVariableNamesToCompare(SimulationSymbolTable simSymbolTable1, SimulationSymbolTable simSymbolTable2) {
    java.util.HashSet<String> hashSet = new java.util.HashSet<String>();
    // 
    // get Variables from Simulation 1
    // 
    Variable[] simVars = simSymbolTable1.getVariables();
    for (int i = 0; simVars != null && i < simVars.length; i++) {
        if (simVars[i] instanceof VolVariable || simVars[i] instanceof StochVolVariable || simVars[i] instanceof MemVariable || simVars[i] instanceof VolumeRegionVariable || simVars[i] instanceof MembraneRegionVariable || simVars[i] instanceof FilamentVariable || simVars[i] instanceof FilamentRegionVariable) {
            hashSet.add(simVars[i].getName());
        }
        Constant sensitivityParameter = simSymbolTable1.getSimulation().getSolverTaskDescription().getSensitivityParameter();
        if (sensitivityParameter != null) {
            if (simVars[i] instanceof VolVariable) {
                hashSet.add(SensVariable.getSensName((VolVariable) simVars[i], sensitivityParameter));
            }
        }
    }
    // 
    // add Variables from Simulation 2
    // 
    simVars = simSymbolTable2.getVariables();
    for (int i = 0; simVars != null && i < simVars.length; i++) {
        if (simVars[i] instanceof VolVariable || simVars[i] instanceof MemVariable || simVars[i] instanceof VolumeRegionVariable || simVars[i] instanceof MembraneRegionVariable || simVars[i] instanceof FilamentVariable || simVars[i] instanceof FilamentRegionVariable) {
            hashSet.add(simVars[i].getName());
        }
        Constant sensitivityParameter = simSymbolTable2.getSimulation().getSolverTaskDescription().getSensitivityParameter();
        if (sensitivityParameter != null) {
            if (simVars[i] instanceof VolVariable) {
                hashSet.add(SensVariable.getSensName((VolVariable) simVars[i], sensitivityParameter));
            }
        }
    }
    return (String[]) hashSet.toArray(new String[hashSet.size()]);
}
Also used : SensVariable(cbit.vcell.solver.ode.SensVariable) FilamentVariable(cbit.vcell.math.FilamentVariable) VolVariable(cbit.vcell.math.VolVariable) StochVolVariable(cbit.vcell.math.StochVolVariable) MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) MemVariable(cbit.vcell.math.MemVariable) FilamentRegionVariable(cbit.vcell.math.FilamentRegionVariable) Variable(cbit.vcell.math.Variable) MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) VolVariable(cbit.vcell.math.VolVariable) StochVolVariable(cbit.vcell.math.StochVolVariable) FilamentRegionVariable(cbit.vcell.math.FilamentRegionVariable) Constant(cbit.vcell.math.Constant) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) MemVariable(cbit.vcell.math.MemVariable) FilamentVariable(cbit.vcell.math.FilamentVariable) StochVolVariable(cbit.vcell.math.StochVolVariable) HashSet(java.util.HashSet)

Example 3 with FilamentRegionVariable

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

the class MathTestingUtilities method comparePDEResultsWithExact.

/**
 * Insert the method's description here.
 * Creation date: (8/20/2003 12:58:10 PM)
 */
public static SimulationComparisonSummary comparePDEResultsWithExact(SimulationSymbolTable simSymbolTable, PDEDataManager dataManager, String type, double absErrorThreshold, double relErrorThreshold) throws DataAccessException, ExpressionException {
    java.util.Hashtable<String, DataErrorSummary> tempVarHash = new java.util.Hashtable<String, DataErrorSummary>();
    double[] timeArray = dataManager.getDataSetTimes();
    Variable[] vars = simSymbolTable.getVariables();
    CartesianMesh mesh = dataManager.getMesh();
    MathDescription mathDesc = simSymbolTable.getSimulation().getMathDescription();
    // Get volumeSubdomains from mathDesc/mesh and store in lookupTable
    int numVol = mesh.getSizeX() * mesh.getSizeY() * mesh.getSizeZ();
    CompartmentSubDomain[] volSubDomainLookup = new CompartmentSubDomain[numVol];
    for (int i = 0; i < numVol; i++) {
        int subVolumeIndex = mesh.getSubVolumeFromVolumeIndex(i);
        SubVolume subVolume = mathDesc.getGeometry().getGeometrySpec().getSubVolume(subVolumeIndex);
        CompartmentSubDomain compSubDomain = mathDesc.getCompartmentSubDomain(subVolume.getName());
        volSubDomainLookup[i] = compSubDomain;
    }
    // Get membraneSubdomains from mathDesc/mesh and store in lookupTable
    int numMem = mesh.getMembraneElements().length;
    MembraneSubDomain[] memSubDomainLookup = new MembraneSubDomain[numMem];
    for (int i = 0; i < numMem; i++) {
        int insideVolIndex = mesh.getMembraneElements()[i].getInsideVolumeIndex();
        int outsideVolIndex = mesh.getMembraneElements()[i].getOutsideVolumeIndex();
        MembraneSubDomain memSubDomain = mathDesc.getMembraneSubDomain(volSubDomainLookup[insideVolIndex], volSubDomainLookup[outsideVolIndex]);
        memSubDomainLookup[i] = memSubDomain;
    }
    double[] valueArray = new double[4];
    SimpleSymbolTable symbolTable = new SimpleSymbolTable(new String[] { "t", "x", "y", "z" });
    int tIndex = symbolTable.getEntry("t").getIndex();
    int xIndex = symbolTable.getEntry("x").getIndex();
    int yIndex = symbolTable.getEntry("y").getIndex();
    int zIndex = symbolTable.getEntry("z").getIndex();
    SimulationComparisonSummary simComparisonSummary = new SimulationComparisonSummary();
    String hashKey = new String("");
    long dataLength = 0;
    // for each var, do the following :
    for (int i = 0; i < vars.length; i++) {
        if (vars[i] instanceof VolVariable || vars[i] instanceof MemVariable || vars[i] instanceof FilamentVariable || vars[i] instanceof VolumeRegionVariable || vars[i] instanceof MembraneRegionVariable || vars[i] instanceof FilamentRegionVariable) {
            // for each time in timeArray,
            for (int j = 0; j < timeArray.length; j++) {
                if (type.equals(TestCaseNew.EXACT_STEADY)) {
                    if (j != (timeArray.length - 1)) {
                        continue;
                    }
                }
                // get data block from varName, data from datablock
                SimDataBlock simDataBlock = dataManager.getSimDataBlock(vars[i].getName(), timeArray[j]);
                double[] data = simDataBlock.getData();
                dataLength = data.length;
                SubDomain subDomain = null;
                Coordinate subDomainCoord = null;
                // for each point in data block ...
                for (int k = 0; k < dataLength; k++) {
                    // Get subdomain from mesh (from the lookupTable), get coordinates (x,y,z) from mesh, evaluate EXACT SOLN at that coord
                    if (vars[i] instanceof VolVariable) {
                        subDomain = volSubDomainLookup[k];
                        subDomainCoord = mesh.getCoordinateFromVolumeIndex(k);
                    } else if (vars[i] instanceof MemVariable) {
                        subDomain = memSubDomainLookup[k];
                        subDomainCoord = mesh.getCoordinateFromMembraneIndex(k);
                    } else {
                        throw new RuntimeException("Var " + vars[i].getName() + " not supported yet!");
                    }
                    hashKey = vars[i].getName() + ":" + subDomain.getName();
                    DataErrorSummary tempVar = (DataErrorSummary) tempVarHash.get(hashKey);
                    if (tempVar == null) {
                        Expression exp = new Expression(subDomain.getEquation(vars[i]).getExactSolution());
                        exp.bindExpression(simSymbolTable);
                        exp = MathUtilities.substituteFunctions(exp, simSymbolTable);
                        exp = exp.flatten();
                        exp.bindExpression(symbolTable);
                        tempVar = new DataErrorSummary(exp);
                        tempVarHash.put(hashKey, tempVar);
                    }
                    // time
                    valueArray[tIndex] = timeArray[j];
                    // x
                    valueArray[xIndex] = subDomainCoord.getX();
                    // y
                    valueArray[yIndex] = subDomainCoord.getY();
                    // z
                    valueArray[zIndex] = subDomainCoord.getZ();
                    // EXACT soln at coord subDomainCoord
                    double value = tempVar.getExactExp().evaluateVector(valueArray);
                    tempVar.addDataValues(value, data[k], timeArray[j], k, absErrorThreshold, relErrorThreshold);
                }
            // end for (k)
            }
        // end for (j)
        }
    // end - if (var)
    }
    // end for (i)
    Enumeration<String> enumKeys = tempVarHash.keys();
    while (enumKeys.hasMoreElements()) {
        String key = enumKeys.nextElement();
        DataErrorSummary tempVarSummary = tempVarHash.get(key);
        simComparisonSummary.addVariableComparisonSummary(new VariableComparisonSummary(key, tempVarSummary.getMinRef(), tempVarSummary.getMaxRef(), tempVarSummary.getMaxAbsoluteError(), tempVarSummary.getMaxRelativeError(), tempVarSummary.getL2Norm(), tempVarSummary.getTimeAtMaxAbsoluteError(), tempVarSummary.getIndexAtMaxAbsoluteError(), tempVarSummary.getTimeAtMaxRelativeError(), tempVarSummary.getIndexAtMaxRelativeError()));
    }
    return simComparisonSummary;
}
Also used : MembraneSubDomain(cbit.vcell.math.MembraneSubDomain) MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) InsideVariable(cbit.vcell.math.InsideVariable) SensVariable(cbit.vcell.solver.ode.SensVariable) FilamentVariable(cbit.vcell.math.FilamentVariable) VolVariable(cbit.vcell.math.VolVariable) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) ReservedVariable(cbit.vcell.math.ReservedVariable) MemVariable(cbit.vcell.math.MemVariable) OutsideVariable(cbit.vcell.math.OutsideVariable) FilamentRegionVariable(cbit.vcell.math.FilamentRegionVariable) Variable(cbit.vcell.math.Variable) MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) MathDescription(cbit.vcell.math.MathDescription) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) SubDomain(cbit.vcell.math.SubDomain) MembraneSubDomain(cbit.vcell.math.MembraneSubDomain) MemVariable(cbit.vcell.math.MemVariable) SimDataBlock(cbit.vcell.simdata.SimDataBlock) SubVolume(cbit.vcell.geometry.SubVolume) AnalyticSubVolume(cbit.vcell.geometry.AnalyticSubVolume) VolVariable(cbit.vcell.math.VolVariable) FilamentRegionVariable(cbit.vcell.math.FilamentRegionVariable) CartesianMesh(cbit.vcell.solvers.CartesianMesh) SimpleSymbolTable(cbit.vcell.parser.SimpleSymbolTable) Coordinate(org.vcell.util.Coordinate) Expression(cbit.vcell.parser.Expression) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) FilamentVariable(cbit.vcell.math.FilamentVariable)

Example 4 with FilamentRegionVariable

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

the class SimulationSymbolTable method createAnnotatedFunctionsList.

public Vector<AnnotatedFunction> createAnnotatedFunctionsList(MathDescription mathDescription) throws InconsistentDomainException {
    // Get the list of (volVariables) in the simulation. Needed to determine 'type' of  functions
    boolean bSpatial = getSimulation().isSpatial();
    String[] variableNames = null;
    VariableType[] variableTypes = null;
    if (bSpatial) {
        Variable[] allVariables = getVariables();
        Vector<Variable> varVector = new Vector<Variable>();
        for (int i = 0; i < allVariables.length; i++) {
            if ((allVariables[i] instanceof VolVariable) || (allVariables[i] instanceof VolumeRegionVariable) || (allVariables[i] instanceof MemVariable) || (allVariables[i] instanceof MembraneRegionVariable) || (allVariables[i] instanceof FilamentVariable) || (allVariables[i] instanceof FilamentRegionVariable) || (allVariables[i] instanceof PointVariable) || (allVariables[i] instanceof ParticleVariable) || (allVariables[i] instanceof InsideVariable) || (allVariables[i] instanceof OutsideVariable)) {
                varVector.addElement(allVariables[i]);
            } else if (allVariables[i] instanceof Constant || (allVariables[i] instanceof Function)) {
            } else {
                System.err.println("SimulationSymbolTable.createAnnotatedFunctionsList() found unexpected variable type " + allVariables[i].getClass().getSimpleName() + " in spatial simulation");
            }
        }
        variableNames = new String[varVector.size()];
        for (int i = 0; i < variableNames.length; i++) {
            variableNames[i] = varVector.get(i).getName();
        }
        // Lookup table for variableType for each variable in 'variables' array.
        variableTypes = new VariableType[variableNames.length];
        for (int i = 0; i < variableNames.length; i++) {
            variableTypes[i] = VariableType.getVariableType(varVector.get(i));
        }
    }
    // 
    // Bind and substitute functions to simulation before storing them in the '.functions' file
    // 
    Function[] functions = getFunctions();
    Vector<AnnotatedFunction> annotatedFunctionVector = new Vector<AnnotatedFunction>();
    for (int i = 0; i < functions.length; i++) {
        if (isFunctionSaved(functions[i])) {
            String errString = "";
            VariableType funcType = null;
            try {
                Expression substitutedExp = substituteFunctions(functions[i].getExpression());
                substitutedExp.bindExpression(this);
                functions[i].setExpression(substitutedExp.flatten());
            } catch (MathException e) {
                e.printStackTrace(System.out);
                errString = errString + ", " + e.getMessage();
            // throw new RuntimeException(e.getMessage());
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                errString = errString + ", " + e.getMessage();
            // throw new RuntimeException(e.getMessage());
            }
            // 
            // get function's data type from the types of it's identifiers
            // 
            funcType = bSpatial ? getFunctionVariableType(functions[i], mathDescription, variableNames, variableTypes, bSpatial) : VariableType.NONSPATIAL;
            AnnotatedFunction annotatedFunc = new AnnotatedFunction(functions[i].getName(), functions[i].getExpression(), functions[i].getDomain(), errString, funcType, FunctionCategory.PREDEFINED);
            annotatedFunctionVector.addElement(annotatedFunc);
        }
    }
    return annotatedFunctionVector;
}
Also used : MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) ReservedVariable(cbit.vcell.math.ReservedVariable) PointVariable(cbit.vcell.math.PointVariable) ParticleVariable(cbit.vcell.math.ParticleVariable) MemVariable(cbit.vcell.math.MemVariable) InsideVariable(cbit.vcell.math.InsideVariable) OutsideVariable(cbit.vcell.math.OutsideVariable) FilamentRegionVariable(cbit.vcell.math.FilamentRegionVariable) Variable(cbit.vcell.math.Variable) FilamentVariable(cbit.vcell.math.FilamentVariable) VolVariable(cbit.vcell.math.VolVariable) MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) ParticleVariable(cbit.vcell.math.ParticleVariable) Constant(cbit.vcell.math.Constant) InsideVariable(cbit.vcell.math.InsideVariable) ExpressionException(cbit.vcell.parser.ExpressionException) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) Function(cbit.vcell.math.Function) MemVariable(cbit.vcell.math.MemVariable) Vector(java.util.Vector) VariableType(cbit.vcell.math.VariableType) VolVariable(cbit.vcell.math.VolVariable) FilamentRegionVariable(cbit.vcell.math.FilamentRegionVariable) Expression(cbit.vcell.parser.Expression) MathException(cbit.vcell.math.MathException) FilamentVariable(cbit.vcell.math.FilamentVariable) PointVariable(cbit.vcell.math.PointVariable) OutsideVariable(cbit.vcell.math.OutsideVariable)

Example 5 with FilamentRegionVariable

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

the class XmlReader method getFilamentRegionVariable.

/**
 * This method returns a FilamentRegionVariable object from a XML Element.
 * Creation date: (5/16/2001 2:56:34 PM)
 * @return cbit.vcell.math.FilamentRegionVariable
 * @param param org.jdom.Element
 */
private FilamentRegionVariable getFilamentRegionVariable(Element param) {
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    // -- create new FilamentRegionVariable object
    FilamentRegionVariable filRegVariable = new FilamentRegionVariable(name, domain);
    transcribeComments(param, filRegVariable);
    return filRegVariable;
}
Also used : FilamentRegionVariable(cbit.vcell.math.FilamentRegionVariable) MembraneSubDomain(cbit.vcell.math.MembraneSubDomain) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) FilamentSubDomain(cbit.vcell.math.FilamentSubDomain) PointSubDomain(cbit.vcell.math.PointSubDomain) Domain(cbit.vcell.math.Variable.Domain)

Aggregations

FilamentRegionVariable (cbit.vcell.math.FilamentRegionVariable)8 FilamentVariable (cbit.vcell.math.FilamentVariable)7 MemVariable (cbit.vcell.math.MemVariable)7 MembraneRegionVariable (cbit.vcell.math.MembraneRegionVariable)7 Variable (cbit.vcell.math.Variable)7 VolVariable (cbit.vcell.math.VolVariable)7 VolumeRegionVariable (cbit.vcell.math.VolumeRegionVariable)7 InsideVariable (cbit.vcell.math.InsideVariable)5 OutsideVariable (cbit.vcell.math.OutsideVariable)5 ReservedVariable (cbit.vcell.math.ReservedVariable)4 Expression (cbit.vcell.parser.Expression)4 SensVariable (cbit.vcell.solver.ode.SensVariable)4 CompartmentSubDomain (cbit.vcell.math.CompartmentSubDomain)3 Constant (cbit.vcell.math.Constant)3 MembraneSubDomain (cbit.vcell.math.MembraneSubDomain)3 FilamentSubDomain (cbit.vcell.math.FilamentSubDomain)2 Function (cbit.vcell.math.Function)2 MathDescription (cbit.vcell.math.MathDescription)2 ParticleVariable (cbit.vcell.math.ParticleVariable)2 PointSubDomain (cbit.vcell.math.PointSubDomain)2