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

Example 36 with Variable

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

the class NFsimXMLWriter method getListOfParameters.

private static Element getListOfParameters(MathDescription mathDesc, SimulationSymbolTable simulationSymbolTable) throws SolverException {
    Element listOfParametersElement = new Element("ListOfParameters");
    for (Variable var : simulationSymbolTable.getVariables()) {
        Double value = null;
        if (var instanceof Constant || var instanceof Function) {
            Expression valExpression = var.getExpression();
            Expression substitutedValExpr = null;
            try {
                substitutedValExpr = simulationSymbolTable.substituteFunctions(valExpression);
            } catch (Exception e) {
                e.printStackTrace(System.out);
                throw new SolverException("Constant or Function " + var.getName() + " substitution failed : exp = \"" + var.getExpression().infix() + "\": " + e.getMessage());
            }
            try {
                value = substitutedValExpr.evaluateConstant();
            } catch (ExpressionException e) {
                System.out.println("constant or function " + var.getName() + " = " + substitutedValExpr.infix() + " does not have a constant value");
            }
            Element parameterElement = new Element("Parameter");
            parameterElement.setAttribute("id", var.getName());
            if (value != null) {
                parameterElement.setAttribute("type", "Constant");
                parameterElement.setAttribute("value", value.toString());
            } else {
                // function, see getListOfFunctions() below
                continue;
            }
            listOfParametersElement.addContent(parameterElement);
        }
    }
    return listOfParametersElement;
}

Example 37 with Variable

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

the class NFsimXMLWriter method getListOfFunctions.

private static Element getListOfFunctions(MathDescription mathDesc, SimulationSymbolTable simulationSymbolTable) throws SolverException {
    Element listOfParametersElement = new Element("ListOfFunctions");
    for (Variable var : simulationSymbolTable.getVariables()) {
        Double value = null;
        if (var instanceof Constant || var instanceof Function) {
            Expression valExpression = var.getExpression();
            Expression substitutedValExpr = null;
            try {
                substitutedValExpr = simulationSymbolTable.substituteFunctions(valExpression);
            } catch (Exception e) {
                e.printStackTrace(System.out);
                throw new SolverException("Constant or Function " + var.getName() + " substitution failed : exp = \"" + var.getExpression().infix() + "\": " + e.getMessage());
            }
            try {
                value = substitutedValExpr.evaluateConstant();
            } catch (ExpressionException e) {
                System.out.println("constant or function " + var.getName() + " = " + substitutedValExpr.infix() + " does not have a constant value");
            }
            Element functionElement = new Element("Function");
            functionElement.setAttribute("id", var.getName());
            if (value != null) {
                // parameter, see getListOfParameters() above
                continue;
            } else {
                Element listOfReferencesElement = new Element("ListOfReferences");
                String[] references = valExpression.getSymbols();
                for (int i = 0; i < references.length; i++) {
                    String reference = references[i];
                    Element referenceElement = new Element("Reference");
                    referenceElement.setAttribute("name", reference);
                    Variable referenceVariable = simulationSymbolTable.getVariable(reference);
                    Double referenceValue = null;
                    Expression referenceExpression = referenceVariable.getExpression();
                    Expression substitutedReferenceExpression = null;
                    if (referenceExpression != null) {
                        try {
                            substitutedReferenceExpression = simulationSymbolTable.substituteFunctions(referenceExpression);
                        } catch (Exception e) {
                            e.printStackTrace(System.out);
                            throw new SolverException("Constant or Function " + var.getName() + " substitution failed : exp = \"" + var.getExpression().infix() + "\": " + e.getMessage());
                        }
                        try {
                            referenceValue = substitutedReferenceExpression.evaluateConstant();
                        } catch (ExpressionException e) {
                            System.out.println("constant or function " + var.getName() + " = " + substitutedValExpr.infix() + " does not have a constant value");
                        }
                    }
                    if (referenceVariable instanceof ParticleObservable) {
                        referenceElement.setAttribute("type", "Observable");
                    } else if (referenceVariable instanceof Function) {
                        if (referenceValue != null) {
                            referenceElement.setAttribute("type", "ConstantExpression");
                        } else {
                            referenceElement.setAttribute("type", "Function");
                        }
                    } else {
                        // constant
                        referenceElement.setAttribute("type", "ConstantExpression");
                    }
                    listOfReferencesElement.addContent(referenceElement);
                }
                functionElement.addContent(listOfReferencesElement);
                Element expressionElement = new Element("Expression");
                String functionExpression = valExpression.infix();
                expressionElement.setText(functionExpression);
                functionElement.addContent(expressionElement);
            }
            listOfParametersElement.addContent(functionElement);
        }
    }
    return listOfParametersElement;
}

Example 38 with Variable

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

the class ModelOptimizationMapping method getRemappedReferenceData.

/**
 * Gets the constraintData property (cbit.vcell.opt.ConstraintData) value.
 * @return The constraintData property value.
 * @see #setConstraintData
 */
private ReferenceData getRemappedReferenceData(MathMapping mathMapping) throws MappingException {
    if (modelOptimizationSpec.getReferenceData() == null) {
        return null;
    }
    // 
    // make sure time is mapped
    // 
    ReferenceData refData = modelOptimizationSpec.getReferenceData();
    ReferenceDataMappingSpec[] refDataMappingSpecs = modelOptimizationSpec.getReferenceDataMappingSpecs();
    RowColumnResultSet rowColResultSet = new RowColumnResultSet();
    Vector<SymbolTableEntry> modelObjectList = new Vector<SymbolTableEntry>();
    Vector<double[]> dataList = new Vector<double[]>();
    // 
    // find bound columns, (time is always mapped to the first column)
    // 
    int mappedColumnCount = 0;
    for (int i = 0; i < refDataMappingSpecs.length; i++) {
        SymbolTableEntry modelObject = refDataMappingSpecs[i].getModelObject();
        if (modelObject != null) {
            int mappedColumnIndex = mappedColumnCount;
            if (modelObject instanceof Model.ReservedSymbol && ((ReservedSymbol) modelObject).isTime()) {
                mappedColumnIndex = 0;
            }
            String origRefDataColumnName = refDataMappingSpecs[i].getReferenceDataColumnName();
            int origRefDataColumnIndex = refData.findColumn(origRefDataColumnName);
            if (origRefDataColumnIndex < 0) {
                throw new RuntimeException("reference data column named '" + origRefDataColumnName + "' not found");
            }
            double[] columnData = refData.getDataByColumn(origRefDataColumnIndex);
            if (modelObjectList.contains(modelObject)) {
                throw new RuntimeException("multiple reference data columns mapped to same model object '" + modelObject.getName() + "'");
            }
            modelObjectList.insertElementAt(modelObject, mappedColumnIndex);
            dataList.insertElementAt(columnData, mappedColumnIndex);
            mappedColumnCount++;
        }
    }
    // 
    if (modelObjectList.size() == 0) {
        throw new RuntimeException("reference data was not associated with model");
    }
    if (modelObjectList.size() == 1) {
        throw new RuntimeException("reference data was not associated with model, must map time and at least one other column");
    }
    boolean bFoundTimeVar = false;
    for (SymbolTableEntry ste : modelObjectList) {
        if (ste instanceof Model.ReservedSymbol && ((ReservedSymbol) ste).isTime()) {
            bFoundTimeVar = true;
            break;
        }
    }
    if (!bFoundTimeVar) {
        throw new RuntimeException("must map time column of reference data to model");
    }
    // 
    for (int i = 0; i < modelObjectList.size(); i++) {
        SymbolTableEntry modelObject = (SymbolTableEntry) modelObjectList.elementAt(i);
        try {
            // Find by name because MathSybolMapping has different 'objects' than refDataMapping 'objects'
            Variable variable = mathMapping.getMathSymbolMapping().findVariableByName(modelObject.getName());
            if (variable != null) {
                String symbol = variable.getName();
                rowColResultSet.addDataColumn(new ODESolverResultSetColumnDescription(symbol));
            } else if (modelObject instanceof Model.ReservedSymbol && ((Model.ReservedSymbol) modelObject).isTime()) {
                Model.ReservedSymbol time = (Model.ReservedSymbol) modelObject;
                String symbol = time.getName();
                rowColResultSet.addDataColumn(new ODESolverResultSetColumnDescription(symbol));
            }
        } catch (MathException | MatrixException | ExpressionException | ModelException e) {
            e.printStackTrace();
            throw new MappingException(e.getMessage(), e);
        }
    }
    // 
    // populate data columns (time and rest)
    // 
    double[] weights = new double[rowColResultSet.getColumnDescriptionsCount()];
    weights[0] = 1.0;
    int numRows = ((double[]) dataList.elementAt(0)).length;
    int numColumns = modelObjectList.size();
    for (int j = 0; j < numRows; j++) {
        double[] row = new double[numColumns];
        for (int i = 0; i < numColumns; i++) {
            row[i] = ((double[]) dataList.elementAt(i))[j];
            if (i > 0) {
                weights[i] += row[i] * row[i];
            }
        }
        rowColResultSet.addRow(row);
    }
    for (int i = 0; i < numColumns; i++) {
        if (weights[i] == 0) {
            weights[i] = 1;
        } else {
            weights[i] = 1 / weights[i];
        }
    }
    SimpleReferenceData remappedRefData = new SimpleReferenceData(rowColResultSet, weights);
    return remappedRefData;
}

Example 39 with Variable

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

the class ConstructedSolutionTemplate method initialize.

/**
 * Insert the method's description here.
 * Creation date: (5/12/2003 11:04:13 AM)
 * @param mathDesc cbit.vcell.math.MathDescription
 */
private void initialize(cbit.vcell.math.MathDescription mathDesc) {
    // 
    // for all valid combinations of variables/domains ... add a solution template with a default solution.
    // 
    java.util.Vector solutionTemplateList = new java.util.Vector();
    Enumeration enumSubDomains = mathDesc.getSubDomains();
    while (enumSubDomains.hasMoreElements()) {
        SubDomain subDomain = (SubDomain) enumSubDomains.nextElement();
        Enumeration enumEquations = subDomain.getEquations();
        while (enumEquations.hasMoreElements()) {
            Equation equation = (Equation) enumEquations.nextElement();
            Variable var = equation.getVariable();
            String baseName = " " + var.getName() + "_" + subDomain.getName();
            String amplitudeName = baseName + "_A";
            String tau1Name = baseName + "_tau1";
            String tau2Name = baseName + "_tau2";
            if (equation instanceof OdeEquation) {
                try {
                    Expression exp = new Expression(amplitudeName + " * (1.0 + exp(-t/" + tau1Name + ")*sin(2*" + Math.PI + "/" + tau2Name + "*t))");
                    solutionTemplateList.add(new SolutionTemplate(equation.getVariable().getName(), subDomain.getName(), exp));
                } catch (cbit.vcell.parser.ExpressionException e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException(e.getMessage());
                }
            } else if (equation instanceof PdeEquation) {
                try {
                    Expression exp = new Expression(amplitudeName + " * (1.0 + exp(-t/" + tau1Name + ") + " + tau2Name + "*x)");
                    solutionTemplateList.add(new SolutionTemplate(equation.getVariable().getName(), subDomain.getName(), exp));
                } catch (cbit.vcell.parser.ExpressionException e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException(e.getMessage());
                }
            }
        }
    }
    this.solutionTemplates = (SolutionTemplate[]) org.vcell.util.BeanUtils.getArray(solutionTemplateList, SolutionTemplate.class);
}

Example 40 with Variable

use of cbit.vcell.math.Variable 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;
}