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

Example 26 with Domain

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

the class MathTestingUtilities method constructExactMath.

/**
 * constructExactMath()
 *
 * take an equation of the form:
 *
 *     d A
 *     --- = F(A,t)
 *     d t
 *
 * and create a new equation with a known exact solution 'A_exact' by adding a forcing function R(t)
 *
 *     d A
 *     --- = F(A,t) + R(t)
 *     d t
 *
 * where:
 *
 *             d A_exact
 *      R(t) = --------- - F(A_exact,t)
 *                d t
 *
 * solving for R(t) is done analytically.
 *
 * Creation date: (1/21/2003 10:47:54 AM)
 * @return cbit.vcell.math.MathDescription
 * @param mathDesc cbit.vcell.math.MathDescription
 */
public static MathDescription constructExactMath(MathDescription mathDesc, java.util.Random random, ConstructedSolutionTemplate constructedSolutionTemplate) throws ExpressionException, MathException, MappingException {
    if (mathDesc.hasFastSystems()) {
        throw new RuntimeException("SolverTest.constructExactMath() suppport for fastSystems not yet implemented.");
    }
    MathDescription exactMath = null;
    try {
        exactMath = (MathDescription) BeanUtils.cloneSerializable(mathDesc);
        exactMath.setDescription("constructed exact solution from MathDescription (" + mathDesc.getName() + ")");
        exactMath.setName("exact from " + mathDesc.getName());
    } catch (Throwable e) {
        e.printStackTrace(System.out);
        throw new RuntimeException("error cloning MathDescription: " + e.getMessage());
    }
    // 
    // preload the VariableHash with existing Variables (and Constants,Functions,etc) and then sort all at once.
    // 
    VariableHash varHash = new VariableHash();
    Enumeration<Variable> enumVar = exactMath.getVariables();
    while (enumVar.hasMoreElements()) {
        varHash.addVariable(enumVar.nextElement());
    }
    java.util.Enumeration<SubDomain> subDomainEnum = exactMath.getSubDomains();
    while (subDomainEnum.hasMoreElements()) {
        SubDomain subDomain = subDomainEnum.nextElement();
        Domain domain = new Domain(subDomain);
        java.util.Enumeration<Equation> equationEnum = subDomain.getEquations();
        if (subDomain instanceof MembraneSubDomain) {
            MembraneSubDomain memSubDomain = (MembraneSubDomain) subDomain;
            AnalyticSubVolume insideAnalyticSubVolume = (AnalyticSubVolume) exactMath.getGeometry().getGeometrySpec().getSubVolume(memSubDomain.getInsideCompartment().getName());
            Function[] outwardNormalFunctions = getOutwardNormal(insideAnalyticSubVolume.getExpression(), "_" + insideAnalyticSubVolume.getName());
            for (int i = 0; i < outwardNormalFunctions.length; i++) {
                varHash.addVariable(outwardNormalFunctions[i]);
            }
        }
        while (equationEnum.hasMoreElements()) {
            Equation equation = equationEnum.nextElement();
            if (equation.getExactSolution() != null) {
                throw new RuntimeException("exact solution already exists");
            }
            Enumeration<Constant> origMathConstants = mathDesc.getConstants();
            if (equation instanceof OdeEquation) {
                OdeEquation odeEquation = (OdeEquation) equation;
                Expression substitutedRateExp = substituteWithExactSolution(odeEquation.getRateExpression(), (CompartmentSubDomain) subDomain, exactMath);
                SolutionTemplate solutionTemplate = constructedSolutionTemplate.getSolutionTemplate(equation.getVariable().getName(), subDomain.getName());
                String varName = odeEquation.getVariable().getName();
                String initName = null;
                while (origMathConstants.hasMoreElements()) {
                    Constant constant = origMathConstants.nextElement();
                    if (constant.getName().startsWith(varName + "_" + subDomain.getName() + DiffEquMathMapping.MATH_FUNC_SUFFIX_SPECIES_INIT_CONC_UNIT_PREFIX)) {
                        initName = constant.getName();
                    }
                }
                String exactName = varName + "_" + subDomain.getName() + "_exact";
                String errorName = varName + "_" + subDomain.getName() + "_error";
                String origRateName = "_" + varName + "_" + subDomain.getName() + "_origRate";
                String substitutedRateName = "_" + varName + "_" + subDomain.getName() + "_substitutedRate";
                String exactTimeDerivativeName = "_" + varName + "_" + subDomain.getName() + "_exact_dt";
                Expression exactExp = solutionTemplate.getTemplateExpression();
                Expression errorExp = new Expression(exactName + " - " + varName);
                Expression origRateExp = new Expression(odeEquation.getRateExpression());
                Expression exactTimeDerivativeExp = exactExp.differentiate("t").flatten();
                Expression newRate = new Expression(origRateName + " - " + substitutedRateName + " + " + exactTimeDerivativeName);
                Constant[] constants = solutionTemplate.getConstants();
                for (int i = 0; i < constants.length; i++) {
                    varHash.addVariable(constants[i]);
                }
                Expression initExp = new Expression(exactExp);
                initExp.substituteInPlace(new Expression("t"), new Expression(0.0));
                varHash.addVariable(new Function(initName, initExp.flatten(), domain));
                varHash.addVariable(new Function(exactName, exactExp, domain));
                varHash.addVariable(new Function(errorName, errorExp, domain));
                varHash.addVariable(new Function(exactTimeDerivativeName, exactTimeDerivativeExp, domain));
                varHash.addVariable(new Function(origRateName, origRateExp, domain));
                varHash.addVariable(new Function(substitutedRateName, substitutedRateExp, domain));
                odeEquation.setRateExpression(newRate);
                odeEquation.setInitialExpression(new Expression(initName));
                odeEquation.setExactSolution(new Expression(exactName));
            } else if (equation instanceof PdeEquation) {
                PdeEquation pdeEquation = (PdeEquation) equation;
                Expression substitutedRateExp = substituteWithExactSolution(pdeEquation.getRateExpression(), (CompartmentSubDomain) subDomain, exactMath);
                SolutionTemplate solutionTemplate = constructedSolutionTemplate.getSolutionTemplate(equation.getVariable().getName(), subDomain.getName());
                String varName = pdeEquation.getVariable().getName();
                String initName = null;
                while (origMathConstants.hasMoreElements()) {
                    Constant constant = origMathConstants.nextElement();
                    if (constant.getName().startsWith(varName + "_" + subDomain.getName() + DiffEquMathMapping.MATH_FUNC_SUFFIX_SPECIES_INIT_CONC_UNIT_PREFIX)) {
                        initName = constant.getName();
                    }
                }
                String diffusionRateName = "_" + varName + "_" + subDomain.getName() + "_diffusionRate";
                String exactName = varName + "_" + subDomain.getName() + "_exact";
                String errorName = varName + "_" + subDomain.getName() + "_error";
                String origRateName = "_" + varName + "_" + subDomain.getName() + "_origRate";
                String substitutedRateName = "_" + varName + "_" + subDomain.getName() + "_substitutedRate";
                String exactTimeDerivativeName = "_" + varName + "_" + subDomain.getName() + "_exact_dt";
                String exactDxName = "_" + varName + "_" + subDomain.getName() + "_exact_dx";
                String exactDyName = "_" + varName + "_" + subDomain.getName() + "_exact_dy";
                String exactDzName = "_" + varName + "_" + subDomain.getName() + "_exact_dz";
                String exactDx2Name = "_" + varName + "_" + subDomain.getName() + "_exact_dx2";
                String exactDy2Name = "_" + varName + "_" + subDomain.getName() + "_exact_dy2";
                String exactDz2Name = "_" + varName + "_" + subDomain.getName() + "_exact_dz2";
                String exactLaplacianName = "_" + varName + "_" + subDomain.getName() + "_exact_laplacian";
                Expression exactExp = solutionTemplate.getTemplateExpression();
                Expression errorExp = new Expression(exactName + " - " + varName);
                Expression origRateExp = new Expression(pdeEquation.getRateExpression());
                Expression initExp = new Expression(exactExp);
                initExp.substituteInPlace(new Expression("t"), new Expression(0.0));
                initExp = initExp.flatten();
                Expression exactTimeDerivativeExp = exactExp.differentiate("t").flatten();
                Expression exactDxExp = exactExp.differentiate("x").flatten();
                Expression exactDx2Exp = exactDxExp.differentiate("x").flatten();
                Expression exactDyExp = exactExp.differentiate("y").flatten();
                Expression exactDy2Exp = exactDxExp.differentiate("y").flatten();
                Expression exactDzExp = exactExp.differentiate("z").flatten();
                Expression exactDz2Exp = exactDxExp.differentiate("z").flatten();
                Expression exactLaplacianExp = Expression.add(Expression.add(exactDx2Exp, exactDy2Exp), exactDz2Exp).flatten();
                Expression newRate = new Expression(origRateName + " - " + substitutedRateName + " - ((" + diffusionRateName + ")*" + exactLaplacianName + ")" + " + " + exactTimeDerivativeName);
                Constant[] constants = solutionTemplate.getConstants();
                for (int i = 0; i < constants.length; i++) {
                    varHash.addVariable(constants[i]);
                }
                varHash.addVariable(new Function(initName, initExp, domain));
                varHash.addVariable(new Function(diffusionRateName, new Expression(pdeEquation.getDiffusionExpression()), domain));
                varHash.addVariable(new Function(exactName, exactExp, domain));
                varHash.addVariable(new Function(errorName, errorExp, domain));
                varHash.addVariable(new Function(exactTimeDerivativeName, exactTimeDerivativeExp, domain));
                varHash.addVariable(new Function(origRateName, origRateExp, domain));
                varHash.addVariable(new Function(substitutedRateName, substitutedRateExp, domain));
                varHash.addVariable(new Function(exactDxName, exactDxExp, domain));
                varHash.addVariable(new Function(exactDyName, exactDyExp, domain));
                varHash.addVariable(new Function(exactDzName, exactDzExp, domain));
                varHash.addVariable(new Function(exactDx2Name, exactDx2Exp, domain));
                varHash.addVariable(new Function(exactDy2Name, exactDy2Exp, domain));
                varHash.addVariable(new Function(exactDz2Name, exactDz2Exp, domain));
                varHash.addVariable(new Function(exactLaplacianName, exactLaplacianExp, domain));
                pdeEquation.setRateExpression(newRate);
                pdeEquation.setInitialExpression(new Expression(initName));
                pdeEquation.setDiffusionExpression(new Expression(diffusionRateName));
                pdeEquation.setExactSolution(new Expression(exactName));
                CompartmentSubDomain compartmentSubDomain = (CompartmentSubDomain) subDomain;
                if (compartmentSubDomain.getBoundaryConditionXm().isDIRICHLET()) {
                    Expression origExp = pdeEquation.getBoundaryXm();
                    if (origExp != null) {
                        Expression substitutedExp = substituteWithExactSolution(origExp, compartmentSubDomain, exactMath);
                        pdeEquation.setBoundaryXm(new Expression(origExp + "-" + substitutedExp + "+" + exactExp));
                    } else {
                        pdeEquation.setBoundaryXm(exactExp);
                    }
                } else if (compartmentSubDomain.getBoundaryConditionXm().isNEUMANN()) {
                    Expression origExp = pdeEquation.getBoundaryXm();
                    if (origExp != null) {
                        Expression substitutedExp = substituteWithExactSolution(origExp, compartmentSubDomain, exactMath);
                        pdeEquation.setBoundaryXm(new Expression(origExp + "-" + substitutedExp + "-" + diffusionRateName + "*" + exactDxName));
                    } else {
                        pdeEquation.setBoundaryXm(new Expression("-" + diffusionRateName + "*" + exactDxName));
                    }
                } else {
                    throw new RuntimeException("unsupported boundary condition type " + compartmentSubDomain.getBoundaryConditionXm());
                }
                if (compartmentSubDomain.getBoundaryConditionXp().isDIRICHLET()) {
                    Expression origExp = pdeEquation.getBoundaryXp();
                    if (origExp != null) {
                        Expression substitutedExp = substituteWithExactSolution(origExp, compartmentSubDomain, exactMath);
                        pdeEquation.setBoundaryXp(new Expression(origExp + "-" + substitutedExp + "+" + exactExp));
                    } else {
                        pdeEquation.setBoundaryXp(exactExp);
                    }
                } else if (compartmentSubDomain.getBoundaryConditionXp().isNEUMANN()) {
                    Expression origExp = pdeEquation.getBoundaryXp();
                    if (origExp != null) {
                        Expression substitutedExp = substituteWithExactSolution(origExp, compartmentSubDomain, exactMath);
                        pdeEquation.setBoundaryXp(new Expression(origExp + "-" + substitutedExp + "+" + diffusionRateName + "*" + exactDxName));
                    } else {
                        pdeEquation.setBoundaryXp(new Expression(diffusionRateName + "*" + exactDxName));
                    }
                } else {
                    throw new RuntimeException("unsupported boundary condition type " + compartmentSubDomain.getBoundaryConditionXp());
                }
                if (compartmentSubDomain.getBoundaryConditionYm().isDIRICHLET()) {
                    Expression origExp = pdeEquation.getBoundaryYm();
                    if (origExp != null) {
                        Expression substitutedExp = substituteWithExactSolution(origExp, compartmentSubDomain, exactMath);
                        pdeEquation.setBoundaryYm(new Expression(origExp + "-" + substitutedExp + "+" + exactExp));
                    } else {
                        pdeEquation.setBoundaryYm(exactExp);
                    }
                } else if (compartmentSubDomain.getBoundaryConditionYm().isNEUMANN()) {
                    Expression origExp = pdeEquation.getBoundaryYm();
                    if (origExp != null) {
                        Expression substitutedExp = substituteWithExactSolution(origExp, compartmentSubDomain, exactMath);
                        pdeEquation.setBoundaryYm(new Expression(origExp + "-" + substitutedExp + "-" + diffusionRateName + "*" + exactDyName));
                    } else {
                        pdeEquation.setBoundaryYm(new Expression("-" + diffusionRateName + "*" + exactDyName));
                    }
                } else {
                    throw new RuntimeException("unsupported boundary condition type " + compartmentSubDomain.getBoundaryConditionYm());
                }
                if (compartmentSubDomain.getBoundaryConditionYp().isDIRICHLET()) {
                    Expression origExp = pdeEquation.getBoundaryYp();
                    if (origExp != null) {
                        Expression substitutedExp = substituteWithExactSolution(origExp, compartmentSubDomain, exactMath);
                        pdeEquation.setBoundaryYp(new Expression(origExp + "-" + substitutedExp + "+" + exactExp));
                    } else {
                        pdeEquation.setBoundaryYp(exactExp);
                    }
                } else if (compartmentSubDomain.getBoundaryConditionYp().isNEUMANN()) {
                    Expression origExp = pdeEquation.getBoundaryYp();
                    if (origExp != null) {
                        Expression substitutedExp = substituteWithExactSolution(origExp, compartmentSubDomain, exactMath);
                        pdeEquation.setBoundaryYp(new Expression(origExp + "-" + substitutedExp + "+" + diffusionRateName + "*" + exactDyName));
                    } else {
                        pdeEquation.setBoundaryYp(new Expression(diffusionRateName + "*" + exactDyName));
                    }
                } else {
                    throw new RuntimeException("unsupported boundary condition type " + compartmentSubDomain.getBoundaryConditionYp());
                }
                if (compartmentSubDomain.getBoundaryConditionZm().isDIRICHLET()) {
                    Expression origExp = pdeEquation.getBoundaryZm();
                    if (origExp != null) {
                        Expression substitutedExp = substituteWithExactSolution(origExp, compartmentSubDomain, exactMath);
                        pdeEquation.setBoundaryZm(new Expression(origExp + "-" + substitutedExp + "+" + exactExp));
                    } else {
                        pdeEquation.setBoundaryZm(exactExp);
                    }
                } else if (compartmentSubDomain.getBoundaryConditionZm().isNEUMANN()) {
                    Expression origExp = pdeEquation.getBoundaryZm();
                    if (origExp != null) {
                        Expression substitutedExp = substituteWithExactSolution(origExp, compartmentSubDomain, exactMath);
                        pdeEquation.setBoundaryZm(new Expression(origExp + "-" + substitutedExp + "-" + diffusionRateName + "*" + exactDzName));
                    } else {
                        pdeEquation.setBoundaryZm(new Expression("-" + diffusionRateName + "*" + exactDzName));
                    }
                } else {
                    throw new RuntimeException("unsupported boundary condition type " + compartmentSubDomain.getBoundaryConditionXm());
                }
                if (compartmentSubDomain.getBoundaryConditionZp().isDIRICHLET()) {
                    Expression origExp = pdeEquation.getBoundaryZp();
                    if (origExp != null) {
                        Expression substitutedExp = substituteWithExactSolution(origExp, compartmentSubDomain, exactMath);
                        pdeEquation.setBoundaryZp(new Expression(origExp + "-" + substitutedExp + "+" + exactExp));
                    } else {
                        pdeEquation.setBoundaryZp(exactExp);
                    }
                } else if (compartmentSubDomain.getBoundaryConditionZp().isNEUMANN()) {
                    Expression origExp = pdeEquation.getBoundaryZp();
                    if (origExp != null) {
                        Expression substitutedExp = substituteWithExactSolution(origExp, compartmentSubDomain, exactMath);
                        pdeEquation.setBoundaryZp(new Expression(origExp + "-" + substitutedExp + "+" + diffusionRateName + "*" + exactDzName));
                    } else {
                        pdeEquation.setBoundaryZp(new Expression(diffusionRateName + "*" + exactDzName));
                    }
                } else {
                    throw new RuntimeException("unsupported boundary condition type " + compartmentSubDomain.getBoundaryConditionZp());
                }
            } else {
                throw new RuntimeException("SolverTest.constructedExactMath(): equation type " + equation.getClass().getName() + " not yet implemented");
            }
        }
        if (subDomain instanceof MembraneSubDomain) {
            MembraneSubDomain membraneSubDomain = (MembraneSubDomain) subDomain;
            Enumeration<JumpCondition> enumJumpConditions = membraneSubDomain.getJumpConditions();
            while (enumJumpConditions.hasMoreElements()) {
                JumpCondition jumpCondition = enumJumpConditions.nextElement();
                Expression origInfluxExp = jumpCondition.getInFluxExpression();
                Expression origOutfluxExp = jumpCondition.getOutFluxExpression();
                Expression substitutedInfluxExp = substituteWithExactSolution(origInfluxExp, membraneSubDomain, exactMath);
                Expression substitutedOutfluxExp = substituteWithExactSolution(origOutfluxExp, membraneSubDomain, exactMath);
                String varName = jumpCondition.getVariable().getName();
                String origInfluxName = "_" + varName + "_" + subDomain.getName() + "_origInflux";
                String origOutfluxName = "_" + varName + "_" + subDomain.getName() + "_origOutflux";
                String substitutedInfluxName = "_" + varName + "_" + subDomain.getName() + "_substitutedInflux";
                String substitutedOutfluxName = "_" + varName + "_" + subDomain.getName() + "_substitutedOutflux";
                String diffusionRateInsideName = "_" + varName + "_" + membraneSubDomain.getInsideCompartment().getName() + "_diffusionRate";
                String diffusionRateOutsideName = "_" + varName + "_" + membraneSubDomain.getOutsideCompartment().getName() + "_diffusionRate";
                String exactInsideDxName = "_" + varName + "_" + membraneSubDomain.getInsideCompartment().getName() + "_exact_dx";
                String exactInsideDyName = "_" + varName + "_" + membraneSubDomain.getInsideCompartment().getName() + "_exact_dy";
                String exactInsideDzName = "_" + varName + "_" + membraneSubDomain.getInsideCompartment().getName() + "_exact_dz";
                String exactOutsideDxName = "_" + varName + "_" + membraneSubDomain.getOutsideCompartment().getName() + "_exact_dx";
                String exactOutsideDyName = "_" + varName + "_" + membraneSubDomain.getOutsideCompartment().getName() + "_exact_dy";
                String exactOutsideDzName = "_" + varName + "_" + membraneSubDomain.getOutsideCompartment().getName() + "_exact_dz";
                String outwardNormalXName = "_" + membraneSubDomain.getInsideCompartment().getName() + "_Nx";
                String outwardNormalYName = "_" + membraneSubDomain.getInsideCompartment().getName() + "_Ny";
                String outwardNormalZName = "_" + membraneSubDomain.getInsideCompartment().getName() + "_Nz";
                String exactInfluxName = "_" + varName + "_" + membraneSubDomain.getName() + "_exactInflux";
                String exactOutfluxName = "_" + varName + "_" + membraneSubDomain.getName() + "_exactOutflux";
                Expression exactInfluxExp = new Expression(diffusionRateInsideName + " * (" + outwardNormalXName + "*" + exactInsideDxName + " + " + outwardNormalYName + "*" + exactInsideDyName + " + " + outwardNormalZName + "*" + exactInsideDzName + ")");
                Expression exactOutfluxExp = new Expression("-" + diffusionRateOutsideName + " * (" + outwardNormalXName + "*" + exactOutsideDxName + " + " + outwardNormalYName + "*" + exactOutsideDyName + " + " + outwardNormalZName + "*" + exactOutsideDzName + ")");
                Expression newInfluxExp = new Expression(origInfluxName + " - " + substitutedInfluxName + " + " + exactInfluxName);
                Expression newOutfluxExp = new Expression(origOutfluxName + " - " + substitutedOutfluxName + " + " + exactOutfluxName);
                varHash.addVariable(new Function(origInfluxName, origInfluxExp, domain));
                varHash.addVariable(new Function(origOutfluxName, origOutfluxExp, domain));
                varHash.addVariable(new Function(exactInfluxName, exactInfluxExp, domain));
                varHash.addVariable(new Function(exactOutfluxName, exactOutfluxExp, domain));
                varHash.addVariable(new Function(substitutedInfluxName, substitutedInfluxExp, domain));
                varHash.addVariable(new Function(substitutedOutfluxName, substitutedOutfluxExp, domain));
                jumpCondition.setInFlux(newInfluxExp);
                jumpCondition.setOutFlux(newOutfluxExp);
            }
        }
    }
    exactMath.setAllVariables(varHash.getAlphabeticallyOrderedVariables());
    if (!exactMath.isValid()) {
        throw new RuntimeException("generated Math is not valid: " + exactMath.getWarning());
    }
    return exactMath;
}

Example 27 with Domain

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

the class MathTestingUtilities method getOutwardNormalFromInsideOutsideFunction.

/**
 * Insert the method's description here.
 * Creation date: (1/23/2003 10:30:23 PM)
 * @return cbit.vcell.parser.Expression
 * @param analyticSubDomainExp cbit.vcell.parser.Expression
 */
public static Function[] getOutwardNormalFromInsideOutsideFunction(Expression insideOutsideFunction, String baseName) throws ExpressionException, MappingException {
    java.util.Vector<Function> varList = new java.util.Vector<Function>();
    Expression F = new Expression(insideOutsideFunction);
    F.bindExpression(null);
    F = F.flatten();
    if (insideOutsideFunction.isRelational() || insideOutsideFunction.isLogical()) {
        throw new RuntimeException("expecting smooth function for analytic function");
    }
    String F_name = baseName + "_F";
    String F_dx_name = baseName + "_F_dx";
    Expression F_dx = F.differentiate("x").flatten();
    String F_dy_name = baseName + "_F_dy";
    Expression F_dy = F.differentiate("y").flatten();
    String F_dz_name = baseName + "_F_dz";
    Expression F_dz = F.differentiate("z").flatten();
    String normalLengthName = baseName + "_F_d_length";
    Expression normalLength = new Expression("sqrt(pow(" + F_dx_name + ",2)+pow(" + F_dy_name + ",2)+pow(" + F_dz_name + ",2))");
    String distanceToSurfaceName = baseName + "_distance";
    Expression distanceToSurface = new Expression("abs(" + F_name + ")/" + normalLengthName);
    String normalXName = baseName + "_Nx";
    Expression normalX = new Expression(F_dx_name + "/" + normalLengthName);
    String normalYName = baseName + "_Ny";
    Expression normalY = new Expression(F_dy_name + "/" + normalLengthName);
    String normalZName = baseName + "_Nz";
    Expression normalZ = new Expression(F_dz_name + "/" + normalLengthName);
    Domain domain = null;
    varList.add(new Function(F_name, F, domain));
    varList.add(new Function(F_dx_name, F_dx, domain));
    varList.add(new Function(F_dy_name, F_dy, domain));
    varList.add(new Function(F_dz_name, F_dz, domain));
    varList.add(new Function(normalLengthName, normalLength, domain));
    varList.add(new Function(normalXName, normalX, domain));
    varList.add(new Function(normalYName, normalY, domain));
    varList.add(new Function(normalZName, normalZ, domain));
    varList.add(new Function(distanceToSurfaceName, distanceToSurface, domain));
    return (Function[]) BeanUtils.getArray(varList, Function.class);
}

Example 28 with Domain

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

the class DataInfoProvider method isDefined.

public boolean isDefined(DataIdentifier dataIdentifier, int dataIndex) {
    try {
        Domain varDomain = dataIdentifier.getDomain();
        if (varDomain == null || dataIdentifier.getVariableType().equals(VariableType.POSTPROCESSING)) {
            return true;
        }
        VariableType varType = dataIdentifier.getVariableType();
        if (pdeDataContext.getCartesianMesh().isChomboMesh() && !Double.isNaN(pdeDataContext.getDataValues()[dataIndex])) {
            return true;
        }
        if (varType.equals(VariableType.VOLUME) || varType.equals(VariableType.VOLUME_REGION)) {
            int subvol = pdeDataContext.getCartesianMesh().getSubVolumeFromVolumeIndex(dataIndex);
            if (simulationModelInfo.getVolumeNameGeometry(subvol) == null || simulationModelInfo.getVolumeNameGeometry(subvol).equals(varDomain.getName())) {
                return true;
            }
        } else if (varType.equals(VariableType.MEMBRANE) || varType.equals(VariableType.MEMBRANE_REGION)) {
            String memSubdomainName = pdeDataContext.getCartesianMesh().getMembraneSubdomainNamefromMemIndex(dataIndex);
            if (varDomain.getName().equals(memSubdomainName)) {
                return true;
            }
        }
    } catch (Exception e) {
        e.printStackTrace();
    }
    return false;
}

Example 29 with Domain

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

the class DataSetControllerImpl method adjustMembraneAdjacentVolumeValues.

private void adjustMembraneAdjacentVolumeValues(OutputContext outputContext, double[][] dataToAdjust, boolean bTimeFormat, SimDataBlock fullDataValueSource, int[] volumeDataIndexes, int[] membraneIndexesInOut, VCDataIdentifier vcdID, String varName, CartesianMesh mesh, TimeInfo timeInfo) throws Exception {
    if (membraneIndexesInOut == null || membraneIndexesInOut.length == 0) {
        return;
    }
    if (bTimeFormat) {
        if (dataToAdjust.length != volumeDataIndexes.length + 1 || dataToAdjust[0].length != timeInfo.desiredTimeValues.length) {
            throw new IllegalArgumentException(this.getClass().getName() + ".adjustMembraneAdjacentVolumeValues array format wrong for time flag=" + bTimeFormat);
        }
    } else {
        if (dataToAdjust.length != timeInfo.desiredTimeValues.length || dataToAdjust[0].length != volumeDataIndexes.length) {
            throw new IllegalArgumentException(this.getClass().getName() + ".adjustMembraneAdjacentVolumeValues array format wrong for time flag=" + bTimeFormat);
        }
    }
    boolean bIsSpecial = false;
    AnnotatedFunction insideFunction = null;
    AnnotatedFunction outsideFunction = null;
    VCData vcData = getVCData(vcdID);
    DataIdentifier[] myDataIdentifers = getDataIdentifiers(outputContext, vcdID);
    for (int i = 0; i < myDataIdentifers.length; i++) {
        if (myDataIdentifers[i].getName().equals(varName)) {
            if (myDataIdentifers[i].getVariableType().equals(VariableType.MEMBRANE)) {
                throw new IllegalArgumentException(this.getClass().getName() + ".adjustMembraneAdjacentVolumeValues Not for Membrane Variables");
            }
            Expression insideExp = null;
            Expression outsideExp = null;
            if (myDataIdentifers[i].isFunction()) {
                AnnotatedFunction sourceFunction = null;
                AnnotatedFunction[] functionsArr = getFunctions(outputContext, vcdID);
                for (int j = 0; j < functionsArr.length; j++) {
                    if (functionsArr[j].getName().equals(varName)) {
                        // need to subsitute and flatten the expression since we no longer store simplified expression.
                        if (vcData instanceof SimulationData) {
                            sourceFunction = ((SimulationData) vcData).simplifyFunction(functionsArr[j]);
                        } else {
                            throw new Exception("DataSetControllerImpl::getTimeSeriesValues_private(): has to be SimulationData to get time plot.");
                        }
                        break;
                    }
                }
                Vector<DataSetIdentifier> dependencyList = identifyDataDependencies(sourceFunction);
                insideExp = new Expression(sourceFunction.getExpression());
                outsideExp = new Expression(sourceFunction.getExpression());
                for (int j = 0; j < dependencyList.size(); j++) {
                    insideExp.substituteInPlace(new Expression(dependencyList.elementAt(j).getName()), new Expression(dependencyList.elementAt(j).getName() + InsideVariable.INSIDE_VARIABLE_SUFFIX));
                    outsideExp.substituteInPlace(new Expression(dependencyList.elementAt(j).getName()), new Expression(dependencyList.elementAt(j).getName() + OutsideVariable.OUTSIDE_VARIABLE_SUFFIX));
                }
            } else {
                insideExp = new Expression(varName + InsideVariable.INSIDE_VARIABLE_SUFFIX);
                outsideExp = new Expression(varName + OutsideVariable.OUTSIDE_VARIABLE_SUFFIX);
            }
            if (insideExp != null && outsideExp != null) {
                insideExp.bindExpression(vcData);
                outsideExp.bindExpression(vcData);
                // TODO domain
                Domain domain = null;
                insideFunction = new AnnotatedFunction("", insideExp, domain, "", VariableType.MEMBRANE, FunctionCategory.PREDEFINED);
                outsideFunction = new AnnotatedFunction("", outsideExp, domain, "", VariableType.MEMBRANE, FunctionCategory.PREDEFINED);
                insideFunction.setExpression(insideExp.flatten());
                outsideFunction.setExpression(outsideExp.flatten());
                FieldFunctionArguments[] insideExpFieldFunctionArgs = FieldUtilities.getFieldFunctionArguments(insideExp);
                FieldFunctionArguments[] outsideExpFieldFunctionArgs = FieldUtilities.getFieldFunctionArguments(outsideExp);
                bIsSpecial = !isAllowOptimizedTimeDataRetrieval() || hasGradient(insideExp) || hasGradient(outsideExp) || (insideExpFieldFunctionArgs != null && insideExpFieldFunctionArgs.length > 0) || (outsideExpFieldFunctionArgs != null && outsideExpFieldFunctionArgs.length > 0);
                if (bIsSpecial && fullDataValueSource == null) {
                    throw new IllegalArgumentException(this.getClass().getName() + ".adjustMembraneAdjacentVolumeValues: special values need SimDataBlock");
                }
            }
            break;
        }
    }
    int crossingCount = 0;
    for (int j = 0; j < membraneIndexesInOut.length; j++) {
        if (membraneIndexesInOut[j] != -1) {
            crossingCount += 1;
        }
    }
    if (crossingCount > 0) {
        int[] crossingCondensedIndexes = new int[crossingCount];
        int[] crossingCondensedOrigLocation = new int[crossingCount];
        crossingCount = 0;
        for (int j = 0; j < membraneIndexesInOut.length; j++) {
            if (membraneIndexesInOut[j] != -1) {
                crossingCondensedOrigLocation[crossingCount] = j;
                crossingCondensedIndexes[crossingCount] = membraneIndexesInOut[j];
                crossingCount += 1;
            }
        }
        MultiFunctionIndexes mfi_inside = null;
        MultiFunctionIndexes mfi_outside = null;
        for (int j = 0; j < crossingCount; j++) {
            double specialInsideVal = (bIsSpecial ? interpolateVolDataValToMemb(mesh, crossingCondensedIndexes[j], fullDataValueSource, true, false) : 0);
            double specialOutsideVal = (bIsSpecial ? interpolateVolDataValToMemb(mesh, crossingCondensedIndexes[j], fullDataValueSource, false, false) : 0);
            VolumeIndexNearFar vinf_inside = interpolateFindNearFarIndex(mesh, crossingCondensedIndexes[j], true, false);
            VolumeIndexNearFar vinf_outside = interpolateFindNearFarIndex(mesh, crossingCondensedIndexes[j], false, false);
            if (vinf_inside.volIndexNear == volumeDataIndexes[crossingCondensedOrigLocation[j]]) {
                if (!bIsSpecial && mfi_inside == null) {
                    mfi_inside = new MultiFunctionIndexes(vcdID, insideFunction, crossingCondensedIndexes, timeInfo.wantsTheseTimes, null, outputContext);
                }
                for (int k = 0; k < timeInfo.desiredTimeValues.length; k++) {
                    if (bTimeFormat) {
                        dataToAdjust[crossingCondensedOrigLocation[j] + 1][k] = (bIsSpecial ? specialInsideVal : mfi_inside.evaluateTimeFunction(outputContext, k, j));
                    } else {
                        dataToAdjust[k][crossingCondensedOrigLocation[j]] = (bIsSpecial ? specialInsideVal : mfi_inside.evaluateTimeFunction(outputContext, k, j));
                    }
                }
            } else if (vinf_outside.volIndexNear == volumeDataIndexes[crossingCondensedOrigLocation[j]]) {
                if (!bIsSpecial && mfi_outside == null) {
                    mfi_outside = new MultiFunctionIndexes(vcdID, outsideFunction, crossingCondensedIndexes, timeInfo.wantsTheseTimes, null, outputContext);
                }
                for (int k = 0; k < timeInfo.desiredTimeValues.length; k++) {
                    if (bTimeFormat) {
                        dataToAdjust[crossingCondensedOrigLocation[j] + 1][k] = (bIsSpecial ? specialOutsideVal : mfi_outside.evaluateTimeFunction(outputContext, k, j));
                    } else {
                        dataToAdjust[k][crossingCondensedOrigLocation[j]] = (bIsSpecial ? specialOutsideVal : mfi_outside.evaluateTimeFunction(outputContext, k, j));
                    }
                }
            } else {
                throw new Exception("couldn't match 'near' indexes");
            }
        }
    } else {
        throw new IllegalArgumentException("No non-null membrane crossing indexes found");
    }
}

Example 30 with Domain

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

the class SimulationData method getVarAndFunctionDataIdentifiers.

/**
 * This method was created in VisualAge.
 * @return java.lang.String[]
 */
public synchronized DataIdentifier[] getVarAndFunctionDataIdentifiers(OutputContext outputContext) throws IOException, DataAccessException {
    // Is this zip format?
    boolean bIsChombo = false;
    try {
        bIsChombo = isChombo();
    } catch (FileNotFoundException e) {
        e.printStackTrace(System.out);
    }
    File zipFile1 = getZipFile(bIsChombo, null);
    File zipFile2 = getZipFile(bIsChombo, 0);
    bZipFormat1 = false;
    bZipFormat2 = false;
    if (zipFile1.exists()) {
        bZipFormat1 = true;
    } else if (zipFile2.exists()) {
        bZipFormat2 = true;
    }
    refreshLogFile();
    if (!isComsol()) {
        try {
            refreshMeshFile();
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage());
        }
    }
    if (!isRulesData && !getIsODEData() && !isComsol() && dataFilenames != null) {
        // read variables only when I have never read the file since variables don't change
        if (dataSetIdentifierList.size() == 0) {
            File file = getPDEDataFile(0.0);
            DataSet dataSet = getPDEDataSet(file, 0.0);
            String[] varNames = dataSet.getDataNames();
            int[] varTypeInts = dataSet.getVariableTypeIntegers();
            if (varNames == null) {
                return null;
            }
            dataSetIdentifierList.clear();
            for (int i = 0; i < varNames.length; i++) {
                VariableType varType = null;
                try {
                    varType = VariableType.getVariableTypeFromInteger(varTypeInts[i]);
                } catch (IllegalArgumentException e) {
                    if (LG.isEnabledFor(Level.WARN)) {
                        LG.warn("Exception typing " + varNames[i] + " has unsupported type " + varTypeInts[i] + ": " + e.getMessage());
                    }
                    varType = SimulationData.getVariableTypeFromLength(mesh, dataSet.getDataLength(varNames[i]));
                }
                Domain domain = Variable.getDomainFromCombinedIdentifier(varNames[i]);
                String varName = Variable.getNameFromCombinedIdentifier(varNames[i]);
                dataSetIdentifierList.addElement(new DataSetIdentifier(varName, varType, domain));
            }
            refreshDataProcessingOutputInfo(outputContext);
            if (dataProcessingOutputInfo != null) {
                for (int i = 0; i < dataProcessingOutputInfo.getVariableNames().length; i++) {
                    if (dataProcessingOutputInfo.getPostProcessDataType(dataProcessingOutputInfo.getVariableNames()[i]).equals(DataProcessingOutputInfo.PostProcessDataType.image)) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(dataProcessingOutputInfo.getVariableNames()[i], VariableType.POSTPROCESSING, null));
                    }
                }
            }
        }
        // always read functions file since functions might change
        getFunctionDataIdentifiers(outputContext);
    }
    if ((isRulesData || getIsODEData()) && dataSetIdentifierList.size() == 0) {
        ODEDataBlock odeDataBlock = getODEDataBlock();
        if (odeDataBlock == null) {
            throw new DataAccessException("Results are not availabe yet. Please try again later.");
        }
        ODESimData odeSimData = odeDataBlock.getODESimData();
        int colCount = odeSimData.getColumnDescriptionsCount();
        // assume index=0 is time "t"
        int DATA_OFFSET = 1;
        dataSetIdentifierList.clear();
        for (int i = 0; i < (colCount - DATA_OFFSET); i++) {
            String varName = odeSimData.getColumnDescriptions(i + DATA_OFFSET).getDisplayName();
            // TODO domain
            Domain domain = null;
            dataSetIdentifierList.addElement(new DataSetIdentifier(varName, VariableType.NONSPATIAL, domain));
        }
    }
    if (isComsol() && dataSetIdentifierList.size() == 0) {
        ComsolSimFiles comsolSimFiles = getComsolSimFiles();
        if (comsolSimFiles.simTaskXMLFile != null) {
            try {
                String xmlString = FileUtils.readFileToString(comsolSimFiles.simTaskXMLFile);
                SimulationTask simTask = XmlHelper.XMLToSimTask(xmlString);
                Enumeration<Variable> variablesEnum = simTask.getSimulation().getMathDescription().getVariables();
                while (variablesEnum.hasMoreElements()) {
                    Variable var = variablesEnum.nextElement();
                    if (var instanceof VolVariable) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.VOLUME, var.getDomain()));
                    } else if (var instanceof MemVariable) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.MEMBRANE, var.getDomain()));
                    } else if (var instanceof Function) {
                        VariableType varType = VariableType.UNKNOWN;
                        if (var.getDomain() != null && var.getDomain().getName() != null) {
                            SubDomain subDomain = simTask.getSimulation().getMathDescription().getSubDomain(var.getDomain().getName());
                            if (subDomain instanceof CompartmentSubDomain) {
                                varType = VariableType.VOLUME;
                            } else if (subDomain instanceof MembraneSubDomain) {
                                varType = VariableType.MEMBRANE;
                            } else if (subDomain instanceof FilamentSubDomain) {
                                throw new RuntimeException("filament subdomains not supported");
                            } else if (subDomain instanceof PointSubDomain) {
                                varType = VariableType.POINT_VARIABLE;
                            }
                        }
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), varType, var.getDomain()));
                    } else if (var instanceof Constant) {
                        System.out.println("ignoring Constant " + var.getName());
                    } else if (var instanceof InsideVariable) {
                        System.out.println("ignoring InsideVariable " + var.getName());
                    } else if (var instanceof OutsideVariable) {
                        System.out.println("ignoring OutsideVariable " + var.getName());
                    } else {
                        throw new RuntimeException("unexpected variable " + var.getName() + " of type " + var.getClass().getName());
                    }
                }
            } catch (XmlParseException | ExpressionException e) {
                e.printStackTrace();
                throw new RuntimeException("failed to read sim task file, msg: " + e.getMessage(), e);
            }
        }
    }
    DataIdentifier[] dis = new DataIdentifier[dataSetIdentifierList.size()];
    for (int i = 0; i < dataSetIdentifierList.size(); i++) {
        DataSetIdentifier dsi = (DataSetIdentifier) dataSetIdentifierList.elementAt(i);
        String displayName = dsi.getName();
        if (dsi.isFunction()) {
            AnnotatedFunction f = null;
            for (int j = 0; j < annotatedFunctionList.size(); j++) {
                AnnotatedFunction function = (AnnotatedFunction) annotatedFunctionList.elementAt(j);
                if (function.getName().equals(dsi.getName())) {
                    f = function;
                    break;
                }
            }
            if (f != null) {
                displayName = f.getDisplayName();
            }
        }
        dis[i] = new DataIdentifier(dsi.getName(), dsi.getVariableType(), dsi.getDomain(), dsi.isFunction(), displayName);
    }
    return dis;
}