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

Example 6 with FastRate

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

the class IDAFileWriter method writeEquations.

/**
 * Insert the method's description here.
 * Creation date: (3/8/00 10:31:52 PM)
 */
protected String writeEquations(HashMap<Discontinuity, String> discontinuityNameMap) throws MathException, ExpressionException {
    Simulation simulation = simTask.getSimulation();
    StringBuffer sb = new StringBuffer();
    MathDescription mathDescription = simulation.getMathDescription();
    if (mathDescription.hasFastSystems()) {
        // 
        // define vector of original variables
        // 
        SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
        CompartmentSubDomain subDomain = (CompartmentSubDomain) mathDescription.getSubDomains().nextElement();
        FastSystem fastSystem = subDomain.getFastSystem();
        FastSystemAnalyzer fs_Analyzer = new FastSystemAnalyzer(fastSystem, simSymbolTable);
        int numIndependent = fs_Analyzer.getNumIndependentVariables();
        int systemDim = mathDescription.getStateVariableNames().size();
        int numDependent = systemDim - numIndependent;
        // 
        // get all variables from fast system (dependent and independent)
        // 
        HashSet<String> fastSystemVarHash = new HashSet<String>();
        Enumeration<Variable> dependentfastSystemVarEnum = fs_Analyzer.getDependentVariables();
        while (dependentfastSystemVarEnum.hasMoreElements()) {
            fastSystemVarHash.add(dependentfastSystemVarEnum.nextElement().getName());
        }
        Enumeration<Variable> independentfastSystemVarEnum = fs_Analyzer.getIndependentVariables();
        while (independentfastSystemVarEnum.hasMoreElements()) {
            fastSystemVarHash.add(independentfastSystemVarEnum.nextElement().getName());
        }
        // 
        // get all equations including for variables that are not in the fastSystem (ode equations for "slow system")
        // 
        RationalExpMatrix origInitVector = new RationalExpMatrix(systemDim, 1);
        RationalExpMatrix origSlowRateVector = new RationalExpMatrix(systemDim, 1);
        RationalExpMatrix origVarColumnVector = new RationalExpMatrix(systemDim, 1);
        Enumeration<Equation> enumEquations = subDomain.getEquations();
        int varIndex = 0;
        while (enumEquations.hasMoreElements()) {
            Equation equation = enumEquations.nextElement();
            origVarColumnVector.set_elem(varIndex, 0, new RationalExp(equation.getVariable().getName()));
            Expression rateExpr = equation.getRateExpression();
            rateExpr.bindExpression(varsSymbolTable);
            rateExpr = MathUtilities.substituteFunctions(rateExpr, varsSymbolTable);
            origSlowRateVector.set_elem(varIndex, 0, new RationalExp("(" + rateExpr.flatten().infix() + ")"));
            Expression initExpr = new Expression(equation.getInitialExpression());
            initExpr.substituteInPlace(new Expression("t"), new Expression(0.0));
            initExpr = MathUtilities.substituteFunctions(initExpr, varsSymbolTable).flatten();
            origInitVector.set_elem(varIndex, 0, new RationalExp("(" + initExpr.flatten().infix() + ")"));
            varIndex++;
        }
        // 
        // make symbolic matrix for fast invariants (from FastSystem's fastInvariants as well as a new fast invariant for each variable not included in the fast system.
        // 
        RationalExpMatrix fastInvarianceMatrix = new RationalExpMatrix(numDependent, systemDim);
        int row = 0;
        for (int i = 0; i < origVarColumnVector.getNumRows(); i++) {
            // 
            if (!fastSystemVarHash.contains(origVarColumnVector.get(i, 0).infixString())) {
                fastInvarianceMatrix.set_elem(row, i, RationalExp.ONE);
                row++;
            }
        }
        Enumeration<FastInvariant> enumFastInvariants = fastSystem.getFastInvariants();
        while (enumFastInvariants.hasMoreElements()) {
            FastInvariant fastInvariant = enumFastInvariants.nextElement();
            Expression fastInvariantExpression = fastInvariant.getFunction();
            for (int col = 0; col < systemDim; col++) {
                Expression coeff = fastInvariantExpression.differentiate(origVarColumnVector.get(col, 0).infixString()).flatten();
                coeff = simSymbolTable.substituteFunctions(coeff);
                fastInvarianceMatrix.set_elem(row, col, RationalExpUtils.getRationalExp(coeff));
            }
            row++;
        }
        for (int i = 0; i < systemDim; i++) {
            sb.append("VAR " + origVarColumnVector.get(i, 0).infixString() + " INIT " + origInitVector.get(i, 0).infixString() + ";\n");
        }
        RationalExpMatrix fullMatrix = null;
        RationalExpMatrix inverseFullMatrix = null;
        RationalExpMatrix newSlowRateVector = null;
        try {
            RationalExpMatrix fastMat = ((RationalExpMatrix) fastInvarianceMatrix.transpose().findNullSpace());
            fullMatrix = new RationalExpMatrix(systemDim, systemDim);
            row = 0;
            for (int i = 0; i < fastInvarianceMatrix.getNumRows(); i++) {
                for (int col = 0; col < systemDim; col++) {
                    fullMatrix.set_elem(row, col, fastInvarianceMatrix.get(i, col));
                }
                row++;
            }
            for (int i = 0; i < fastMat.getNumRows(); i++) {
                for (int col = 0; col < systemDim; col++) {
                    fullMatrix.set_elem(row, col, fastMat.get(i, col));
                }
                row++;
            }
            inverseFullMatrix = new RationalExpMatrix(systemDim, systemDim);
            inverseFullMatrix.identity();
            RationalExpMatrix copyOfFullMatrix = new RationalExpMatrix(fullMatrix);
            copyOfFullMatrix.gaussianElimination(inverseFullMatrix);
            newSlowRateVector = new RationalExpMatrix(numDependent, 1);
            newSlowRateVector.matmul(fastInvarianceMatrix, origSlowRateVector);
        } catch (MatrixException ex) {
            ex.printStackTrace();
            throw new MathException(ex.getMessage());
        }
        sb.append("TRANSFORM\n");
        for (row = 0; row < systemDim; row++) {
            for (int col = 0; col < systemDim; col++) {
                sb.append(fullMatrix.get(row, col).getConstant().doubleValue() + " ");
            }
            sb.append("\n");
        }
        sb.append("INVERSETRANSFORM\n");
        for (row = 0; row < systemDim; row++) {
            for (int col = 0; col < systemDim; col++) {
                sb.append(inverseFullMatrix.get(row, col).getConstant().doubleValue() + " ");
            }
            sb.append("\n");
        }
        int numDifferential = numDependent;
        int numAlgebraic = numIndependent;
        sb.append("RHS DIFFERENTIAL " + numDifferential + " ALGEBRAIC " + numAlgebraic + "\n");
        int equationIndex = 0;
        while (equationIndex < numDependent) {
            // print row of mass matrix followed by slow rate corresponding to fast invariant
            Expression slowRateExp = new Expression(newSlowRateVector.get(equationIndex, 0).infixString()).flatten();
            slowRateExp.bindExpression(simSymbolTable);
            slowRateExp = MathUtilities.substituteFunctions(slowRateExp, varsSymbolTable).flatten();
            Vector<Discontinuity> v = slowRateExp.getDiscontinuities();
            for (Discontinuity od : v) {
                od = getSubsitutedAndFlattened(od, varsSymbolTable);
                String dname = discontinuityNameMap.get(od);
                if (dname == null) {
                    dname = ROOT_VARIABLE_PREFIX + discontinuityNameMap.size();
                    discontinuityNameMap.put(od, dname);
                }
                slowRateExp.substituteInPlace(od.getDiscontinuityExp(), new Expression("(" + dname + "==1)"));
            }
            sb.append(slowRateExp.infix() + ";\n");
            equationIndex++;
        }
        Enumeration<FastRate> enumFastRates = fastSystem.getFastRates();
        while (enumFastRates.hasMoreElements()) {
            // print the fastRate for this row
            Expression fastRateExp = new Expression(enumFastRates.nextElement().getFunction());
            fastRateExp = MathUtilities.substituteFunctions(fastRateExp, varsSymbolTable).flatten();
            Vector<Discontinuity> v = fastRateExp.getDiscontinuities();
            for (Discontinuity od : v) {
                od = getSubsitutedAndFlattened(od, varsSymbolTable);
                String dname = discontinuityNameMap.get(od);
                if (dname == null) {
                    dname = ROOT_VARIABLE_PREFIX + discontinuityNameMap.size();
                    discontinuityNameMap.put(od, dname);
                }
                fastRateExp.substituteInPlace(od.getDiscontinuityExp(), new Expression("(" + dname + "==1)"));
            }
            sb.append(fastRateExp.flatten().infix() + ";\n");
            equationIndex++;
        }
    } else {
        for (int i = 0; i < getStateVariableCount(); i++) {
            StateVariable stateVar = getStateVariable(i);
            Expression initExpr = new Expression(stateVar.getInitialRateExpression());
            initExpr = MathUtilities.substituteFunctions(initExpr, varsSymbolTable);
            initExpr.substituteInPlace(new Expression("t"), new Expression(0.0));
            sb.append("VAR " + stateVar.getVariable().getName() + " INIT " + initExpr.flatten().infix() + ";\n");
        }
        sb.append("TRANSFORM\n");
        for (int row = 0; row < getStateVariableCount(); row++) {
            for (int col = 0; col < getStateVariableCount(); col++) {
                sb.append((row == col ? 1 : 0) + " ");
            }
            sb.append("\n");
        }
        sb.append("INVERSETRANSFORM\n");
        for (int row = 0; row < getStateVariableCount(); row++) {
            for (int col = 0; col < getStateVariableCount(); col++) {
                sb.append((row == col ? 1 : 0) + " ");
            }
            sb.append("\n");
        }
        sb.append("RHS DIFFERENTIAL " + getStateVariableCount() + " ALGEBRAIC 0\n");
        for (int i = 0; i < getStateVariableCount(); i++) {
            StateVariable stateVar = getStateVariable(i);
            Expression rateExpr = new Expression(stateVar.getRateExpression());
            rateExpr = MathUtilities.substituteFunctions(rateExpr, varsSymbolTable).flatten();
            Vector<Discontinuity> v = rateExpr.getDiscontinuities();
            for (Discontinuity od : v) {
                od = getSubsitutedAndFlattened(od, varsSymbolTable);
                String dname = discontinuityNameMap.get(od);
                if (dname == null) {
                    dname = ROOT_VARIABLE_PREFIX + discontinuityNameMap.size();
                    discontinuityNameMap.put(od, dname);
                }
                rateExpr.substituteInPlace(od.getDiscontinuityExp(), new Expression("(" + dname + "==1)"));
            }
            sb.append(rateExpr.infix() + ";\n");
        }
    }
    return sb.toString();
}

Example 7 with FastRate

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

the class MathTestingUtilities method constructOdesForSensitivity.

// 
// This method is used to solve for sensitivity of variables to a given parameter.
// The mathDescription and the sensitivity parameter are passed as arguments.
// New variables and ODEs are constructed according to the rule listed below and are added to the mathDescription.
// The method returns the modified mathDescription.
// 
public static MathDescription constructOdesForSensitivity(MathDescription mathDesc, Constant sensParam) throws ExpressionException, MathException, MappingException {
    // 
    // For each ODE :
    // 
    // dX/dt = F(X, P)
    // 
    // (where P is the sensitivity parameter)
    // 
    // we create two other ODEs :
    // 
    // dX_1/dt = F(X_1, P_1)    and
    // 
    // dX_2/dt = F(X_2, P_2)
    // 
    // where P_1 = P + epsilon, and
    // P_2 = P - epsilon.
    // 
    // We keep the initial conditions for both the new ODEs to be the same,
    // i.e., X_1_init = X_2_init.
    // 
    // Then, solving for X_1 & X_2, sensitivity of X wrt P can be computed as :
    // 
    // dX = (X_1 - X_2)
    // --	 -----------   .
    // dP	 (P_1 - P_2)
    // 
    // 
    // REMOVE PRINTS AFTER CHECKING !!!
    System.out.println(" \n\n------------  Old Math Description -----------------");
    System.out.println(mathDesc.getVCML_database());
    if (mathDesc.getGeometry().getDimension() > 0) {
        throw new RuntimeException("Suppport for Spatial systems not yet implemented.");
    }
    VariableHash varHash = new VariableHash();
    Enumeration<Variable> enumVar = mathDesc.getVariables();
    while (enumVar.hasMoreElements()) {
        varHash.addVariable(enumVar.nextElement());
    }
    // 
    // Get 2 values of senstivity parameter (P + epsilon) & (P - epsilon)
    // 
    Constant epsilon = new Constant("epsilon", new Expression(sensParam.getConstantValue() * 1e-3));
    Constant sensParam1 = new Constant(sensParam.getName() + "_1", new Expression(sensParam.getConstantValue() + epsilon.getConstantValue()));
    Constant sensParam2 = new Constant(sensParam.getName() + "_2", new Expression(sensParam.getConstantValue() - epsilon.getConstantValue()));
    // 
    // Iterate through each subdomain (only 1 in compartmental case), and each equation in the subdomain
    // 
    Enumeration<SubDomain> subDomainEnum = mathDesc.getSubDomains();
    // 
    // Create a vector of equations to store the 2 equations for each ODE variable in the subdomain.
    // Later, add it to the equations list in the subdomain.
    // 
    Vector<Equation> equnsVector = new Vector<Equation>();
    Vector<Variable> varsVector = new Vector<Variable>();
    Vector<Variable> var1s = new Vector<Variable>();
    Vector<Variable> var2s = new Vector<Variable>();
    while (subDomainEnum.hasMoreElements()) {
        SubDomain subDomain = subDomainEnum.nextElement();
        Enumeration<Equation> equationEnum = subDomain.getEquations();
        Domain domain = new Domain(subDomain);
        while (equationEnum.hasMoreElements()) {
            Equation equation = equationEnum.nextElement();
            if (equation instanceof OdeEquation) {
                OdeEquation odeEquation = (OdeEquation) equation;
                // Similar to substituteWithExactSolutions, to bind and substitute functions in the ODE
                Expression substitutedRateExp = substituteFunctions(odeEquation.getRateExpression(), mathDesc);
                String varName = odeEquation.getVariable().getName();
                VolVariable var = new VolVariable(varName, domain);
                varsVector.addElement(var);
                // 
                // Create the variable var1, and get the initExpr and rateExpr from the original ODE.
                // Substitute the new vars (var1 and param1) in the old initExpr and rateExpr and create a new ODE
                // 
                String varName1 = new String("__" + varName + "_1");
                Expression initExpr1 = odeEquation.getInitialExpression();
                Expression rateExpr1 = new Expression(substitutedRateExp);
                rateExpr1.substituteInPlace(new Expression(varName), new Expression(varName1));
                rateExpr1.substituteInPlace(new Expression(sensParam.getName()), new Expression(sensParam1.getName()));
                VolVariable var1 = new VolVariable(varName1, domain);
                var1s.addElement(var1);
                OdeEquation odeEqun1 = new OdeEquation(var1, initExpr1, rateExpr1);
                equnsVector.addElement(odeEqun1);
                // 
                // Create the variable var2, and get the initExpr and rateExpr from the original ODE.
                // Substitute the new vars (var2 and param2) in the old initExpr and rateExpr and create a new ODE
                // 
                String varName2 = new String("__" + varName + "_2");
                Expression initExpr2 = odeEquation.getInitialExpression();
                Expression rateExpr2 = new Expression(substitutedRateExp);
                rateExpr2.substituteInPlace(new Expression(varName), new Expression(varName2));
                rateExpr2.substituteInPlace(new Expression(sensParam.getName()), new Expression(sensParam2.getName()));
                VolVariable var2 = new VolVariable(varName2, domain);
                var2s.addElement(var2);
                OdeEquation odeEqun2 = new OdeEquation(var2, initExpr2, rateExpr2);
                equnsVector.addElement(odeEqun2);
                // 
                // Create a function for the sensitivity function expression (X1-X2)/(P1-P2), and save in varHash
                // 
                Expression diffVar = Expression.add(new Expression(var1.getName()), Expression.negate(new Expression(var2.getName())));
                Expression diffParam = Expression.add(new Expression(sensParam1.getName()), Expression.negate(new Expression(sensParam2.getName())));
                Expression sensitivityExpr = Expression.mult(diffVar, Expression.invert(diffParam));
                Function sens_Func = new Function("__sens" + varName + "_wrt_" + sensParam.getName(), sensitivityExpr, domain);
                varHash.addVariable(epsilon);
                varHash.addVariable(sensParam1);
                varHash.addVariable(sensParam2);
                varHash.addVariable(var1);
                varHash.addVariable(var2);
                varHash.addVariable(sens_Func);
            } else {
                // sensitivity not implemented for PDEs or other equation types.
                throw new RuntimeException("SolverTest.constructedExactMath(): equation type " + equation.getClass().getName() + " not yet implemented");
            }
        }
        // 
        // Need to substitute the new variables in the new ODEs.
        // i.e., if Rate Expr for ODE_1 for variable X_1 contains variable Y, variable Z, etc.
        // Rate Expr is already substituted with X_1, but it also needs substitute Y with Y_1, Z with Z_1, etc.
        // So get the volume variables, from the vectors for vars, var_1s and var_2s
        // Substitute the rate expressions for the newly added ODEs in equnsVector.
        // 
        Variable[] vars = (Variable[]) BeanUtils.getArray(varsVector, Variable.class);
        Variable[] var_1s = (Variable[]) BeanUtils.getArray(var1s, Variable.class);
        Variable[] var_2s = (Variable[]) BeanUtils.getArray(var2s, Variable.class);
        Vector<Equation> newEqunsVector = new Vector<Equation>();
        for (int i = 0; i < equnsVector.size(); i++) {
            Equation equn = equnsVector.elementAt(i);
            Expression initEx = equn.getInitialExpression();
            Expression rateEx = equn.getRateExpression();
            for (int j = 0; j < vars.length; j++) {
                if (equn.getVariable().getName().endsWith("_1")) {
                    rateEx.substituteInPlace(new Expression(vars[j].getName()), new Expression(var_1s[j].getName()));
                } else if (equn.getVariable().getName().endsWith("_2")) {
                    rateEx.substituteInPlace(new Expression(vars[j].getName()), new Expression(var_2s[j].getName()));
                }
            }
            OdeEquation odeEqun = new OdeEquation(equn.getVariable(), initEx, rateEx);
            newEqunsVector.addElement(odeEqun);
        }
        // 
        for (int i = 0; i < newEqunsVector.size(); i++) {
            mathDesc.getSubDomain(subDomain.getName()).addEquation((Equation) newEqunsVector.elementAt(i));
        }
        // 
        // FAST SYSTEM
        // If the subdomain has a fast system, create a new fast system by substituting the high-low variables/parameters
        // in the expressions for the fastInvariants and fastRates and adding them to the fast system.
        // 
        Vector<FastInvariant> invarsVector = new Vector<FastInvariant>();
        Vector<FastRate> ratesVector = new Vector<FastRate>();
        Enumeration<FastInvariant> fastInvarsEnum = null;
        Enumeration<FastRate> fastRatesEnum = null;
        // Get the fast invariants and fast rates in the system.
        FastSystem fastSystem = subDomain.getFastSystem();
        if (fastSystem != null) {
            fastInvarsEnum = fastSystem.getFastInvariants();
            fastRatesEnum = fastSystem.getFastRates();
            // 
            while (fastInvarsEnum.hasMoreElements()) {
                FastInvariant fastInvar = fastInvarsEnum.nextElement();
                Expression fastInvarExpr = fastInvar.getFunction();
                fastInvarExpr = MathUtilities.substituteFunctions(fastInvarExpr, mathDesc);
                Expression fastInvarExpr1 = new Expression(fastInvarExpr);
                Expression fastInvarExpr2 = new Expression(fastInvarExpr);
                for (int i = 0; i < vars.length; i++) {
                    fastInvarExpr1.substituteInPlace(new Expression(vars[i].getName()), new Expression(var_1s[i].getName()));
                    fastInvarExpr2.substituteInPlace(new Expression(vars[i].getName()), new Expression(var_2s[i].getName()));
                }
                fastInvarExpr1.substituteInPlace(new Expression(sensParam.getName()), new Expression(sensParam1.getName()));
                FastInvariant fastInvar1 = new FastInvariant(fastInvarExpr1);
                invarsVector.addElement(fastInvar1);
                fastInvarExpr2.substituteInPlace(new Expression(sensParam.getName()), new Expression(sensParam2.getName()));
                FastInvariant fastInvar2 = new FastInvariant(fastInvarExpr2);
                invarsVector.addElement(fastInvar2);
            }
            // Add the newly created fast invariants to the existing list of fast invariants in the fast system.
            for (int i = 0; i < invarsVector.size(); i++) {
                FastInvariant inVar = (FastInvariant) invarsVector.elementAt(i);
                fastSystem.addFastInvariant(inVar);
            }
            // 
            while (fastRatesEnum.hasMoreElements()) {
                FastRate fastRate = fastRatesEnum.nextElement();
                Expression fastRateExpr = fastRate.getFunction();
                fastRateExpr = MathUtilities.substituteFunctions(fastRateExpr, mathDesc);
                Expression fastRateExpr1 = new Expression(fastRateExpr);
                Expression fastRateExpr2 = new Expression(fastRateExpr);
                for (int i = 0; i < vars.length; i++) {
                    fastRateExpr1.substituteInPlace(new Expression(vars[i].getName()), new Expression(var_1s[i].getName()));
                    fastRateExpr2.substituteInPlace(new Expression(vars[i].getName()), new Expression(var_2s[i].getName()));
                }
                fastRateExpr1.substituteInPlace(new Expression(sensParam.getName()), new Expression(sensParam1.getName()));
                FastRate fastRate1 = new FastRate(fastRateExpr1);
                ratesVector.addElement(fastRate1);
                fastRateExpr2.substituteInPlace(new Expression(sensParam.getName()), new Expression(sensParam2.getName()));
                FastRate fastRate2 = new FastRate(fastRateExpr2);
                ratesVector.addElement(fastRate2);
            }
            // Add the newly created fast rates to the existing list of fast rates in the fast system.
            for (int i = 0; i < ratesVector.size(); i++) {
                FastRate rate = (FastRate) ratesVector.elementAt(i);
                fastSystem.addFastRate(rate);
            }
        }
    }
    // Reset all variables in mathDesc.
    mathDesc.setAllVariables(varHash.getAlphabeticallyOrderedVariables());
    // REMOVE PRINTS AFTER CHECKING
    System.out.println(" \n\n------------  New Math Description -----------------");
    System.out.println(mathDesc.getVCML_database());
    return mathDesc;
}

Example 8 with FastRate

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

the class MathDescriptionCellRenderer method getTreeCellRendererComponent.

/**
 * Insert the method's description here.
 * Creation date: (7/27/2000 6:41:57 PM)
 * @return java.awt.Component
 */
public java.awt.Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
    JLabel component = (JLabel) super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
    boolean bLoaded = false;
    // 
    try {
        if (value instanceof BioModelNode) {
            BioModelNode node = (BioModelNode) value;
            if (node.getUserObject() instanceof PdeEquation) {
                PdeEquation pdeEquation = (PdeEquation) node.getUserObject();
                Variable var = pdeEquation.getVariable();
                component.setToolTipText("PDE Equation");
                // \u2207 = nabla ... del operator
                // \u2219 = dot
                String DEL = "\u2207";
                // "\u2202";     //  '\u2202' is partial differentiation    'd' is regular diff
                String PARTIAL_DIFF = "d";
                String Super2 = "\u00b2";
                String DOT = "\u2219";
                // String diffusionTerm = DEL+" "+DOT+" "+"("+pdeEquation.getDiffusionExpression()+" "+DEL+" "+var.getName()+")";
                String diffusionTerm = "";
                if (pdeEquation.getVelocityX() != null || pdeEquation.getVelocityY() != null || pdeEquation.getVelocityZ() != null) {
                    if (pdeEquation.getDiffusionExpression().isZero()) {
                        // reaction/advection
                        diffusionTerm = "- " + DEL + " " + DOT + "( velocity " + var.getName() + " )";
                    } else {
                        // reaction/diffusion/advection
                        diffusionTerm = DEL + " " + DOT + " (" + pdeEquation.getDiffusionExpression().infix() + " " + DEL + "  " + var.getName() + "   -   velocity " + var.getName() + ")";
                    }
                } else {
                    diffusionTerm = "(" + pdeEquation.getDiffusionExpression().infix() + ") " + DEL + Super2 + " " + var.getName();
                }
                String gradTerm = "";
                if (pdeEquation.getGradientX() != null && !pdeEquation.getGradientX().isZero()) {
                    gradTerm += " + " + PARTIAL_DIFF + "[" + pdeEquation.getGradientX().infix() + "]/" + PARTIAL_DIFF + "x";
                }
                if (pdeEquation.getGradientY() != null && !pdeEquation.getGradientY().isZero()) {
                    gradTerm += " + " + PARTIAL_DIFF + "[" + pdeEquation.getGradientY().infix() + "]/" + PARTIAL_DIFF + "y";
                }
                if (pdeEquation.getGradientZ() != null && !pdeEquation.getGradientZ().isZero()) {
                    gradTerm += " + " + PARTIAL_DIFF + "[" + pdeEquation.getGradientZ().infix() + "]/" + PARTIAL_DIFF + "z";
                }
                String sourceTerm = pdeEquation.getRateExpression().infix();
                if (!sourceTerm.equals("0.0")) {
                    component.setText(PARTIAL_DIFF + "[" + var.getName() + "]/" + PARTIAL_DIFF + "t = " + diffusionTerm + gradTerm + " + " + sourceTerm);
                } else {
                    component.setText(PARTIAL_DIFF + "[" + var.getName() + "]/" + PARTIAL_DIFF + "t = " + diffusionTerm + gradTerm);
                }
            } else if (node.getUserObject() instanceof OdeEquation) {
                OdeEquation odeEquation = (OdeEquation) node.getUserObject();
                Variable var = odeEquation.getVariable();
                component.setToolTipText("ODE Equation");
                component.setText("d[" + var.getName() + "]/dt = " + odeEquation.getRateExpression().infix());
            } else if (node.getUserObject() instanceof MembraneRegionEquation) {
                MembraneRegionEquation membraneRegionEquation = (MembraneRegionEquation) node.getUserObject();
                Variable var = membraneRegionEquation.getVariable();
                component.setToolTipText("Membrane Region Equation");
                component.setText("Membrane Region Equation for " + var.getName());
            } else if (node.getUserObject() instanceof JumpCondition) {
                JumpCondition jumpCondition = (JumpCondition) node.getUserObject();
                Variable var = jumpCondition.getVariable();
                component.setToolTipText("Jump Condition");
                component.setText("Flux for " + var.getName());
            } else if (node.getUserObject() instanceof Constant) {
                Constant constant = (Constant) node.getUserObject();
                component.setToolTipText("Constant");
                component.setText(constant.getName() + " = " + constant.getExpression().infix());
            } else if (node.getUserObject() instanceof Function) {
                Function function = (Function) node.getUserObject();
                component.setToolTipText("Function");
                component.setText(function.getName() + " = " + function.getExpression().infix());
            } else if (node.getUserObject() instanceof SubDomain) {
                SubDomain subDomain = (SubDomain) node.getUserObject();
                component.setToolTipText("SubDomain");
                component.setText(subDomain.getName());
            } else if (node.getUserObject() instanceof FastSystem) {
                component.setToolTipText("Fast System");
                component.setText("Fast System");
            } else if (node.getUserObject() instanceof FastInvariant) {
                FastInvariant fi = (FastInvariant) node.getUserObject();
                component.setToolTipText("Fast Invariant");
                component.setText("fast invariant: " + fi.getFunction().infix());
            } else if (node.getUserObject() instanceof FastRate) {
                FastRate fr = (FastRate) node.getUserObject();
                component.setToolTipText("Fast Rate");
                component.setText("fast rate: " + fr.getFunction().infix());
            } else if (node.getUserObject() instanceof Annotation) {
                Annotation annotation = (Annotation) node.getUserObject();
                component.setToolTipText("Annotation");
                component.setText("\"" + annotation + "\"");
            } else {
            }
            if (selectedFont == null && component.getFont() != null) {
                selectedFont = component.getFont().deriveFont(Font.BOLD);
            }
            if (unselectedFont == null && component.getFont() != null) {
                unselectedFont = component.getFont().deriveFont(Font.PLAIN);
            }
            if (bLoaded) {
                component.setFont(selectedFont);
            } else {
                component.setFont(unselectedFont);
            }
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
    }
    // 
    return component;
}

Example 9 with FastRate

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

the class MathDescriptionTreeModel method createBaseTree.

/**
 * Insert the method's description here.
 * Creation date: (11/28/00 1:06:51 PM)
 * @return cbit.vcell.desktop.BioModelNode
 * @param docManager cbit.vcell.clientdb.DocumentManager
 */
private BioModelNode createBaseTree() {
    if (getMathDescription() == null) {
        return new BioModelNode(" ", false);
    }
    // 
    // make root node
    // 
    BioModelNode rootNode = new BioModelNode("math description", true);
    // 
    // create subTree of Constants
    // 
    BioModelNode constantRootNode = new BioModelNode("constants", true);
    Enumeration<Constant> enum1 = getMathDescription().getConstants();
    while (enum1.hasMoreElements()) {
        Constant constant = enum1.nextElement();
        BioModelNode constantNode = new BioModelNode(constant, false);
        constantRootNode.add(constantNode);
    }
    if (constantRootNode.getChildCount() > 0) {
        rootNode.add(constantRootNode);
    }
    // 
    // create subTree of Functions
    // 
    BioModelNode functionRootNode = new BioModelNode("functions", true);
    Enumeration<Function> enum2 = getMathDescription().getFunctions();
    while (enum2.hasMoreElements()) {
        Function function = enum2.nextElement();
        BioModelNode functionNode = new BioModelNode(function, false);
        functionRootNode.add(functionNode);
    }
    if (functionRootNode.getChildCount() > 0) {
        rootNode.add(functionRootNode);
    }
    // 
    // create subTree of VolumeSubDomains and MembraneSubDomains
    // 
    BioModelNode volumeRootNode = new BioModelNode("volume domains", true);
    BioModelNode membraneRootNode = new BioModelNode("membrane domains", true);
    Enumeration<SubDomain> enum3 = getMathDescription().getSubDomains();
    while (enum3.hasMoreElements()) {
        SubDomain subDomain = enum3.nextElement();
        if (subDomain instanceof cbit.vcell.math.CompartmentSubDomain) {
            CompartmentSubDomain volumeSubDomain = (CompartmentSubDomain) subDomain;
            BioModelNode volumeSubDomainNode = new BioModelNode(volumeSubDomain, true);
            if (// stochastic subtree
            getMathDescription().isNonSpatialStoch()) {
                // add stoch variable initial conditions
                BioModelNode varIniConditionNode = new BioModelNode("variable_initial_conditions", true);
                for (VarIniCondition varIni : volumeSubDomain.getVarIniConditions()) {
                    BioModelNode varIniNode = new BioModelNode(varIni, false);
                    varIniConditionNode.add(varIniNode);
                }
                volumeSubDomainNode.add(varIniConditionNode);
                // add jump processes
                for (JumpProcess jp : volumeSubDomain.getJumpProcesses()) {
                    BioModelNode jpNode = new BioModelNode(jp, true);
                    // add probability rate.
                    String probRate = "P_" + jp.getName();
                    BioModelNode prNode = new BioModelNode("probability_rate = " + probRate, false);
                    jpNode.add(prNode);
                    // add Actions
                    Enumeration<Action> actions = Collections.enumeration(jp.getActions());
                    while (actions.hasMoreElements()) {
                        Action action = actions.nextElement();
                        BioModelNode actionNode = new BioModelNode(action, false);
                        jpNode.add(actionNode);
                    }
                    volumeSubDomainNode.add(jpNode);
                }
            } else // non-stochastic subtree
            {
                // 
                // add equation children
                // 
                Enumeration<Equation> eqnEnum = volumeSubDomain.getEquations();
                while (eqnEnum.hasMoreElements()) {
                    Equation equation = eqnEnum.nextElement();
                    BioModelNode equationNode = new BioModelNode(equation, false);
                    volumeSubDomainNode.add(equationNode);
                }
                // 
                // add fast system
                // 
                FastSystem fastSystem = volumeSubDomain.getFastSystem();
                if (fastSystem != null) {
                    BioModelNode fsNode = new BioModelNode(fastSystem, true);
                    Enumeration<FastInvariant> enumFI = fastSystem.getFastInvariants();
                    while (enumFI.hasMoreElements()) {
                        FastInvariant fi = enumFI.nextElement();
                        fsNode.add(new BioModelNode(fi, false));
                    }
                    Enumeration<FastRate> enumFR = fastSystem.getFastRates();
                    while (enumFR.hasMoreElements()) {
                        FastRate fr = enumFR.nextElement();
                        fsNode.add(new BioModelNode(fr, false));
                    }
                    volumeSubDomainNode.add(fsNode);
                }
            }
            volumeRootNode.add(volumeSubDomainNode);
        } else if (subDomain instanceof MembraneSubDomain) {
            MembraneSubDomain membraneSubDomain = (MembraneSubDomain) subDomain;
            BioModelNode membraneSubDomainNode = new BioModelNode(membraneSubDomain, true);
            // 
            // add equation children
            // 
            Enumeration<Equation> eqnEnum = membraneSubDomain.getEquations();
            while (eqnEnum.hasMoreElements()) {
                Equation equation = eqnEnum.nextElement();
                BioModelNode equationNode = new BioModelNode(equation, false);
                membraneSubDomainNode.add(equationNode);
            }
            // 
            // add jump condition children
            // 
            Enumeration<JumpCondition> jcEnum = membraneSubDomain.getJumpConditions();
            while (jcEnum.hasMoreElements()) {
                JumpCondition jumpCondition = jcEnum.nextElement();
                BioModelNode jcNode = new BioModelNode(jumpCondition, false);
                membraneSubDomainNode.add(jcNode);
            }
            // 
            // add fast system
            // 
            FastSystem fastSystem = membraneSubDomain.getFastSystem();
            if (fastSystem != null) {
                BioModelNode fsNode = new BioModelNode(fastSystem, true);
                Enumeration<FastInvariant> enumFI = fastSystem.getFastInvariants();
                while (enumFI.hasMoreElements()) {
                    FastInvariant fi = enumFI.nextElement();
                    fsNode.add(new BioModelNode(fi, false));
                }
                Enumeration<FastRate> enumFR = fastSystem.getFastRates();
                while (enumFR.hasMoreElements()) {
                    FastRate fr = enumFR.nextElement();
                    fsNode.add(new BioModelNode(fr, false));
                }
                membraneSubDomainNode.add(fsNode);
            }
            membraneRootNode.add(membraneSubDomainNode);
        }
    }
    if (volumeRootNode.getChildCount() > 0) {
        rootNode.add(volumeRootNode);
    }
    if (membraneRootNode.getChildCount() > 0) {
        rootNode.add(membraneRootNode);
    }
    return rootNode;
}

Example 10 with FastRate

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

the class FastSystemAnalyzer method refreshSubstitutedRateExps.

/**
 */
private void refreshSubstitutedRateExps() throws MathException, ExpressionException {
    // 
    // refresh PseudoConstants (temp constants involved with fastInvariants)
    // 
    pseudoConstantList.removeAllElements();
    Enumeration<FastInvariant> enum_fi = fastSystem.getFastInvariants();
    while (enum_fi.hasMoreElements()) {
        FastInvariant fi = enum_fi.nextElement();
        fi.getFunction().bindExpression(this);
        PseudoConstant pc = new PseudoConstant(getAvailablePseudoConstantName(), fi.getFunction(), MathMapping_4_8.nullDomain);
        pseudoConstantList.addElement(pc);
    // System.out.println("FastSystem.refreshSubstitutedRateExps() __C"+i+" = "+fi.getFunction());
    }
    // 
    // build expressions for dependent variables in terms of independent vars
    // and pseudoConstants
    // 
    dependencyExpList.removeAllElements();
    for (int row = 0; row < dependentVarList.size(); row++) {
        Expression exp = new Expression("0.0;");
        // 
        for (int col = 0; col < independentVarList.size(); col++) {
            Variable indepVar = (Variable) independentVarList.elementAt(col);
            RationalExp coefExp = dependencyMatrix.get(row, col).simplify();
            if (!coefExp.isZero()) {
                exp = Expression.add(exp, new Expression(coefExp.infixString() + "*" + indepVar.getName()));
            }
        }
        // 
        for (int col = independentVarList.size(); col < dependencyMatrix.getNumCols(); col++) {
            PseudoConstant pc = (PseudoConstant) pseudoConstantList.elementAt(col - independentVarList.size());
            RationalExp coefExp = dependencyMatrix.get(row, col);
            if (!coefExp.isZero()) {
                exp = Expression.add(exp, new Expression(coefExp.infixString() + "*" + pc.getName()));
            }
        }
        exp.bindExpression(null);
        exp = exp.flatten();
        exp.bindExpression(this);
        // System.out.println("FastSystem.refreshSubstitutedRateExps() "+((Variable)dependentVarList.elementAt(row)).getName()+" = "+exp.toString()+";");
        dependencyExpList.addElement(exp);
    }
    // 
    // flatten functions, then substitute expressions for dependent vars into rate expressions
    // 
    fastRateExpList.removeAllElements();
    // VariableSymbolTable combinedSymbolTable = getCombinedSymbolTable();
    Enumeration<FastRate> enum_fr = fastSystem.getFastRates();
    while (enum_fr.hasMoreElements()) {
        FastRate fr = enum_fr.nextElement();
        Expression exp = new Expression(MathUtilities.substituteFunctions(new Expression(fr.getFunction()), this));
        // System.out.println("FastSystem.refreshSubstitutedRateExps() fast rate before substitution = "+exp.toString());
        for (int j = 0; j < dependentVarList.size(); j++) {
            Variable depVar = (Variable) dependentVarList.elementAt(j);
            Expression subExp = new Expression((Expression) dependencyExpList.elementAt(j));
            exp.substituteInPlace(new Expression(depVar.getName()), subExp);
        }
        exp.bindExpression(null);
        exp = exp.flatten();
        // System.out.println("FastSystem.refreshSubstitutedRateExps() fast rate after substitution  = "+exp.toString());
        exp.bindExpression(this);
        fastRateExpList.addElement(exp);
    }
}