Examples with RationalNumber cbit.vcell.matrix.RationalNumber used on opensource projects

Example 1 with RationalNumber

use of cbit.vcell.matrix.RationalNumber in project vcell by virtualcell.

the class RationalExpUtils method getRationalExp.

private static RationalExp getRationalExp(SimpleNode node, boolean bAllowFunctions) throws ExpressionException {
    if (node == null) {
        return null;
    }
    if (node instanceof ASTAndNode || node instanceof ASTOrNode || node instanceof ASTNotNode || node instanceof ASTRelationalNode || node instanceof DerivativeNode || node instanceof ASTLaplacianNode) {
        throw new ExpressionException("sub-expression " + node.infixString(SimpleNode.LANGUAGE_DEFAULT) + " cannot be translated to a Rational Expression");
    } else if (node instanceof ASTFuncNode) {
        if (((ASTFuncNode) node).getFunction() == FunctionType.POW) {
            try {
                double constantExponent = node.jjtGetChild(1).evaluateConstant();
                if (constantExponent != Math.floor(constantExponent)) {
                    throw new ExpressionException("sub-expression " + node.infixString(SimpleNode.LANGUAGE_DEFAULT) + " cannot be translated to a Rational Expression, exponent is not an integer");
                }
                int intExponent = (int) constantExponent;
                if (intExponent == 0) {
                    return RationalExp.ONE;
                }
                RationalExp base = getRationalExp((SimpleNode) node.jjtGetChild(0), bAllowFunctions);
                if (intExponent < 0) {
                    base = base.inverse();
                    intExponent = -intExponent;
                }
                RationalExp baseUnit = new RationalExp(base);
                for (int i = 1; i < intExponent; i++) {
                    base = base.mult(baseUnit);
                }
                return base;
            } catch (ExpressionException e) {
                throw new ExpressionException("sub-expression " + node.infixString(SimpleNode.LANGUAGE_DEFAULT) + " cannot be translated to a Rational Expression, exponent is not constant");
            }
        } else {
            if (bAllowFunctions) {
                return new RationalExp(((ASTFuncNode) node).infixString(SimpleNode.LANGUAGE_DEFAULT));
            } else {
                throw new ExpressionException("sub-expression " + node.infixString(SimpleNode.LANGUAGE_DEFAULT) + " cannot be translated to a Rational Expression");
            }
        }
    } else if (node instanceof ASTPowerNode) {
        try {
            double constantExponent = node.jjtGetChild(1).evaluateConstant();
            if (constantExponent != Math.floor(constantExponent)) {
                throw new ExpressionException("sub-expression " + node.infixString(SimpleNode.LANGUAGE_DEFAULT) + " cannot be translated to a Rational Expression, exponent is not an integer");
            }
            int intExponent = (int) constantExponent;
            if (intExponent == 0) {
                return RationalExp.ONE;
            }
            RationalExp base = getRationalExp((SimpleNode) node.jjtGetChild(0), bAllowFunctions);
            if (intExponent < 0) {
                base = base.inverse();
                intExponent = -intExponent;
            }
            RationalExp baseUnit = new RationalExp(base);
            for (int i = 1; i < intExponent; i++) {
                base = base.mult(baseUnit);
            }
            return base;
        } catch (ExpressionException e) {
            throw new ExpressionException("sub-expression " + node.infixString(SimpleNode.LANGUAGE_DEFAULT) + " cannot be translated to a Rational Expression, exponent is not constant");
        }
    } else if (node instanceof ASTAddNode) {
        RationalExp exp = RationalExp.ZERO;
        for (int i = 0; i < node.jjtGetNumChildren(); i++) {
            exp = exp.add(getRationalExp((SimpleNode) node.jjtGetChild(i), bAllowFunctions));
        }
        return exp;
    } else if (node instanceof ASTMinusTermNode) {
        return getRationalExp((SimpleNode) node.jjtGetChild(0), bAllowFunctions).minus();
    } else if (node instanceof ASTMultNode) {
        if (node.jjtGetNumChildren() == 1) {
            return getRationalExp((SimpleNode) node.jjtGetChild(0), bAllowFunctions);
        }
        RationalExp exp = RationalExp.ONE;
        for (int i = 0; i < node.jjtGetNumChildren(); i++) {
            exp = exp.mult(getRationalExp((SimpleNode) node.jjtGetChild(i), bAllowFunctions));
        }
        return exp;
    } else if (node instanceof ASTInvertTermNode) {
        SimpleNode child = (SimpleNode) node.jjtGetChild(0);
        return getRationalExp(child, bAllowFunctions).inverse();
    } else if (node instanceof ASTFloatNode) {
        // return TBD instead of dimensionless.
        RationalNumber r = RationalNumber.getApproximateFraction(((ASTFloatNode) node).value.doubleValue());
        return new RationalExp(r);
    // } else if (node instanceof ASTFuncNode) {
    // String functionName = ((ASTFuncNode)node).getName();
    // if (functionName.equalsIgnoreCase("pow")) {
    // SimpleNode child0 =  (SimpleNode)node.jjtGetChild(0);
    // SimpleNode child1 =  (SimpleNode)node.jjtGetChild(1);
    // VCUnitDefinition unit0 = getRationalExp(child0);
    // VCUnitDefinition unit1 = getRationalExp(child1);
    // if (!unit1.compareEqual(VCUnitDefinition.UNIT_DIMENSIONLESS) && !unit1.compareEqual(VCUnitDefinition.UNIT_TBD)){
    // throw new VCUnitException("exponent of '"+node.infixString(SimpleNode.LANGUAGE_DEFAULT,SimpleNode.NAMESCOPE_DEFAULT)+"' has units of "+unit0);
    // }
    // if (unit0.compareEqual(VCUnitDefinition.UNIT_DIMENSIONLESS) || unit0.isTBD()){
    // return unit0;
    // }
    // try {
    // double d = ((SimpleNode)node.jjtGetChild(1)).evaluateConstant();
    // RationalNumber rn = RationalNumber.getApproximateFraction(d);
    // return unit0.raiseTo(rn);
    // }catch(ExpressionException e){
    // return VCUnitDefinition.UNIT_TBD;  // ????? don't know the unit now
    // }
    // }
    // } else if (node instanceof ASTPowerNode) {
    // SimpleNode child0 =  (SimpleNode)node.jjtGetChild(0);
    // SimpleNode child1 =  (SimpleNode)node.jjtGetChild(1);
    // VCUnitDefinition unit0 = getRationalExp(child0);
    // VCUnitDefinition unit1 = getRationalExp(child1);
    // if (!unit1.compareEqual(VCUnitDefinition.UNIT_DIMENSIONLESS) && !unit1.compareEqual(VCUnitDefinition.UNIT_TBD)){
    // throw new VCUnitException("exponent of '"+node.infixString(SimpleNode.LANGUAGE_DEFAULT,SimpleNode.NAMESCOPE_DEFAULT)+"' has units of "+unit0);
    // }
    // if (unit0.compareEqual(VCUnitDefinition.UNIT_DIMENSIONLESS)){
    // return VCUnitDefinition.UNIT_DIMENSIONLESS;
    // }
    // boolean bConstantExponent = false;
    // double exponentValue = 1;
    // try {
    // exponentValue = child1.evaluateConstant();
    // bConstantExponent = true;
    // }catch(ExpressionException e){
    // bConstantExponent = false;
    // }
    // if (bConstantExponent){ //
    // if (unit0.isTBD()){
    // return VCUnitDefinition.UNIT_TBD;
    // }else{
    // RationalNumber rn = RationalNumber.getApproximateFraction(exponentValue);
    // return unit0.raiseTo(rn);
    // }
    // }else{
    // return VCUnitDefinition.UNIT_TBD;
    // }
    } else if (node instanceof ASTIdNode) {
        return new RationalExp(((ASTIdNode) node).name);
    } else {
        throw new ExpressionException("node type " + node.getClass().toString() + " not supported yet");
    }
}

Example 2 with RationalNumber

use of cbit.vcell.matrix.RationalNumber in project vcell by virtualcell.

the class SpeciesContextSpec method initializeForSpatial.

public void initializeForSpatial() {
    if (getDiffusionParameter() != null && getDiffusionParameter().getExpression() != null && getDiffusionParameter().getExpression().isZero()) {
        Expression e = null;
        ModelUnitSystem modelUnitSystem = getSimulationContext().getModel().getUnitSystem();
        VCUnitDefinition micronsqpersecond = modelUnitSystem.getInstance("um2.s-1");
        if (speciesContext.getStructure() instanceof Feature) {
            RationalNumber rn = RationalNumber.getApproximateFraction(micronsqpersecond.convertTo(10, getDiffusionParameter().getUnitDefinition()));
            e = new Expression(rn.doubleValue());
        } else if (speciesContext.getStructure() instanceof Membrane) {
            RationalNumber rn = RationalNumber.getApproximateFraction(micronsqpersecond.convertTo(0.1, getDiffusionParameter().getUnitDefinition()));
            e = new Expression(rn.doubleValue());
        } else {
            RationalNumber rn = RationalNumber.getApproximateFraction(micronsqpersecond.convertTo(1.0, getDiffusionParameter().getUnitDefinition()));
            e = new Expression(rn.doubleValue());
        }
        try {
            getDiffusionParameter().setExpression(e);
        } catch (ExpressionBindingException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Error while initializing diffusion rate, " + e1.getMessage());
        }
    }
}

Example 3 with RationalNumber

use of cbit.vcell.matrix.RationalNumber in project vcell by virtualcell.

the class StructureAnalyzer method refreshTotalDependancies.

/**
 * This method was created by a SmartGuide.
 * @param b cbit.vcell.math.Matrix
 * @param vars java.lang.String[]
 */
public static StructureAnalyzer.Dependency[] refreshTotalDependancies(RationalMatrix nullSpaceMatrix, SpeciesContextMapping[] speciesContextMappings, AbstractMathMapping argMathMapping, boolean bFast) throws Exception {
    // System.out.println("StructureAnalyzer.refreshTotalDependancies()");
    SimulationContext argSimContext = argMathMapping.getSimulationContext();
    if (nullSpaceMatrix == null) {
        // System.out.println("the matrix has full rank, there are no dependencies");
        return new StructureAnalyzer.Dependency[0];
    }
    if (speciesContextMappings.length != nullSpaceMatrix.getNumCols()) {
        // throw new Exception("varName array not same dimension as b matrix");
        System.out.println("varName array not same dimension as b matrix");
        nullSpaceMatrix.show();
        for (int i = 0; i < speciesContextMappings.length; i++) {
            System.out.println("scm[" + i + "] is " + speciesContextMappings[i].getSpeciesContext().getName());
        }
    }
    System.out.println("there are " + nullSpaceMatrix.getNumRows() + " dependencies, " + nullSpaceMatrix.getNumCols() + " columns.");
    long startTime = System.currentTimeMillis();
    Vector<Dependency> dependencyList = new Vector<Dependency>();
    for (int i = 0; i < nullSpaceMatrix.getNumRows(); i++) {
        // 
        // find first variable
        // 
        ArrayList<Expression> el = new ArrayList<Expression>();
        ArrayList<Expression> cel = new ArrayList<Expression>();
        String constantName = null;
        SpeciesContextMapping firstSCM = null;
        boolean bFirst = true;
        for (int j = 0; j < nullSpaceMatrix.getNumCols(); j++) {
            RationalNumber coeff = nullSpaceMatrix.get_elem(i, j);
            if (coeff.doubleValue() != 0.0) {
                if (bFirst) {
                    if (coeff.doubleValue() != 1.0) {
                        System.out.println("i=" + i + " j=" + j);
                        nullSpaceMatrix.show();
                        throw new Exception("expecting a coefficient of 1.0, instead coeff = " + coeff.infix());
                    }
                    firstSCM = speciesContextMappings[j];
                    // 
                    // first term of dependancy expression   ("K_CalciumCyt")
                    // 
                    SpeciesContext firstSC = firstSCM.getSpeciesContext();
                    constantName = DiffEquMathMapping.PARAMETER_MASS_CONSERVATION_PREFIX + firstSC.getName() + DiffEquMathMapping.PARAMETER_MASS_CONSERVATION_SUFFIX;
                    Expression exp = new Expression(constantName);
                    el.add(exp);
                    // 
                    // first term of K expression
                    // 
                    StructureMapping firstSM = argSimContext.getGeometryContext().getStructureMapping(firstSC.getStructure());
                    SpeciesContextSpec firstSCS = argSimContext.getReactionContext().getSpeciesContextSpec(firstSC);
                    SymbolTableEntry scSTE = null;
                    if (bFast) {
                        scSTE = firstSCS.getSpeciesContext();
                    } else {
                        scSTE = firstSCS.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
                    }
                    Expression constantExp = Expression.mult(new Expression(coeff), firstSM.getNormalizedConcentrationCorrection(argSimContext, argMathMapping), new Expression(scSTE, argMathMapping.getNameScope()));
                    cel.add(constantExp);
                    bFirst = false;
                } else {
                    // 
                    // add term to dependancy expression     (" - 2*IP3Cyt ")
                    // 
                    SpeciesContextMapping scm = speciesContextMappings[j];
                    SpeciesContext sc = scm.getSpeciesContext();
                    StructureMapping sm = argSimContext.getGeometryContext().getStructureMapping(sc.getStructure());
                    SpeciesContextSpec scs = argSimContext.getReactionContext().getSpeciesContextSpec(sc);
                    Expression negate = Expression.negate(Expression.mult(new Expression(coeff), sm.getNormalizedConcentrationCorrection(argSimContext, argMathMapping), new Expression(sc, argMathMapping.getNameScope())));
                    el.add(negate);
                    // 
                    // add term to K expression
                    // 
                    SymbolTableEntry scSTE = null;
                    if (bFast) {
                        scSTE = sc;
                    } else {
                        scSTE = scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
                    }
                    Expression mult = Expression.mult(new Expression(coeff), sm.getNormalizedConcentrationCorrection(argSimContext, argMathMapping), new Expression(scSTE, argMathMapping.getNameScope()));
                    cel.add(mult);
                }
            }
        }
        if (firstSCM != null) {
            // 
            // store totalMass parameter (e.g. K_xyz_total = xyz_init + wzy_init)
            // 
            // MathMapping.MathMappingParameter totalMassParameter = mathMapping.addMathMappingParameter(constantName,constantExp.flatten(),MathMapping.PARAMETER_ROLE_TOTALMASS,cbit.vcell.units.VCUnitDefinition.UNIT_uM);
            // 
            // store dependency parameter (e.g. xyz = K_xyz_total - wzy)
            // 
            StructureMapping sm = argSimContext.getGeometryContext().getStructureMapping(firstSCM.getSpeciesContext().getStructure());
            Expression invert = Expression.invert(sm.getNormalizedConcentrationCorrection(argSimContext, argMathMapping));
            Dependency dependency = new Dependency();
            // exp = Expression.mult(exp,invert);
            // exp = exp.flatten();							// old way
            // System.out.println(exp.infix());
            // //exp.bindExpression(mathMapping_temp);
            // //firstSCM.setDependencyExpression(exp);
            // dependency.dependencyExpression = exp;
            Expression[] ev = el.toArray(new Expression[el.size()]);
            Expression e = Expression.add(ev);
            e = Expression.mult(e, invert);
            // new way
            e = e.flatten();
            // System.out.println(e.infix());
            // e.bindExpression(mathMapping_temp);
            // firstSCM.setDependencyExpression(e);
            dependency.dependencyExpression = e;
            dependency.speciesContextMapping = firstSCM;
            dependency.invariantSymbolName = constantName;
            // Expression slow = constantExp.flatten();		// old way, very slow
            // dependency.conservedMoietyExpression = slow;
            Expression[] cev = cel.toArray(new Expression[cel.size()]);
            Expression ce = Expression.add(cev);
            // new way, much faster
            ce = ce.flatten();
            dependency.conservedMoietyExpression = ce;
            dependencyList.add(dependency);
        }
    }
    long endTime = System.currentTimeMillis();
    long elapsedTime = endTime - startTime;
    System.out.println("     " + elapsedTime + " milliseconds");
    return (StructureAnalyzer.Dependency[]) BeanUtils.getArray(dependencyList, StructureAnalyzer.Dependency.class);
}

Example 4 with RationalNumber

use of cbit.vcell.matrix.RationalNumber in project vcell by virtualcell.

the class AbstractMathMapping method getUnitFactorAsRationalExp.

/**
 * This method was created in VisualAge.
 * @return Expression
 */
public RationalExp getUnitFactorAsRationalExp(VCUnitDefinition unitFactor) {
    if (unitFactor.isEquivalent(getSimulationContext().getModel().getUnitSystem().getInstance_DIMENSIONLESS())) {
        return RationalExp.ONE;
    }
    for (MathMappingParameter p : fieldMathMappingParameters) {
        if (p instanceof UnitFactorParameter && p.getUnitDefinition().isEquivalent(unitFactor)) {
            return new RationalExp(p.getName());
        }
    }
    RationalNumber factor = unitFactor.getDimensionlessScale();
    String name = PARAMETER_K_UNITFACTOR_PREFIX + TokenMangler.fixTokenStrict(unitFactor.getSymbol().replace("-", "_neg_"));
    UnitFactorParameter unitFactorParameter = new UnitFactorParameter(name, new Expression(factor), unitFactor);
    MathMappingParameter[] newMathMappingParameters = (MathMappingParameter[]) BeanUtils.addElement(this.fieldMathMappingParameters, unitFactorParameter);
    try {
        setMathMapppingParameters(newMathMappingParameters);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException(e.getMessage());
    }
    return new RationalExp(factor);
}

Example 5 with RationalNumber

use of cbit.vcell.matrix.RationalNumber in project vcell by virtualcell.

the class AbstractMathMapping method getUnitFactor.

/**
 * This method was created in VisualAge.
 * @return Expression
 */
public Expression getUnitFactor(VCUnitDefinition unitFactor) {
    if (unitFactor.isEquivalent(getSimulationContext().getModel().getUnitSystem().getInstance_DIMENSIONLESS())) {
        return new Expression(1.0);
    }
    for (MathMappingParameter p : fieldMathMappingParameters) {
        if (p instanceof UnitFactorParameter && p.getUnitDefinition().isEquivalent(unitFactor)) {
            return new Expression(p, getNameScope());
        }
    }
    RationalNumber factor = unitFactor.getDimensionlessScale();
    String name = PARAMETER_K_UNITFACTOR_PREFIX + TokenMangler.fixTokenStrict(unitFactor.getSymbol().replace("-", "_neg_"));
    UnitFactorParameter unitFactorParameter = new UnitFactorParameter(name, new Expression(factor), unitFactor);
    MathMappingParameter[] newMathMappingParameters = (MathMappingParameter[]) BeanUtils.addElement(this.fieldMathMappingParameters, unitFactorParameter);
    try {
        setMathMapppingParameters(newMathMappingParameters);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException(e.getMessage());
    }
    return new Expression(unitFactorParameter, getNameScope());
}