Examples with ExplicitFitObjectiveFunction cbit.vcell.opt.ExplicitFitObjectiveFunction used on opensource projects

Example 1 with ExplicitFitObjectiveFunction

use of cbit.vcell.opt.ExplicitFitObjectiveFunction in project vcell by virtualcell.

the class ReactionDominantTest method solve.

private OptimizationResultSet solve() throws ExpressionException, IOException {
    Expression Fbleached_bleachFastExp = new Expression(Fbleached_bleachFast);
    Expression OmegaExp = new Expression(strOmega);
    Expression Omega_cExp = new Expression(strOmega_c);
    Expression WExp = new Expression(strW);
    Fbleached_bleachFastExp.substituteInPlace(OmegaExp, new Expression(Omega));
    Fbleached_bleachFastExp.substituteInPlace(Omega_cExp, new Expression(Omega_c));
    Fbleached_bleachFastExp.substituteInPlace(WExp, new Expression(W));
    Parameter[] parameters = new Parameter[] { para_alpha, para_Kon_star, para_Koff };
    // Expression Fbleached_bleachFast = Fbleached_bleachFastExp.flatten();
    // choose optimization solver, currently we have Powell and CFSQP
    PowellOptimizationSolver optService = new PowellOptimizationSolver();
    OptimizationSpec optSpec = new OptimizationSpec();
    // create simple reference data
    double[][] realData = new double[2][t.length];
    for (int i = 0; i < t.length; i++) {
        realData[0][i] = t[i];
        realData[1][i] = data_bleached[i];
    }
    String[] colNames = new String[] { "t", "intensity" };
    double[] weights = new double[] { 1.0, 1.0 };
    SimpleReferenceData refData = new SimpleReferenceData(colNames, weights, realData);
    // send to optimization service
    ExplicitFitObjectiveFunction.ExpressionDataPair oneExpDataPair = new ExplicitFitObjectiveFunction.ExpressionDataPair(Fbleached_bleachFastExp.flatten(), 1);
    ExplicitFitObjectiveFunction.ExpressionDataPair[] expDataPairs = new ExplicitFitObjectiveFunction.ExpressionDataPair[] { oneExpDataPair };
    optSpec.setObjectiveFunction(new ExplicitFitObjectiveFunction(expDataPairs, refData));
    optSpec.setComputeProfileDistributions(true);
    // get the initial guess to send it to the f() function. ....
    for (int i = 0; i < parameters.length; i++) {
        optSpec.addParameter(parameters[i]);
    }
    // Parameters in OptimizationSolverSpec are solver type and objective function change tolerance.
    OptimizationSolverSpec optSolverSpec = new OptimizationSolverSpec(OptimizationSolverSpec.SOLVERTYPE_POWELL, 0.000001);
    OptSolverCallbacks optSolverCallbacks = new DefaultOptSolverCallbacks();
    OptimizationResultSet optResultSet = null;
    optResultSet = optService.solve(optSpec, optSolverSpec, optSolverCallbacks);
    String[] paramNames = optResultSet.getOptSolverResultSet().getParameterNames();
    ArrayList<ProfileDistribution> profileDistributionList = optResultSet.getOptSolverResultSet().getProfileDistributionList();
    for (int i = 0; i < profileDistributionList.size(); i++) {
        outputProfileLikelihood(profileDistributionList.get(i), i, paramNames[i], new File(fileDir));
    }
    return optResultSet;
}

Example 2 with ExplicitFitObjectiveFunction

use of cbit.vcell.opt.ExplicitFitObjectiveFunction in project vcell by virtualcell.

the class CurveFitting method solve.

public static OptimizationResultSet solve(ExplicitFitObjectiveFunction.ExpressionDataPair[] expDataPairs, Parameter[] parameters, double[] time, double[][] data, String[] colNames, Weights weights) throws ExpressionException, OptimizationException, IOException {
    // choose optimization solver, currently we have Powell and CFSQP
    PowellOptimizationSolver optService = new PowellOptimizationSolver();
    OptimizationSpec optSpec = new OptimizationSpec();
    // create simple reference data, columns: t + dataColumns
    double[][] realData = new double[1 + data.length][time.length];
    for (// add time column
    int i = 0; // add time column
    i < time.length; // add time column
    i++) {
        realData[0][i] = time[i];
    }
    for (// add each data column to realData
    int i = 0; // add each data column to realData
    i < data.length; // add each data column to realData
    i++) {
        for (int j = 0; j < time.length; j++) {
            realData[1 + i][j] = data[i][j];
        }
    }
    SimpleReferenceData refData = new SimpleReferenceData(colNames, weights, realData);
    // send to optimization service
    optSpec.setObjectiveFunction(new ExplicitFitObjectiveFunction(expDataPairs, refData));
    double[] parameterValues = new double[parameters.length];
    for (int i = 0; i < parameters.length; i++) {
        parameterValues[i] = parameters[i].getInitialGuess();
        System.out.println("initial " + parameters[i].getName() + " = " + parameterValues[i] + ";\tLB = " + parameters[i].getLowerBound() + ";\tUB = " + parameters[i].getUpperBound());
    }
    // get the initial guess to send it to the f() function. ....
    for (int i = 0; i < parameters.length; i++) {
        optSpec.addParameter(parameters[i]);
    }
    // Parameters in OptimizationSolverSpec are solver type and objective function change tolerance.
    OptimizationSolverSpec optSolverSpec = new OptimizationSolverSpec(OptimizationSolverSpec.SOLVERTYPE_POWELL, 0.000001);
    OptSolverCallbacks optSolverCallbacks = new DefaultOptSolverCallbacks();
    OptimizationResultSet optResultSet = null;
    optResultSet = optService.solve(optSpec, optSolverSpec, optSolverCallbacks);
    return optResultSet;
}

Example 3 with ExplicitFitObjectiveFunction

use of cbit.vcell.opt.ExplicitFitObjectiveFunction in project vcell by virtualcell.

the class CurveFitting method solve.

public static OptimizationResultSet solve(ExplicitFitObjectiveFunction.ExpressionDataPair[] expDataPairs, Parameter[] parameters, double[] time, double[][] data, String[] colNames, Weights weights) throws ExpressionException, OptimizationException, IOException {
    // choose optimization solver, currently we have Powell
    PowellOptimizationSolver optService = new PowellOptimizationSolver();
    OptimizationSpec optSpec = new OptimizationSpec();
    // create simple reference data, columns: t + dataColumns
    double[][] realData = new double[1 + data.length][time.length];
    for (// add time column
    int i = 0; // add time column
    i < time.length; // add time column
    i++) {
        realData[0][i] = time[i];
    }
    for (// add each data column to realData
    int i = 0; // add each data column to realData
    i < data.length; // add each data column to realData
    i++) {
        for (int j = 0; j < time.length; j++) {
            realData[1 + i][j] = data[i][j];
        }
    }
    SimpleReferenceData refData = new SimpleReferenceData(colNames, weights, realData);
    // send to optimization service
    optSpec.setObjectiveFunction(new ExplicitFitObjectiveFunction(expDataPairs, refData));
    double[] parameterValues = new double[parameters.length];
    for (int i = 0; i < parameters.length; i++) {
        parameterValues[i] = parameters[i].getInitialGuess();
        System.out.println("initial " + parameters[i].getName() + " = " + parameterValues[i] + ";\tLB = " + parameters[i].getLowerBound() + ";\tUB = " + parameters[i].getUpperBound());
    }
    // get the initial guess to send it to the f() function. ....
    for (int i = 0; i < parameters.length; i++) {
        optSpec.addParameter(parameters[i]);
    }
    // Parameters in OptimizationSolverSpec are solver type and objective function change tolerance.
    OptimizationSolverSpec optSolverSpec = new OptimizationSolverSpec(OptimizationSolverSpec.SOLVERTYPE_POWELL, 0.000001);
    OptSolverCallbacks optSolverCallbacks = new DefaultOptSolverCallbacks();
    OptimizationResultSet optResultSet = null;
    optResultSet = optService.solve(optSpec, optSolverSpec, optSolverCallbacks);
    return optResultSet;
}

Example 4 with ExplicitFitObjectiveFunction

use of cbit.vcell.opt.ExplicitFitObjectiveFunction in project vcell by virtualcell.

the class OptXmlWriter method getObjectiveFunctionXML.

public static Element getObjectiveFunctionXML(OptimizationSpec optimizationSpec) {
    Element objectiveFunctionElement = new Element(OptXmlTags.ObjectiveFunction_Tag);
    ObjectiveFunction objectiveFunction = optimizationSpec.getObjectiveFunction();
    if (objectiveFunction instanceof ExplicitObjectiveFunction) {
        ExplicitObjectiveFunction explicitObjectiveFunction = (ExplicitObjectiveFunction) objectiveFunction;
        objectiveFunctionElement.setAttribute(OptXmlTags.ObjectiveFunctionType_Attr, OptXmlTags.ObjectiveFunctionType_Attr_Explicit);
        Element expressionElement = new Element(OptXmlTags.Expression_Tag);
        expressionElement.addContent(explicitObjectiveFunction.getExpression().infix());
        objectiveFunctionElement.addContent(expressionElement);
    } else if (objectiveFunction instanceof ExplicitFitObjectiveFunction) {
        ExplicitFitObjectiveFunction explicitFitObjectiveFunction = (ExplicitFitObjectiveFunction) objectiveFunction;
        objectiveFunctionElement.setAttribute(OptXmlTags.ObjectiveFunctionType_Attr, OptXmlTags.ObjectiveFunctionType_Attr_ExplicitFit);
        // add expression list
        Element expressionListElement = new Element(OptXmlTags.ExpressionList_Tag);
        objectiveFunctionElement.addContent(expressionListElement);
        ExplicitFitObjectiveFunction.ExpressionDataPair[] expDataPairs = explicitFitObjectiveFunction.getExpressionDataPairs();
        for (int i = 0; i < expDataPairs.length; i++) {
            Element expressionElement = new Element(OptXmlTags.Expression_Tag);
            expressionElement.setAttribute(OptXmlTags.ExpRefDataColumnIndex_Attr, expDataPairs[i].getReferenceDataIndex() + "");
            expressionElement.addContent(expDataPairs[i].getFitFunction().infix());
            expressionListElement.addContent(expressionElement);
        }
        if (explicitFitObjectiveFunction.getReferenceData() instanceof SimpleReferenceData) {
            Element dataElement = getDataXML(explicitFitObjectiveFunction.getReferenceData());
            objectiveFunctionElement.addContent(dataElement);
        } else {
            throw new OptimizationException("Optimization XML Writer exports SimpleReferenceData only.");
        }
    } else if (objectiveFunction instanceof PdeObjectiveFunction) {
        PdeObjectiveFunction pdeObjectiveFunction = (PdeObjectiveFunction) objectiveFunction;
        objectiveFunctionElement.setAttribute(OptXmlTags.ObjectiveFunctionType_Attr, OptXmlTags.ObjectiveFunctionType_Attr_PDE);
        SpatialReferenceData refData = pdeObjectiveFunction.getReferenceData();
        Element dataElement = getDataXML(refData);
        objectiveFunctionElement.addContent(dataElement);
        Element modelElement = getModelXML(pdeObjectiveFunction, optimizationSpec.getParameterNames());
        objectiveFunctionElement.addContent(modelElement);
        Simulation tempSim = new Simulation(pdeObjectiveFunction.getMathDescription());
        SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(tempSim, 0);
        // 
        for (int i = 1; i < refData.getNumVariables(); i++) {
            Element modelMappingElement = new Element(OptXmlTags.ModelMapping_Tag);
            modelMappingElement.setAttribute(OptXmlTags.ModelMappingDataColumn_Attr, refData.getVariableNames()[i]);
            modelMappingElement.setAttribute(OptXmlTags.ModelMappingWeight_Attr, String.valueOf(refData.getVariableWeights()[i]));
            Expression mappingExpression = null;
            try {
                Variable var = pdeObjectiveFunction.getMathDescription().getVariable(refData.getVariableNames()[i]);
                if (var instanceof Function) {
                    Expression exp = new Expression(var.getExpression());
                    exp.bindExpression(simSymbolTable);
                    exp = MathUtilities.substituteFunctions(exp, simSymbolTable);
                    mappingExpression = exp.flatten();
                } else {
                    mappingExpression = new Expression(var.getName());
                }
            } catch (ExpressionException e) {
                e.printStackTrace();
                throw new OptimizationException(e.getMessage());
            }
            modelMappingElement.addContent(mappingExpression.infix());
            objectiveFunctionElement.addContent(modelMappingElement);
        }
    }
    return objectiveFunctionElement;
}

Example 5 with ExplicitFitObjectiveFunction

use of cbit.vcell.opt.ExplicitFitObjectiveFunction in project vcell by virtualcell.

the class OptUtils method getAugmentedObjectiveFunction.

/**
 * Insert the method's description here.
 * Creation date: (8/4/2005 3:26:14 PM)
 * @return function.AugmentedObjectiveFunction
 * @param optSpec cbit.vcell.opt.OptimizationSpec
 * @param power double
 * @param mu double
 */
public static AugmentedObjectiveFunction getAugmentedObjectiveFunction(OptimizationSpec optSpec, double power, double mu, OptSolverCallbacks optSolverCallbacks) throws cbit.vcell.parser.ExpressionException {
    Parameter[] parameters = optSpec.getParameters();
    // 
    // build symbol list
    // 
    String[] origSymbols = optSpec.getParameterNames();
    String[] scaledSymbols = optSpec.getScaledParameterNames();
    double[] scaleFactors = optSpec.getScaleFactors();
    ScalarFunction objFunction = null;
    if (optSpec.getObjectiveFunction() instanceof ExplicitObjectiveFunction) {
        ExplicitObjectiveFunction explicitObjectiveFunction = (ExplicitObjectiveFunction) optSpec.getObjectiveFunction();
        // 
        // build objective function
        // 
        objFunction = new DynamicScalarFunction(explicitObjectiveFunction.getScaledExpression(origSymbols, scaledSymbols, scaleFactors), scaledSymbols);
    } else if (optSpec.getObjectiveFunction() instanceof ImplicitObjectiveFunction) {
        ImplicitObjectiveFunction implicitObjectiveFunction = (ImplicitObjectiveFunction) optSpec.getObjectiveFunction();
        // 
        // build objective function
        // 
        objFunction = implicitObjectiveFunction.getObjectiveFunction();
    } else if (optSpec.getObjectiveFunction() instanceof ExplicitFitObjectiveFunction) {
        ExplicitFitObjectiveFunction explicitFitObjectiveFunction = (ExplicitFitObjectiveFunction) optSpec.getObjectiveFunction();
        objFunction = explicitFitObjectiveFunction.getScalarFunction();
    } else {
        throw new RuntimeException("unsupported objective function type : " + optSpec.getObjectiveFunction().getClass().getName());
    }
    // 
    // build equality and inequality constraints
    // 
    DynamicVectorFunction equalityConstraints = null;
    DynamicVectorFunction inequalityConstraints = null;
    Constraint[] constraints = optSpec.getConstraints();
    Vector equExpList = new Vector();
    Vector inequExpList = new Vector();
    // 
    for (int i = 0; i < constraints.length; i++) {
        ConstraintType type = constraints[i].getConstraintType();
        if (type.equals(ConstraintType.LinearEquality) || type.equals(ConstraintType.NonlinearEquality)) {
            equExpList.add(constraints[i].getExpression());
        } else {
            inequExpList.add(constraints[i].getExpression());
        }
    }
    // 
    for (int i = 0; i < parameters.length; i++) {
        if (!Double.isInfinite(parameters[i].getLowerBound())) {
            inequExpList.add(new Expression("(" + parameters[i].getLowerBound() + " - " + parameters[i].getName() + ")/" + scaleFactors[i]));
        }
        if (!Double.isInfinite(parameters[i].getUpperBound())) {
            inequExpList.add(new Expression("(" + parameters[i].getName() + " - " + parameters[i].getUpperBound() + ")/" + scaleFactors[i]));
        }
    }
    if (equExpList.size() > 0) {
        Expression[] exps = (Expression[]) org.vcell.util.BeanUtils.getArray(equExpList, Expression.class);
        equalityConstraints = new DynamicVectorFunction(exps, origSymbols);
    }
    if (inequExpList.size() > 0) {
        Expression[] exps = (Expression[]) org.vcell.util.BeanUtils.getArray(inequExpList, Expression.class);
        inequalityConstraints = new DynamicVectorFunction(exps, origSymbols);
    }
    AugmentedObjectiveFunction augmentedObjFunc = new AugmentedObjectiveFunction(objFunction, equalityConstraints, inequalityConstraints, power, mu, optSolverCallbacks);
    return augmentedObjFunc;
}