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

Example 1 with OptimizationStatus

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

the class OptXmlReader method getOptRunResultSet.

private static OptRunResultSet getOptRunResultSet(Element optRunElement) throws DataConversionException {
    double bestObjectFuncValue = optRunElement.getAttribute(OptXmlTags.OptSolverResultSetBestObjectiveFunction_Attr).getDoubleValue();
    long numObjectFuncEvals = optRunElement.getAttribute(OptXmlTags.OptSolverResultSetNumObjectiveFunctionEvaluations_Attr).getLongValue();
    String status = optRunElement.getAttributeValue(OptXmlTags.OptSolverResultSetStatus_Attr);
    Attribute statusMessageAttr = optRunElement.getAttribute(OptXmlTags.OptSolverResultSetStatusMessage_Attr);
    List<Element> paramElementList = optRunElement.getChildren(OptXmlTags.Parameter_Tag);
    String[] parameterNames = new String[paramElementList.size()];
    double[] parameterValues = new double[paramElementList.size()];
    int count = 0;
    for (Element parameterElement : paramElementList) {
        parameterNames[count] = parameterElement.getAttributeValue(OptXmlTags.ParameterName_Attr);
        parameterValues[count] = Double.parseDouble(parameterElement.getAttributeValue(OptXmlTags.ParameterBestValue_Attr));
        count++;
    }
    int statusID = OptimizationStatus.statusFromXMLName(status);
    String statusMessage = null;
    if (statusMessageAttr != null) {
        statusMessage = statusMessageAttr.getValue();
    }
    OptimizationStatus optimizationStatus = new OptimizationStatus(statusID, statusMessage);
    OptRunResultSet optRun = new OptRunResultSet(parameterValues, new Double(bestObjectFuncValue), numObjectFuncEvals, optimizationStatus);
    return optRun;
}

Example 2 with OptimizationStatus

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

the class CopasiOptimizationSolver method solveRemoteApi.

public static OptimizationResultSet solveRemoteApi(ParameterEstimationTaskSimulatorIDA parestSimulator, ParameterEstimationTask parameterEstimationTask, CopasiOptSolverCallbacks optSolverCallbacks, MathMappingCallback mathMappingCallback) throws IOException, ExpressionException, OptimizationException {
    try {
        OptProblem optProblem = CopasiServicePython.makeOptProblem(parameterEstimationTask);
        boolean bIgnoreCertProblems = true;
        boolean bIgnoreHostMismatch = true;
        // e.g. vcell.serverhost=vcellapi.cam.uchc.edu:8080
        String serverHost = PropertyLoader.getRequiredProperty(PropertyLoader.vcellServerHost);
        String[] parts = serverHost.split(":");
        String host = parts[0];
        int port = Integer.parseInt(parts[1]);
        VCellApiClient apiClient = new VCellApiClient(host, port, bIgnoreCertProblems, bIgnoreHostMismatch);
        TSerializer serializer = new TSerializer(new TJSONProtocol.Factory());
        String optProblemJson = serializer.toString(optProblem);
        String optimizationId = apiClient.submitOptimization(optProblemJson);
        // 20 second minute timeout
        final long TIMEOUT_MS = 1000 * 20;
        long startTime = System.currentTimeMillis();
        OptRun optRun = null;
        while ((System.currentTimeMillis() - startTime) < TIMEOUT_MS) {
            if (optSolverCallbacks.getStopRequested()) {
                throw new RuntimeException(STOP_REQUESTED);
            }
            String optRunJson = apiClient.getOptRunJson(optimizationId);
            TDeserializer deserializer = new TDeserializer(new TJSONProtocol.Factory());
            optRun = new OptRun();
            deserializer.deserialize(optRun, optRunJson.getBytes());
            OptRunStatus status = optRun.status;
            if (status == OptRunStatus.Complete) {
                System.out.println("job " + optimizationId + ": status " + status + " " + optRun.getOptResultSet().toString());
                break;
            }
            if (status == OptRunStatus.Failed) {
                throw new RuntimeException("optimization failed, message=" + optRun.statusMessage);
            }
            System.out.println("job " + optimizationId + ": status " + status);
            try {
                Thread.sleep(1000);
            } catch (InterruptedException e) {
            }
        }
        System.out.println("done with optimization");
        OptResultSet optResultSet = optRun.getOptResultSet();
        int numFittedParameters = optResultSet.getOptParameterValues().size();
        String[] paramNames = new String[numFittedParameters];
        double[] paramValues = new double[numFittedParameters];
        for (int pIndex = 0; pIndex < numFittedParameters; pIndex++) {
            OptParameterValue optParamValue = optResultSet.getOptParameterValues().get(pIndex);
            paramNames[pIndex] = optParamValue.parameterName;
            paramValues[pIndex] = optParamValue.bestValue;
        }
        OptimizationStatus status = new OptimizationStatus(OptimizationStatus.NORMAL_TERMINATION, optRun.statusMessage);
        OptRunResultSet optRunResultSet = new OptRunResultSet(paramValues, optResultSet.objectiveFunction, optResultSet.numFunctionEvaluations, status);
        OptSolverResultSet copasiOptSolverResultSet = new OptSolverResultSet(paramNames, optRunResultSet);
        RowColumnResultSet copasiRcResultSet = parestSimulator.getRowColumnRestultSetByBestEstimations(parameterEstimationTask, paramNames, paramValues);
        OptimizationResultSet copasiOptimizationResultSet = new OptimizationResultSet(copasiOptSolverResultSet, copasiRcResultSet);
        System.out.println("-----------SOLUTION FROM VCellAPI---------------\n" + optResultSet.toString());
        return copasiOptimizationResultSet;
    } catch (Exception e) {
        e.printStackTrace(System.out);
        if (e.getMessage() != null && e.getMessage().equals(STOP_REQUESTED)) {
            throw UserCancelException.CANCEL_GENERIC;
        }
        throw new OptimizationException(e.getCause() != null ? e.getCause().getMessage() : e.getMessage());
    }
}

Example 3 with OptimizationStatus

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

the class CopasiOptimizationSolver method solveLocalPython.

public static OptimizationResultSet solveLocalPython(ParameterEstimationTaskSimulatorIDA parestSimulator, ParameterEstimationTask parameterEstimationTask, CopasiOptSolverCallbacks optSolverCallbacks, MathMappingCallback mathMappingCallback) throws IOException, ExpressionException, OptimizationException {
    File dir = Files.createTempDirectory("parest", new FileAttribute<?>[] {}).toFile();
    try {
        String prefix = "testing_" + Math.abs(new Random().nextInt(10000));
        File optProblemThriftFile = new File(dir, prefix + ".optprob.bin");
        File optRunFile = new File(dir, prefix + ".optrun.bin");
        // 
        // Setup Python COPASI opt problem and write to disk
        // 
        OptProblem optProblem = CopasiServicePython.makeOptProblem(parameterEstimationTask);
        CopasiServicePython.writeOptProblem(optProblemThriftFile, optProblem);
        // 
        // run Python COPASI opt problem
        // 
        CopasiServicePython.runCopasiPython(optProblemThriftFile, optRunFile);
        if (!optRunFile.exists()) {
            throw new RuntimeException("COPASI optimization output file not found:\n" + optRunFile.getAbsolutePath());
        }
        OptRun optRun = CopasiServicePython.readOptRun(optRunFile);
        OptResultSet optResultSet = optRun.getOptResultSet();
        int numFittedParameters = optResultSet.getOptParameterValues().size();
        String[] paramNames = new String[numFittedParameters];
        double[] paramValues = new double[numFittedParameters];
        for (int pIndex = 0; pIndex < numFittedParameters; pIndex++) {
            OptParameterValue optParamValue = optResultSet.getOptParameterValues().get(pIndex);
            paramNames[pIndex] = optParamValue.parameterName;
            paramValues[pIndex] = optParamValue.bestValue;
        }
        OptimizationStatus status = new OptimizationStatus(OptimizationStatus.NORMAL_TERMINATION, optRun.statusMessage);
        OptRunResultSet optRunResultSet = new OptRunResultSet(paramValues, optResultSet.objectiveFunction, optResultSet.numFunctionEvaluations, status);
        OptSolverResultSet copasiOptSolverResultSet = new OptSolverResultSet(paramNames, optRunResultSet);
        RowColumnResultSet copasiRcResultSet = parestSimulator.getRowColumnRestultSetByBestEstimations(parameterEstimationTask, paramNames, paramValues);
        OptimizationResultSet copasiOptimizationResultSet = new OptimizationResultSet(copasiOptSolverResultSet, copasiRcResultSet);
        System.out.println("-----------SOLUTION FROM PYTHON---------------\n" + optResultSet.toString());
        return copasiOptimizationResultSet;
    } catch (Throwable e) {
        e.printStackTrace(System.out);
        throw new OptimizationException(e.getCause() != null ? e.getCause().getMessage() : e.getMessage());
    } finally {
        if (dir != null && dir.exists()) {
            FileUtils.deleteDirectory(dir);
        }
    }
}

Example 4 with OptimizationStatus

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

the class PowellOptimizationSolver method solve.

/**
 * Insert the method's description here.
 * Creation date: (3/5/00 11:15:15 PM)
 * @return double[]
 * @param optSpec cbit.vcell.opt.OptimizationSpec
 * @exception java.io.IOException The exception description.
 * @exception cbit.vcell.parser.ExpressionException The exception description.
 * @exception cbit.vcell.opt.OptimizationException The exception description.
 */
public OptimizationResultSet solve(OptimizationSpec os, OptimizationSolverSpec optSolverSpec, OptSolverCallbacks optSolverCallbacks) throws java.io.IOException, cbit.vcell.parser.ExpressionException, OptimizationException {
    final double power = 2.0;
    final double MU_START = 0.1;
    final double MU_END = 100000.0;
    final double MU_STEP = 10.0;
    AugmentedObjectiveFunction augmentedObjFunc = OptUtils.getAugmentedObjectiveFunction(os, power, MU_START, optSolverCallbacks);
    // 
    // initialize starting guess
    // 
    Parameter[] parameters = os.getParameters();
    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]);
    }
    // 
    // get initial direction set
    // 
    double[][] xi = new double[parameterValues.length][parameterValues.length];
    for (int i = 0; i < parameterValues.length; i++) {
        for (int j = 0; j < parameterValues.length; j++) {
            xi[i][j] = (i == j ? 1.0 : 0.0);
        }
    }
    final double ftol = 1e-6;
    double fret = augmentedObjFunc.f(parameterValues);
    PowellSolver powellSolver = new PowellSolver();
    for (double mu = MU_START; mu <= MU_END; mu *= MU_STEP) {
        try {
            if (optSolverCallbacks.getStopRequested()) {
                break;
            }
            augmentedObjFunc.setMu(mu);
            fret = powellSolver.powell(parameterValues.length, parameterValues, xi, ftol, augmentedObjFunc);
            System.out.println("mu=" + mu + ", function value=" + fret);
            if (augmentedObjFunc.getPenalty(parameterValues) == 0.0) {
                break;
            }
        } catch (Exception ex) {
            ex.printStackTrace();
            break;
        }
    }
    OptimizationStatus optStatus = new OptimizationStatus(OptimizationStatus.NORMAL_TERMINATION, "Normal Termination");
    ODESolverResultSet odeSolverResultSet = null;
    if (optSolverCallbacks.getStopRequested()) {
        optStatus = new OptimizationStatus(OptimizationStatus.STOPPED_BY_USER, "Stopped by user");
    }
    parameterValues = optSolverCallbacks.getBestEvaluation().getParameterValues();
    fret = optSolverCallbacks.getBestEvaluation().getObjectiveFunctionValue();
    odeSolverResultSet = optSolverCallbacks.getBestResultSet();
    for (int i = 0; i < parameters.length; i++) {
        System.out.println("final " + parameters[i].getName() + " = " + parameterValues[i]);
    }
    OptRunResultSet bestResult = new OptRunResultSet(parameterValues, new Double(fret), optSolverCallbacks.getEvaluationCount(), optStatus);
    return new OptimizationResultSet(new OptSolverResultSet(os.getParameterNames(), bestResult), odeSolverResultSet);
}