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

Example 1 with OptimizationException

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

the class ParameterEstimationRunTaskPanel method solve.

private void solve() throws NumberFormatException {
    CopasiOptimizationMethod com = optimizationMethodParameterTableModel.copasiOptimizationMethod;
    OptimizationSolverSpec optSolverSpec = new OptimizationSolverSpec(com);
    // get num runs for stochstic opt mehtods before starting solving...
    if (com.getType().isStochasticMethod()) {
        int numRuns = Integer.parseInt(((String) numberOfRunComboBox.getSelectedItem()));
        optSolverSpec.setNumOfRuns(numRuns);
    }
    parameterEstimationTask.setOptimizationSolverSpec(optSolverSpec);
    parameterEstimationTask.getModelOptimizationSpec().setComputeProfileDistributions(computeProfileDistributionsCheckBox.isSelected());
    optSolverCallbacks.reset();
    Double endValue = com.getEndValue();
    optSolverCallbacks.setEvaluation(0, Double.POSITIVE_INFINITY, 0, endValue, 0);
    // (endValue != null);
    getRunStatusDialog().showProgressBar(com);
    Collection<AsynchClientTask> taskList = ClientRequestManager.updateMath(this, parameterEstimationTask.getSimulationContext(), false, NetworkGenerationRequirements.ComputeFullStandardTimeout);
    AsynchClientTask task1 = new AsynchClientTask("checking issues", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            StringBuffer issueText = new StringBuffer();
            java.util.Vector<Issue> issueList = new java.util.Vector<Issue>();
            IssueContext issueContext = new IssueContext();
            parameterEstimationTask.gatherIssues(issueContext, issueList);
            boolean bFailed = false;
            for (int i = 0; i < issueList.size(); i++) {
                Issue issue = (Issue) issueList.elementAt(i);
                issueText.append(issue.getMessage() + "\n");
                if (issue.getSeverity() == Issue.SEVERITY_ERROR) {
                    bFailed = true;
                    break;
                }
            }
            if (bFailed) {
                throw new OptimizationException(issueText.toString());
            }
            parameterEstimationTask.refreshMappings();
        }
    };
    taskList.add(task1);
    AsynchClientTask task2 = new AsynchClientTask("solving", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            MathMappingCallback mathMappingCallback = new MathMappingCallbackTaskAdapter(getClientTaskStatusSupport());
            // OptimizationResultSet optResultSet = CopasiOptimizationSolver.solveLocalPython(new ParameterEstimationTaskSimulatorIDA(),parameterEstimationTask,optSolverCallbacks,mathMappingCallback);
            OptimizationResultSet optResultSet = CopasiOptimizationSolver.solveRemoteApi(new ParameterEstimationTaskSimulatorIDA(), parameterEstimationTask, optSolverCallbacks, mathMappingCallback);
            hashTable.put(ORS_KEY, optResultSet);
        }
    };
    taskList.add(task2);
    AsynchClientTask setResultTask = new AsynchClientTask("set results", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            OptimizationResultSet optResultSet = (OptimizationResultSet) hashTable.get(ORS_KEY);
            parameterEstimationTask.setOptimizationResultSet(optResultSet);
        }
    };
    taskList.add(setResultTask);
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), taskList.toArray(new AsynchClientTask[taskList.size()]), getRunStatusDialog(), true, true, true, null, false);
}

Example 2 with OptimizationException

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

the class LocalOptimizationService method solve.

/**
 * solve method comment.
 */
public OptimizationResultSet solve(OptimizationSpec optSpec, OptimizationSolverSpec optSolverSpec, OptSolverCallbacks optSolverCallbacks) {
    OptimizationSolver optSolver = null;
    if (optSolverSpec.getSolverType().equals(OptimizationSolverSpec.SOLVERTYPE_POWELL)) {
        optSolver = new PowellOptimizationSolver();
    // }else if (optSolverSpec.getSolverType().equals(OptimizationSolverSpec.SOLVERTYPE_CONJUGATE_GRADIENT)){
    // optSolver = new ConjugateGradientOptimizationSolver();
    } else {
        throw new RuntimeException("unsupported solver type '" + optSolverSpec.getSolverType() + "'");
    }
    OptimizationResultSet optResultSet = null;
    try {
        optResultSet = optSolver.solve(optSpec, optSolverSpec, optSolverCallbacks);
    } catch (IOException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException(e.getMessage());
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException(e.getMessage());
    } catch (OptimizationException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException(e.getMessage());
    }
    return optResultSet;
}

Example 3 with OptimizationException

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

the class FRAPDataAnalysis method fitRecovery_reacOffRateOnly.

/**
 * Method fitRecovery2.
 * @param frapData, the original image info.
 * @param fixedParameter: the fixed parameter from profile likelihood distribution analysis.
 * @param measurementError: the measurementError is used as weights for calculating objectiveFunction errors.
 * @return FrapDataAnalysisResults.ReactionOnlyAnalysisRestults
 * @throws ExpressionException
 */
public static FrapDataAnalysisResults.ReactionOnlyAnalysisRestults fitRecovery_reacOffRateOnly(FRAPData frapData, Parameter fixedParam, double[][] measurementError, int startIndexForRecovery) throws ExpressionException, OptimizationException, IOException {
    // int startIndexForRecovery = getRecoveryIndex(frapData);
    // 
    // get unnormalized average background fluorescence at each time point
    // 
    double[] temp_background = frapData.getAvgBackGroundIntensity();
    // the prebleachAvg has backgroud subtracted.
    double[] preBleachAvgXYZ = FrapDataUtils.calculatePreBleachAverageXYZ(frapData, startIndexForRecovery);
    // tempBeachedAverage and tempCellROIAverage have subtracted background and divided by prebleach average. the following array has data for the full time duration.
    double[] tempBeachedAverage = getAverageROIIntensity(frapData, frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name()), preBleachAvgXYZ, temp_background);
    double[] tempCellROIAverage = getAverageROIIntensity(frapData, frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name()), preBleachAvgXYZ, temp_background);
    double[] temp_time = frapData.getImageDataset().getImageTimeStamps();
    // get bleached and cell roi data starting from first post bleach
    // The time points start from the first post bleach
    double[] bleachedAverage = new double[tempBeachedAverage.length - startIndexForRecovery];
    // time points start from the first post bleach
    double[] cellROIAverage = new double[tempCellROIAverage.length - startIndexForRecovery];
    // Time points stat from the first post bleach
    double[] time = new double[temp_time.length - startIndexForRecovery];
    System.arraycopy(tempBeachedAverage, startIndexForRecovery, bleachedAverage, 0, bleachedAverage.length);
    System.arraycopy(tempCellROIAverage, startIndexForRecovery, cellROIAverage, 0, cellROIAverage.length);
    System.arraycopy(temp_time, startIndexForRecovery, time, 0, time.length);
    // initialize reaction off rate analysis results
    FrapDataAnalysisResults.ReactionOnlyAnalysisRestults offRateAnalysisResults = new FrapDataAnalysisResults.ReactionOnlyAnalysisRestults();
    /**
     *curve fitting
     */
    // index 0: cell ROI intensity average at time 0, I_cell_ini. index 1: bleached intensity average at time 0, I_bleached_ini
    double[] inputParamValues = new double[] { cellROIAverage[0], bleachedAverage[0] };
    // if fixed parameter is null, then outputs are bwm rate, koff rate, fitting parameter A. Otherwise outputs are two out of three.
    double[] outputParamValues = null;
    // create data array,first col is cell average, second col is bleached average.
    double[][] fitData = new double[2][];
    fitData[0] = cellROIAverage;
    fitData[1] = bleachedAverage;
    // create element weights array, first col is cell data weights, second col is bleached data weights
    double[][] weightData = new double[time.length][2];
    double[] cellROIMeasurementError = measurementError[FRAPData.VFRAP_ROI_ENUM.ROI_CELL.ordinal()];
    double[] bleachedROIMeasurementError = measurementError[FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.ordinal()];
    for (// elementWeight, first dimension is number of rows(time points), second dimension is number of variables(fitDatasets)
    int i = 0; // elementWeight, first dimension is number of rows(time points), second dimension is number of variables(fitDatasets)
    i < time.length; // elementWeight, first dimension is number of rows(time points), second dimension is number of variables(fitDatasets)
    i++) {
        weightData[i][0] = 1 / (cellROIMeasurementError[i] * cellROIMeasurementError[i]);
        weightData[i][1] = 1 / (bleachedROIMeasurementError[i] * bleachedROIMeasurementError[i]);
    }
    ElementWeights eleWeights = new ElementWeights(weightData);
    if (fixedParam == null) {
        // call curvefitting
        // bwmrate, fitting parameter A & reaction off rate
        outputParamValues = new double[3];
        double error = CurveFitting.fitRecovery_reacKoffRateOnly(time, fitData, inputParamValues, outputParamValues, fixedParam, eleWeights);
        // set objective function value
        offRateAnalysisResults.setObjectiveFunctionValue(error);
        // set reaction off rate analysis results
        offRateAnalysisResults.setBleachWhileMonitoringTau(outputParamValues[0]);
        offRateAnalysisResults.setFittingParamA(outputParamValues[1]);
        offRateAnalysisResults.setOffRate(outputParamValues[2]);
        // set cell intensity expression ( only t left in expression)
        Expression cellIntensityExp = new Expression(FRAPOptFunctions.FUNC_CELL_INTENSITY);
        cellIntensityExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_I_inicell), new Expression(cellROIAverage[0]));
        // subsitute bwmRate
        cellIntensityExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_BWM_RATE), new Expression(outputParamValues[0]));
        // undo time shift
        cellIntensityExp.substituteInPlace(new Expression(ReservedVariable.TIME.getName()), new Expression(ReservedVariable.TIME.getName() + "-" + time[0]));
        offRateAnalysisResults.setFitBleachWhileMonitorExpression(cellIntensityExp);
        // set bleached region intensity expression ( only t left in expression)
        Expression bleachIntensityExp = new Expression(FRAPOptFunctions.FUNC_RECOVERY_BLEACH_REACTION_DOMINANT);
        bleachIntensityExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_I_inibleached), new Expression(bleachedAverage[0]));
        // subsitute bwmRate
        bleachIntensityExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_BWM_RATE), new Expression(outputParamValues[0]));
        // subsitute parameter A
        bleachIntensityExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_A), new Expression(outputParamValues[1]));
        // reaction off rate
        bleachIntensityExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_KOFF), new Expression(outputParamValues[2]));
        // undo time shift
        bleachIntensityExp.substituteInPlace(new Expression(ReservedVariable.TIME.getName()), new Expression(ReservedVariable.TIME.getName() + "-" + time[0]));
        offRateAnalysisResults.setOffRateFitExpression(bleachIntensityExp);
    } else {
        if (fixedParam != null && fixedParam.getName().equals(FRAPModel.MODEL_PARAMETER_NAMES[FRAPModel.INDEX_BLEACH_MONITOR_RATE])) {
            // fitting parameter A & reaction off rate
            outputParamValues = new double[2];
            double error = CurveFitting.fitRecovery_reacKoffRateOnly(time, fitData, inputParamValues, outputParamValues, fixedParam, eleWeights);
            // set objective function value
            offRateAnalysisResults.setObjectiveFunctionValue(error);
            // set reaction off rate analysis results
            offRateAnalysisResults.setBleachWhileMonitoringTau(fixedParam.getInitialGuess());
            offRateAnalysisResults.setFittingParamA(outputParamValues[0]);
            offRateAnalysisResults.setOffRate(outputParamValues[1]);
            // set cell intensity expression ( only t left in expression)
            Expression cellIntensityExp = new Expression(FRAPOptFunctions.FUNC_CELL_INTENSITY);
            cellIntensityExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_I_inicell), new Expression(cellROIAverage[0]));
            // subsitute bwmRate
            cellIntensityExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_BWM_RATE), new Expression(fixedParam.getInitialGuess()));
            // undo time shift
            cellIntensityExp.substituteInPlace(new Expression(ReservedVariable.TIME.getName()), new Expression(ReservedVariable.TIME.getName() + "-" + time[0]));
            offRateAnalysisResults.setFitBleachWhileMonitorExpression(cellIntensityExp);
            // set bleached region intensity expression ( only t left in expression)
            Expression bleachIntensityExp = new Expression(FRAPOptFunctions.FUNC_RECOVERY_BLEACH_REACTION_DOMINANT);
            bleachIntensityExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_I_inibleached), new Expression(bleachedAverage[0]));
            // subsitute bwmRate
            bleachIntensityExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_BWM_RATE), new Expression(fixedParam.getInitialGuess()));
            // subsitute parameter A
            bleachIntensityExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_A), new Expression(outputParamValues[0]));
            // reaction off rate
            bleachIntensityExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_KOFF), new Expression(outputParamValues[1]));
            // undo time shift
            bleachIntensityExp.substituteInPlace(new Expression(ReservedVariable.TIME.getName()), new Expression(ReservedVariable.TIME.getName() + "-" + time[0]));
            offRateAnalysisResults.setOffRateFitExpression(bleachIntensityExp);
        } else if (fixedParam != null && fixedParam.getName().equals(FRAPModel.MODEL_PARAMETER_NAMES[FRAPModel.INDEX_OFF_RATE])) {
            // bwmRate & fitting parameter A
            outputParamValues = new double[2];
            double error = CurveFitting.fitRecovery_reacKoffRateOnly(time, fitData, inputParamValues, outputParamValues, fixedParam, eleWeights);
            // set objective function value
            offRateAnalysisResults.setObjectiveFunctionValue(error);
            // set reaction off rate analysis results
            offRateAnalysisResults.setBleachWhileMonitoringTau(outputParamValues[0]);
            offRateAnalysisResults.setFittingParamA(outputParamValues[1]);
            offRateAnalysisResults.setOffRate(fixedParam.getInitialGuess());
            // set cell intensity expression ( only t left in expression)
            Expression cellIntensityExp = new Expression(FRAPOptFunctions.FUNC_CELL_INTENSITY);
            cellIntensityExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_I_inicell), new Expression(cellROIAverage[0]));
            // subsitute bwmRate
            cellIntensityExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_BWM_RATE), new Expression(outputParamValues[0]));
            // undo time shift
            cellIntensityExp.substituteInPlace(new Expression(ReservedVariable.TIME.getName()), new Expression(ReservedVariable.TIME.getName() + "-" + time[0]));
            offRateAnalysisResults.setFitBleachWhileMonitorExpression(cellIntensityExp);
            // set bleached region intensity expression ( only t left in expression)
            Expression bleachIntensityExp = new Expression(FRAPOptFunctions.FUNC_RECOVERY_BLEACH_REACTION_DOMINANT);
            bleachIntensityExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_I_inibleached), new Expression(bleachedAverage[0]));
            // subsitute bwmRate
            bleachIntensityExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_BWM_RATE), new Expression(outputParamValues[0]));
            // subsitute parameter A
            bleachIntensityExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_A), new Expression(outputParamValues[1]));
            // reaction off rate
            bleachIntensityExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_KOFF), new Expression(fixedParam.getInitialGuess()));
            // undo time shift
            bleachIntensityExp.substituteInPlace(new Expression(ReservedVariable.TIME.getName()), new Expression(ReservedVariable.TIME.getName() + "-" + time[0]));
            offRateAnalysisResults.setOffRateFitExpression(bleachIntensityExp);
        } else {
            throw new OptimizationException("Unknown fixed parameter:" + fixedParam.getName());
        }
    }
    return offRateAnalysisResults;
}

Example 4 with OptimizationException

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

the class OptimizationService method optimize.

public static OptimizationResultSet optimize(ParameterEstimationTask parameterEstimationTask) throws Exception {
    // if (OperatingSystemInfo.getInstance().isMac()){
    // throw new RuntimeException("parameter estimation not currently available on Mac\n\n   try Windows or Linux.\n\n   coming soon on Mac.");
    // }
    copasiOptCallbacks.reset();
    updateMath(parameterEstimationTask.getSimulationContext(), NetworkGenerationRequirements.ComputeFullStandardTimeout);
    StringBuffer issueText = new StringBuffer();
    java.util.Vector<Issue> issueList = new java.util.Vector<Issue>();
    IssueContext issueContext = new IssueContext();
    parameterEstimationTask.gatherIssues(issueContext, issueList);
    boolean bFailed = false;
    for (int i = 0; i < issueList.size(); i++) {
        Issue issue = (Issue) issueList.elementAt(i);
        issueText.append(issue.getMessage() + "\n");
        if (issue.getSeverity() == Issue.SEVERITY_ERROR) {
            bFailed = true;
            break;
        }
    }
    if (bFailed) {
        throw new OptimizationException(issueText.toString());
    }
    parameterEstimationTask.refreshMappings();
    OptimizationResultSet optResultSet = CopasiOptimizationSolver.solveLocalPython(new ParameterEstimationTaskSimulatorIDA(), parameterEstimationTask, copasiOptCallbacks, callback);
    return optResultSet;
}

Example 5 with OptimizationException

use of cbit.vcell.opt.OptimizationException 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());
    }
}