Examples with ODESolverResultSet cbit.vcell.solver.ode.ODESolverResultSet used on opensource projects

Example 16 with ODESolverResultSet

use of cbit.vcell.solver.ode.ODESolverResultSet in project vcell by virtualcell.

the class FRAPEstimationPanel_NotUsed method displayFit.

private void displayFit(FrapDataAnalysisResults.DiffusionOnlyAnalysisRestults diffAnalysisResults, double[] frapDataTimeStamps, int startIndexForRecovery) {
    if (diffAnalysisResults == null) {
        FRAPParameterEstimateEnum.DIFFUSION_RATE.value = null;
        FRAPParameterEstimateEnum.MOBILE_FRACTION.value = null;
        FRAPParameterEstimateEnum.IMMOBILE_FRATION.value = null;
        FRAPParameterEstimateEnum.START_TIME_RECOVERY.value = null;
        FRAPParameterEstimateEnum.BLEACH_RATE_MONITOR.value = null;
        multisourcePlotPane.setDataSources(null);
    } else {
        FRAPParameterEstimateEnum.DIFFUSION_RATE.value = (diffAnalysisResults.getRecoveryDiffusionRate() == null ? null : diffAnalysisResults.getRecoveryDiffusionRate());
        FRAPParameterEstimateEnum.MOBILE_FRACTION.value = (diffAnalysisResults.getMobilefraction() == null ? null : diffAnalysisResults.getMobilefraction());
        FRAPParameterEstimateEnum.IMMOBILE_FRATION.value = (FRAPParameterEstimateEnum.MOBILE_FRACTION.value == null ? null : 1.0 - FRAPParameterEstimateEnum.MOBILE_FRACTION.value);
        FRAPParameterEstimateEnum.BLEACH_RATE_MONITOR.value = (diffAnalysisResults.getBleachWhileMonitoringTau() == null ? null : diffAnalysisResults.getBleachWhileMonitoringTau());
        // int startIndexForRecovery = FRAPDataAnalysis.getRecoveryIndex(initFRAPData);
        // 
        // Experiment - Cell ROI Average
        // 
        double[] temp_background = initFRAPData.getAvgBackGroundIntensity();
        double[] preBleachAvgXYZ = FrapDataUtils.calculatePreBleachAverageXYZ(initFRAPData, startIndexForRecovery);
        double[] cellRegionData = FRAPDataAnalysis.getAverageROIIntensity(initFRAPData, initFRAPData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name()), preBleachAvgXYZ, temp_background);
        ReferenceData expCellAvgData = new SimpleReferenceData(new String[] { "t", "CellROIAvg" }, new double[] { 1.0, 1.0 }, new double[][] { frapDataTimeStamps, cellRegionData });
        DataSource expCellAvgDataSource = new DataSource.DataSourceReferenceData("expCellAvg", expCellAvgData);
        // 
        // Analytic - Cell ROI Average with Bleach while monitor
        // 
        ODESolverResultSet bleachWhileMonitorOdeSolverResultSet = new ODESolverResultSet();
        bleachWhileMonitorOdeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription("t"));
        try {
            bleachWhileMonitorOdeSolverResultSet.addFunctionColumn(new FunctionColumnDescription(diffAnalysisResults.getFitBleachWhileMonitorExpression(), "CellROI_BleachWhileMonitor", null, "bleachWhileMonitorFit", true));
        } catch (ExpressionException e) {
            e.printStackTrace();
        }
        for (int i = startIndexForRecovery; i < frapDataTimeStamps.length; i++) {
            bleachWhileMonitorOdeSolverResultSet.addRow(new double[] { frapDataTimeStamps[i] });
        }
        // 
        // extend if necessary to plot theoretical curve to 4*tau
        // 
        {
            double T = frapDataTimeStamps[frapDataTimeStamps.length - 1];
            double deltaT = frapDataTimeStamps[frapDataTimeStamps.length - 1] - frapDataTimeStamps[frapDataTimeStamps.length - 2];
            while (T + deltaT < 6 * diffAnalysisResults.getRecoveryTau()) {
                bleachWhileMonitorOdeSolverResultSet.addRow(new double[] { T });
                T += deltaT;
            }
        }
        DataSource bleachWhileMonitorDataSource = new DataSource.DataSourceRowColumnResultSet("bleachwm", bleachWhileMonitorOdeSolverResultSet);
        // Recovery curve
        double[] bleachRegionData = FRAPDataAnalysis.getAverageROIIntensity(initFRAPData, initFRAPData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name()), preBleachAvgXYZ, temp_background);
        ;
        ReferenceData expRefData = new SimpleReferenceData(new String[] { "t", "BleachROIAvg" }, new double[] { 1.0, 1.0 }, new double[][] { frapDataTimeStamps, bleachRegionData });
        DataSource expDataSource = new DataSource.DataSourceReferenceData("experiment", expRefData);
        ODESolverResultSet fitOdeSolverResultSet = new ODESolverResultSet();
        fitOdeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription("t"));
        try {
            fitOdeSolverResultSet.addFunctionColumn(new FunctionColumnDescription(diffAnalysisResults.getDiffFitExpression(), // "('"+FrapDataAnalysisResults.BLEACH_TYPE_NAMES[bleachEstimationComboBox.getSelectedIndex()]+"')",
            "BleachROI_Recovery", null, "recoveryFit", true));
        } catch (ExpressionException e) {
            e.printStackTrace();
        }
        for (int i = startIndexForRecovery; i < frapDataTimeStamps.length; i++) {
            fitOdeSolverResultSet.addRow(new double[] { frapDataTimeStamps[i] });
        }
        // 
        // extend if necessary to plot theoretical curve to 4*tau
        // 
        double T = frapDataTimeStamps[frapDataTimeStamps.length - 1];
        double deltaT = frapDataTimeStamps[frapDataTimeStamps.length - 1] - frapDataTimeStamps[frapDataTimeStamps.length - 2];
        while (T + deltaT < 6 * diffAnalysisResults.getRecoveryTau()) {
            fitOdeSolverResultSet.addRow(new double[] { T });
            T += deltaT;
        }
        DataSource fitDataSource = new DataSource.DataSourceRowColumnResultSet("fit", fitOdeSolverResultSet);
        multisourcePlotPane.setDataSources(new DataSource[] { expDataSource, fitDataSource, expCellAvgDataSource, bleachWhileMonitorDataSource });
        multisourcePlotPane.selectAll();
    }
    table.repaint();
}

Example 17 with ODESolverResultSet

use of cbit.vcell.solver.ode.ODESolverResultSet in project vcell by virtualcell.

the class EstParams_ReactionOffRatePanel method displayResults.

private void displayResults(FRAPData frapData, int startIndexRecovery) throws ExpressionException, DivideByZeroException {
    Parameter[] currentParams = offRateParamPanel.getCurrentParameters();
    if (frapData == null || currentParams == null) {
        multisourcePlotPane.setDataSources(null);
    } else {
        double[] frapDataTimeStamps = frapData.getImageDataset().getImageTimeStamps();
        // Experiment - Cell ROI Average
        double[] temp_background = frapData.getAvgBackGroundIntensity();
        double[] preBleachAvgXYZ = FrapDataUtils.calculatePreBleachAverageXYZ(frapData, startIndexRecovery);
        /*double[] cellRegionData = FRAPDataAnalysis.getAverageROIIntensity(frapData, frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name()),preBleachAvgXYZ,temp_background);
			ReferenceData expCellAvgData = new SimpleReferenceData(new String[] { ReservedSymbol.TIME.getName(), "CellROIAvg" }, new double[] { 1.0, 1.0 }, new double[][] {frapDataTimeStamps, cellRegionData });
			DataSource expCellAvgDataSource = new DataSource.DataSourceReferenceData("exp", expCellAvgData);
			//Analytic - Cell ROI Average with Bleach while monitor
			ODESolverResultSet bleachWhileMonitorOdeSolverResultSet = new ODESolverResultSet();
			bleachWhileMonitorOdeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(ReservedSymbol.TIME.getName()));
			Expression cellAvgExp = new Expression(FRAPOptFunctions.FUNC_CELL_INTENSITY);
			// substitute parameter values 
			cellAvgExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_I_inicell), new Expression(cellRegionData[startIndexRecovery]));
			cellAvgExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_BWM_RATE), new Expression(currentParams[FRAPModel.INDEX_BLEACH_MONITOR_RATE].getInitialGuess()));
			// time shift
			cellAvgExp.substituteInPlace(new Expression(ReservedSymbol.TIME.getName()), new Expression(ReservedSymbol.TIME.getName()+"-"+frapDataTimeStamps[startIndexRecovery]));
			try {
				bleachWhileMonitorOdeSolverResultSet.addFunctionColumn(
					new FunctionColumnDescription(
						cellAvgExp,
						"CellROIAvg",
						null,"bleachWhileMonitorFit",true));
			} catch (ExpressionException e) {
				e.printStackTrace();
			}
			for (int i = startIndexRecovery; i < frapDataTimeStamps.length; i++) 
			{
				bleachWhileMonitorOdeSolverResultSet.addRow(new double[] { frapDataTimeStamps[i] });
			}
			DataSource bleachWhileMonitorDataSource = new DataSource.DataSourceOdeSolverResultSet("fit", bleachWhileMonitorOdeSolverResultSet);*/
        // experimental bleach region average intensity curve
        double[] bleachRegionData = FRAPDataAnalysis.getAverageROIIntensity(frapData, frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name()), preBleachAvgXYZ, temp_background);
        ;
        ReferenceData expRefData = new SimpleReferenceData(new String[] { ReservedVariable.TIME.getName(), "BleachROIAvg" }, new double[] { 1.0, 1.0 }, new double[][] { frapDataTimeStamps, bleachRegionData });
        DataSource expBleachDataSource = new DataSource.DataSourceReferenceData("exp", expRefData);
        // Analytic - bleach region average intensity with bleach while monitoring rate
        ODESolverResultSet koffFitOdeSolverResultSet = new ODESolverResultSet();
        koffFitOdeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(ReservedVariable.TIME.getName()));
        Expression bleachedAvgExp = frapWorkspace.getWorkingFrapStudy().getFrapOptFunc().getRecoveryExpressionWithCurrentParameters(currentParams);
        try {
            koffFitOdeSolverResultSet.addFunctionColumn(new FunctionColumnDescription(bleachedAvgExp, "BleachROIAvg", null, "recoveryFit", true));
        } catch (ExpressionException e) {
            e.printStackTrace();
        }
        double[] truncatedTimes = new double[frapDataTimeStamps.length - startIndexRecovery];
        for (int i = startIndexRecovery; i < frapDataTimeStamps.length; i++) {
            koffFitOdeSolverResultSet.addRow(new double[] { frapDataTimeStamps[i] });
            truncatedTimes[i - startIndexRecovery] = frapDataTimeStamps[i];
        }
        setCurrentEstimationResults(frapWorkspace.getWorkingFrapStudy().getFrapOptFunc().createData(bleachedAvgExp.flatten(), truncatedTimes));
        DataSource koffFitDataSource = new DataSource.DataSourceRowColumnResultSet("fit", koffFitOdeSolverResultSet);
        multisourcePlotPane.setDataSources(new DataSource[] { expBleachDataSource, koffFitDataSource /*, expCellAvgDataSource , bleachWhileMonitorDataSource*/
        });
        multisourcePlotPane.selectAll();
    }
}

Example 18 with ODESolverResultSet

use of cbit.vcell.solver.ode.ODESolverResultSet in project vcell by virtualcell.

the class EstParams_TwoDiffComponentPanel method plotDerivedSimulationResults.

private void plotDerivedSimulationResults(AnalysisParameters[] anaParams) {
    try {
        String description = null;
        int totalROIlen = FRAPData.VFRAP_ROI_ENUM.values().length;
        boolean[] wantsROITypes = new boolean[totalROIlen];
        System.arraycopy(frapWorkspace.getWorkingFrapStudy().getSelectedROIsForErrorCalculation(), 0, wantsROITypes, 0, totalROIlen);
        ODESolverResultSet fitOdeSolverResultSet = new ODESolverResultSet();
        fitOdeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription("t"));
        for (int j = 0; j < totalROIlen; j++) {
            if (!wantsROITypes[j]) {
                continue;
            }
            String currentROIName = FRAPData.VFRAP_ROI_ENUM.values()[j].name();
            String name = (description == null ? /*"sim D="+diffusionRates[diffusionRateIndex]+"::"*/
            "" : description) + currentROIName;
            fitOdeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(name));
        }
        int totalWantedROIlen = 0;
        for (int i = 0; i < wantsROITypes.length; i++) {
            if (wantsROITypes[i]) {
                totalWantedROIlen++;
            }
        }
        // 
        // populate time
        // 
        double[] shiftedSimTimes = frapOptData.getReducedExpTimePoints();
        int startIndexRecovery = frapOptData.getExpFrapStudy().getStartingIndexForRecovery();
        for (int j = 0; j < shiftedSimTimes.length; j++) {
            double[] row = new double[totalWantedROIlen + 1];
            row[0] = shiftedSimTimes[j] + frapOptData.getExpFrapStudy().getFrapData().getImageDataset().getImageTimeStamps()[startIndexRecovery];
            fitOdeSolverResultSet.addRow(row);
        }
        // populate values
        double[][] currentOptFitData = diffTwoPanel.getCurrentFitData();
        // store results
        setCurrentEstimationResults(currentOptFitData);
        if (allDataHash != null && currentOptFitData != null) {
            // populate optimization data---convert it to odeSoverResultSet and further put into datasource
            int columncounter = 0;
            for (int j = 0; j < totalROIlen; j++) {
                if (!wantsROITypes[j]) {
                    continue;
                }
                // if(!isSimData) //opt data
                // {
                double[] values = currentOptFitData[j];
                for (int k = 0; k < values.length; k++) {
                    fitOdeSolverResultSet.setValue(k, columncounter + /*j*/
                    1, values[k]);
                }
                // }
                columncounter++;
            }
            // anaParams[0] is the key in allDataHash to get the dataSource[]:exp & sim
            DataSource[] selectedRowDataSourceArr = allDataHash.get(anaParams[0]);
            if (selectedRowDataSourceArr != null) {
                // referenceData is the exp data
                final DataSource expDataSource = /*new DataSource(referenceData,"exp")*/
                selectedRowDataSourceArr[SpatialAnalysisResults.ARRAY_INDEX_EXPDATASOURCE];
                DataSource optDataSource = new DataSource.DataSourceRowColumnResultSet("opt", fitOdeSolverResultSet);
                // 
                DataSource[] newDataSourceArr = new DataSource[2];
                newDataSourceArr[SpatialAnalysisResults.ARRAY_INDEX_EXPDATASOURCE] = expDataSource;
                newDataSourceArr[SpatialAnalysisResults.ARRAY_INDEX_SIMDATASOURCE] = optDataSource;
                if (currentOptFitData == null) {
                    multisourcePlotPane.setDataSources(null);
                } else {
                    // the following paragraph of code is just to get selected color for selected ROIs
                    // and make them the same as we show on ChooseModel_RoiForErrorPanel/RoiForErrorPanel
                    // double valid ROI colors (not include cell and background)
                    int validROISize = FRAPData.VFRAP_ROI_ENUM.values().length - 2;
                    Color[] fullColors = ColorUtil.generateAutoColor(validROISize * 2, getBackground(), new Integer(0));
                    boolean[] selectedROIs = frapWorkspace.getWorkingFrapStudy().getSelectedROIsForErrorCalculation();
                    int selectedROICounter = 0;
                    for (int i = 0; i < selectedROIs.length; i++) {
                        if (selectedROIs[i]) {
                            selectedROICounter++;
                        }
                    }
                    // double the size, each ROI is a comparison of exp and sim
                    Color[] selectedColors = new Color[selectedROICounter * 2];
                    int selectedColorIdx = 0;
                    for (int i = 0; i < selectedROIs.length; i++) {
                        if (selectedROIs[i] && i == 0) {
                            selectedColors[selectedColorIdx] = fullColors[i];
                            selectedColors[selectedColorIdx + selectedROICounter] = fullColors[i + validROISize];
                            selectedColorIdx++;
                        }
                        if (// skip cell and background ROIs
                        selectedROIs[i] && i > 2) {
                            selectedColors[selectedColorIdx] = fullColors[i - 2];
                            selectedColors[selectedColorIdx + selectedROICounter] = fullColors[i - 2 + validROISize];
                            selectedColorIdx++;
                        }
                    }
                    int[] selectedIndices = multisourcePlotPane.getUnsortedSelectedIndices();
                    multisourcePlotPane.setDataSources(newDataSourceArr, selectedColors);
                    if (selectedIndices.length == 0) {
                        multisourcePlotPane.selectAll();
                    } else {
                        multisourcePlotPane.setUnsortedSelectedIndices(selectedIndices);
                    }
                }
            }
        }
    } catch (Exception e2) {
        e2.printStackTrace();
        DialogUtils.showErrorDialog(this, "Error graphing Optimizer data " + e2.getMessage());
    }
}

Example 19 with ODESolverResultSet

use of cbit.vcell.solver.ode.ODESolverResultSet in project vcell by virtualcell.

the class TestingFrameworkWindowManager method generateTestCriteriaReport.

/**
 * Insert the method's description here.
 * Creation date: (8/18/2003 5:36:47 PM)
 */
private String generateTestCriteriaReport(TestCaseNew testCase, TestCriteriaNew testCriteria, Simulation testSim, TFGenerateReport.VCDocumentAndSimInfo userSelectedRefSimInfo) /*,VCDocument refDoc,VCDocument testDocument*/
{
    if (testSim.getScanCount() != 1) {
        throw new RuntimeException("paramater scan is not supported in Math Testing Framework");
    }
    SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(testSim, 0);
    String simReportStatus = null;
    String simReportStatusMessage = null;
    StringBuffer reportTCBuffer = new StringBuffer();
    VariableComparisonSummary[] failVarSummaries = null;
    VariableComparisonSummary[] allVarSummaries = null;
    double absErr = 0;
    double relErr = 0;
    if (testCriteria != null) {
        absErr = testCriteria.getMaxAbsError().doubleValue();
        relErr = testCriteria.getMaxRelError().doubleValue();
    }
    try {
        VCDocument testDoc = null;
        if (testCase instanceof TestCaseNewMathModel) {
            MathModelInfo mmInfo = ((TestCaseNewMathModel) testCase).getMathModelInfo();
            MathModel mathModel = getRequestManager().getDocumentManager().getMathModel(mmInfo);
            testDoc = mathModel;
        } else if (testCase instanceof TestCaseNewBioModel) {
            TestCaseNewBioModel bioTestCase = (TestCaseNewBioModel) testCase;
            // bioTestCase.
            BioModelInfo bmInfo = bioTestCase.getBioModelInfo();
            BioModel bioModel = getRequestManager().getDocumentManager().getBioModel(bmInfo);
            testDoc = bioModel;
        }
        TFGenerateReport.VCDocumentAndSimInfo refVCDocumentAndSimInfo = null;
        if (userSelectedRefSimInfo == null) {
            SimulationInfo refSimInfo = testCriteria.getRegressionSimInfo();
            if (refSimInfo != null) {
                VCDocument refDoc = null;
                if (testCriteria instanceof TestCriteriaNewMathModel) {
                    MathModelInfo mmInfo = ((TestCriteriaNewMathModel) testCriteria).getRegressionMathModelInfo();
                    MathModel mathModel = getRequestManager().getDocumentManager().getMathModel(mmInfo);
                    refDoc = mathModel;
                } else if (testCriteria instanceof TestCriteriaNewBioModel) {
                    BioModelInfo bmInfo = ((TestCriteriaNewBioModel) testCriteria).getRegressionBioModelInfo();
                    BioModel bioModel = getRequestManager().getDocumentManager().getBioModel(bmInfo);
                    refDoc = bioModel;
                }
                refVCDocumentAndSimInfo = new TFGenerateReport.VCDocumentAndSimInfo(refSimInfo, refDoc);
            }
            reportTCBuffer.append("\t\t" + testSim.getName() + (refVCDocumentAndSimInfo != null ? " (Using TestCrit RegrRefSim)" : "") + " : " + "\n");
        } else {
            refVCDocumentAndSimInfo = userSelectedRefSimInfo;
            reportTCBuffer.append("\t\t" + testSim.getName() + " (Using UserDefined RegrRefSim '" + userSelectedRefSimInfo.getSimInfo().getAuthoritativeVCSimulationIdentifier() + "') : " + "\n");
        }
        if (testCase.getType().equals(TestCaseNew.REGRESSION) && refVCDocumentAndSimInfo == null) {
            reportTCBuffer.append("\t\t\tNo reference SimInfo, SimInfoKey=" + testCriteria.getSimInfo().getVersion().getName() + ". Cannot perform Regression Test!\n");
            simReportStatus = TestCriteriaNew.TCRIT_STATUS_NOREFREGR;
        } else {
            VCDataIdentifier vcdID = new VCSimulationDataIdentifier(testSim.getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), 0);
            DataManager simDataManager = getRequestManager().getDataManager(null, vcdID, testSim.isSpatial());
            double[] timeArray = null;
            // can be histogram, so there won't be time array
            try {
                timeArray = simDataManager.getDataSetTimes();
            } catch (Exception ex) {
                ex.printStackTrace(System.out);
            }
            NonspatialStochSimOptions stochOpt = testSim.getSolverTaskDescription().getStochOpt();
            if ((stochOpt == null || stochOpt.getNumOfTrials() == 1) && (timeArray == null || timeArray.length == 0)) {
                reportTCBuffer.append("\t\t\tNO DATA : Simulation not run yet.\n");
                simReportStatus = TestCriteriaNew.TCRIT_STATUS_NODATA;
            } else {
                // SPATIAL simulation
                if (testSim.getMathDescription().isSpatial()) {
                    PDEDataManager pdeDataManager = (PDEDataManager) simDataManager;
                    // Get EXACT solution if test case type is EXACT, Compare with numerical
                    if (testCase.getType().equals(TestCaseNew.EXACT) || testCase.getType().equals(TestCaseNew.EXACT_STEADY)) {
                        SimulationComparisonSummary simCompSummary = MathTestingUtilities.comparePDEResultsWithExact(simSymbolTable, pdeDataManager, testCase.getType(), testCriteria.getMaxAbsError(), testCriteria.getMaxRelError());
                        // Failed var summaries
                        failVarSummaries = simCompSummary.getFailingVariableComparisonSummaries(absErr, relErr);
                        allVarSummaries = simCompSummary.getVariableComparisonSummaries();
                        if (failVarSummaries.length > 0) {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_FAILEDVARS;
                            // Failed simulation
                            reportTCBuffer.append("\t\tTolerance test FAILED \n");
                            reportTCBuffer.append("\t\tFailed Variables : \n");
                            for (int m = 0; m < failVarSummaries.length; m++) {
                                reportTCBuffer.append("\t\t\t" + failVarSummaries[m].toShortString() + "\n");
                            }
                        } else {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_PASSED;
                            reportTCBuffer.append("\t\tTolerance test PASSED \n");
                        }
                        reportTCBuffer.append("\t\tPassed Variables : \n");
                        // Check if varSummary exists in failed summaries list. If not, simulation passed.
                        for (int m = 0; m < allVarSummaries.length; m++) {
                            if (!BeanUtils.arrayContains(failVarSummaries, allVarSummaries[m])) {
                                reportTCBuffer.append("\t\t\t" + allVarSummaries[m].toShortString() + "\n");
                            }
                        }
                    // Get CONSTRUCTED solution if test case type is CONSTRUCTED, Compare with numerical
                    } else if (testCase.getType().equals(TestCaseNew.CONSTRUCTED)) {
                        SimulationComparisonSummary simCompSummary = MathTestingUtilities.comparePDEResultsWithExact(simSymbolTable, pdeDataManager, testCase.getType(), testCriteria.getMaxAbsError(), testCriteria.getMaxRelError());
                        // Failed var summaries
                        failVarSummaries = simCompSummary.getFailingVariableComparisonSummaries(absErr, relErr);
                        allVarSummaries = simCompSummary.getVariableComparisonSummaries();
                        if (failVarSummaries.length > 0) {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_FAILEDVARS;
                            // Failed simulation
                            reportTCBuffer.append("\t\tTolerance test FAILED \n");
                            reportTCBuffer.append("\t\tFailed Variables : \n");
                            for (int m = 0; m < failVarSummaries.length; m++) {
                                reportTCBuffer.append("\t\t\t" + failVarSummaries[m].toShortString() + "\n");
                            }
                        } else {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_PASSED;
                            reportTCBuffer.append("\t\tTolerance test PASSED \n");
                        }
                        reportTCBuffer.append("\t\tPassed Variables : \n");
                        // Check if varSummary exists in failed summaries list. If not, simulation passed.
                        for (int m = 0; m < allVarSummaries.length; m++) {
                            if (!BeanUtils.arrayContains(failVarSummaries, allVarSummaries[m])) {
                                reportTCBuffer.append("\t\t\t" + allVarSummaries[m].toShortString() + "\n");
                            }
                        }
                    } else if (testCase.getType().equals(TestCaseNew.REGRESSION)) {
                        Simulation refSim = ((ClientDocumentManager) getRequestManager().getDocumentManager()).getSimulation(refVCDocumentAndSimInfo.getSimInfo());
                        VCDataIdentifier refVcdID = new VCSimulationDataIdentifier(refVCDocumentAndSimInfo.getSimInfo().getAuthoritativeVCSimulationIdentifier(), 0);
                        PDEDataManager refDataManager = (PDEDataManager) getRequestManager().getDataManager(null, refVcdID, refSim.isSpatial());
                        if (refSim.getScanCount() != 1) {
                            throw new RuntimeException("paramater scan is not supported in Math Testing Framework");
                        }
                        SimulationSymbolTable refSimSymbolTable = new SimulationSymbolTable(refSim, 0);
                        String[] varsToCompare = getVariableNamesToCompare(simSymbolTable, refSimSymbolTable);
                        SimulationComparisonSummary simCompSummary = MathTestingUtilities.comparePDEResults(simSymbolTable, pdeDataManager, refSimSymbolTable, refDataManager, varsToCompare, testCriteria.getMaxAbsError(), testCriteria.getMaxRelError(), refVCDocumentAndSimInfo.getVCDocument(), getDataInfoProvider(refVCDocumentAndSimInfo.getVCDocument(), refDataManager.getPDEDataContext(), refSim.getName()), testDoc, getDataInfoProvider(testDoc, pdeDataManager.getPDEDataContext(), testSim.getName()));
                        // Failed var summaries
                        failVarSummaries = simCompSummary.getFailingVariableComparisonSummaries(absErr, relErr);
                        allVarSummaries = simCompSummary.getVariableComparisonSummaries();
                        if (failVarSummaries.length > 0) {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_FAILEDVARS;
                            // Failed simulation
                            reportTCBuffer.append("\t\tTolerance test FAILED \n");
                            reportTCBuffer.append("\t\tFailed Variables : \n");
                            for (int m = 0; m < failVarSummaries.length; m++) {
                                reportTCBuffer.append("\t\t\t" + failVarSummaries[m].toShortString() + "\n");
                            }
                        } else {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_PASSED;
                            reportTCBuffer.append("\t\tTolerance test PASSED \n");
                        }
                        reportTCBuffer.append("\t\tPassed Variables : \n");
                        // Check if varSummary exists in failed summaries list. If not, simulation passed.
                        for (int m = 0; m < allVarSummaries.length; m++) {
                            if (!BeanUtils.arrayContains(failVarSummaries, allVarSummaries[m])) {
                                reportTCBuffer.append("\t\t\t" + allVarSummaries[m].toShortString() + "\n");
                            }
                        }
                    }
                } else {
                    // NON-SPATIAL CASE
                    ODEDataManager odeDataManager = (ODEDataManager) simDataManager;
                    ODESolverResultSet numericalResultSet = odeDataManager.getODESolverResultSet();
                    // Get EXACT result set if test case type is EXACT, Compare with numerical
                    if (testCase.getType().equals(TestCaseNew.EXACT) || testCase.getType().equals(TestCaseNew.EXACT_STEADY)) {
                        ODESolverResultSet exactResultSet = MathTestingUtilities.getExactResultSet(testSim.getMathDescription(), timeArray, testSim.getSolverTaskDescription().getSensitivityParameter());
                        String[] varsToCompare = getVariableNamesToCompare(simSymbolTable, simSymbolTable);
                        SimulationComparisonSummary simCompSummary_exact = MathTestingUtilities.compareResultSets(numericalResultSet, exactResultSet, varsToCompare, testCase.getType(), testCriteria.getMaxAbsError(), testCriteria.getMaxRelError());
                        // Get all the variable comparison summaries and the failed ones to print out report for EXACT solution comparison.
                        failVarSummaries = simCompSummary_exact.getFailingVariableComparisonSummaries(absErr, relErr);
                        allVarSummaries = simCompSummary_exact.getVariableComparisonSummaries();
                        if (failVarSummaries.length > 0) {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_FAILEDVARS;
                            // Failed simulation
                            reportTCBuffer.append("\t\tTolerance test FAILED \n");
                            reportTCBuffer.append("\t\tFailed Variables : \n");
                            for (int m = 0; m < failVarSummaries.length; m++) {
                                reportTCBuffer.append("\t\t\t" + failVarSummaries[m].toShortString() + "\n");
                            }
                        } else {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_PASSED;
                            reportTCBuffer.append("\t\tTolerance test PASSED \n");
                        }
                        reportTCBuffer.append("\t\tPassed Variables : \n");
                        // Check if varSummary exists in failed summaries list. If not, simulation passed.
                        for (int m = 0; m < allVarSummaries.length; m++) {
                            if (!BeanUtils.arrayContains(failVarSummaries, allVarSummaries[m])) {
                                reportTCBuffer.append("\t\t\t" + allVarSummaries[m].toShortString() + "\n");
                            }
                        }
                    // Get CONSTRUCTED result set if test case type is CONSTRUCTED , compare with numerical
                    } else if (testCase.getType().equals(TestCaseNew.CONSTRUCTED)) {
                        ODESolverResultSet constructedResultSet = MathTestingUtilities.getConstructedResultSet(testSim.getMathDescription(), timeArray);
                        String[] varsToCompare = getVariableNamesToCompare(simSymbolTable, simSymbolTable);
                        SimulationComparisonSummary simCompSummary_constr = MathTestingUtilities.compareResultSets(numericalResultSet, constructedResultSet, varsToCompare, testCase.getType(), testCriteria.getMaxAbsError(), testCriteria.getMaxRelError());
                        // Get all the variable comparison summaries and the failed ones to print out report for CONSTRUCTED solution comparison.
                        failVarSummaries = simCompSummary_constr.getFailingVariableComparisonSummaries(absErr, relErr);
                        allVarSummaries = simCompSummary_constr.getVariableComparisonSummaries();
                        if (failVarSummaries.length > 0) {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_FAILEDVARS;
                            // Failed simulation
                            reportTCBuffer.append("\t\tTolerance test FAILED \n");
                            reportTCBuffer.append("\t\tFailed Variables : \n");
                            for (int m = 0; m < failVarSummaries.length; m++) {
                                reportTCBuffer.append("\t\t\t" + failVarSummaries[m].toShortString() + "\n");
                            }
                        } else {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_PASSED;
                            reportTCBuffer.append("\t\tTolerance test PASSED \n");
                        }
                        reportTCBuffer.append("\t\tPassed Variables : \n");
                        // Check if varSummary exists in failed summaries list. If not, simulation passed.
                        for (int m = 0; m < allVarSummaries.length; m++) {
                            if (!BeanUtils.arrayContains(failVarSummaries, allVarSummaries[m])) {
                                reportTCBuffer.append("\t\t\t" + allVarSummaries[m].toShortString() + "\n");
                            }
                        }
                    } else if (testCase.getType().equals(TestCaseNew.REGRESSION)) {
                        Simulation refSim = ((ClientDocumentManager) getRequestManager().getDocumentManager()).getSimulation(testCriteria.getRegressionSimInfo());
                        if (refSim.getScanCount() != 1) {
                            throw new RuntimeException("paramater scan is not supported in Math Testing Framework");
                        }
                        SimulationSymbolTable refSimSymbolTable = new SimulationSymbolTable(refSim, 0);
                        String[] varsToTest = getVariableNamesToCompare(simSymbolTable, refSimSymbolTable);
                        VCDataIdentifier refVcdID = new VCSimulationDataIdentifier(refVCDocumentAndSimInfo.getSimInfo().getAuthoritativeVCSimulationIdentifier(), 0);
                        ODEDataManager refDataManager = (ODEDataManager) getRequestManager().getDataManager(null, refVcdID, refSim.isSpatial());
                        ODESolverResultSet referenceResultSet = refDataManager.getODESolverResultSet();
                        SimulationComparisonSummary simCompSummary_regr = null;
                        int interpolationOrder = 1;
                        SolverTaskDescription solverTaskDescription = refSim.getSolverTaskDescription();
                        if (solverTaskDescription.getOutputTimeSpec().isDefault() && ((DefaultOutputTimeSpec) solverTaskDescription.getOutputTimeSpec()).getKeepEvery() == 1) {
                            SolverDescription solverDescription = solverTaskDescription.getSolverDescription();
                            if ((!solverDescription.supportsAll(SolverDescription.DiscontinutiesFeatures)) || !refSim.getMathDescription().hasDiscontinuities()) {
                                interpolationOrder = solverDescription.getTimeOrder();
                            }
                        }
                        simCompSummary_regr = MathTestingUtilities.compareUnEqualResultSets(numericalResultSet, referenceResultSet, varsToTest, testCriteria.getMaxAbsError(), testCriteria.getMaxRelError(), interpolationOrder);
                        // Get all the variable comparison summaries and the failed ones to print out report for CONSTRUCTED solution comparison.
                        failVarSummaries = simCompSummary_regr.getFailingVariableComparisonSummaries(absErr, relErr);
                        allVarSummaries = simCompSummary_regr.getVariableComparisonSummaries();
                        if (failVarSummaries.length > 0) {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_FAILEDVARS;
                            // Failed simulation
                            reportTCBuffer.append("\t\tTolerance test FAILED \n");
                            reportTCBuffer.append("\t\tFailed Variables : \n");
                            for (int m = 0; m < failVarSummaries.length; m++) {
                                reportTCBuffer.append("\t\t\t" + failVarSummaries[m].toShortString() + "\n");
                            }
                        } else {
                            simReportStatus = TestCriteriaNew.TCRIT_STATUS_PASSED;
                            reportTCBuffer.append("\t\tTolerance test PASSED \n");
                        }
                        reportTCBuffer.append("\t\tPassed Variables : \n");
                        // Check if varSummary exists in failed summaries list. If not, simulation passed.
                        for (int m = 0; m < allVarSummaries.length; m++) {
                            if (!BeanUtils.arrayContains(failVarSummaries, allVarSummaries[m])) {
                                reportTCBuffer.append("\t\t\t" + allVarSummaries[m].toShortString() + "\n");
                            }
                        }
                    }
                }
            }
        }
    } catch (Throwable e) {
        simReportStatus = TestCriteriaNew.TCRIT_STATUS_RPERROR;
        simReportStatusMessage = e.getClass().getName() + " " + e.getMessage();
        reportTCBuffer.append("\t\t" + simReportStatusMessage + "\n");
        e.printStackTrace(System.out);
    }
    if (userSelectedRefSimInfo == null) {
        try {
            // Remove any test results already present for testCriteria
            RemoveTestResultsOP removeResultsOP = new RemoveTestResultsOP(new BigDecimal[] { testCriteria.getTCritKey() });
            // testResultsOPsVector.add(removeResultsOP);
            getRequestManager().getDocumentManager().doTestSuiteOP(removeResultsOP);
            // Create new AddTestREsultsOP object for the current simulation./testCriteria.
            if (allVarSummaries != null) {
                AddTestResultsOP testResultsOP = new AddTestResultsOP(testCriteria.getTCritKey(), allVarSummaries);
                // testResultsOPsVector.add(testResultsOP);
                // Write the testResults for simulation/TestCriteria into the database ...
                getRequestManager().getDocumentManager().doTestSuiteOP(testResultsOP);
            }
            // Update report status
            updateTCritStatus(testCriteria, simReportStatus, simReportStatusMessage);
        } catch (Throwable e) {
            reportTCBuffer.append("\t\tUpdate DB Results failed. " + e.getClass().getName() + " " + e.getMessage() + "\n");
            try {
                getRequestManager().getDocumentManager().doTestSuiteOP(new EditTestCriteriaOPReportStatus(testCriteria.getTCritKey(), TestCriteriaNew.TCRIT_STATUS_RPERROR, e.getClass().getName() + " " + e.getMessage()));
            } catch (Throwable e2) {
            // Nothing more can be done
            }
        }
    }
    return reportTCBuffer.toString();
}

Example 20 with ODESolverResultSet

use of cbit.vcell.solver.ode.ODESolverResultSet in project vcell by virtualcell.

the class MergedDatasetViewer method refreshData.

/**
 * Insert the method's description here.
 * Creation date: (6/11/2004 2:43:49 PM)
 * @exception org.vcell.util.DataAccessException The exception description.
 */
public void refreshData() throws org.vcell.util.DataAccessException {
    if (isODEData) {
        ODESolverResultSet osr = null;
        osr = odeDataViewer.getOdeSolverResultSet();
        if (osr != null) {
            odeDataViewer.setOdeSolverResultSet(osr);
        }
    } else {
        pdeDataViewer.getPdeDataContext().refreshTimes();
    }
}