Examples with SimulationSymbolTable cbit.vcell.solver.SimulationSymbolTable used on opensource projects

Example 16 with SimulationSymbolTable

use of cbit.vcell.solver.SimulationSymbolTable in project vcell by virtualcell.

the class SimulationWorkspace method checkSimulationParameters.

/**
 * Insert the method's description here.
 * Creation date: (5/11/2004 2:57:10 PM)
 * @return boolean
 * @param simulation cbit.vcell.solver.Simulation
 */
private static boolean checkSimulationParameters(Simulation simulation, Component parent) {
    SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(simulation, 0);
    String errorMessage = null;
    long maxTimepoints = Simulation.MAX_LIMIT_NON_SPATIAL_TIMEPOINTS;
    long warningTimepoints = Simulation.WARNING_NON_SPATIAL_TIMEPOINTS;
    boolean bSpatial = simulation.isSpatial();
    if (bSpatial) {
        maxTimepoints = Simulation.MAX_LIMIT_SPATIAL_TIMEPOINTS;
        warningTimepoints = Simulation.WARNING_SPATIAL_TIMEPOINTS;
    }
    long maxSizeBytes = megabytesToBytes(Simulation.MAX_LIMIT_0DE_MEGABYTES);
    long warningSizeBytes = megabytesToBytes(Simulation.WARNING_0DE_MEGABYTES);
    if (bSpatial) {
        maxSizeBytes = megabytesToBytes(Simulation.MAX_LIMIT_PDE_MEGABYTES);
        warningSizeBytes = megabytesToBytes(Simulation.WARNING_PDE_MEGABYTES);
    } else if (simulation.getMathDescription().isNonSpatialStoch()) {
        maxSizeBytes = megabytesToBytes(Simulation.MAX_LIMIT_STOCH_MEGABYTES);
        warningSizeBytes = megabytesToBytes(Simulation.WARNING_STOCH_MEGABYTES);
    }
    long expectedNumTimePoints = getExpectedNumTimePoints(simulation);
    long expectedSizeBytes = getExpectedSizeBytes(simSymbolTable);
    // 
    // check for error conditions (hard limits on resources) ... Note: each user should have it's own limits (and quotas).
    // 
    SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
    SolverDescription solverDescription = solverTaskDescription.getSolverDescription();
    if (expectedNumTimePoints > maxTimepoints) {
        errorMessage = "Errors in Simulation: '" + simulation.getName() + "'!\n" + "The simulation has too many timepoints (" + expectedNumTimePoints + ") to be saved, which has exceeded our limit.\n\n" + "maximum saving timepoints limits are:\n" + "     " + Simulation.MAX_LIMIT_NON_SPATIAL_TIMEPOINTS + " for compartmental simulations\n" + "     " + Simulation.MAX_LIMIT_SPATIAL_TIMEPOINTS + " for spatial simulations\n" + "suggested saving timepoints limits are:\n" + "     " + Simulation.WARNING_NON_SPATIAL_TIMEPOINTS + " for compartmental simulations\n" + "     " + Simulation.WARNING_SPATIAL_TIMEPOINTS + " for spatial simulations\n" + "Try saving fewer timepoints\n" + "If you need to exceed the quota, please contact us";
        // not used for multiple stochastic run
        if (solverTaskDescription.getStochOpt() != null && solverTaskDescription.getStochOpt().getNumOfTrials() > 1) {
            errorMessage = null;
        }
    } else if (expectedSizeBytes > maxSizeBytes) {
        errorMessage = "Errors in Simulation: '" + simulation.getName() + "'!\n" + "The simulation's result dataset (" + CodeUtil.humanBytePrint(expectedSizeBytes) + ") is too large, which has exceeded our limit.\n\n" + "maximum size limits are:\n" + "     " + Simulation.MAX_LIMIT_0DE_MEGABYTES + " MB for compartmental ODE simulations\n" + "     " + Simulation.MAX_LIMIT_PDE_MEGABYTES + " MB for spatial simulations\n" + "     " + Simulation.MAX_LIMIT_STOCH_MEGABYTES + " MB for compartmental stochastic simulations\n" + "suggested size limits are:\n" + "     " + Simulation.WARNING_0DE_MEGABYTES + " MB for compartmental ODE simulations\n" + "     " + Simulation.WARNING_PDE_MEGABYTES + " MB for spatial simulations\n" + "     " + Simulation.WARNING_STOCH_MEGABYTES + " MB for compartmental stochastic simulations\n" + "Try saving fewer timepoints or using a smaller mesh (if spatial)\n" + "If you need to exceed the quota, please contact us";
        // not used for multiple stochastic run
        if (solverTaskDescription.getStochOpt() != null && solverTaskDescription.getStochOpt().getNumOfTrials() > 1) {
            errorMessage = null;
        }
    } else if (simulation.getScanCount() > Simulation.MAX_LIMIT_SCAN_JOBS) {
        errorMessage = "Errors in Simulation: '" + simulation.getName() + "'!\n" + "The simulation generates too many simulations (" + simulation.getScanCount() + ") required for parameter scan, which has exceeded our limit.\n\n" + "maximum number of parameter sets is: " + Simulation.MAX_LIMIT_SCAN_JOBS + " \n" + "suggested limit for number of parameter sets is: " + Simulation.WARNING_SCAN_JOBS + " \n" + "Try choosing fewer parameters or reducing the size of scan for each parameter.";
        // not used for multiple stochastic run
        if (simulation.getMathDescription().isNonSpatialStoch() && solverTaskDescription.getStochOpt() != null && solverTaskDescription.getStochOpt().getNumOfTrials() > 1) {
            errorMessage = null;
        }
    } else if (solverDescription.equals(SolverDescription.SundialsPDE)) {
        if (solverTaskDescription.getOutputTimeSpec().isDefault()) {
            DefaultOutputTimeSpec dot = (DefaultOutputTimeSpec) solverTaskDescription.getOutputTimeSpec();
            int maxNumberOfSteps = dot.getKeepEvery() * dot.getKeepAtMost();
            double maximumTimeStep = solverTaskDescription.getTimeStep().getMaximumTimeStep();
            double maxSimTime = maxNumberOfSteps * maximumTimeStep;
            double endingTime = solverTaskDescription.getTimeBounds().getEndingTime();
            if (maxSimTime < endingTime) {
                errorMessage = "Errors in Simulation: '" + simulation.getName() + "'!\n" + "The maximum possible simulation time (keepEvery * maxTimestep * keepAtMost = " + maxSimTime + ") is less than simulation end time (" + endingTime + ").\n\n" + "You have chosen a variable time step solver and specified a maximum number of time steps of " + maxNumberOfSteps + " (keepEvery*keepAtMost).  " + "Actual time steps are often small, but even if all steps were at the maximum time step of " + maximumTimeStep + ", the simulation end time of " + endingTime + " would not be reached. \n\n" + "Either adjust the parameters or choose the \"Output Interval\" option.";
            }
        }
    } else if (simulation.getMathDescription().isNonSpatialStoch() && !(solverDescription.isNonSpatialStochasticSolver())) {
        // to guarantee stochastic model uses stochastic methods and deterministic model uses ODE/PDE methods.
        errorMessage = "Errors in Simulation: '" + simulation.getName() + "'!\n" + "Stochastic simulation(s) must use stochastic solver(s).\n" + solverDescription.getDisplayLabel() + " is not a stochastic solver!";
    } else if (!simulation.getMathDescription().isNonSpatialStoch() && (solverDescription.isNonSpatialStochasticSolver())) {
        errorMessage = "Errors in Simulation: '" + simulation.getName() + "'!\n" + "ODE/PDE simulation(s) must use ODE/PDE solver(s).\n" + solverDescription.getDisplayLabel() + " is not a ODE/PDE solver!";
    } else if (simulation.getSolverTaskDescription().getSolverDescription().isChomboSolver()) {
        MeshSpecification meshSpecification = simulation.getMeshSpecification();
        boolean bCellCentered = simulation.hasCellCenteredMesh();
        if (meshSpecification != null && !meshSpecification.isAspectRatioOK(1e-4, bCellCentered)) {
            errorMessage = "Non uniform spatial step is detected. This will affect the accuracy of the solution.\n\n" + "\u0394x=" + meshSpecification.getDx(bCellCentered) + "\n" + "\u0394y=" + meshSpecification.getDy(bCellCentered) + (meshSpecification.getGeometry().getDimension() < 3 ? "" : "\n\u0394z=" + meshSpecification.getDz(bCellCentered));
        }
    } else {
        errorMessage = null;
    }
    if (errorMessage != null) {
        DialogUtils.showErrorDialog(parent, errorMessage);
        return false;
    } else if (simulation.getSolverTaskDescription().getSolverDescription().isChomboSolver()) {
        Geometry geometry = simulation.getMathDescription().getGeometry();
        ChomboMeshValidator meshValidator = new ChomboMeshValidator(geometry, simulation.getSolverTaskDescription().getChomboSolverSpec());
        ChomboMeshRecommendation chomboMeshRecommendation = meshValidator.computeMeshSpecs();
        boolean bValid = chomboMeshRecommendation.validate();
        if (!bValid) {
            String option = DialogUtils.showWarningDialog(parent, "Error", chomboMeshRecommendation.getErrorMessage(), chomboMeshRecommendation.getDialogOptions(), ChomboMeshRecommendation.optionClose);
            if (ChomboMeshRecommendation.optionSuggestions.equals(option)) {
                DialogUtils.showInfoDialog(parent, ChomboMeshRecommendation.optionSuggestions, chomboMeshRecommendation.getMeshSuggestions());
            }
        }
        return bValid;
    } else {
        String warningMessage = null;
        // don't check warning message for stochastic multiple trials, let it run.
        if (simulation.getMathDescription().isNonSpatialStoch() && simulation.getSolverTaskDescription().getStochOpt() != null && simulation.getSolverTaskDescription().getStochOpt().getNumOfTrials() > 1) {
            return true;
        }
        // 
        if (expectedNumTimePoints > warningTimepoints) {
            warningMessage = "Warnings from Simulation: '" + simulation.getName() + "'!\n" + "The simulation has large number of saving timepoints (" + expectedNumTimePoints + "), suggested saving timepoints limits are:\n" + "     " + Simulation.WARNING_NON_SPATIAL_TIMEPOINTS + " for compartmental simulations\n" + "     " + Simulation.WARNING_SPATIAL_TIMEPOINTS + " for spatial simulations\n" + "Try saving fewer timepoints";
        } else if (expectedSizeBytes > warningSizeBytes) {
            warningMessage = "Warnings from Simulation: '" + simulation.getName() + "'!\n" + "The simulation has large result dataset (" + (expectedSizeBytes / 1000000L) + "MB), suggested size limits are:\n" + "     " + Simulation.WARNING_0DE_MEGABYTES + " MB for compartmental ODE simulations\n" + "     " + Simulation.WARNING_PDE_MEGABYTES + " MB for spatial simulations\n" + "     " + Simulation.WARNING_STOCH_MEGABYTES + " MB for compartmental stochastic simulations\n" + "Try saving fewer timepoints or using a coarser mesh if spatial.";
        } else if (simulation.getScanCount() > Simulation.WARNING_SCAN_JOBS) {
            warningMessage = "Warnings from Simulation: '" + simulation.getName() + "'!\n" + "The simulation generates a large number of simulations (" + simulation.getScanCount() + ") required for parameter scan.\n" + "maximum number of parameter sets is: " + Simulation.MAX_LIMIT_SCAN_JOBS + " \n" + "suggested limit for the number of parameter sets is: " + Simulation.WARNING_SCAN_JOBS + " \n" + "Try choosing fewer parameters or reducing the size of scan for each parameter.";
        }
        if (solverDescription.equals(SolverDescription.SundialsPDE)) {
            if (solverTaskDescription.getErrorTolerance().getRelativeErrorTolerance() > 1e-4) {
                String msg = "Warnings from Simulation: '" + simulation.getName() + "'!\n" + "Warning: it is not reccomended to use a relative tolerance that is greater than \n1e-4 for " + solverDescription.getDisplayLabel() + ".";
                warningMessage = warningMessage == null ? msg : warningMessage + "\n\n" + msg;
            }
        } else if (solverDescription.isSemiImplicitPdeSolver()) {
            if (solverTaskDescription.getErrorTolerance().getRelativeErrorTolerance() > 1e-8) {
                String msg = "Warnings from Simulation: '" + simulation.getName() + "'!\n" + "Warning: it is not reccomended to use a relative tolerance that is greater than \n1e-8 for " + solverDescription.getDisplayLabel() + ".";
                warningMessage = warningMessage == null ? msg : warningMessage + "\n\n" + msg;
            }
        }
        MeshSpecification meshSpecification = simulation.getMeshSpecification();
        boolean bCellCentered = simulation.hasCellCenteredMesh();
        if (meshSpecification != null && !meshSpecification.isAspectRatioOK(bCellCentered)) {
            warningMessage = (warningMessage == null ? "" : warningMessage + "\n\n") + "Non uniform spatial step is detected. This might affect the accuracy of the solution.\n\n" + "\u0394x=" + meshSpecification.getDx(bCellCentered) + "\n" + "\u0394y=" + meshSpecification.getDy(bCellCentered) + (meshSpecification.getGeometry().getDimension() < 3 ? "" : "\n\u0394z=" + meshSpecification.getDz(bCellCentered));
        }
        if (warningMessage != null) {
            String result = DialogUtils.showWarningDialog(parent, warningMessage + "\n\nDo you want to continue anyway?", new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
            return (result != null && result.equals(UserMessage.OPTION_OK));
        } else {
            return true;
        }
    }
}

Example 17 with SimulationSymbolTable

use of cbit.vcell.solver.SimulationSymbolTable in project vcell by virtualcell.

the class FRAPStudyPanel method refreshPDEDisplay.

protected void refreshPDEDisplay(DisplayChoice choice) throws Exception {
    Simulation sim = null;
    FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
    if (fStudy == null || fStudy.getBioModel() == null || fStudy.getBioModel().getSimulations() == null || fStudy.getBioModel().getSimulations().length < 1) {
        return;
    }
    sim = fStudy.getBioModel().getSimulations()[0];
    FieldFunctionArguments[] fieldFunctionArgs = FieldUtilities.getFieldFunctionArguments(sim.getMathDescription());
    FieldDataIdentifierSpec[] fieldDataIdentifierSpecs = new FieldDataIdentifierSpec[fieldFunctionArgs.length];
    for (int i = 0; i < fieldDataIdentifierSpecs.length; i++) {
        fieldDataIdentifierSpecs[i] = new FieldDataIdentifierSpec(fieldFunctionArgs[i], fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier());
    }
    PDEDataViewer flourViewer = getFlourDataViewer();
    PDEDataManager dataManager = null;
    if (choice == DisplayChoice.EXTTIMEDATA) {
        flourViewer.setSimulation(null);
        flourViewer.setPdeDataContext(null);
        flourViewer.setDataIdentifierFilter(new DataIdentifierFilter() {

            private String ALL_DATAIDENTIFIERS = "All";

            private String EXP_NORM_FLUOR = "Exp. Norm. Fluor";

            private String SIM_NORM_FLUOR = "Sim. Norm. Fluor";

            private String DEFAULT_VIEW = "Default View (more...)";

            private String[] filterSetNames = new String[] { ALL_DATAIDENTIFIERS, EXP_NORM_FLUOR, SIM_NORM_FLUOR, DEFAULT_VIEW };

            public boolean accept(String filterSetName, List<AnnotatedFunction> myFunctionList, DataIdentifier dataidentifier) {
                if (filterSetName.equals(ALL_DATAIDENTIFIERS)) {
                    return true;
                } else if (filterSetName.equals(EXP_NORM_FLUOR)) {
                    return dataidentifier.getName().indexOf(NORM_FLUOR_VAR) != -1;
                } else if (filterSetName.equals(SIM_NORM_FLUOR)) {
                    boolean a = (dataidentifier.getName().indexOf(REACTION_RATE_PREFIX) == -1) && ((dataidentifier.getName().indexOf(FRAPStudy.SPECIES_NAME_PREFIX_COMBINED) != -1) || (dataidentifier.getName().indexOf(FRAPStudy.SPECIES_NAME_PREFIX_IMMOBILE) != -1) || (dataidentifier.getName().indexOf(FRAPStudy.SPECIES_NAME_PREFIX_MOBILE) != -1) || (dataidentifier.getName().indexOf(FRAPStudy.SPECIES_NAME_PREFIX_SLOW_MOBILE) != -1));
                    return a;
                } else if (filterSetName.equals(DEFAULT_VIEW)) {
                    boolean a = (dataidentifier.getName().indexOf(REACTION_RATE_PREFIX) == -1) && ((dataidentifier.getName().indexOf(NORM_FLUOR_VAR) != -1) || (dataidentifier.getName().indexOf(NORM_SIM_VAR) != -1));
                    return a;
                }
                throw new IllegalArgumentException("DataIdentifierFilter: Unknown filterSetName " + filterSetName);
            }

            public String getDefaultFilterName() {
                return DEFAULT_VIEW;
            }

            public String[] getFilterSetNames() {
                return filterSetNames;
            }

            public boolean isAcceptAll(String filterSetName) {
                return filterSetName.equals(ALL_DATAIDENTIFIERS);
            }

            @Override
            public void setPostProcessingMode(boolean bPostProcessingMode) {
            // TODO Auto-generated method stub
            }

            @Override
            public boolean isPostProcessingMode() {
                // TODO Auto-generated method stub
                return false;
            }

            @Override
            public ArrayList<DataIdentifier> accept(String filterSetName, List<AnnotatedFunction> myFunctionList, DataIdentifier[] dataidentifiers) {
                if (filterSetName.equals(DEFAULT_VIEW)) {
                    ArrayList<DataIdentifier> dataIds = new ArrayList<>();
                    if (dataidentifiers != null) {
                        for (int i = 0; i < dataidentifiers.length; i++) {
                            dataIds.add(dataidentifiers[i]);
                        }
                    }
                    return dataIds;
                }
                throw new RuntimeException("Not Implemented for FRAP");
            }
        });
        ExternalDataIdentifier timeSeriesExtDataID = fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier();
        ExternalDataIdentifier maskExtDataID = fStudy.getRoiExternalDataInfo().getExternalDataIdentifier();
        // add sim
        int jobIndex = 0;
        SimulationJob simJob = new SimulationJob(sim, jobIndex, fieldDataIdentifierSpecs);
        // add function to display normalized fluorence data
        Norm_Exp_Fluor = new Expression(Norm_Exp_Fluor_Str);
        SimulationSymbolTable simSymbolTable = simJob.getSimulationSymbolTable();
        if (// one diffusing component
        simSymbolTable.getVariable(FRAPStudy.SPECIES_NAME_PREFIX_SLOW_MOBILE) == null) {
            Norm_Sim = new Expression(Norm_Sim_One_Diff_Str);
        } else // two diffusing components
        {
            Norm_Sim = new Expression(Norm_Sim_Two_Diff_Str);
        }
        AnnotatedFunction[] func = { new AnnotatedFunction(NORM_FLUOR_VAR, Norm_Exp_Fluor, null, null, VariableType.VOLUME, FunctionCategory.OLDUSERDEFINED), new AnnotatedFunction(NORM_SIM_VAR, Norm_Sim, null, null, VariableType.VOLUME, FunctionCategory.OLDUSERDEFINED) };
        VCDataIdentifier[] dataIDs = new VCDataIdentifier[] { timeSeriesExtDataID, maskExtDataID, simJob.getVCDataIdentifier() };
        VCDataIdentifier vcDataId = new MergedDataInfo(LocalWorkspace.getDefaultOwner(), dataIDs, FRAPStudy.VFRAP_DS_PREFIX);
        outputContext = new OutputContext(func);
        dataManager = new PDEDataManager(outputContext, getLocalWorkspace().getVCDataManager(), vcDataId);
        ClientPDEDataContext pdeDataContext = new ClientPDEDataContext(dataManager);
        pdeDataContext.refreshIdentifiers();
        flourViewer.setSimulation(sim);
        flourViewer.setPdeDataContext(pdeDataContext);
        SimulationModelInfo simModelInfo = new SimulationWorkspaceModelInfo(fStudy.getBioModel().getSimulationContext(sim), sim.getName());
        flourViewer.setSimulationModelInfo(simModelInfo);
        getLocalWorkspace().getDataSetControllerImpl().addDataJobListener(flourViewer);
        ((VirtualFrapWindowManager) flourViewer.getDataViewerManager()).setLocalWorkSpace(getLocalWorkspace());
        // do now show post data processing for VFRAP
        flourViewer.setPostProcessingPanelVisible(false);
        flourViewer.repaint();
    }
}

Example 18 with SimulationSymbolTable

use of cbit.vcell.solver.SimulationSymbolTable in project vcell by virtualcell.

the class MathOverridesTableModel method updateKeys.

private void updateKeys(MathOverrides mathOverrides) {
    fieldKeys = new String[0];
    if (mathOverrides != null) {
        if (getEditable()) {
            // show all
            fieldKeys = mathOverrides.getAllConstantNames();
        } else {
            // summary, show only overriden ones
            fieldKeys = mathOverrides.getOverridenConstantNames();
        }
        Arrays.sort(fieldKeys);
        simSymbolTable = new SimulationSymbolTable(getMathOverrides().getSimulation(), 0);
    }
}

Example 19 with SimulationSymbolTable

use of cbit.vcell.solver.SimulationSymbolTable 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 SimulationSymbolTable

use of cbit.vcell.solver.SimulationSymbolTable in project vcell by virtualcell.

the class FiniteVolumeFileWriter method getDiscontinuityTimes.

private void getDiscontinuityTimes(Vector<Discontinuity> discontinuities, TreeSet<Double> discontinuityTimes) throws ExpressionException, MathException {
    Simulation simulation = simTask.getSimulation();
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    for (Discontinuity discontinuity : discontinuities) {
        Expression rfexp = discontinuity.getRootFindingExp();
        rfexp.bindExpression(simSymbolTable);
        rfexp = simSymbolTable.substituteFunctions(rfexp).flatten();
        String[] symbols = rfexp.getSymbols();
        if (symbols == null) {
            continue;
        }
        boolean bHasT = false;
        for (String symbol : symbols) {
            if (symbol.equals(ReservedVariable.TIME.getName())) {
                bHasT = true;
            }
        }
        if (bHasT) {
            if (symbols.length != 1) {
                throw new ExpressionException(simulation.getSolverTaskDescription().getSolverDescription().getDisplayLabel() + ": time discontinuity " + discontinuity.getDiscontinuityExp().infix() + " can only be a function of time");
            }
            Expression deriv = rfexp.differentiate(ReservedVariable.TIME.getName());
            // we don't allow 5t < 3
            double d = deriv.evaluateConstant();
            if (d != 1 && d != -1) {
                throw new ExpressionException(simulation.getSolverTaskDescription().getSolverDescription().getDisplayLabel() + ": time discontinuity " + discontinuity.getDiscontinuityExp().infix() + " is not allowed.");
            }
            rfexp.substituteInPlace(new Expression(ReservedVariable.TIME.getName()), new Expression(0));
            rfexp.flatten();
            double st = Math.abs(rfexp.evaluateConstant());
            discontinuityTimes.add(st);
        }
    }
/*Simulation simulation = simTask.getSimulation();
	SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
	MonadicFunctionRootFinder rootFinder = new Bisection();
	
	for (Discontinuity discontinuity : discontinuities) {
		Expression rfexp = discontinuity.getRootFindingExp();
		rfexp.bindExpression(simSymbolTable);
		rfexp = simSymbolTable.substituteFunctions(rfexp).flatten();
		String[] symbols = rfexp.getSymbols();
		boolean bHasT = false;
		for (String symbol : symbols) {
			if (symbol.equals(ReservedVariable.TIME.getName())) {
				bHasT = true;
			}
		}
		if (bHasT) {
			if (symbols.length != 1) {
				System.err.println(simulation.getSolverTaskDescription().getSolverDescription().getDisplayLabel() 
						+  ": discontinuity " + discontinuity.getDiscontinuityExp().infix() + " is not just a function of time, not handled properly by solver");
				continue;
			}
		
			double startTime = simulation.getSolverTaskDescription().getTimeBounds().getStartingTime();
			double endTime = simulation.getSolverTaskDescription().getTimeBounds().getEndingTime();
			findAllRoots(rfexp,startTime,endTime,rootFinder,discontinuityTimes,false);
		}
	} ---------------------------------JIM's CODE COMMENTTED FOR FUTURE DEVELOPMENT*/
}