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

Example 21 with SimulationInfo

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

the class VCellClientDataServiceImpl method getSimsFromOpenModels.

@Override
public List<SimulationDataSetRef> getSimsFromOpenModels() {
    ArrayList<SimulationDataSetRef> simulationDataSetRefs = new ArrayList<SimulationDataSetRef>();
    for (TopLevelWindowManager windowManager : vcellClient.getMdiManager().getWindowManagers()) {
        Simulation[] simulations = null;
        VCDocument modelDocument = null;
        if (windowManager instanceof BioModelWindowManager) {
            BioModelWindowManager selectedBioWindowManager = (BioModelWindowManager) windowManager;
            BioModel bioModel = selectedBioWindowManager.getBioModel();
            simulations = bioModel.getSimulations();
            modelDocument = bioModel;
        // simOwnerCount = bioModel.getNumSimulationContexts();
        } else if (windowManager instanceof MathModelWindowManager) {
            MathModelWindowManager selectedMathWindowManager = (MathModelWindowManager) windowManager;
            MathModel mathModel = selectedMathWindowManager.getMathModel();
            simulations = mathModel.getSimulations();
            modelDocument = mathModel;
        // simOwnerCount = 1;
        }
        if (simulations != null) {
            for (Simulation simulation : simulations) {
                if (!isVtkSupported(simulation)) {
                    continue;
                }
                Origin origin = simulation.getMathDescription().getGeometry().getOrigin();
                Extent extent = simulation.getMathDescription().getGeometry().getExtent();
                SimulationInfo simInfo = simulation.getSimulationInfo();
                SimulationStatus simStatus = vcellClient.getRequestManager().getServerSimulationStatus(simInfo);
                for (int jobIndex = 0; jobIndex < simulation.getScanCount(); jobIndex++) {
                    if (simStatus != null && simStatus.getHasData()) {
                        SimulationDataSetRef simulationDataSetReference = VCellClientDataServiceImpl.createSimulationDataSetRef(simulation, modelDocument, jobIndex, false);
                        simulationDataSetRefs.add(simulationDataSetReference);
                    }
                }
            }
        }
    }
    File localSimDir = ResourceUtil.getLocalSimDir(User.tempUser.getName());
    String[] simtaskFilenames = localSimDir.list((dir, name) -> (name.endsWith(".simtask.xml")));
    for (String simtaskFilename : simtaskFilenames) {
        try {
            SimulationTask simTask = XmlHelper.XMLToSimTask(org.apache.commons.io.FileUtils.readFileToString(new File(localSimDir, simtaskFilename)));
            VCDocument modelDocument = null;
            SimulationDataSetRef simulationDataSetReference = VCellClientDataServiceImpl.createSimulationDataSetRef(simTask.getSimulation(), modelDocument, simTask.getSimulationJob().getJobIndex(), true);
            simulationDataSetRefs.add(simulationDataSetReference);
        } catch (ExpressionException | XmlParseException | IOException e) {
            e.printStackTrace();
        }
    }
    return simulationDataSetRefs;
}

Example 22 with SimulationInfo

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

the class TestingFrameworkWindowPanel method getUserSelectedSimulationInfo.

private TFGenerateReport.VCDocumentAndSimInfo getUserSelectedSimulationInfo() throws Exception {
    final String CANCEL_STRING = "Cancel";
    final String BM_STRING = "BioModel";
    final String MM_STRING = "MathModel";
    String result = PopupGenerator.showWarningDialog(this, "Choose Reference Model Type.", new String[] { BM_STRING, MM_STRING, CANCEL_STRING }, CANCEL_STRING);
    if (result == null || result.equals(CANCEL_STRING)) {
        throw UserCancelException.CANCEL_GENERIC;
    }
    VCDocumentInfo userDefinedRegrRefModel = null;
    VCDocument vcDocument = null;
    if (result.equals(BM_STRING)) {
        userDefinedRegrRefModel = getTestingFrameworkWindowManager().getRequestManager().selectBioModelInfo(getTestingFrameworkWindowManager());
        vcDocument = getTestingFrameworkWindowManager().getRequestManager().getDocumentManager().getBioModel(userDefinedRegrRefModel.getVersion().getVersionKey());
    } else {
        userDefinedRegrRefModel = getTestingFrameworkWindowManager().getRequestManager().selectMathModelInfo(getTestingFrameworkWindowManager());
        vcDocument = getTestingFrameworkWindowManager().getRequestManager().getDocumentManager().getMathModel(userDefinedRegrRefModel.getVersion().getVersionKey());
    }
    SimulationInfo simInfo = getTestingFrameworkWindowManager().getUserSelectedRefSimInfo(getTestingFrameworkWindowManager().getRequestManager(), userDefinedRegrRefModel);
    TFGenerateReport.VCDocumentAndSimInfo vcDocumentAndsimInfo = new TFGenerateReport.VCDocumentAndSimInfo(simInfo, vcDocument);
    return vcDocumentAndsimInfo;
}

Example 23 with SimulationInfo

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

the class TestingFrmwkTreeModel method createTestCaseSubTree.

/**
 * Insert the method's description here.
 * Creation date: (11/28/00 1:06:51 PM)
 * @return cbit.vcell.desktop.BioModelNode
 * @param docManager cbit.vcell.clientdb.DocumentManager
 */
private BioModelNode createTestCaseSubTree(TestCaseNew testCase) throws DataAccessException {
    // 
    // add 'test case' node
    // 
    BioModelNode testCaseNode = new BioModelNode(testCase, true);
    TestCriteriaNew[] tCriteria = testCase.getTestCriterias();
    // Sort
    if (tCriteria != null && tCriteria.length > 0) {
        java.util.Arrays.sort(tCriteria, new java.util.Comparator<TestCriteriaNew>() {

            public int compare(TestCriteriaNew tc1, TestCriteriaNew tc2) {
                return tc1.getSimInfo().getVersion().getName().compareTo(tc2.getSimInfo().getVersion().getName());
            }

            public boolean equals(Object obj) {
                return false;
            }
        });
        // 
        // False => sim has not been run; True => for a regression test, the ref SimInfo is not set.
        boolean bRefSimNull = false;
        for (int t = 0; t < tCriteria.length; t += 1) {
            TestCriteriaNew tcInfo = tCriteria[t];
            BioModelNode simInfoNode = new BioModelNode(tcInfo, true);
            String tcInfoStr = null;
            if (tcInfo != null) {
                tcInfoStr = "TestCriteria : LimitAbsError = " + tcInfo.getMaxAbsError() + "; LimitRelError = " + tcInfo.getMaxRelError() + "; ";
                if (testCase.getType().equals(TestCaseNew.REGRESSION)) {
                    if (tcInfo.getRegressionSimInfo() != null) {
                        SimulationInfo refSimInfo = tcInfo.getRegressionSimInfo();
                        if (refSimInfo != null) {
                            if (tcInfo instanceof TestCriteriaNewMathModel) {
                                tcInfoStr = tcInfoStr + "MathModel : " + ((TestCriteriaNewMathModel) tcInfo).getRegressionMathModelInfo().getVersion().getName() + "; ";
                                tcInfoStr = tcInfoStr + "SimInfo : " + refSimInfo.getName();
                            } else if (tcInfo instanceof TestCriteriaNewBioModel) {
                                tcInfoStr = tcInfoStr + "BioModel : " + ((TestCriteriaNewBioModel) tcInfo).getRegressionBioModelInfo().getVersion().getName() + "; ";
                                tcInfoStr = tcInfoStr + "SimInfo : " + refSimInfo.getName();
                            }
                        }
                    } else {
                        tcInfoStr = tcInfoStr + " REFERENCE SIMULATION NOT SET YET";
                        bRefSimNull = true;
                    }
                }
                BioModelNode testCriteriaNode = new BioModelNode(tcInfoStr, false);
                simInfoNode.add(testCriteriaNode);
            }
            // Add sim results if present (by adding the reportInfo subtree ...)
            BioModelNode reportInfoNode = createSimulationSubTree(tcInfo, simInfoNode, bRefSimNull);
            if (reportInfoNode != null) {
                simInfoNode.add(reportInfoNode);
            }
            testCaseNode.add(simInfoNode);
        }
    }
    return testCaseNode;
}

Example 24 with SimulationInfo

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

the class CheckBeforeDelete method checkLostResults.

/**
 * Insert the method's description here.
 * Creation date: (6/1/2004 3:44:03 PM)
 * @return cbit.vcell.solver.SolverResultSetInfo[]
 * @param mathmodel cbit.vcell.mathmodel.Mathmodel
 */
private Simulation[] checkLostResults(MathModel oldMathmodel, MathModel newlySavedMathmodel, cbit.vcell.clientdb.DocumentManager documentManager, Simulation[] submittedSimulations) throws Exception {
    // 
    // before deleting old version, prompt user if old simulation results will not be availlable in new edition
    // 
    Vector<Simulation> lostResultsSimulationList = new Vector<Simulation>();
    Simulation[] oldSimulations = oldMathmodel.getSimulations();
    for (int i = 0; i < oldSimulations.length; i++) {
        Simulation oldSimulation = oldSimulations[i];
        // SolverResultSetInfo rsInfo = null;
        SimulationStatus simStatus = null;
        SimulationInfo oldSimInfo = oldSimulation.getSimulationInfo();
        if (oldSimInfo != null) {
            // 
            // we need to ask for previous sim results (here we need possible translation to ask for parent's results).
            // 
            simStatus = documentManager.getServerSimulationStatus(oldSimInfo.getAuthoritativeVCSimulationIdentifier());
        }
        if (simStatus != null && simStatus.getHasData()) {
            // 
            // results exist in old version (the Mathmodel to be deleted) for SimulationInfo "oldSimInfo"
            // Users should be warned when they are going to loose any simulation results in any unexpected way.
            // 
            // WARN if the lost data is because new simulation is not mathematically equivalent to old edition
            // (different MathDescription key)
            // 
            // IGNORE if the lost data is from edits of a Simulation only (same MathDescription)
            // (same MathDescription key, different Simulation key)
            // 
            // IGNORE if Simulation has been deleted
            // (Simulation not found in current Mathmodel)
            // 
            // IGNORE if Simulation has been submitted for running
            // 
            boolean bDataInNewEdition = false;
            Simulation[] newSimulations = newlySavedMathmodel.getSimulations();
            Simulation correspondingSimulation = null;
            for (int j = 0; j < newSimulations.length; j++) {
                if (newSimulations[j].getName().equals(oldSimulation.getName())) {
                    correspondingSimulation = newSimulations[j];
                    if (correspondingSimulation.getKey().equals(oldSimulation.getKey())) {
                        // 
                        // exactly same simulation (same key), so no lost data
                        // 
                        bDataInNewEdition = true;
                    } else if (correspondingSimulation.getSimulationVersion().getParentSimulationReference() != null) {
                        // 
                        // new simulation changed but points to same results
                        // 
                        bDataInNewEdition = true;
                    }
                    break;
                }
            }
            if (!bDataInNewEdition && correspondingSimulation != null) {
                // 
                // result set (for "rsInfo") will be lost, should we ignore this fact?
                // 
                boolean bIgnore = false;
                // 
                // ignore if only Simulation has been edited (same MathDescription)
                // 
                MathDescription mdCorr = correspondingSimulation.getMathDescription();
                MathDescription mdOld = oldSimulation.getMathDescription();
                if (mdCorr.getKey().equals(mdOld.getKey())) {
                    bIgnore = true;
                }
                // 
                for (int j = 0; submittedSimulations != null && j < submittedSimulations.length; j++) {
                    if (correspondingSimulation.getName().equals(submittedSimulations[j].getName())) {
                        bIgnore = true;
                    }
                }
                // 
                if (!bIgnore) {
                    lostResultsSimulationList.add(correspondingSimulation);
                }
            }
        }
    }
    return (Simulation[]) BeanUtils.getArray(lostResultsSimulationList, Simulation.class);
}

Example 25 with SimulationInfo

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

the class RunSims method run.

/**
 * Insert the method's description here.
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
public void run(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    DocumentWindowManager documentWindowManager = (DocumentWindowManager) hashTable.get(CommonTask.DOCUMENT_WINDOW_MANAGER.name);
    ClientSimManager clientSimManager = (ClientSimManager) hashTable.get("clientSimManager");
    // DocumentManager documentManager = (DocumentManager)hashTable.get(CommonTask.DOCUMENT_MANAGER.name);
    JobManager jobManager = (JobManager) hashTable.get("jobManager");
    Simulation[] simulations = (Simulation[]) hashTable.get("simulations");
    Hashtable<Simulation, Throwable> failures = new Hashtable<Simulation, Throwable>();
    if (simulations != null && simulations.length > 0) {
        // we need to get the new ones if a save occurred...
        if (hashTable.containsKey(SaveDocument.DOC_KEY)) {
            VCDocument savedDocument = (VCDocument) hashTable.get(SaveDocument.DOC_KEY);
            Simulation[] allSims = null;
            if (savedDocument instanceof BioModel) {
                allSims = ((BioModel) savedDocument).getSimulations();
            } else if (savedDocument instanceof MathModel) {
                allSims = ((MathModel) savedDocument).getSimulations();
            }
            Vector<Simulation> v = new Vector<Simulation>();
            for (int i = 0; i < simulations.length; i++) {
                for (int j = 0; j < allSims.length; j++) {
                    if (simulations[i].getName().equals(allSims[j].getName())) {
                        v.add(allSims[j]);
                        break;
                    }
                }
            }
            simulations = (Simulation[]) BeanUtils.getArray(v, Simulation.class);
        }
        for (Simulation sim : simulations) {
            try {
                int dimension = sim.getMathDescription().getGeometry().getDimension();
                if (clientSimManager.getSimulationStatus(sim).isCompleted()) {
                    // completed
                    String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_1, sim.getName());
                    String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                    if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                        continue;
                    }
                }
                DataProcessingInstructions dataProcessingInstructions = sim.getDataProcessingInstructions();
                try {
                    if (dataProcessingInstructions != null) {
                        dataProcessingInstructions.getSampleImageFieldData(sim.getVersion().getOwner());
                    }
                } catch (Exception ex) {
                    DialogUtils.showErrorDialog(documentWindowManager.getComponent(), "Problem found in simulation '" + sim.getName() + "':\n" + ex.getMessage());
                    continue;
                }
                if (dimension > 0) {
                    MeshSpecification meshSpecification = sim.getMeshSpecification();
                    boolean bCellCentered = sim.hasCellCenteredMesh();
                    if (meshSpecification != null && !meshSpecification.isAspectRatioOK(bCellCentered)) {
                        String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_2, sim.getName(), "\u0394x=" + meshSpecification.getDx(bCellCentered) + "\n" + "\u0394y=" + meshSpecification.getDy(bCellCentered) + (dimension < 3 ? "" : "\n\u0394z=" + meshSpecification.getDz(bCellCentered)));
                        String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                        if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                            continue;
                        }
                    }
                    if (sim.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.Smoldyn)) {
                        if (!isSmoldynTimeStepOK(sim)) {
                            double s = smoldynTimestepVars.getSpatialResolution();
                            double dMax = smoldynTimestepVars.getMaxDiffusion();
                            double condn = (s * s) / (2.0 * dMax);
                            String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_3, Double.toString(s), Double.toString(dMax), Double.toString(condn));
                            DialogUtils.showErrorDialog(documentWindowManager.getComponent(), warningMessage);
                            continue;
                        }
                    }
                    // check the number of regions if the simulation mesh is coarser.
                    Geometry mathGeometry = sim.getMathDescription().getGeometry();
                    ISize newSize = meshSpecification.getSamplingSize();
                    ISize defaultSize = mathGeometry.getGeometrySpec().getDefaultSampledImageSize();
                    if (!sim.getSolverTaskDescription().getSolverDescription().isChomboSolver()) {
                        int defaultTotalVolumeElements = mathGeometry.getGeometrySurfaceDescription().getVolumeSampleSize().getXYZ();
                        int newTotalVolumeElements = meshSpecification.getSamplingSize().getXYZ();
                        if (defaultTotalVolumeElements > newTotalVolumeElements) {
                            // coarser
                            Geometry resampledGeometry = (Geometry) BeanUtils.cloneSerializable(mathGeometry);
                            GeometrySurfaceDescription geoSurfaceDesc = resampledGeometry.getGeometrySurfaceDescription();
                            geoSurfaceDesc.setVolumeSampleSize(newSize);
                            geoSurfaceDesc.updateAll();
                            if (mathGeometry.getGeometrySurfaceDescription().getGeometricRegions() == null) {
                                mathGeometry.getGeometrySurfaceDescription().updateAll();
                            }
                            int defaultNumGeometricRegions = mathGeometry.getGeometrySurfaceDescription().getGeometricRegions().length;
                            int numGeometricRegions = geoSurfaceDesc.getGeometricRegions().length;
                            if (numGeometricRegions != defaultNumGeometricRegions) {
                                String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_4, newSize.getX() + (dimension > 1 ? " x " + newSize.getY() : "") + (dimension > 2 ? " x " + newSize.getZ() : ""), sim.getName(), numGeometricRegions, defaultNumGeometricRegions);
                                String result = PopupGenerator.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                                if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                                    continue;
                                }
                            }
                        }
                        if (mathGeometry.getGeometrySpec().hasImage()) {
                            // if it's an image.
                            if (defaultSize.getX() + 1 < newSize.getX() || defaultSize.getY() + 1 < newSize.getY() || defaultSize.getZ() + 1 < newSize.getZ()) {
                                // finer
                                String defaultSizeString = (defaultSize.getX() + 1) + (dimension > 1 ? " x " + (defaultSize.getY() + 1) : "") + (dimension > 2 ? " x " + (defaultSize.getZ() + 1) : "");
                                String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_5, newSize.getX() + (dimension > 1 ? " x " + newSize.getY() : "") + (dimension > 2 ? " x " + newSize.getZ() : ""), sim.getName(), defaultSizeString, defaultSizeString);
                                String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                                if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                                    continue;
                                }
                            }
                        }
                    }
                    boolean bGiveWarning = false;
                    for (int i = 0; i < sim.getScanCount(); i++) {
                        if (sim.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.SundialsPDE)) {
                            SimulationJob simJob = new SimulationJob(sim, i, null);
                            if (simJob.getSimulationSymbolTable().hasTimeVaryingDiffusionOrAdvection()) {
                                bGiveWarning = true;
                                break;
                            }
                        }
                    }
                    if (bGiveWarning) {
                        String warningMessage = VCellErrorMessages.RunSims_6;
                        String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                        if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                            continue;
                        }
                    }
                }
                SimulationInfo simInfo = sim.getSimulationInfo();
                if (simInfo != null) {
                    // 
                    // translate to common ancestral simulation (oldest mathematically equivalent simulation)
                    // 
                    SimulationStatus simulationStatus = jobManager.startSimulation(simInfo.getAuthoritativeVCSimulationIdentifier(), sim.getScanCount());
                    // updateStatus
                    clientSimManager.updateStatusFromStartRequest(sim, simulationStatus);
                } else {
                    // this should really not happen...
                    throw new RuntimeException(">>>>>>>>>> trying to run an unsaved simulation...");
                }
            } catch (Throwable exc) {
                exc.printStackTrace(System.out);
                failures.put(sim, exc);
            }
        }
    }
    // we deal with individual request failures here, passing down only other things (that break the whole thing down) to dispatcher
    if (!failures.isEmpty()) {
        Enumeration<Simulation> en = failures.keys();
        while (en.hasMoreElements()) {
            Simulation sim = en.nextElement();
            Throwable exc = (Throwable) failures.get(sim);
            // // updateStatus
            // SimulationStatus simulationStatus = clientSimManager.updateStatusFromStartRequest(sim, true, exc.getMessage());
            // notify user
            PopupGenerator.showErrorDialog(documentWindowManager, "Failed to start simulation'" + sim.getName() + "'\n" + exc.getMessage());
        }
    }
}