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

Example 41 with VCSimulationDataIdentifier

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

the class SimulationData method getChomboFiles.

@Override
public ChomboFiles getChomboFiles() throws IOException, XmlParseException, ExpressionException {
    if (chomboFileIterationIndices == null) {
        throw new RuntimeException("SimulationData.chomboFileIterationIndices is null, can't process Chombo HDF5 files");
    }
    if (!(getVcDataId() instanceof VCSimulationDataIdentifier)) {
        throw new RuntimeException("SimulationData.getVcDataId() is not a VCSimulationDataIdentifier (type is " + getVcDataId().getClass().getName() + "), can't process chombo HDF5 files");
    }
    VCSimulationDataIdentifier vcDataID = (VCSimulationDataIdentifier) getVcDataId();
    String expectedMeshfile = vcDataID.getID() + ".mesh.hdf5";
    File meshFile = amplistorHelper.getFile(expectedMeshfile);
    ChomboFiles chomboFiles = new ChomboFiles(vcDataID.getSimulationKey(), vcDataID.getJobIndex(), meshFile);
    String simtaskFilePath = vcDataID.getID() + "_0.simtask.xml";
    File simtaskFile = amplistorHelper.getFile(simtaskFilePath);
    if (!simtaskFile.exists()) {
        throw new RuntimeException("Chombo dataset mission .simtask.xml file, please rerun");
    }
    String xmlString = FileUtils.readFileToString(simtaskFile);
    SimulationTask simTask = XmlHelper.XMLToSimTask(xmlString);
    if (!simTask.getSimulation().getSolverTaskDescription().getChomboSolverSpec().isSaveChomboOutput() && !simTask.getSimulation().getSolverTaskDescription().isParallel()) {
        throw new RuntimeException("Export of Chombo simulations to VTK requires chombo data, select 'Chombo' data format in simulation solver options and rerun simulation.");
    }
    CartesianMeshChombo chomboMesh = (CartesianMeshChombo) mesh;
    FeaturePhaseVol[] featurePhaseVols = chomboMesh.getFeaturePhaseVols();
    for (int timeIndex : chomboFileIterationIndices) {
        if (featurePhaseVols == null) {
            // for old format which doesn't have featurephasevols, we need to try ivol up to 20 for each feature
            Enumeration<SubDomain> subdomainEnum = simTask.getSimulation().getMathDescription().getSubDomains();
            while (subdomainEnum.hasMoreElements()) {
                SubDomain subDomain = subdomainEnum.nextElement();
                if (subDomain instanceof CompartmentSubDomain) {
                    for (int ivol = 0; ivol < 20; ++ivol) {
                        // can be many vol, let us try 20
                        findChomboFeatureVolFile(chomboFiles, vcDataID, subDomain.getName(), ivol, timeIndex);
                    }
                }
            }
        } else {
            // note: some feature + ivol doesn't have a file if there are no variables defined in that feature
            for (FeaturePhaseVol pfv : featurePhaseVols) {
                findChomboFeatureVolFile(chomboFiles, vcDataID, pfv.feature, pfv.ivol, timeIndex);
            }
        }
    }
    return chomboFiles;
}

Example 42 with VCSimulationDataIdentifier

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

the class VtkMeshGenerator method generateVtkMeshes.

private void generateVtkMeshes(User owner, KeyValue simKey, int jobIndex) throws DataAccessException, IOException {
    VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simKey, owner);
    VCSimulationDataIdentifier vcdataID = new VCSimulationDataIdentifier(vcSimID, jobIndex);
    Cachetable cacheTable = new Cachetable(MessageConstants.MINUTE_IN_MS * 20);
    DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(cacheTable, new File(PropertyLoader.getRequiredProperty(PropertyLoader.primarySimDataDirInternalProperty)), new File(PropertyLoader.getRequiredProperty(PropertyLoader.secondarySimDataDirInternalProperty)));
    ExportServiceImpl exportServiceImpl = new ExportServiceImpl();
    DataServerImpl dataServerImpl = new DataServerImpl(dataSetControllerImpl, exportServiceImpl);
    // @SuppressWarnings("unused")
    if (!dataSetControllerImpl.getIsMovingBoundary(vcdataID)) {
        // 
        // precompute single static vtk mesh
        // 
        VtuFileContainer vtuFileContainer = dataServerImpl.getEmptyVtuMeshFiles(owner, vcdataID, 0);
    } else {
        // 
        // precompute static vtk mesh for each saved time point
        // 
        double[] times = dataServerImpl.getDataSetTimes(owner, vcdataID);
        for (int i = 0; i < times.length; i++) {
            VtuFileContainer vtuFileContainer = dataServerImpl.getEmptyVtuMeshFiles(owner, vcdataID, i);
        }
    }
}

Example 43 with VCSimulationDataIdentifier

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

the class DataSetControllerImplTest method setUp.

@Before
public void setUp() throws Exception {
    System.setProperty(PropertyLoader.installationRoot, new File("../").getAbsolutePath());
    String message = "installation directory is " + PropertyLoader.getRequiredProperty(PropertyLoader.installationRoot);
    ResourceUtil.setNativeLibraryDirectory();
    NativeLib.HDF5.load();
    Cachetable cachetable = new Cachetable(2000);
    File resourcesDirectory = new File("src/test/resources/simdata");
    File primarydir = resourcesDirectory;
    File secondarydir = resourcesDirectory;
    KeyValue simKey = new KeyValue("1771409053");
    VCSimulationIdentifier vcSimId = new VCSimulationIdentifier(new KeyValue("1771409053"), User.tempUser);
    vcDataIdentifier = new VCSimulationDataIdentifier(vcSimId, 0);
    dsc = new DataSetControllerImpl(cachetable, primarydir, secondarydir);
}

Example 44 with VCSimulationDataIdentifier

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

the class NagiosVCellCheck method checkVCell.

private static String checkVCell(VCELL_CHECK_LEVEL checkLevel, String rmiHostName, int rmiPort, String rmiBootstrapStubName, String vcellNagiosPassword, int warningTimeout, int criticalTimeout) throws Exception {
    long startTime = System.currentTimeMillis();
    SimulationStatusPersistent lastSimStatus = null;
    if (rmiHostName == null || rmiPort == -1) {
        throw new UnexpectedTestStateException("Host name/ip and rmiPort required for testing, rmihostname=" + rmiHostName + " rmiport=" + rmiPort);
    }
    String rmiUrl = "//" + rmiHostName + ":" + rmiPort + "/" + rmiBootstrapStubName;
    VCellBootstrap vcellBootstrap = null;
    try {
        vcellBootstrap = (VCellBootstrap) Naming.lookup(rmiUrl);
    } catch (Exception e) {
        throw new UnexpectedTestStateException("Error during bootstrap lookup, " + e.getClass().getSimpleName() + " " + e.getMessage());
    }
    if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.CONNECT_1.ordinal()) {
        if (vcellNagiosPassword == null) {
            throw new UnexpectedTestStateException("vcellNagios Password required for " + VCELL_CHECK_LEVEL.CONNECT_1.toString() + " and above");
        }
        VCellConnection vcellConnection = vcellBootstrap.getVCellConnection(new UserLoginInfo("vcellNagios", new DigestedPassword(vcellNagiosPassword)));
        if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.INFOS_2.ordinal()) {
            VCInfoContainer vcInfoContainer = vcellConnection.getUserMetaDbServer().getVCInfoContainer();
            if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.LOAD_3.ordinal()) {
                KeyValue bioModelKey = null;
                final String testModelName = "Solver Suite 5.1 (BETA only ode)";
                for (BioModelInfo bioModelInfo : vcInfoContainer.getBioModelInfos()) {
                    if (bioModelInfo.getVersion().getName().equals(testModelName)) {
                        bioModelKey = bioModelInfo.getVersion().getVersionKey();
                        break;
                    }
                }
                BigString bioModelXML = vcellConnection.getUserMetaDbServer().getBioModelXML(bioModelKey);
                BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
                bioModel.refreshDependencies();
                if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.DATA_4.ordinal()) {
                    final String testSimContextName = "non-spatial ODE";
                    SimulationContext simulationContext = bioModel.getSimulationContext(testSimContextName);
                    final String testSimName = "Copy of combined ida/cvode";
                    Simulation simulation = simulationContext.getSimulation(testSimName);
                    if (simulation == null) {
                        throw new UnexpectedTestStateException("Couldn't find sim '" + testSimName + "' for " + checkLevel.toString());
                    }
                    VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(simulation.getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), 0);
                    ArrayList<AnnotatedFunction> outputFunctionsList = simulationContext.getOutputFunctionContext().getOutputFunctionsList();
                    OutputContext outputContext = new OutputContext(outputFunctionsList.toArray(new AnnotatedFunction[outputFunctionsList.size()]));
                    double[] times = vcellConnection.getDataSetController().getDataSetTimes(vcSimulationDataIdentifier);
                    ODESimData odeSimData = vcellConnection.getDataSetController().getODEData(vcSimulationDataIdentifier);
                    // SimDataBlock simDataBlock = vcellConnection.getDataSetController().getSimDataBlock(outputContext, vcSimulationDataIdentifier, "RanC_cyt",times[times.length-1]);
                    if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.RUN_5.ordinal()) {
                        KeyValue copy1Key = null;
                        KeyValue copy2Key = null;
                        try {
                            if (simulationContext.getSimulations().length != 1) {
                                throw new UnexpectedTestStateException("Expecting only 1 sim to be copied for " + checkLevel.toString());
                            }
                            SimulationStatusPersistent simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(simulation.getVersion().getVersionKey());
                            if (!simulationStatus.isCompleted()) {
                                throw new UnexpectedTestStateException("Expecting completed sim to copy for " + checkLevel.toString());
                            }
                            String copyModelName = testModelName + "_" + rmiHostName + "_" + rmiPort;
                            for (BioModelInfo bioModelInfo : vcInfoContainer.getBioModelInfos()) {
                                if (bioModelInfo.getVersion().getName().equals(copyModelName)) {
                                    throw new UnexpectedTestStateException("Messy test environment, not expecting " + copyModelName + " to exist at this point");
                                }
                            }
                            BigString copyBioModelXMLStr = vcellConnection.getUserMetaDbServer().saveBioModelAs(bioModelXML, copyModelName, null);
                            BioModel copyBioModel = XmlHelper.XMLToBioModel(new XMLSource(copyBioModelXMLStr.toString()));
                            copy1Key = copyBioModel.getVersion().getVersionKey();
                            copyBioModel.refreshDependencies();
                            Simulation copySim = copyBioModel.getSimulationContext(testSimContextName).copySimulation(copyBioModel.getSimulationContext(testSimContextName).getSimulation(testSimName));
                            final String copyTestSimName = "test";
                            copySim.setName(copyTestSimName);
                            copyBioModel.refreshDependencies();
                            copyBioModelXMLStr = new BigString(XmlHelper.bioModelToXML(copyBioModel));
                            copyBioModelXMLStr = vcellConnection.getUserMetaDbServer().saveBioModel(copyBioModelXMLStr, null);
                            copyBioModel = XmlHelper.XMLToBioModel(new XMLSource(copyBioModelXMLStr.toString()));
                            copy2Key = copyBioModel.getVersion().getVersionKey();
                            copyBioModel.refreshDependencies();
                            Simulation newSimulation = copyBioModel.getSimulationContext(testSimContextName).getSimulation(copyTestSimName);
                            simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(newSimulation.getVersion().getVersionKey());
                            if (simulationStatus != null && !simulationStatus.isNeverRan()) {
                                throw new UnexpectedTestStateException("Expecting new sim to have 'never ran' status for " + checkLevel.toString());
                            }
                            VCSimulationIdentifier newSimID = new VCSimulationIdentifier(newSimulation.getVersion().getVersionKey(), copyBioModel.getVersion().getOwner());
                            vcellConnection.getSimulationController().startSimulation(newSimID, 1);
                            lastSimStatus = simulationStatus;
                            MessageEvent[] messageEvents = null;
                            while (simulationStatus == null || (!simulationStatus.isStopped() && !simulationStatus.isCompleted() && !simulationStatus.isFailed())) {
                                Thread.sleep(200);
                                if (((System.currentTimeMillis() - startTime) / 1000) > criticalTimeout) {
                                    vcellConnection.getSimulationController().stopSimulation(newSimID);
                                    vcellConnection.getMessageEvents();
                                    break;
                                }
                                simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(newSimulation.getVersion().getVersionKey());
                                if (simulationStatus != null && !simulationStatus.toString().equals((lastSimStatus == null ? null : lastSimStatus.toString()))) {
                                    lastSimStatus = simulationStatus;
                                }
                                messageEvents = vcellConnection.getMessageEvents();
                            }
                        } finally {
                            try {
                                if (copy1Key != null) {
                                    vcellConnection.getUserMetaDbServer().deleteBioModel(copy1Key);
                                }
                            } catch (Exception e) {
                                e.printStackTrace();
                            }
                            try {
                                if (copy2Key != null) {
                                    vcellConnection.getUserMetaDbServer().deleteBioModel(copy2Key);
                                }
                            } catch (Exception e) {
                                e.printStackTrace();
                            }
                        }
                    }
                }
            }
        }
    }
    long endTime = System.currentTimeMillis();
    if (criticalTimeout != -1 && ((endTime - startTime) / 1000) > criticalTimeout) {
        throw new Exception(checkLevel.toString() + " test exceeded criticalTimeout=" + criticalTimeout + " seconds lastSimStatus=" + lastSimStatus);
    }
    if (warningTimeout != -1 && ((endTime - startTime) / 1000) > warningTimeout) {
        throw new WarningTestConditionException(checkLevel.toString() + " test exceeded warningTimeout=" + warningTimeout + " seconds lastSimStatus=" + lastSimStatus);
    }
    return vcellBootstrap.getVCellSoftwareVersion();
}

Example 45 with VCSimulationDataIdentifier

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

the class ImportImageROIsFrom2DVCellOp method importROIs.

public ImageROIs importROIs(File vcellSimLogFile, String bleachedMaskVarName, String cellSubvolumeName, String ecSubvolumeName) throws Exception {
    VCSimulationIdentifier vcSimulationIdentifier = VCellSimReader.getVCSimulationIdentifierFromVCellSimulationData(vcellSimLogFile);
    VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(vcSimulationIdentifier, 0);
    DataSetControllerImpl dataSetControllerImpl = VCellSimReader.getDataSetControllerImplFromVCellSimulationData(vcellSimLogFile);
    CartesianMesh cartesianMesh = dataSetControllerImpl.getMesh(vcSimulationDataIdentifier);
    // get rois from log file
    if (bleachedMaskVarName == null) {
        throw new RuntimeException("bleachedMathVarName not set");
    }
    double[] rawROIBleached = dataSetControllerImpl.getSimDataBlock(null, vcSimulationDataIdentifier, bleachedMaskVarName, 0).getData();
    short[] scaledCellDataShort = new short[rawROIBleached.length];
    short[] scaledBleachedDataShort = new short[rawROIBleached.length];
    short[] scaledBackgoundDataShort = new short[rawROIBleached.length];
    for (int j = 0; j < scaledCellDataShort.length; j++) {
        boolean isCell = cartesianMesh.getCompartmentSubdomainNamefromVolIndex(j).equals(cellSubvolumeName);
        boolean isBackground = cartesianMesh.getCompartmentSubdomainNamefromVolIndex(j).equals(ecSubvolumeName);
        if (isCell) {
            scaledCellDataShort[j] = 1;
        }
        if (isBackground) {
            scaledBackgoundDataShort[j] = 1;
        }
        if (rawROIBleached[j] > 0.2) {
            scaledBleachedDataShort[j] = 1;
        }
    }
    UShortImage cellImage = new UShortImage(scaledCellDataShort, cartesianMesh.getOrigin(), cartesianMesh.getExtent(), cartesianMesh.getSizeX(), cartesianMesh.getSizeY(), cartesianMesh.getSizeZ());
    UShortImage bleachedImage = new UShortImage(scaledBleachedDataShort, cartesianMesh.getOrigin(), cartesianMesh.getExtent(), cartesianMesh.getSizeX(), cartesianMesh.getSizeY(), cartesianMesh.getSizeZ());
    UShortImage backgroundImage = new UShortImage(scaledBackgoundDataShort, cartesianMesh.getOrigin(), cartesianMesh.getExtent(), cartesianMesh.getSizeX(), cartesianMesh.getSizeY(), cartesianMesh.getSizeZ());
    ROI cellROI = new ROI(cellImage, "cellROI");
    ROI bleachedROI = new ROI(bleachedImage, "bleachedROI");
    ROI backgroundROI = new ROI(backgroundImage, "backgroundROI");
    ImageROIs imageRois = new ImageROIs();
    imageRois.cellROI_2D = cellROI;
    imageRois.bleachedROI_2D = bleachedROI;
    imageRois.backgroundROI_2D = backgroundROI;
    return imageRois;
}