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

Example 56 with VCSimulationIdentifier

use of cbit.vcell.solver.VCSimulationIdentifier 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 57 with VCSimulationIdentifier

use of cbit.vcell.solver.VCSimulationIdentifier 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;
}

Example 58 with VCSimulationIdentifier

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

the class ImportRawTimeSeriesFrom2DVCellConcentrationsOp method importRawTimeSeries.

private static ImageDataset importRawTimeSeries(File vcellSimLogFile, String fluorFunctionName, Double maxIntensity, boolean bNoise, final ClientTaskStatusSupport progressListener) throws Exception {
    VCSimulationIdentifier vcSimulationIdentifier = VCellSimReader.getVCSimulationIdentifierFromVCellSimulationData(vcellSimLogFile);
    VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(vcSimulationIdentifier, 0);
    DataSetControllerImpl dataSetControllerImpl = VCellSimReader.getDataSetControllerImplFromVCellSimulationData(vcellSimLogFile);
    final DataJobEvent[] bStatus = new DataJobEvent[] { null };
    DataJobListener dataJobListener = new DataJobListener() {

        public void dataJobMessage(DataJobEvent event) {
            bStatus[0] = event;
            if (progressListener != null) {
                progressListener.setProgress((int) (event.getProgress() / 100.0 * .75));
            }
        }
    };
    dataSetControllerImpl.addDataJobListener(dataJobListener);
    DataIdentifier[] dataIdentifiers = VCellSimReader.getDataIdentiferListFromVCellSimulationData(vcellSimLogFile, 0);
    DataIdentifier variableNameDataIdentifier = null;
    for (int i = 0; i < dataIdentifiers.length; i++) {
        if (dataIdentifiers[i].getName().equals(fluorFunctionName)) {
            variableNameDataIdentifier = dataIdentifiers[i];
            break;
        }
    }
    if (variableNameDataIdentifier == null) {
        throw new IllegalArgumentException("Variable " + fluorFunctionName + " not found.");
    }
    if (!variableNameDataIdentifier.getVariableType().equals(VariableType.VOLUME)) {
        throw new IllegalArgumentException("Variable " + fluorFunctionName + " is not VOLUME type.");
    }
    double[] times = dataSetControllerImpl.getDataSetTimes(vcSimulationDataIdentifier);
    CartesianMesh cartesianMesh = dataSetControllerImpl.getMesh(vcSimulationDataIdentifier);
    BitSet allBitset = new BitSet(cartesianMesh.getNumVolumeElements());
    allBitset.set(0, cartesianMesh.getNumVolumeElements() - 1);
    TimeSeriesJobSpec timeSeriesJobSpec = new TimeSeriesJobSpec(new String[] { fluorFunctionName }, new BitSet[] { allBitset }, times[0], 1, times[times.length - 1], true, false, VCDataJobID.createVCDataJobID(VCellSimReader.getDotUser(), true));
    TSJobResultsSpaceStats tsJobResultsSpaceStats = (TSJobResultsSpaceStats) dataSetControllerImpl.getTimeSeriesValues(null, vcSimulationDataIdentifier, timeSeriesJobSpec);
    // wait for job to finish
    while (bStatus[0] == null || bStatus[0].getEventTypeID() != DataJobEvent.DATA_COMPLETE) {
        Thread.sleep(100);
    }
    double allTimesMin = tsJobResultsSpaceStats.getMinimums()[0][0];
    double allTimesMax = allTimesMin;
    for (int i = 0; i < times.length; i++) {
        allTimesMin = Math.min(allTimesMin, tsJobResultsSpaceStats.getMinimums()[0][i]);
        allTimesMax = Math.max(allTimesMax, tsJobResultsSpaceStats.getMaximums()[0][i]);
    }
    // double SCALE_MAX = maxIntensity.doubleValue();/*Math.pow(2,16)-1;*///Scale to 16 bits
    double linearScaleFactor = 1;
    if (maxIntensity != null) {
        linearScaleFactor = maxIntensity.doubleValue() / allTimesMax;
    }
    System.out.println("alltimesMin=" + allTimesMin + " allTimesMax=" + allTimesMax + " linearScaleFactor=" + linearScaleFactor);
    UShortImage[] scaledDataImages = new UShortImage[times.length];
    Random rnd = new Random();
    int shortMax = 65535;
    // set messge to load variable
    if (progressListener != null) {
        progressListener.setMessage("Loading variable " + fluorFunctionName + "...");
    }
    for (int i = 0; i < times.length; i++) {
        double[] rawData = dataSetControllerImpl.getSimDataBlock(null, vcSimulationDataIdentifier, fluorFunctionName, times[i]).getData();
        short[] scaledDataShort = new short[rawData.length];
        for (int j = 0; j < scaledDataShort.length; j++) {
            double scaledRawDataJ = rawData[j] * linearScaleFactor;
            if (bNoise) {
                double ran = rnd.nextGaussian();
                double scaledRawDataJ_withNoise = Math.max(0, (scaledRawDataJ + ran * Math.sqrt(scaledRawDataJ)));
                scaledRawDataJ_withNoise = Math.min(shortMax, scaledRawDataJ_withNoise);
                int scaledValue = (int) (scaledRawDataJ_withNoise);
                scaledDataShort[j] &= 0x0000;
                scaledDataShort[j] |= 0x0000FFFF & scaledValue;
            } else {
                int scaledValue = (int) (scaledRawDataJ);
                scaledDataShort[j] &= 0x0000;
                scaledDataShort[j] |= 0x0000FFFF & scaledValue;
            }
        }
        scaledDataImages[i] = new UShortImage(scaledDataShort, cartesianMesh.getOrigin(), cartesianMesh.getExtent(), cartesianMesh.getSizeX(), cartesianMesh.getSizeY(), cartesianMesh.getSizeZ());
        if (progressListener != null) {
            int progress = (int) (((i + 1) * 1.0 / times.length) * 100);
            progressListener.setProgress(progress);
        }
    }
    ImageDataset rawImageDataSet = new ImageDataset(scaledDataImages, times, cartesianMesh.getSizeZ());
    return rawImageDataSet;
}

Example 59 with VCSimulationIdentifier

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

the class RunFakeSimOp method runRefSimulation.

public ImageTimeSeries<UShortImage> runRefSimulation(LocalWorkspace localWorkspace, Simulation simulation, double max_intensity, double bleachBlackoutStartTime, double bleachBlackoutStopTime, boolean hasNoise, ClientTaskStatusSupport progressListener) throws Exception {
    User owner = LocalWorkspace.getDefaultOwner();
    KeyValue simKey = LocalWorkspace.createNewKeyValue();
    runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), simulation, progressListener);
    Extent extent = simulation.getMathDescription().getGeometry().getExtent();
    Origin origin = simulation.getMathDescription().getGeometry().getOrigin();
    VCDataIdentifier vcDataIdentifier = new VCSimulationDataIdentifier(new VCSimulationIdentifier(simulation.getKey(), simulation.getVersion().getOwner()), 0);
    CartesianMesh mesh = localWorkspace.getDataSetControllerImpl().getMesh(vcDataIdentifier);
    ISize isize = new ISize(mesh.getSizeX(), mesh.getSizeY(), mesh.getSizeZ());
    double[] dataTimes = localWorkspace.getDataSetControllerImpl().getDataSetTimes(vcDataIdentifier);
    DataProcessingOutputDataValues dataProcessingOutputDataValues = (DataProcessingOutputDataValues) localWorkspace.getDataSetControllerImpl().doDataOperation(new DataProcessingOutputDataValuesOP(vcDataIdentifier, SimulationContext.FLUOR_DATA_NAME, TimePointHelper.createAllTimeTimePointHelper(), DataIndexHelper.createSliceDataIndexHelper(0), null, null));
    ArrayList<SourceDataInfo> sourceDataInfoArr = dataProcessingOutputDataValues.createSourceDataInfos(new ISize(mesh.getSizeX(), mesh.getSizeY(), 1), origin, extent);
    // find scale factor to scale up the data to avoid losing precision when casting double to short
    double maxDataValue = 0;
    for (int i = 0; i < dataTimes.length; i++) {
        if (sourceDataInfoArr.get(i).getMinMax() != null) {
            maxDataValue = Math.max(maxDataValue, sourceDataInfoArr.get(i).getMinMax().getMax());
        } else {
            double[] doubleData = (double[]) sourceDataInfoArr.get(i).getData();
            for (int j = 0; j < doubleData.length; j++) {
                maxDataValue = Math.max(maxDataValue, doubleData[j]);
            }
        }
    }
    double scale = max_intensity / maxDataValue;
    ArrayList<UShortImage> outputImages = new ArrayList<UShortImage>();
    ArrayList<Double> outputTimes = new ArrayList<Double>();
    for (int i = 0; i < dataTimes.length; i++) {
        if (dataTimes[i] < bleachBlackoutStartTime || dataTimes[i] > bleachBlackoutStopTime) {
            // saving each time step 2D double array to a UShortImage
            double[] doubleData = (double[]) sourceDataInfoArr.get(i).getData();
            short[] shortData = new short[isize.getX() * isize.getY()];
            for (int j = 0; j < shortData.length; j++) {
                double dData = doubleData[j] * scale;
                if (dData < 0 || dData > 65535.0) {
                    throw new RuntimeException("scaled pixel out of range of unsigned 16 bit integer, original simulated value = " + doubleData[j] + ", scale = " + scale + ", scaled value = " + dData);
                }
                short sData = (short) (0x0000ffff & ((int) dData));
                if (hasNoise && dData > 0.0) {
                    if (dData > 20) {
                        shortData[j] = (short) (0x0000ffff & (int) RandomVariable.normal(dData, Math.sqrt(dData)));
                    } else {
                        shortData[j] = (short) (0x0000ffff & RandomVariable.poisson(dData));
                    }
                } else {
                    shortData[j] = sData;
                }
            }
            outputTimes.add(dataTimes[i]);
            outputImages.add(new UShortImage(shortData, sourceDataInfoArr.get(i).getOrigin(), sourceDataInfoArr.get(i).getExtent(), sourceDataInfoArr.get(i).getXSize(), sourceDataInfoArr.get(i).getYSize(), 1));
            if (progressListener != null) {
                int progress = (int) (((i + 1) * 1.0 / dataTimes.length) * 100);
                progressListener.setProgress(progress);
            }
        }
    }
    double[] outputTimesArray = new double[outputTimes.size()];
    for (int i = 0; i < outputTimes.size(); i++) {
        outputTimesArray[i] = outputTimes.get(i);
    }
    ImageTimeSeries<UShortImage> fakeFluorTimeSeries = new ImageTimeSeries<UShortImage>(UShortImage.class, outputImages.toArray(new UShortImage[0]), outputTimesArray, 1);
    return fakeFluorTimeSeries;
}