Examples with DataSetControllerImpl cbit.vcell.simdata.DataSetControllerImpl used on opensource projects

Example 21 with DataSetControllerImpl

use of cbit.vcell.simdata.DataSetControllerImpl in project vcell by virtualcell.

the class LocalVCellConnectionFactory method createVCellConnection.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.server.VCellConnection
 */
public VCellConnection createVCellConnection() throws AuthenticationException, ConnectionException {
    try {
        if (connectionFactory == null) {
            connectionFactory = DatabaseService.getInstance().createConnectionFactory();
        }
        KeyFactory keyFactory = connectionFactory.getKeyFactory();
        LocalVCellConnection.setDatabaseResources(connectionFactory, keyFactory);
        AdminDBTopLevel adminDbTopLevel = new AdminDBTopLevel(connectionFactory);
        boolean bEnableRetry = false;
        boolean isLocal = true;
        User user = adminDbTopLevel.getUser(userLoginInfo.getUserName(), userLoginInfo.getDigestedPassword(), bEnableRetry, isLocal);
        if (user != null) {
            userLoginInfo.setUser(user);
        } else {
            throw new AuthenticationException("failed to authenticate as user " + userLoginInfo.getUserName());
        }
        DatabaseServerImpl databaseServerImpl = new DatabaseServerImpl(connectionFactory, keyFactory);
        boolean bCache = false;
        Cachetable cacheTable = null;
        DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(cacheTable, new File(PropertyLoader.getRequiredProperty(PropertyLoader.primarySimDataDirInternalProperty)), new File(PropertyLoader.getRequiredProperty(PropertyLoader.secondarySimDataDirInternalProperty)));
        SimulationDatabaseDirect simulationDatabase = new SimulationDatabaseDirect(adminDbTopLevel, databaseServerImpl, bCache);
        ExportServiceImpl exportServiceImpl = new ExportServiceImpl();
        LocalVCellConnection vcConn = new LocalVCellConnection(userLoginInfo, simulationDatabase, dataSetControllerImpl, exportServiceImpl);
        linkHDFLib();
        return vcConn;
    } catch (Throwable exc) {
        lg.error(exc.getMessage(), exc);
        throw new ConnectionException(exc.getMessage());
    }
}

Example 22 with DataSetControllerImpl

use of cbit.vcell.simdata.DataSetControllerImpl 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 23 with DataSetControllerImpl

use of cbit.vcell.simdata.DataSetControllerImpl 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;
}