Examples with ImageDataset cbit.vcell.VirtualMicroscopy.ImageDataset used on opensource projects

Example 36 with ImageDataset

use of cbit.vcell.VirtualMicroscopy.ImageDataset in project vcell by virtualcell.

the class FrapDataUtils method saveImageDatasetAsExternalData.

public static void saveImageDatasetAsExternalData(FRAPData frapData, LocalWorkspace localWorkspace, ExternalDataIdentifier newImageExtDataID, int startingIndexForRecovery, CartesianMesh cartesianMesh) throws ObjectNotFoundException, FileNotFoundException {
    ImageDataset imageDataset = frapData.getImageDataset();
    if (imageDataset.getSizeC() > 1) {
        throw new RuntimeException("FRAPData.saveImageDatasetAsExternalData(): multiple channels not yet supported");
    }
    Extent extent = imageDataset.getExtent();
    ISize isize = imageDataset.getISize();
    // not include the prebleach
    int numImageToStore = imageDataset.getSizeT() - startingIndexForRecovery;
    // original fluor data and back ground average
    double[][][] pixData = new double[numImageToStore][2][];
    double[] timesArray = new double[numImageToStore];
    double[] bgAvg = frapData.getAvgBackGroundIntensity();
    for (int tIndex = startingIndexForRecovery; tIndex < imageDataset.getSizeT(); tIndex++) {
        // images according to zIndex at specific time points(tIndex)
        short[] originalData = imageDataset.getPixelsZ(0, tIndex);
        double[] doubleData = new double[originalData.length];
        double[] expandBgAvg = new double[originalData.length];
        for (int i = 0; i < originalData.length; i++) {
            doubleData[i] = 0x0000ffff & originalData[i];
            expandBgAvg[i] = bgAvg[tIndex];
        }
        pixData[tIndex - startingIndexForRecovery][0] = doubleData;
        pixData[tIndex - startingIndexForRecovery][1] = expandBgAvg;
        timesArray[tIndex - startingIndexForRecovery] = imageDataset.getImageTimeStamps()[tIndex] - imageDataset.getImageTimeStamps()[startingIndexForRecovery];
    }
    // changed in March 2008. Though biomodel is not created, we still let user save to xml file.
    Origin origin = new Origin(0, 0, 0);
    FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
    fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
    fdos.cartesianMesh = cartesianMesh;
    fdos.doubleSpecData = pixData;
    fdos.specEDI = newImageExtDataID;
    fdos.varNames = new String[] { SimulationContext.FLUOR_DATA_NAME, "bg_average" };
    fdos.owner = LocalWorkspace.getDefaultOwner();
    fdos.times = timesArray;
    fdos.variableTypes = new VariableType[] { VariableType.VOLUME, VariableType.VOLUME };
    fdos.origin = origin;
    fdos.extent = extent;
    fdos.isize = isize;
    localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
}

Example 37 with ImageDataset

use of cbit.vcell.VirtualMicroscopy.ImageDataset in project vcell by virtualcell.

the class FRAPData method crop.

/**
 * Method crop.
 * @param rect Rectangle
 * @return FRAPData
 * @throws ImageException
 */
@Override
public FRAPData crop(Rectangle rect) throws ImageException {
    ImageDataset croppedImageDataset = getImageDataset().crop(rect);
    ROI[] rois = getRois();
    ROI[] croppedROIs = new ROI[rois.length];
    ROI currentlyDisplayedROI = getCurrentlyDisplayedROI();
    ROI croppedCurrentROI = null;
    for (int i = 0; i < croppedROIs.length; i++) {
        croppedROIs[i] = rois[i].crop(rect);
        if (currentlyDisplayedROI == rois[i]) {
            croppedCurrentROI = croppedROIs[i];
        }
    }
    FRAPData croppedFrapData = new FRAPData(croppedImageDataset, croppedROIs);
    setCurrentlyDisplayedROI(croppedCurrentROI);
    return croppedFrapData;
}

Example 38 with ImageDataset

use of cbit.vcell.VirtualMicroscopy.ImageDataset 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 39 with ImageDataset

use of cbit.vcell.VirtualMicroscopy.ImageDataset in project vcell by virtualcell.

the class ImportRawTimeSeriesFrom2DVCellConcentrationsOp method importRawTimeSeries.

public ImageTimeSeries<UShortImage> importRawTimeSeries(File vcellSimLogFile, String fluorFunctionName, double maxIntensity, boolean bNoise) throws Exception {
    ClientTaskStatusSupport clientTaskStatusSupport = null;
    ImageDataset timeRawData = importRawTimeSeries(vcellSimLogFile, fluorFunctionName, maxIntensity, bNoise, clientTaskStatusSupport);
    ImageTimeSeries<UShortImage> imageTimeSeries = new ImageTimeSeries<UShortImage>(UShortImage.class, timeRawData.getAllImages(), timeRawData.getImageTimeStamps(), 1);
    return imageTimeSeries;
}

Example 40 with ImageDataset

use of cbit.vcell.VirtualMicroscopy.ImageDataset in project vcell by virtualcell.

the class ImportRawTimeSeriesFromExperimentImagesOp method importRawTimeSeries.

public ImageTimeSeries<UShortImage> importRawTimeSeries(File[] expTimeSeriesFiles, double timeInterval) throws Exception {
    boolean isTimeSeries = true;
    ClientTaskStatusSupport clientTaskStatusSupport = null;
    ImageDataset rawTimeData = ImageDatasetReaderService.getInstance().getImageDatasetReader().readImageDatasetFromMultiFiles(expTimeSeriesFiles, clientTaskStatusSupport, isTimeSeries, timeInterval);
    ImageTimeSeries<UShortImage> imageTimeSeries = new ImageTimeSeries<UShortImage>(UShortImage.class, rawTimeData.getAllImages(), rawTimeData.getImageTimeStamps(), 1);
    return imageTimeSeries;
}