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

Example 91 with UShortImage

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

the class GenerateNormalizedFrapDataOp method generate.

public NormalizedFrapDataResults generate(ImageTimeSeries<UShortImage> rawImageTimeSeries, ROI backgroundROI_2D, Integer indexPostbleach) throws Exception {
    UShortImage firstImage = rawImageTimeSeries.getAllImages()[0];
    ISize isize = firstImage.getISize();
    int nX = isize.getX();
    int nY = isize.getY();
    int nZ = isize.getZ();
    int numTimes = rawImageTimeSeries.getSizeT();
    Extent extent = firstImage.getExtent();
    org.vcell.util.Origin origin = firstImage.getOrigin();
    if (indexPostbleach == 0) {
        throw new RuntimeException("no prebleach images found - indexOfFirstPostbleach is 0");
    }
    // 
    // find average "dark count" in background of pre-bleach images (for background subtraction)
    // 
    float avgBackground = 0.0f;
    int numPrebleach = indexPostbleach;
    for (int i = 0; i < numPrebleach; i++) {
        avgBackground += getAverage(rawImageTimeSeries.getAllImages()[i], backgroundROI_2D);
    }
    avgBackground /= numPrebleach;
    // 
    // find averaged prebleach image (corrected for background).
    // 
    int numPostbleachImages = numTimes - numPrebleach;
    // holds new averaged image pixels
    float[] prebleachAveragePixels = new float[nX * nY * nZ];
    for (int i = 0; i < numPrebleach; i++) {
        short[] currPrebleachImage = rawImageTimeSeries.getAllImages()[i].getPixels();
        for (int j = 0; j < isize.getXYZ(); j++) {
            float intPixel = 0x0000ffff & ((int) currPrebleachImage[j]);
            prebleachAveragePixels[j] += intPixel / numPrebleach;
        }
    }
    FloatImage prebleachAverageImage = new FloatImage(prebleachAveragePixels, origin, extent, nX, nY, nZ);
    // 
    // create normalized dataset
    // 
    // normalized postbleach = (origPostbleach - background)/(prebleach - background)
    // 
    FloatImage[] normalizedImages = new FloatImage[numPostbleachImages];
    double[] postbleachTimeStamps = new double[numPostbleachImages];
    for (int i = 0; i < numPostbleachImages; i++) {
        double[] origTimeStamps = rawImageTimeSeries.getImageTimeStamps();
        postbleachTimeStamps[i] = origTimeStamps[indexPostbleach + i] - origTimeStamps[indexPostbleach];
        float[] normalizedPixels = new float[isize.getXYZ()];
        normalizedImages[i] = new FloatImage(normalizedPixels, origin, extent, nX, nY, nZ);
        short[] uncorrectedPixels = rawImageTimeSeries.getAllImages()[i + indexPostbleach].getPixels();
        for (int j = 0; j < isize.getXYZ(); j++) {
            int intPixel = 0x0000ffff & ((int) uncorrectedPixels[j]);
            normalizedPixels[j] = (intPixel - avgBackground) / (Math.max(1, prebleachAveragePixels[j] - avgBackground));
        }
        normalizedImages[i] = new FloatImage(normalizedPixels, origin, extent, nX, nY, nZ);
    }
    ImageTimeSeries<FloatImage> normalizedData = new ImageTimeSeries<FloatImage>(FloatImage.class, normalizedImages, postbleachTimeStamps, nZ);
    NormalizedFrapDataResults results = new NormalizedFrapDataResults();
    results.normalizedFrapData = normalizedData;
    results.prebleachAverage = prebleachAverageImage;
    return results;
}

Example 92 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage 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 93 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage 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 94 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage 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 95 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage 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;
}