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

Example 36 with UShortImage

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

the class GenerateBleachRoiOp method generateBleachRoi.

public ROI generateBleachRoi(Image firstPostbleach, ROI cellROI_2D, Double bleachThreshold) throws ImageException {
    int numPixels = firstPostbleach.getNumXYZ();
    short[] scaledBleachedDataShort = new short[numPixels];
    short[] erodedCellUShort = cellROI_2D.getRoiImages()[0].getBinaryPixels(1);
    // input is already normalized to 1.0 ... if relative to max, then crazy values from outside cell can interfere.
    double bleachThresholdValue = bleachThreshold;
    double[] firstPostbleachImage = firstPostbleach.getDoublePixels();
    for (int j = 0; j < numPixels; j++) {
        boolean isCell = (erodedCellUShort[j] == 1);
        boolean isBleach = firstPostbleachImage[j] < bleachThresholdValue;
        if (isCell && isBleach) {
            scaledBleachedDataShort[j] = 1;
        }
    }
    UShortImage bleachedImage = new UShortImage(scaledBleachedDataShort, firstPostbleach.getOrigin(), firstPostbleach.getExtent(), firstPostbleach.getNumX(), firstPostbleach.getNumY(), firstPostbleach.getNumZ());
    ROI bleachedROI = new ROI(bleachedImage, "bleachedROI");
    return bleachedROI;
}

Example 37 with UShortImage

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

the class GenerateCellROIsFromRawPhotoactivationTimeSeriesOp method generate.

public GeometryRoisAndActivationTiming generate(ImageTimeSeries rawTimeSeriesImages, double cellThreshold) throws Exception {
    Image[] allImages = rawTimeSeriesImages.getAllImages();
    int numPixels = allImages[0].getNumXYZ();
    int numTimes = allImages.length;
    ImageStatistics[] imageStats = new ImageStatistics[numTimes];
    for (int i = 0; i < numTimes; i++) {
        imageStats[i] = allImages[i].getImageStatistics();
    }
    // 
    // find largest change in fluorescence (ratio of total[n+1]/total[n]
    // 
    int indexPostactivation = -1;
    double largestRatio = 0.0;
    for (int tIndex = 0; tIndex < numTimes - 1; tIndex++) {
        double currentRatio = imageStats[tIndex + 1].meanValue / imageStats[tIndex].meanValue;
        if (currentRatio > largestRatio) {
            largestRatio = currentRatio;
            indexPostactivation = tIndex + 1;
        }
    }
    double[] firstImagePixels = allImages[0].getDoublePixels();
    short[] scaledCellDataShort = new short[numPixels];
    short[] scaledBackgoundDataShort = new short[numPixels];
    short[] wholeDomainDataShort = new short[numPixels];
    // 
    // find cell and background by thresholding the first image
    // 
    double cellThresholdValue = cellThreshold * imageStats[0].maxValue;
    for (int j = 0; j < numPixels; j++) {
        boolean isCell = firstImagePixels[j] > cellThresholdValue;
        if (isCell) {
            scaledCellDataShort[j] = 1;
        } else {
            scaledBackgoundDataShort[j] = 1;
        }
    }
    UShortImage cellImage = new UShortImage(scaledCellDataShort, allImages[0].getOrigin(), allImages[0].getExtent(), allImages[0].getNumX(), allImages[0].getNumY(), allImages[0].getNumZ());
    UShortImage backgroundImage = new UShortImage(scaledBackgoundDataShort, allImages[0].getOrigin(), allImages[0].getExtent(), allImages[0].getNumX(), allImages[0].getNumY(), allImages[0].getNumZ());
    Arrays.fill(wholeDomainDataShort, (short) 1);
    UShortImage wholeDomainImage = new UShortImage(wholeDomainDataShort, allImages[0].getOrigin(), allImages[0].getExtent(), allImages[0].getNumX(), allImages[0].getNumY(), allImages[0].getNumZ());
    UShortImage reverseCell = UShortImage.fastDilate(cellImage, 10, wholeDomainImage);
    reverseCell.reverse();
    reverseCell.and(backgroundImage);
    backgroundImage = reverseCell;
    cellImage = new UShortImage(backgroundImage);
    cellImage.reverse();
    ROI cellROI = new ROI(cellImage, "cellROI");
    ROI backgroundROI = new ROI(backgroundImage, "backgroundROI");
    GeometryRoisAndActivationTiming results = new GeometryRoisAndActivationTiming();
    results.cellROI_2D = cellROI;
    results.backgroundROI_2D = backgroundROI;
    results.indexOfFirstPostactivation = indexPostactivation;
    return results;
}

Example 38 with UShortImage

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

the class ImportRawTimeSeriesFromExperimentImageOp method importRawTimeSeries.

public ImageTimeSeries<UShortImage> importRawTimeSeries(File expTimeSeriesFile) throws Exception {
    ClientTaskStatusSupport clientTaskStatusSupport = null;
    ImageDataset rawTimeData = ImageDatasetReaderService.getInstance().getImageDatasetReader().readImageDataset(expTimeSeriesFile.getAbsolutePath(), clientTaskStatusSupport);
    ImageTimeSeries<UShortImage> imageTimeSeries = new ImageTimeSeries<UShortImage>(UShortImage.class, rawTimeData.getAllImages(), rawTimeData.getImageTimeStamps(), 1);
    return imageTimeSeries;
}

Example 39 with UShortImage

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

the class BioformatsImageDatasetReader method getImageDataset.

private ImageDataset getImageDataset(org.vcell.imagedataset.ImageDataset t_imageDataset) throws ImageException {
    List<org.vcell.imagedataset.UShortImage> t_images = t_imageDataset.getImages();
    UShortImage[] images = new UShortImage[t_images.size()];
    for (int i = 0; i < t_images.size(); i++) {
        org.vcell.imagedataset.UShortImage t_image = t_images.get(i);
        short[] pixels = new short[t_image.getPixels().size()];
        for (int p = 0; p < t_image.getPixelsSize(); p++) {
            pixels[p] = t_image.getPixels().get(p);
        }
        Origin origin = new Origin(t_image.getOrigin().x, t_image.getOrigin().y, t_image.getOrigin().z);
        Extent extent = new Extent(t_image.getExtent().x, t_image.getExtent().y, t_image.getExtent().z);
        int numX = t_image.getSize().x;
        int numY = t_image.getSize().y;
        int numZ = t_image.getSize().z;
        UShortImage image = new UShortImage(pixels, origin, extent, numX, numY, numZ);
        images[i] = image;
    }
    ;
    List<Double> t_imageTimeStamps = t_imageDataset.getImageTimeStamps();
    double[] timestamps = new double[t_imageTimeStamps.size()];
    for (int t = 0; t < t_imageTimeStamps.size(); t++) {
        timestamps[t] = t_imageTimeStamps.get(t);
    }
    ImageDataset imageDataset = new ImageDataset(images, timestamps, t_imageDataset.numZ);
    return imageDataset;
}

Example 40 with UShortImage

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

the class MicroscopyXmlReader method getUShortImage.

/**
 * This method returns a VCIMage object from a XML representation.
 * Creation date: (3/16/2001 3:41:24 PM)
 * @param param org.jdom.Element
 * @return VCImage
 * @throws XmlParseException
 */
private UShortImage getUShortImage(Element param) throws XmlParseException {
    // get the attributes
    Element tempelement = param.getChild(XMLTags.ImageDataTag);
    int aNumX = Integer.parseInt(tempelement.getAttributeValue(XMLTags.XAttrTag));
    int aNumY = Integer.parseInt(tempelement.getAttributeValue(XMLTags.YAttrTag));
    int aNumZ = Integer.parseInt(tempelement.getAttributeValue(XMLTags.ZAttrTag));
    int compressSize = Integer.parseInt(tempelement.getAttributeValue(XMLTags.CompressedSizeTag));
    final int BYTES_PER_SHORT = 2;
    int UNCOMPRESSED_SIZE_BYTES = aNumX * aNumY * aNumZ * BYTES_PER_SHORT;
    // getpixels
    String hexEncodedBytes = tempelement.getText();
    byte[] rawBytes = org.vcell.util.Hex.toBytes(hexEncodedBytes);
    ByteArrayInputStream rawByteArrayInputStream = new ByteArrayInputStream(rawBytes);
    InputStream rawInputStream = rawByteArrayInputStream;
    if (compressSize != UNCOMPRESSED_SIZE_BYTES) {
        rawInputStream = new InflaterInputStream(rawByteArrayInputStream);
    }
    byte[] shortsAsBytes = new byte[UNCOMPRESSED_SIZE_BYTES];
    int readCount = 0;
    try {
        while ((readCount += rawInputStream.read(shortsAsBytes, readCount, shortsAsBytes.length - readCount)) != shortsAsBytes.length) {
        }
    } catch (Exception e) {
        e.printStackTrace();
        throw new XmlParseException("error reading image pixels: ", e);
    } finally {
        if (rawInputStream != null) {
            try {
                rawInputStream.close();
            } catch (Exception e2) {
                e2.printStackTrace();
            }
        }
    }
    ByteBuffer byteBuffer = ByteBuffer.wrap(shortsAsBytes);
    short[] shortPixels = new short[aNumX * aNumY * aNumZ];
    for (int i = 0; i < shortPixels.length; i++) {
        shortPixels[i] = byteBuffer.getShort();
    }
    Element extentElement = param.getChild(XMLTags.ExtentTag);
    Extent extent = null;
    if (extentElement != null) {
        extent = vcellXMLReader.getExtent(extentElement);
    }
    Element originElement = param.getChild(XMLTags.OriginTag);
    Origin origin = null;
    if (originElement != null) {
        origin = vcellXMLReader.getOrigin(originElement);
    }
    // //set attributes
    // String name = this.unMangle( param.getAttributeValue(XMLTags.NameAttrTag) );
    // String annotation = param.getChildText(XMLTags.AnnotationTag);
    UShortImage newimage;
    try {
        newimage = new UShortImage(shortPixels, origin, extent, aNumX, aNumY, aNumZ);
    } catch (ImageException e) {
        e.printStackTrace();
        throw new XmlParseException("error reading image: ", e);
    }
    return newimage;
}