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

Example 1 with ImageDataset

use of cbit.vcell.VirtualMicroscopy.ImageDataset 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 2 with ImageDataset

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

the class BioformatsImageDatasetReader method readImageDatasetChannels.

@Override
public ImageDataset[] readImageDatasetChannels(String imageID, ClientTaskStatusSupport status, boolean bMergeChannels, Integer timeIndex, ISize resize) throws Exception {
    try (TTransport transport = new TSocket("localhost", port)) {
        transport.open();
        TProtocol protocol = new TBinaryProtocol(transport);
        ImageDatasetService.Client client = new ImageDatasetService.Client(protocol);
        String fileName = imageID;
        org.vcell.imagedataset.ISize t_resize = null;
        if (resize != null) {
            t_resize = new org.vcell.imagedataset.ISize(resize.getX(), resize.getY(), resize.getZ());
        }
        List<org.vcell.imagedataset.ImageDataset> t_imageDatasetList = client.readImageDatasetChannels(fileName, bMergeChannels, timeIndex, t_resize);
        ImageDataset[] imageDatasets = new ImageDataset[t_imageDatasetList.size()];
        for (int i = 0; i < t_imageDatasetList.size(); i++) {
            imageDatasets[i] = getImageDataset(t_imageDatasetList.get(i));
        }
        return imageDatasets;
    }
}

Example 3 with ImageDataset

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

the class BioformatsImageDatasetReader method readImageDataset.

@Override
public ImageDataset readImageDataset(String imageID, ClientTaskStatusSupport status) throws Exception {
    try (TTransport transport = new TSocket("localhost", port)) {
        transport.open();
        TProtocol protocol = new TBinaryProtocol(transport);
        ImageDatasetService.Client client = new ImageDatasetService.Client(protocol);
        String fileName = imageID;
        org.vcell.imagedataset.ImageDataset t_imageDataset = client.readImageDataset(fileName);
        ImageDataset imageDataset = getImageDataset(t_imageDataset);
        return imageDataset;
    }
}

Example 4 with ImageDataset

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

the class MicroscopyXmlReader method getAnnotatedImageDataset.

public AnnotatedImageDataset getAnnotatedImageDataset(Element param, /*root, frapstudy element*/
ClientTaskStatusSupport progressListener) throws XmlParseException {
    // get frapData element
    Element frapDataElement = param.getChild(MicroscopyXMLTags.FRAPDataTag);
    Element imageDatasetElement = frapDataElement.getChild(MicroscopyXMLTags.ImageDatasetTag);
    ImageDataset imageDataset = null;
    if (imageDatasetElement != null) {
        imageDataset = getImageDataset(imageDatasetElement, progressListener);
    }
    Namespace ns = param.getNamespace();
    List<Element> roiList = frapDataElement.getChildren(MicroscopyXMLTags.ROITag);
    ROI[] rois = new ROI[0];
    int numROIs = roiList.size();
    if (numROIs > 0) {
        rois = new ROI[numROIs];
        Iterator<Element> roiIter = roiList.iterator();
        int index = 0;
        while (roiIter.hasNext()) {
            Element roiElement = roiIter.next();
            rois[index++] = getROI(roiElement);
        }
    }
    // reorder ROIs according to the order of FRAPData.VFRAP_ROI_ENUM
    ROI[] reorderedROIs = AnnotatedImageDataset.reorderROIs(rois);
    AnnotatedImageDataset annotatedImages = new AnnotatedImageDataset(imageDataset, reorderedROIs);
    // After loading all the ROI rings, the progress should set to 100.
    if (progressListener != null) {
        progressListener.setProgress(100);
    }
    return annotatedImages;
}

Example 5 with ImageDataset

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

the class MicroscopyXmlReader method getImageDataset.

/**
 * This method returns a Biomodel object from a XML Element.
 * Creation date: (3/13/2001 12:35:00 PM)
 * @param param org.jdom.Element
 * @return cbit.vcell.biomodel.BioModel
 * @throws XmlParseException
 */
private ImageDataset getImageDataset(Element param, ClientTaskStatusSupport progressListener) throws XmlParseException {
    List<Element> ushortImageElementList = param.getChildren(MicroscopyXMLTags.UShortImageTag);
    Iterator<Element> imageElementIter = ushortImageElementList.iterator();
    UShortImage[] images = new UShortImage[ushortImageElementList.size()];
    // added in Feb 2008, for counting loading progress
    int imageSize = ushortImageElementList.size();
    int imageCount = 0;
    while (imageElementIter.hasNext()) {
        images[imageCount++] = getUShortImage(imageElementIter.next());
        if (progressListener != null) {
            progressListener.setProgress((int) ((imageCount * 100.0) / imageSize));
        }
    }
    Element timeStampListElement = param.getChild(MicroscopyXMLTags.TimeStampListTag);
    double[] timestamps = null;
    if (timeStampListElement != null) {
        String timeStampListText = timeStampListElement.getTextTrim();
        StringTokenizer tokens = new StringTokenizer(timeStampListText, ",\n\r\t ", false);
        ArrayList<Double> times = new ArrayList<Double>();
        while (tokens.hasMoreTokens()) {
            String token = tokens.nextToken();
            times.add(Double.parseDouble(token));
        }
        timestamps = new double[times.size()];
        for (int i = 0; i < timestamps.length; i++) {
            timestamps[i] = times.get(i);
        }
    }
    int numTimeSteps = (timestamps != null) ? (timestamps.length) : (1);
    int numZ = images.length / numTimeSteps;
    ImageDataset imageDataset = new ImageDataset(images, timestamps, numZ);
    return imageDataset;
}