Examples with ImageData omero.gateway.model.ImageData used on opensource projects

Example 1 with ImageData

use of omero.gateway.model.ImageData in project imagej-omero by imagej.

the class DefaultOMEROService method uploadTable.

@Override
public long uploadTable(final OMEROCredentials credentials, final String name, final Table<?, ?> imageJTable, final long imageID) throws ServerError, PermissionDeniedException, CannotCreateSessionException, ExecutionException, DSOutOfServiceException, DSAccessException {
    final TableData omeroTable = convertOMEROTable(imageJTable);
    long id = -1;
    try (final OMEROSession session = new DefaultOMEROSession(credentials)) {
        // Get image
        final BrowseFacility browseFacility = session.getGateway().getFacility(BrowseFacility.class);
        final ImageData image = browseFacility.getImage(session.getSecurityContext(), imageID);
        // attach table to image
        final TablesFacility tablesFacility = session.getGateway().getFacility(TablesFacility.class);
        final TableData stored = tablesFacility.addTable(session.getSecurityContext(), image, name, omeroTable);
        id = stored.getOriginalFileId();
    }
    return id;
}

Example 2 with ImageData

use of omero.gateway.model.ImageData in project imagej-omero by imagej.

the class DefaultOMEROSession method createPixels.

@Override
public RawPixelsStorePrx createPixels(final OMEROFormat.Metadata meta) throws ServerError, FormatException {
    // create a new Image which will house the written pixels
    final ImageData newImage = createImage(meta);
    final long imageID = newImage.getId();
    meta.setImageID(imageID);
    // configure the raw pixels store
    final RawPixelsStorePrx store = session.createRawPixelsStore();
    final long pixelsID = newImage.getDefaultPixels().getId();
    store.setPixelsId(pixelsID, false);
    meta.setPixelsID(pixelsID);
    return store;
}

Example 3 with ImageData

use of omero.gateway.model.ImageData in project imagej-omero by imagej.

the class ModuleAdapter method createOutputLinks.

/**
 * Attempts to attach the outputs to the appropriate items.
 */
private void createOutputLinks(final HashMap<String, Object> inputMap, final HashMap<String, TableData> tables) throws ExecutionException, ServerError, DSOutOfServiceException, DSAccessException {
    final ExperimenterData user = createUser();
    final BrowseFacility browse = gateway.getFacility(BrowseFacility.class);
    final DataManagerFacility dm = gateway.getFacility(DataManagerFacility.class);
    final SecurityContext ctx = new SecurityContext(user.getGroupId());
    final List<ImageData> outImages = getOutputImages(user.getId(), browse, ctx);
    final List<ImageData> inputImages = getInputImages(inputMap, browse, ctx);
    if (!outImages.isEmpty()) {
        attachImagesToDatasets(inputImages, outImages, dm, browse, ctx);
    }
    if (!tables.isEmpty()) {
        if (inputImages.isEmpty())
            throw new IllegalArgumentException("Input image(s) required to upload table to OMERO");
        attachTablesToImages(inputImages, tables, ctx, dm);
    }
}

Example 4 with ImageData

use of omero.gateway.model.ImageData in project imagej-omero by imagej.

the class ModuleAdapter method attachImagesToDatasets.

/**
 * Attaches the given output images to the datasets of the given input images.
 */
private void attachImagesToDatasets(final List<ImageData> inputImages, final List<ImageData> outputImages, final DataManagerFacility dm, final BrowseFacility browse, SecurityContext ctx) throws DSOutOfServiceException, DSAccessException {
    final HashMap<Long, DatasetData> datasets = new HashMap<>();
    // Get all datasets related to the input images
    // FIXME: ImageData has a getDatasets() method, but it is null since the
    // underlying ImageI is unloaded.
    final Collection<DatasetData> allDatasets = browse.getDatasets(ctx);
    for (DatasetData d : allDatasets) {
        Collection<ImageData> allImages = browse.getImagesForDatasets(ctx, Collections.singleton(d.getId()));
        for (ImageData image : allImages) {
            for (ImageData input : inputImages) {
                if (input.getId() == image.getId())
                    datasets.put(d.getId(), d);
            }
        }
    }
    // attach all output images to these datasets
    if (!datasets.isEmpty()) {
        for (Long id : datasets.keySet()) dm.addImagesToDataset(ctx, outputImages, datasets.get(id));
    }
}

Example 5 with ImageData

use of omero.gateway.model.ImageData in project imagej-omero by imagej.

the class DefaultOMEROSession method createImage.

// -- Helper methods --
private ImageData createImage(final OMEROFormat.Metadata meta) throws ServerError, FormatException {
    // create a new Image
    final ImageMetadata imageMeta = meta.get(0);
    final int xLen = axisLength(imageMeta, Axes.X);
    final int yLen = axisLength(imageMeta, Axes.Y);
    final int zLen = axisLength(imageMeta, Axes.Z);
    final int tLen = axisLength(imageMeta, Axes.TIME);
    final int cLen = axisLength(imageMeta, Axes.CHANNEL);
    final int sizeX = xLen == 0 ? 1 : xLen;
    final int sizeY = yLen == 0 ? 1 : yLen;
    final int sizeZ = zLen == 0 ? 1 : zLen;
    final int sizeT = tLen == 0 ? 1 : tLen;
    final int sizeC = cLen == 0 ? 1 : cLen;
    final List<Integer> channelList = new ArrayList<Integer>(sizeC);
    for (int c = 0; c < sizeC; c++) {
        // TODO: Populate actual emission wavelengths?
        channelList.add(c);
    }
    final int pixelType = imageMeta.getPixelType();
    final PixelsType pixelsType = getPixelsType(pixelType);
    final String name = meta.getName();
    final String description = meta.getName();
    final RLong id = session.getPixelsService().createImage(sizeX, sizeY, sizeZ, sizeT, channelList, pixelsType, name, description);
    if (id == null)
        throw new FormatException("Cannot create image");
    // retrieve the newly created Image
    final List<Image> results = session.getContainerService().getImages(Image.class.getName(), Arrays.asList(id.getValue()), null);
    return new ImageData(results.get(0));
}