Examples with ImageServerMetadata qupath.lib.images.servers.ImageServerMetadata used on opensource projects

Example 1 with ImageServerMetadata

use of qupath.lib.images.servers.ImageServerMetadata in project qupath by qupath.

the class CreateTrainingImageCommand method createSparseServer.

/**
 * Create a {@link SparseImageServer} from a collection of images.
 * @param entries project entries that may be added to the image
 * @param predicate predicate used to select annotated regions
 * @param maxWidth the preferred width of the generated image, in pixels (used to determine whether to append a region horizontally or vertically)
 * @param doZ if true, take all slices of a z-stack for each region where available; if false, take the region and create a 2D image
 * @return
 * @throws IOException
 */
static SparseImageServer createSparseServer(Collection<ProjectImageEntry<BufferedImage>> entries, Predicate<PathObject> predicate, int maxWidth, boolean doZ) throws IOException {
    var builder = new SparseImageServer.Builder();
    boolean doT = false;
    int pad = 0;
    int x = 0;
    int y = 0;
    int rowHeight = 0;
    ImageServerMetadata firstMetadata = null;
    int n = 0;
    for (var entry : entries) {
        if (!entry.hasImageData())
            continue;
        var hierarchy = entry.readHierarchy();
        if (hierarchy == null)
            continue;
        var annotations = hierarchy.getAnnotationObjects();
        if (annotations.isEmpty())
            continue;
        try {
            ImageServer<BufferedImage> server = null;
            for (var annotation : annotations) {
                if (!predicate.test(annotation))
                    continue;
                var roi = annotation.getROI();
                var region = ImageRegion.createInstance(roi);
                if (server == null) {
                    server = entry.getServerBuilder().build();
                    if (firstMetadata == null)
                        firstMetadata = server.getMetadata();
                    else {
                        if (firstMetadata.getPixelType() != server.getPixelType()) {
                            logger.warn("Incompatible pixel types {} and {} - will skip regions from {}", server.getPixelType(), firstMetadata.getPixelType(), entry.getImageName());
                            break;
                        }
                        if (firstMetadata.getSizeC() != server.nChannels()) {
                            logger.warn("Incompatible channel counts {} and {} - will skip regions from {}", server.nChannels(), firstMetadata.getSizeC(), entry.getImageName());
                            break;
                        }
                    }
                }
                var croppedServer = new CroppedImageServer(server, region);
                int[] zArray = doZ ? IntStream.range(0, croppedServer.nZSlices()).toArray() : new int[] { 0 };
                int[] tArray = doT ? IntStream.range(0, croppedServer.nTimepoints()).toArray() : new int[] { 0 };
                for (int t : tArray) {
                    for (int z : zArray) {
                        rowHeight = Math.max(region.getHeight(), rowHeight);
                        var regionOutput = ImageRegion.createInstance(x, y, region.getWidth(), region.getHeight(), z, t);
                        for (double downsample : croppedServer.getPreferredDownsamples()) {
                            builder.serverRegion(regionOutput, downsample, croppedServer);
                            n++;
                        }
                    }
                }
                // Increment x
                x += region.getWidth() + pad;
                // Move to next row
                if (x >= maxWidth) {
                    y += rowHeight + pad;
                    rowHeight = 0;
                    x = 0;
                }
            }
        } catch (Exception e) {
            logger.warn("Exception trying to read {}: {}", entry.getImageName(), e.getLocalizedMessage());
        }
    }
    if (n == 0) {
        return null;
    } else
        return builder.build();
}