Merge pull request #83 from chris-allan/ngff-optimization-001

First set of NGFF optimizations

src/main/java/com/glencoesoftware/omero/ms/image/region/ImageRegionRequestHandler.java

@@ -320,8 +320,10 @@ public byte[] renderImageRegion(omero.client client) {
             Map<Long, Pixels> imagePixels = retrievePixDescription(
                     iQuery, Arrays.asList(imageRegionCtx.imageId));
             Pixels pixels = imagePixels.get(imageRegionCtx.imageId);
+            RenderingDef renderingDef =
+                    getRenderingDef(client, imageRegionCtx.imageId);
             if (pixels != null) {
-                return getRegion(client, pixels);
+                return getRegion(client, pixels, renderingDef);
             }
             log.debug("Cannot find Image:{}", imageRegionCtx.imageId);
         } catch (Exception e) {
@@ -338,13 +340,14 @@ public byte[] renderImageRegion(omero.client client) {
      * defined by <code>imageRegionCtx.format</code>.
      * @param client OMERO client to use for querying.
      * @param pixels pixels metadata
+     * @param renderingDef rendering settings to use
      * @return Image region as a byte array.
      * @throws QuantizationException
      */
-    private byte[] getRegion(omero.client client, Pixels pixels)
-            throws IllegalArgumentException, ServerError, IOException,
-                QuantizationException {
-        RenderingDef renderingDef = getRenderingDef(client, pixels.getId());
+    private byte[] getRegion(
+            omero.client client, Pixels pixels, RenderingDef renderingDef)
+                    throws IllegalArgumentException, ServerError, IOException,
+                        QuantizationException {
         return compress(getBufferedImage(render(client, pixels, renderingDef)));
     }
 
@@ -404,6 +407,26 @@ protected byte[] compress(BufferedImage image) throws IOException {
         return toReturn;
     }
 
+    /**
+     * Returns a pixel buffer for a given set of pixels.
+     * @param pixels pixels metadata
+     * @return See above.
+     * @see PixelsService#getPixelBuffer(Pixels)
+     */
+    private PixelBuffer getPixelBuffer(Pixels pixels) {
+        Tracer tracer = Tracing.currentTracer();
+        ScopedSpan span = tracer.startScopedSpan("get_pixel_buffer");
+        try {
+            span.tag("omero.pixels_id", Long.toString(pixels.getId()));
+            return pixelsService.getPixelBuffer(pixels, false);
+        } catch (Exception e) {
+            span.error(e);
+            throw e;
+        } finally {
+            span.finish();
+        }
+    }
+
     /**
      * Prepares an in memory pixel buffer of the desired project pixels based
      * on input.
@@ -419,7 +442,7 @@ private PixelBuffer prepareProjectedPixelBuffer(
         int projectedSizeC = 0;
         ChannelBinding[] channelBindings =
                 renderer.getChannelBindings();
-        PixelBuffer pixelBuffer = pixelsService.getPixelBuffer(pixels, false);
+        PixelBuffer pixelBuffer = getPixelBuffer(pixels);
         int start = Optional
                 .ofNullable(imageRegionCtx.projectionStart)
                 .orElse(0);
@@ -428,7 +451,7 @@ private PixelBuffer prepareProjectedPixelBuffer(
                 .orElse(pixels.getSizeZ() - 1);
         Tracer tracer = Tracing.currentTracer();
         ScopedSpan span = tracer.startScopedSpan(
-                "prepare_porjected_pixel_buffer");
+                "prepare_projected_pixel_buffer");
         try {
             for (int i = 0; i < channelBindings.length; i++) {
                 if (!channelBindings[i].getActive()) {
@@ -494,8 +517,7 @@ protected Array render(
         ScopedSpan span = tracer.startScopedSpan("render_as_packed_int");
         span.tag("omero.pixels_id", pixels.getId().toString());
         Renderer renderer = null;
-        try (PixelBuffer pixelBuffer =
-                pixelsService.getPixelBuffer(pixels, false)) {
+        try (PixelBuffer pixelBuffer = getPixelBuffer(pixels)) {
             renderer = new Renderer(
                 quantumFactory, renderingModels, pixels, renderingDef,
                 pixelBuffer, lutProvider

src/main/java/com/glencoesoftware/omero/ms/image/region/PixelsService.java

@@ -196,7 +196,7 @@ public ZarrPixelBuffer getLabelImagePixelBuffer(Pixels pixels, String uuid)
             throw new IllegalArgumentException("NGFF dir not configured");
         }
         Path root = ngffDir.resolve(getLabelImageSubPath(pixels, uuid));
-        return new ZarrPixelBuffer(root, maxTileLength);
+        return new ZarrPixelBuffer(pixels, root, maxTileLength);
     }
 
     /**
@@ -214,7 +214,8 @@ public PixelBuffer getPixelBuffer(Pixels pixels, boolean write) {
         if (ngffDir != null) {
             try {
                 Path root = ngffDir.resolve(getImageSubPath(pixels));
-                PixelBuffer v = new ZarrPixelBuffer(root, maxTileLength);
+                PixelBuffer v =
+                        new ZarrPixelBuffer(pixels, root, maxTileLength);
                 log.info("Using NGFF Pixel Buffer");
                 return v;
             } catch (Exception e) {

src/main/java/com/glencoesoftware/omero/ms/image/region/ThumbnailCtx.java

@@ -25,6 +25,9 @@
 
 import org.slf4j.LoggerFactory;
 
+import brave.ScopedSpan;
+import brave.Tracer;
+import brave.Tracing;
 import io.vertx.core.MultiMap;
 import ome.io.nio.PixelBuffer;
 import ome.model.enums.Family;
@@ -79,8 +82,8 @@ public class ThumbnailCtx extends ImageRegionCtx {
 
     /**
      * Apply the first resolution level larger than the thumbnail
-     * @param resolutionDescriptions
-     * @return
+     * @param renderer fully initialized renderer
+     * @param pixelBuffer pixel buffer providing data for the image
      */
     @Override
     public void setResolutionLevel(

src/main/java/com/glencoesoftware/omero/ms/image/region/ThumbnailsRequestHandler.java

@@ -94,7 +94,10 @@ public ThumbnailsRequestHandler(
      */
     public Map<Long, byte[]> renderThumbnails(omero.client client) {
         Map<Long, byte[]> thumbnails = new HashMap<Long, byte[]>();
+        ScopedSpan span =
+                Tracing.currentTracer().startScopedSpan("render_thumbnails");
         try {
+            span.tag("omero.image_ids", thumbnailCtx.imageIds.toString());
             ServiceFactoryPrx sf = client.getSession();
             IQueryPrx iQuery = sf.getQueryService();
             long userId = sf.getAdminService().getEventContext().userId;
@@ -123,7 +126,10 @@ public Map<Long, byte[]> renderThumbnails(omero.client client) {
                 thumbnails.put(imageId, thumbnail);
             }
         } catch (Exception e) {
+            span.error(e);
             log.error("Exception while rendering thumbnails", e);
+        } finally {
+            span.finish();
         }
         return thumbnails;
     }

src/main/java/com/glencoesoftware/omero/ms/image/region/ZarrPixelBuffer.java

@@ -41,6 +41,7 @@
 import loci.formats.FormatTools;
 import ome.io.nio.DimensionsOutOfBoundsException;
 import ome.io.nio.PixelBuffer;
+import ome.model.core.Pixels;
 import ome.util.PixelData;
 import ucar.ma2.InvalidRangeException;
 
@@ -49,6 +50,9 @@ public class ZarrPixelBuffer implements PixelBuffer {
     private static final org.slf4j.Logger log =
             LoggerFactory.getLogger(PixelBuffer.class);
 
+    /** Reference to the pixels. */
+    private final Pixels pixels;
+
     /** Root of the OME-NGFF multiscale we are operating on */
     private final Path root;
 
@@ -77,8 +81,9 @@ public class ZarrPixelBuffer implements PixelBuffer {
      * read operations
      * @throws IOException
      */
-    public ZarrPixelBuffer(Path root, Integer maxTileLength)
+    public ZarrPixelBuffer(Pixels pixels, Path root, Integer maxTileLength)
             throws IOException {
+        this.pixels = pixels;
         this.root = root;
         rootGroup = ZarrGroup.open(this.root);
         rootGroupAttributes = rootGroup.getAttributes();
@@ -156,9 +161,7 @@ private int getBytesPerPixel() {
      * @param offset The offset of the region
      * @return byte array of data from the ZarrArray
      */
-    private byte[] getBytes(int[] shape, int[] offset) {
-        ScopedSpan span = Tracing.currentTracer()
-                .startScopedSpan("get_bytes_zarr");
+    private ByteBuffer getBytes(int[] shape, int[] offset) {
         if (shape[4] > maxTileLength) {
             throw new IllegalArgumentException(String.format(
                     "sizeX %d > maxTileLength %d", shape[4], maxTileLength));
@@ -167,7 +170,12 @@ private byte[] getBytes(int[] shape, int[] offset) {
             throw new IllegalArgumentException(String.format(
                     "sizeY %d > maxTileLength %d", shape[3], maxTileLength));
         }
+        ScopedSpan span = Tracing.currentTracer()
+                .startScopedSpan("get_bytes");
         try {
+            span.tag("omero.zarr.shape", Arrays.toString(shape));
+            span.tag("omero.zarr.offset", Arrays.toString(offset));
+            span.tag("omero.zarr.array", array.toString());
             int length = IntStream.of(shape).reduce(1, Math::multiplyExact);
             int bytesPerPixel = getBytesPerPixel();
             ByteBuffer asByteBuffer = ByteBuffer.allocate(
@@ -176,38 +184,38 @@ private byte[] getBytes(int[] shape, int[] offset) {
             switch (dataType) {
                 case u1:
                 case i1:
-                    return (byte[]) array.read(shape, offset);
+                    return ByteBuffer.wrap((byte[]) array.read(shape, offset));
                 case u2:
                 case i2:
                 {
                     short[] data = (short[]) array.read(shape, offset);
                     asByteBuffer.asShortBuffer().put(data);
-                    return asByteBuffer.array();
+                    return asByteBuffer;
                 }
                 case u4:
                 case i4:
                 {
                     int[] data = (int[]) array.read(shape, offset);
                     asByteBuffer.asIntBuffer().put(data);
-                    return asByteBuffer.array();
+                    return asByteBuffer;
                 }
                 case i8:
                 {
                     long[] data = (long[]) array.read(shape, offset);
                     asByteBuffer.asLongBuffer().put(data);
-                    return asByteBuffer.array();
+                    return asByteBuffer;
                 }
                 case f4:
                 {
                     float[] data = (float[]) array.read(shape, offset);
                     asByteBuffer.asFloatBuffer().put(data);
-                    return asByteBuffer.array();
+                    return asByteBuffer;
                 }
                 case f8:
                 {
                     double[] data = (double[]) array.read(shape, offset);
                     asByteBuffer.asDoubleBuffer().put(data);
-                    return asByteBuffer.array();
+                    return asByteBuffer;
                 }
                 default:
                     log.error("Unsupported data type" + dataType);
@@ -221,24 +229,6 @@ private byte[] getBytes(int[] shape, int[] offset) {
         }
     }
 
-    /**
-     * Retrieves the array shapes of all subresolutions of this multiscale
-     * buffer.
-     * @return See above.
-     * @throws IOException
-     */
-    public int[][] getShapes() throws IOException {
-        List<Map<String, String>> datasets = getDatasets();
-        List<int[]> shapes = new ArrayList<int[]>();
-        for (Map<String, String> dataset : datasets) {
-            ZarrArray resolutionArray =
-                    ZarrArray.open(root.resolve(dataset.get("path")));
-            int[] shape = resolutionArray.getShape();
-            shapes.add(0, shape);
-        }
-        return shapes.toArray(new int[shapes.size()][]);
-    }
-
     /**
      * Retrieves the array chunk sizes of all subresolutions of this multiscale
      * buffer.
@@ -424,10 +414,9 @@ public PixelData getTile(Integer z, Integer c, Integer t, Integer x, Integer y,
         try {
             checkBounds(x + w, y + h, z, c, t);
             int[] shape = new int[] { 1, 1, 1, h, w };
-            int[] offsets = new int[] { t, c, z, y, x };
-            byte[] asArray = getBytes(shape, offsets);
+            int[] offset = new int[] { t, c, z, y, x };
             PixelData d = new PixelData(
-                    getPixelsType(), ByteBuffer.wrap(asArray));
+                    getPixelsType(), getBytes(shape, offset));
             d.setOrder(ByteOrder.BIG_ENDIAN);
             return d;
         } catch (DimensionsOutOfBoundsException e) {
@@ -699,11 +688,16 @@ public Dimension getTileSize() {
     @Override
     public List<List<Integer>> getResolutionDescriptions() {
         try {
-            int[][] shapes = getShapes();
+            int resolutionLevels = getResolutionLevels();
             List<List<Integer>> resolutionDescriptions =
                     new ArrayList<List<Integer>>();
-            for (int[] shape : shapes) {
-                resolutionDescriptions.add(Arrays.asList(shape[4], shape[3]));
+            int sizeX = pixels.getSizeX();
+            int sizeY = pixels.getSizeY();
+            for (int i = 0; i < resolutionLevels; i++) {
+                double scale = Math.pow(2, i);
+                resolutionDescriptions.add(
+                        0, Arrays.asList(
+                                (int) (sizeX / scale), (int) (sizeY / scale)));
             }
             return resolutionDescriptions;
         } catch (Exception e) {