wip: toward using prefetching

Author: bogovicj

src/main/java/org/janelia/saalfeldlab/n5/shard/DefaultDatasetAccess.java

@@ -142,6 +142,15 @@ private void readChunksRecursive(
 			// TODO: collect all the elementPos that we will need and prefetch
 			//       Probably best to add a prefetch method to RawShard?
 
+            // Here's an attempt at that.
+            // Don't love that we have to build a list of positions
+            // Consider making DataBlockRequest package private and passing them directly
+            final ArrayList<long[]> positions = new ArrayList<>();
+            for (final ChunkRequest<T> request : requests) {
+                positions.add(request.position.relative(0));
+            }
+            shard.prefetch(positions);
+
 			for (final ChunkRequest<T> request : requests) {
 				final long[] elementPos = request.position.relative(0);
 				final ReadData elementData = shard.getElementData(elementPos);
@@ -1010,7 +1019,7 @@ public List<DataBlock<T>> chunks(final List<ChunkRequest<T>> duplicates) {
 	 * Construct {@code ChunkRequests} from a list of level-0 grid positions
 	 * for reading.
 	 * <p>
-	 * The nesting level ot the returned {@code ChunkRequests} is {@code
+	 * The nesting level of the returned {@code ChunkRequests} is {@code
 	 * grid.numLevels()}, that is level of the highest-order shard + 1. This
 	 * implies that the requests are not guaranteed to be in the same shard (at
 	 * any level. {@link ChunkRequests#split() Splitting} the {@code

src/main/java/org/janelia/saalfeldlab/n5/shard/RawShard.java

@@ -28,6 +28,11 @@
  */
 package org.janelia.saalfeldlab.n5.shard;
 
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import org.janelia.saalfeldlab.n5.readdata.Range;
 import org.janelia.saalfeldlab.n5.readdata.ReadData;
 import org.janelia.saalfeldlab.n5.readdata.segment.Segment;
 import org.janelia.saalfeldlab.n5.readdata.segment.SegmentedReadData;
@@ -86,4 +91,16 @@ public void setElementData(final ReadData data, final long[] pos) {
 		final Segment segment = data == null ? null : SegmentedReadData.wrap(data).segments().get(0);
 		index.set(segment, pos);
 	}
+
+	public void prefetch(List<long[]> positions) {
+
+		final List<Range> ranges = new ArrayList<>(positions.size());
+		for (long[] pos : positions) {
+			final Segment seg = index.get(pos);
+			if (seg != null)
+				ranges.add(sourceData.location(seg));
+		}
+		sourceData.prefetch(ranges);
+	}
+
 }