refactor: migrate previous batching/aggregate work to current development

feat: use the aggregate/prefetch logic with VolatileReadData.

By default, `VolatileReadData.from` now uses AggregatingSliceTrackingLazyRead. This is useful to ensure the default VolatileReadData behaves reasonably even for reading many chunks from the same shard.

Author: cmhulbert

src/main/java/org/janelia/saalfeldlab/n5/readdata/VolatileReadData.java

@@ -1,7 +1,7 @@
 package org.janelia.saalfeldlab.n5.readdata;
 
-import java.io.InputStream;
 import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
+import org.janelia.saalfeldlab.n5.readdata.slices.AggregatingSliceTrackingLazyRead;
 
 /**
  * During its life-time, the content of a {@code VolatileReadData} should not be
@@ -29,7 +29,8 @@ public interface VolatileReadData extends ReadData, AutoCloseable {
 	 * @return a new VolatileReadData
 	 */
 	static VolatileReadData from(final LazyRead lazyRead) {
-		return new LazyReadData(lazyRead);
+		final LazyRead aggregatingLazyRead = new AggregatingSliceTrackingLazyRead(lazyRead);
+		return new LazyReadData(aggregatingLazyRead);
 	}
 
 }

src/main/java/org/janelia/saalfeldlab/n5/readdata/kva/KvaPlayground.java

@@ -28,16 +28,17 @@
  */
 package org.janelia.saalfeldlab.n5.readdata.segment;
 
+import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
+import org.janelia.saalfeldlab.n5.readdata.Range;
+import org.janelia.saalfeldlab.n5.readdata.ReadData;
+
 import java.io.InputStream;
 import java.io.OutputStream;
 import java.nio.ByteBuffer;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
-import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
-import org.janelia.saalfeldlab.n5.readdata.Range;
-import org.janelia.saalfeldlab.n5.readdata.ReadData;
 
 /**
  * Implementation of a {@link SegmentedReadData} wrapper around an existing {@code ReadData} delegate.

src/main/java/org/janelia/saalfeldlab/n5/readdata/kva/LazyRead.java

@@ -1,10 +1,11 @@
-package org.janelia.saalfeldlab.n5.readdata.kva;
-
-import java.util.Collection;
+package org.janelia.saalfeldlab.n5.readdata.slices;
 
 import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
+import org.janelia.saalfeldlab.n5.readdata.LazyRead;
 import org.janelia.saalfeldlab.n5.readdata.Range;
 
+import java.util.Collection;
+
 public class AggregatingSliceTrackingLazyRead extends SliceTrackingLazyRead {
 
 	public AggregatingSliceTrackingLazyRead(final LazyRead delegate) {

src/main/java/org/janelia/saalfeldlab/n5/readdata/kva/LazyReadData.java

@@ -1,9 +1,11 @@
-package org.janelia.saalfeldlab.n5.readdata.kva;
+package org.janelia.saalfeldlab.n5.readdata.slices;
 
-import java.util.Collection;
 import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
+import org.janelia.saalfeldlab.n5.readdata.LazyRead;
 import org.janelia.saalfeldlab.n5.readdata.Range;
 
+import java.util.Collection;
+
 public class DefaultSliceTrackingLazyRead extends SliceTrackingLazyRead {
 
 	public DefaultSliceTrackingLazyRead(final LazyRead delegate) {

src/main/java/org/janelia/saalfeldlab/n5/readdata/kva/VolatileReadData.java

@@ -1,12 +1,14 @@
-package org.janelia.saalfeldlab.n5.readdata.kva;
+package org.janelia.saalfeldlab.n5.readdata.slices;
+
+import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
+import org.janelia.saalfeldlab.n5.readdata.LazyRead;
+import org.janelia.saalfeldlab.n5.readdata.Range;
+import org.janelia.saalfeldlab.n5.readdata.ReadData;
 
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
-import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
-import org.janelia.saalfeldlab.n5.readdata.Range;
-import org.janelia.saalfeldlab.n5.readdata.ReadData;
 
 public abstract class SliceTrackingLazyRead implements LazyRead {
 

src/main/java/org/janelia/saalfeldlab/n5/readdata/segment/DefaultSegmentedReadData.java

@@ -1,9 +1,10 @@
-package org.janelia.saalfeldlab.n5.readdata.kva;
+package org.janelia.saalfeldlab.n5.readdata.slices;
+
+import org.janelia.saalfeldlab.n5.readdata.Range;
 
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.List;
-import org.janelia.saalfeldlab.n5.readdata.Range;
 
 class Slices {