feat: implement dataset codecs inside sharding codecs

* what to do when transpose it outside a shard codec is unclear

Author: bogovicj

src/main/java/org/janelia/saalfeldlab/n5/DatasetAttributes.java

@@ -210,6 +210,8 @@ protected DatasetAccess<?> createDatasetAccess() {
 
 		BlockCodecInfo currentBlockCodecInfo = blockCodecInfo;
 		DataCodecInfo[] currentDataCodecInfos = dataCodecInfos;
+		
+		DatasetCodecInfo[] datasetCodecInfos = this.datasetCodecInfos;
 
 		final NestedGrid grid = new NestedGrid(blockSizes, dimensions);
 		final BlockCodec<?>[] blockCodecs = new BlockCodec[m];
@@ -219,16 +221,33 @@ protected DatasetAccess<?> createDatasetAccess() {
 				final ShardCodecInfo info = (ShardCodecInfo) currentBlockCodecInfo;
 				currentBlockCodecInfo = info.getInnerBlockCodecInfo();
 				currentDataCodecInfos = info.getInnerDataCodecInfos();
+				if (info.getInnerDataCodecInfos() != null) {
+					if (datasetCodecInfos != null && datasetCodecInfos.length > 0) {
+						throw new N5Exception.N5JsonParseException("Found DatasetCodecs both inside and outside of shards. Not handled");
+					}
+					else
+						datasetCodecInfos = info.getInnerDatasetCodecInfos();
+				}
 			}
 		}
 
+		// add dataset codecs
+		blockCodecs[0] = blockCodecWithDatasetCodecs(this, blockCodecs[0], datasetCodecInfos);
+
+		return new DefaultDatasetAccess<>(grid, blockCodecs);
+	}
+
+	@SuppressWarnings("unchecked")
+	private static BlockCodec<?> blockCodecWithDatasetCodecs(final DatasetAttributes attributes, final BlockCodec<?> blockCodec,
+			final DatasetCodecInfo[] datasetCodecInfos) {
+
+		BlockCodec<?> result = blockCodec;
 		if (datasetCodecInfos != null) {
 			for (final DatasetCodecInfo info : datasetCodecInfos) {
-				blockCodecs[0] = DatasetCodec.concatenate(info.create(this), (BlockCodec) blockCodecs[0]);
+				result = DatasetCodec.concatenate(info.create(attributes), (BlockCodec)result);
 			}
 		}
-
-		return new DefaultDatasetAccess<>(grid, blockCodecs);
+		return result;
 	}
 
 	private static int nestingDepth(BlockCodecInfo info) {

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

@@ -65,7 +65,7 @@ public String getType() {
 	@NameConfig.Parameter(value = "index_codecs")
 	private CodecInfo[] indexCodecs;
 
-	private transient DatasetCodecInfo[] innerDatasetCodecInfo;
+	private transient DatasetCodecInfo[] innerDatasetCodecInfos;
 
 	private transient BlockCodecInfo innerBlockCodecInfo;
 
@@ -82,13 +82,15 @@ public String getType() {
 
 	public DefaultShardCodecInfo(
 			final int[] innerBlockSize,
+			final DatasetCodecInfo[] innerDatasetCodecInfos,
 			final BlockCodecInfo innerBlockCodecInfo,
 			final DataCodecInfo[] innerDataCodecInfos,
 			final BlockCodecInfo indexBlockCodecInfo,
 			final DataCodecInfo[] indexDataCodecInfos,
 			final IndexLocation indexLocation) {
 
 		this.innerBlockSize = innerBlockSize;
+		this.innerDatasetCodecInfos = innerDatasetCodecInfos;
 		this.innerBlockCodecInfo = innerBlockCodecInfo;
 		this.innerDataCodecInfos = innerDataCodecInfos;
 		this.indexBlockCodecInfo = indexBlockCodecInfo;
@@ -98,6 +100,23 @@ public DefaultShardCodecInfo(
 		codecs = concatenateCodecs(innerBlockCodecInfo, innerDataCodecInfos);
 		indexCodecs = concatenateCodecs(indexBlockCodecInfo, indexDataCodecInfos);
 	}
+	
+	public DefaultShardCodecInfo(
+			final int[] innerBlockSize,
+			final BlockCodecInfo innerBlockCodecInfo,
+			final DataCodecInfo[] innerDataCodecInfos,
+			final BlockCodecInfo indexBlockCodecInfo,
+			final DataCodecInfo[] indexDataCodecInfos,
+			final IndexLocation indexLocation) {
+
+		this(innerBlockSize,
+				null,
+				innerBlockCodecInfo,
+				innerDataCodecInfos,
+				indexBlockCodecInfo,
+				indexDataCodecInfos,
+				indexLocation);
+	}
 
 	private void build() {
 
@@ -111,7 +130,7 @@ private void build() {
 		// codecs and indexCodecs
 
 		final CodecParser parser = new CodecParser(codecs);
-		innerDatasetCodecInfo = parser.datasetCodecInfos;
+		innerDatasetCodecInfos = parser.datasetCodecInfos;
 		innerBlockCodecInfo = parser.blockCodecInfo;
 		innerDataCodecInfos = parser.dataCodecInfos;
 
@@ -130,6 +149,11 @@ public int[] getInnerBlockSize() {
 		return innerBlockSize;
 	}
 
+	@Override
+	public DatasetCodecInfo[] getInnerDatasetCodecInfos() {
+		return innerDatasetCodecInfos;
+	}
+
 	@Override
 	public BlockCodecInfo getInnerBlockCodecInfo() {
 		return innerBlockCodecInfo;

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

@@ -31,6 +31,7 @@
 import org.janelia.saalfeldlab.n5.DataType;
 import org.janelia.saalfeldlab.n5.codec.BlockCodecInfo;
 import org.janelia.saalfeldlab.n5.codec.DataCodecInfo;
+import org.janelia.saalfeldlab.n5.codec.DatasetCodecInfo;
 import org.janelia.saalfeldlab.n5.shard.ShardIndex.IndexLocation;
 
 public interface ShardCodecInfo extends BlockCodecInfo {
@@ -42,6 +43,12 @@ public interface ShardCodecInfo extends BlockCodecInfo {
 	 */
 	int[] getInnerBlockSize();
 
+	/**
+	 *
+	 * @return the collection of DatasetCodecInfo applied to data blocks for this shard
+	 */
+	DatasetCodecInfo[] getInnerDatasetCodecInfos();
+
 	/**
 	 * BlockCodecInfo for shard elements (either nested shard or DataBlock)
 	 *