fix: transpose codec inside shard codec

Author: bogovicj

src/main/java/org/janelia/saalfeldlab/n5/codec/CodecParser.java

@@ -0,0 +1,61 @@
+package org.janelia.saalfeldlab.n5.codec;
+
+import java.util.ArrayList;
+
+import org.janelia.saalfeldlab.n5.DatasetAttributes;
+import org.janelia.saalfeldlab.n5.N5Exception;
+
+public class CodecParser {
+
+	public DatasetCodecInfo[] datasetCodecInfos;
+	public BlockCodecInfo blockCodecInfo;
+	public DataCodecInfo[] dataCodecInfos;
+
+	public CodecParser(CodecInfo[] codecs) {
+
+		parse(codecs);
+	}
+
+	private void parse(CodecInfo[] codecs) {
+
+		final ArrayList<DataCodecInfo> dataCodecList = new ArrayList<>();
+		final ArrayList<DatasetCodecInfo> datasetCodecList = new ArrayList<>();
+
+		boolean foundBlockCodec = false;
+
+		int i = 0;
+		int blockCodecIndex = -1;
+		for (CodecInfo codec : codecs) {
+			if (!foundBlockCodec) {
+
+				if (codec instanceof BlockCodecInfo) {
+					blockCodecInfo = (BlockCodecInfo)codec;
+					foundBlockCodec = true;
+					blockCodecIndex = i;
+				} else if (codec instanceof DatasetCodecInfo)
+					datasetCodecList.add((DatasetCodecInfo)codec);
+				else
+					throw new N5Exception("Codec at index " + i + " is a DataCodec, but came before a BlockCodec.");
+
+			} else if (codec instanceof BlockCodecInfo)
+				throw new N5Exception("Codec at index " + i + " is a BlockCodec, but came after a BlockCodec at position " + blockCodecIndex);
+			else if (codec instanceof DatasetCodecInfo)
+				throw new N5Exception("Codec at index " + i + " is a DatasetCodec, but came after a BlockCodec at position " + blockCodecIndex);
+			else
+				dataCodecList.add((DataCodecInfo)codec);
+
+			i++;
+		}
+
+		datasetCodecInfos = datasetCodecList.stream().toArray(n -> new DatasetCodecInfo[n]);
+		dataCodecInfos = dataCodecList.stream().toArray(n -> new DataCodecInfo[n]);
+	}
+
+	private static CodecInfo[] concatenateCodecs(DatasetAttributes attributes) {
+
+		final CodecInfo[] codecs = new CodecInfo[attributes.getDataCodecInfos().length + 1];
+		codecs[0] = attributes.getBlockCodecInfo();
+		System.arraycopy(attributes.getDataCodecInfos(), 0, codecs, 1, attributes.getDataCodecInfos().length);
+		return codecs;
+	}
+}

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

@@ -34,7 +34,9 @@
 import org.janelia.saalfeldlab.n5.codec.BlockCodec;
 import org.janelia.saalfeldlab.n5.codec.BlockCodecInfo;
 import org.janelia.saalfeldlab.n5.codec.CodecInfo;
+import org.janelia.saalfeldlab.n5.codec.CodecParser;
 import org.janelia.saalfeldlab.n5.codec.DataCodecInfo;
+import org.janelia.saalfeldlab.n5.codec.DatasetCodecInfo;
 import org.janelia.saalfeldlab.n5.serialization.N5Annotations;
 import org.janelia.saalfeldlab.n5.serialization.NameConfig;
 import org.janelia.saalfeldlab.n5.shard.ShardIndex.IndexLocation;
@@ -63,6 +65,8 @@ public String getType() {
 	@NameConfig.Parameter(value = "index_codecs")
 	private CodecInfo[] indexCodecs;
 
+	private transient DatasetCodecInfo[] innerDatasetCodecInfo;
+
 	private transient BlockCodecInfo innerBlockCodecInfo;
 
 	private transient DataCodecInfo[] innerDataCodecInfos;
@@ -106,14 +110,10 @@ private void build() {
 		// from
 		// codecs and indexCodecs
 
-		if (codecs[0] instanceof BlockCodecInfo)
-			innerBlockCodecInfo = (BlockCodecInfo)codecs[0];
-		else
-			throw new N5Exception("Codec at index " + 0 + " must be a BlockCodec.");
-
-		innerDataCodecInfos = new DataCodecInfo[codecs.length - 1];
-		for (int i = 1; i < codecs.length; i++)
-			innerDataCodecInfos[i - 1] = (DataCodecInfo)codecs[i];
+		final CodecParser parser = new CodecParser(codecs);
+		innerDatasetCodecInfo = parser.datasetCodecInfos;
+		innerBlockCodecInfo = parser.blockCodecInfo;
+		innerDataCodecInfos = parser.dataCodecInfos;
 
 		if (indexCodecs[0] instanceof BlockCodecInfo)
 			indexBlockCodecInfo = (BlockCodecInfo)indexCodecs[0];