Merge remote-tracking branch 'origin/master' into feat/attributesKey

# Conflicts:
#	src/main/java/org/janelia/saalfeldlab/n5/DatasetAttributes.java
#	src/main/java/org/janelia/saalfeldlab/n5/GsonUtils.java

Author: bogovicj

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

@@ -60,24 +60,25 @@
 import java.lang.annotation.RetentionPolicy;
 import java.lang.annotation.Target;
 
-import org.janelia.saalfeldlab.n5.codec.BytesCodec;
-import org.janelia.saalfeldlab.n5.codec.Codec;
+import org.janelia.saalfeldlab.n5.codec.DataCodec;
+import org.janelia.saalfeldlab.n5.codec.DataCodecInfo;
+import org.janelia.saalfeldlab.n5.codec.CodecInfo;
 import org.scijava.annotations.Indexable;
 
 /**
- * This interface is used to indicate that a {@link BytesCodec} can be
+ * This interface is used to indicate that a {@link DataCodec} can be
  * serialized as a "compression" for the N5 format (using the N5 API).
  * <p>
- * N5Readers and N5Writers for the N5 format can declare BytesCodecs that
+ * N5Readers and N5Writers for the N5 format can declare DataCodecs that
  * implement this interface so that the {@link CompressionAdapter} is used for
  * serialization.
  * <p>
- * See also: an alternative method for serializing general {@link Codec}s is
+ * See also: an alternative method for serializing general {@link CodecInfo}s is
  * with the {@link NameConfigAdapter}.
  *
  * @author Stephan Saalfeld
  */
-public interface Compression extends Serializable, BytesCodec {
+public interface Compression extends Serializable, DataCodecInfo, DataCodec {
 
 	/**
 	 * Annotation for runtime discovery of compression schemes.
@@ -110,4 +111,9 @@ default String getType() {
 		else
 			return compressionType.value();
 	}
+
+	@Override
+	default DataCodec create() {
+		return this;
+	}
 }

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

@@ -32,10 +32,10 @@
 import java.util.Arrays;
 import java.util.HashMap;
 
-import org.janelia.saalfeldlab.n5.codec.ArrayCodec;
-import org.janelia.saalfeldlab.n5.codec.BytesCodec;
-import org.janelia.saalfeldlab.n5.codec.DataBlockSerializer;
-import org.janelia.saalfeldlab.n5.codec.N5ArrayCodec;
+import org.janelia.saalfeldlab.n5.codec.BlockCodecInfo;
+import org.janelia.saalfeldlab.n5.codec.BlockCodec;
+import org.janelia.saalfeldlab.n5.codec.DataCodecInfo;
+import org.janelia.saalfeldlab.n5.codec.N5BlockCodecInfo;
 
 /**
  * Mandatory dataset attributes:
@@ -66,38 +66,39 @@ public class DatasetAttributes implements Serializable {
 	private final int[] blockSize;
 	private final DataType dataType;
 
-	private final ArrayCodec arrayCodec;
-	private final BytesCodec[] byteCodecs;
+	private final BlockCodecInfo blockCodecInfo;
+	private final DataCodecInfo[] dataCodecInfos;
 
-	private final DataBlockSerializer<?> dataBlockSerializer;
+	private final BlockCodec<?> blockCodec;
 
 	public DatasetAttributes(
 			final long[] dimensions,
 			final int[] blockSize,
 			final DataType dataType,
-			final ArrayCodec arrayCodec,
-			final BytesCodec... codecs) {
+			final BlockCodecInfo blockCodecInfo,
+			final DataCodecInfo... dataCodecInfos) {
 
 		this.dimensions = dimensions;
 		this.blockSize = blockSize;
 		this.dataType = dataType;
 
-		this.arrayCodec = arrayCodec == null ? defaultArrayCodec() : arrayCodec;
-		byteCodecs = Arrays.stream(codecs).filter(it -> !(it instanceof RawCompression)).toArray(BytesCodec[]::new);
-		dataBlockSerializer = this.arrayCodec.initialize(this, byteCodecs);
+		this.blockCodecInfo = blockCodecInfo == null ? defaultBlockCodecInfo() : blockCodecInfo;
+		this.dataCodecInfos = Arrays.stream(dataCodecInfos).filter(it -> !(it instanceof RawCompression)).toArray(DataCodecInfo[]::new);
+		blockCodec = this.blockCodecInfo.create(this, this.dataCodecInfos);
 	}
 
 	public DatasetAttributes(
 			final long[] dimensions,
 			final int[] blockSize,
 			final DataType dataType,
-			final BytesCodec compression) {
+			final DataCodecInfo compression) {
 
 		this(dimensions, blockSize, dataType, null, compression);
 	}
 
-	protected ArrayCodec defaultArrayCodec() {
-		return new N5ArrayCodec();
+	protected BlockCodecInfo defaultBlockCodecInfo() {
+
+		return new N5BlockCodecInfo();
 	}
 
 	public long[] getDimensions() {
@@ -117,7 +118,7 @@ public int[] getBlockSize() {
 
 	public Compression getCompression() {
 
-		return Arrays.stream(byteCodecs)
+		return Arrays.stream(dataCodecInfos)
 				.filter(it -> it instanceof Compression)
 				.map(it -> (Compression)it)
 				.findFirst()
@@ -130,23 +131,24 @@ public DataType getDataType() {
 	}
 
 	/**
-	 * Get the {@link ArrayCodec} for this dataset.
+	 * Get the {@link BlockCodecInfo} for this dataset.
 	 *
-	 * @return the {@code ArrayCodec} for this dataset
+	 * @return the {@code BlockCodecInfo} for this dataset
 	 */
-	public ArrayCodec getArrayCodec() {
+	public BlockCodecInfo getBlockCodecInfo() {
 
-		return arrayCodec;
+		return blockCodecInfo;
 	}
 
-	public BytesCodec[] getCodecs() {
+	public DataCodecInfo[] getDataCodecInfos() {
 
-		return byteCodecs;
+		return dataCodecInfos;
 	}
 
 	@SuppressWarnings("unchecked")
-	<T> DataBlockSerializer<T> getDataBlockSerializer() {
-		return (DataBlockSerializer<T>) dataBlockSerializer;
+	<T> BlockCodec<T> getBlockCodec() {
+
+		return (BlockCodec<T>) blockCodec;
 	}
 
 	public HashMap<String, Object> asMap() {

src/main/java/org/janelia/saalfeldlab/n5/GsonKeyValueN5Reader.java

@@ -100,7 +100,7 @@ default DataBlock<?> readBlock(
 
 		try {
 			final ReadData blockData = getKeyValueAccess().createReadData(path);
-			return datasetAttributes.getDataBlockSerializer().decode(blockData, gridPosition);
+			return datasetAttributes.getBlockCodec().decode(blockData, gridPosition);
 		} catch (N5Exception.N5NoSuchKeyException e) {
 			return null;
 		}

src/main/java/org/janelia/saalfeldlab/n5/GsonKeyValueN5Writer.java

@@ -246,7 +246,7 @@ default <T> void writeBlock(
 				final LockedChannel lock = getKeyValueAccess().lockForWriting(blockPath);
 				final OutputStream out = lock.newOutputStream()
 		) {
-			datasetAttributes.<T>getDataBlockSerializer().encode(dataBlock).writeTo(out);
+			datasetAttributes.<T>getBlockCodec().encode(dataBlock).writeTo(out);
 		} catch (final IOException | UncheckedIOException e) {
 			throw new N5IOException(
 					"Failed to write block " + Arrays.toString(dataBlock.getGridPosition()) + " into dataset " + path,

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

@@ -63,15 +63,13 @@
 import java.util.regex.Matcher;
 
 import com.google.gson.Gson;
-import com.google.gson.GsonBuilder;
 import com.google.gson.JsonArray;
 import com.google.gson.JsonElement;
 import com.google.gson.JsonObject;
 import com.google.gson.JsonPrimitive;
 import com.google.gson.JsonSyntaxException;
 import com.google.gson.reflect.TypeToken;
 import org.janelia.saalfeldlab.n5.N5Exception.N5JsonParseException;
-import org.janelia.saalfeldlab.n5.codec.Codec;
 
 /**
  * Utility class for working with  JSON.

src/main/java/org/janelia/saalfeldlab/n5/N5KeyValueReader.java

@@ -33,7 +33,7 @@
 
 import com.google.gson.JsonElement;
 import org.janelia.saalfeldlab.n5.cache.N5JsonCache;
-import org.janelia.saalfeldlab.n5.codec.Codec;
+import org.janelia.saalfeldlab.n5.codec.CodecInfo;
 
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
@@ -163,7 +163,7 @@ private boolean inferExistence(String path) {
 	protected GsonBuilder registerGson(final GsonBuilder gsonBuilder) {
 
 		gsonBuilder.registerTypeAdapter(DataType.class, new DataType.JsonAdapter());
-		gsonBuilder.registerTypeHierarchyAdapter(Codec.class, NameConfigAdapter.getJsonAdapter(Codec.class));
+		gsonBuilder.registerTypeHierarchyAdapter(CodecInfo.class, NameConfigAdapter.getJsonAdapter(CodecInfo.class));
 		gsonBuilder.registerTypeHierarchyAdapter(Compression.class, CompressionAdapter.getJsonAdapter());
 		gsonBuilder.disableHtmlEscaping();
 		return gsonBuilder;

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

@@ -38,7 +38,7 @@
  * @param <T>
  * 		type of the data contained in the DataBlock
  */
-public interface DataBlockSerializer<T> {
+public interface BlockCodec<T> {
 
 	ReadData encode(DataBlock<T> dataBlock) throws N5IOException;
 

…eldlab/n5/codec/DataBlockSerializer.java …lia/saalfeldlab/n5/codec/BlockCodec.javasrc/main/java/org/janelia/saalfeldlab/n5/codec/DataBlockSerializer.java renamed to src/main/java/org/janelia/saalfeldlab/n5/codec/BlockCodec.java src/main/java/org/janelia/saalfeldlab/n5/codec/DataBlockSerializer.java renamed to src/main/java/org/janelia/saalfeldlab/n5/codec/BlockCodec.java

@@ -0,0 +1,25 @@
+package org.janelia.saalfeldlab.n5.codec;
+
+import java.util.Arrays;
+import org.janelia.saalfeldlab.n5.DataBlock;
+import org.janelia.saalfeldlab.n5.DatasetAttributes;
+import org.janelia.saalfeldlab.n5.readdata.ReadData;
+
+/**
+ * Metadata and factory for a particular family of {@code BlockCodec}.
+ * <p>
+ * {@code BlockCodec}s encode {@link DataBlock}s into {@link ReadData} and
+ * decode {@link ReadData} into {@link DataBlock}s.
+ */
+public interface BlockCodecInfo extends CodecInfo {
+
+	<T> BlockCodec<T> create(final DatasetAttributes attributes, final DataCodec... codecs);
+
+	default <T> BlockCodec<T> create(final DatasetAttributes attributes, final DataCodecInfo... codecInfos) {
+		final DataCodec[] codecs = new DataCodec[codecInfos.length];
+		Arrays.setAll(codecs, i -> codecInfos[i].create());
+		return create(attributes, codecs);
+	}
+
+	// TODO: Should we have both create() signatures?
+}

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

@@ -11,7 +11,7 @@
  * Zarr.
  */
 @NameConfig.Prefix("codec")
-public interface Codec extends Serializable {
+public interface CodecInfo extends Serializable {
 
 	String getType();
 }