Refactor for compatibility with upcoming Codecs Release

src/main/java/org/janelia/saalfeldlab/n5/Bzip2Compression.java

@@ -60,9 +60,9 @@ public boolean equals(final Object other) {
 	}
 
 	@Override
-	public ReadData decode(final ReadData readData, final int decodedLength) throws IOException {
-		final InputStream inflater = new BZip2CompressorInputStream(readData.inputStream());
-		return ReadData.from(inflater, decodedLength);
+	public ReadData decode(final ReadData readData) throws IOException {
+
+		return ReadData.from(new BZip2CompressorInputStream(readData.inputStream()));
 	}
 
 	@Override

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

@@ -85,15 +85,13 @@ default String getType() {
 	 *
 	 * @param readData
 	 * 		data to decode
-	 * @param decodedLength
-	 * 		length of the decoded data (-1 if unknown)
 	 *
 	 * @return decoded ReadData
 	 *
 	 * @throws IOException
 	 * 		if any I/O error occurs
 	 */
-	ReadData decode(ReadData readData, int decodedLength) throws IOException;
+	ReadData decode(ReadData readData) throws IOException;
 
 	/**
 	 * Encode the given {@code readData}.

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

@@ -95,6 +95,20 @@ static int getNumElements(final int[] size) {
 	 */
 	interface DataBlockFactory<T> {
 
+
+		/**
+		 * Factory for {@link DataBlock DataBlocks}.
+		 *
+		 * @param blockSize
+		 *            the block size
+		 * @param gridPosition
+		 *            the grid position
+		 * @param data
+		 *            the number of elements (not necessarily one element per block
+		 *            element)
+		 * @return the data block
+		 */
 		DataBlock<T> createDataBlock(int[] blockSize, long[] gridPosition, T data);
+
 	}
 }

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

@@ -6,10 +6,10 @@
  * modification, are permitted provided that the following conditions are met:
  *
  * 1. Redistributions of source code must retain the above copyright notice,
- *    this list of conditions and the following disclaimer.
+ * this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
- *    this list of conditions and the following disclaimer in the documentation
- *    and/or other materials provided with the distribution.
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
  *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
@@ -34,10 +34,6 @@
 import com.google.gson.JsonPrimitive;
 import com.google.gson.JsonSerializationContext;
 import com.google.gson.JsonSerializer;
-import org.janelia.saalfeldlab.n5.codec.N5Codecs;
-import org.janelia.saalfeldlab.n5.codec.DataBlockCodec;
-import org.janelia.saalfeldlab.n5.codec.N5Codecs.DataBlockCodecFactory;
-
 /**
  * Enumerates available data types.
  *
@@ -47,101 +43,90 @@ public enum DataType {
 
 	UINT8(
 			"uint8",
-			(blockSize, gridPosition, numElements) -> new ByteArrayDataBlock(
-					blockSize,
-					gridPosition,
-					new byte[numElements]),
-			N5Codecs.BYTE),
+			(blockSize, gridPosition, numElements) -> {
+				ByteArrayDataBlock dataBlock = new ByteArrayDataBlock(blockSize, gridPosition, new byte[numElements]);
+
+
+				return new ByteArrayDataBlock(
+						blockSize,
+						gridPosition,
+						new byte[numElements]);
+			}),
 	UINT16(
 			"uint16",
 			(blockSize, gridPosition, numElements) -> new ShortArrayDataBlock(
 					blockSize,
 					gridPosition,
-					new short[numElements]),
-			N5Codecs.SHORT),
+					new short[numElements])),
 	UINT32(
 			"uint32",
 			(blockSize, gridPosition, numElements) -> new IntArrayDataBlock(
 					blockSize,
 					gridPosition,
-					new int[numElements]),
-			N5Codecs.INT),
+					new int[numElements])),
 	UINT64(
 			"uint64",
 			(blockSize, gridPosition, numElements) -> new LongArrayDataBlock(
 					blockSize,
 					gridPosition,
-					new long[numElements]),
-			N5Codecs.LONG),
+					new long[numElements])),
 	INT8(
 			"int8",
 			(blockSize, gridPosition, numElements) -> new ByteArrayDataBlock(
 					blockSize,
 					gridPosition,
-					new byte[numElements]),
-			N5Codecs.BYTE),
+					new byte[numElements])),
 	INT16(
 			"int16",
 			(blockSize, gridPosition, numElements) -> new ShortArrayDataBlock(
 					blockSize,
 					gridPosition,
-					new short[numElements]),
-			N5Codecs.SHORT),
+					new short[numElements])),
 	INT32(
 			"int32",
 			(blockSize, gridPosition, numElements) -> new IntArrayDataBlock(
 					blockSize,
 					gridPosition,
-					new int[numElements]),
-			N5Codecs.INT),
+					new int[numElements])),
 	INT64(
 			"int64",
 			(blockSize, gridPosition, numElements) -> new LongArrayDataBlock(
 					blockSize,
 					gridPosition,
-					new long[numElements]),
-			N5Codecs.LONG),
+					new long[numElements])),
 	FLOAT32(
 			"float32",
 			(blockSize, gridPosition, numElements) -> new FloatArrayDataBlock(
 					blockSize,
 					gridPosition,
-					new float[numElements]),
-			N5Codecs.FLOAT),
+					new float[numElements])),
 	FLOAT64(
 			"float64",
 			(blockSize, gridPosition, numElements) -> new DoubleArrayDataBlock(
 					blockSize,
 					gridPosition,
-					new double[numElements]),
-			N5Codecs.DOUBLE),
+					new double[numElements])),
 	STRING(
 			"string",
 			(blockSize, gridPosition, numElements) -> new StringDataBlock(
 					blockSize,
 					gridPosition,
-					new String[numElements]),
-			N5Codecs.STRING),
+					new String[numElements])),
 	OBJECT(
 			"object",
 			(blockSize, gridPosition, numElements) -> new ByteArrayDataBlock(
 					blockSize,
 					gridPosition,
-					new byte[numElements]),
-			N5Codecs.OBJECT);
-
+					new byte[numElements]));
 
 	private final String label;
 
 	private final DataBlockFactory dataBlockFactory;
 
-	private final DataBlockCodecFactory<?> dataBlockCodecFactory;
-
-	DataType(final String label, final DataBlockFactory dataBlockFactory, final DataBlockCodecFactory<?> dataBlockCodecFactory) {
+	DataType(final String label, final DataBlockFactory dataBlockFactory) {
 
 		this.label = label;
 		this.dataBlockFactory = dataBlockFactory;
-		this.dataBlockCodecFactory = dataBlockCodecFactory;
 	}
 
 	@Override
@@ -190,19 +175,6 @@ public DataBlock<?> createDataBlock(final int[] blockSize, final long[] gridPosi
 		return dataBlockFactory.createDataBlock(blockSize, gridPosition, DataBlock.getNumElements(blockSize));
 	}
 
-	/**
-	 * Get the default {@link DataBlockCodec}, with the specified {@code
-	 * compression}, for {@link DataBlock DataBlocks} of this {@code DataType}.
-	 * The default codec is used for de/serializing blocks to N5 format.
-	 *
-	 * @param compression
-	 *
-	 * @return the default {@code DataBlockCodec}
-	 */
-	public DataBlockCodec<?> createDataBlockCodec(final Compression compression) {
-		return dataBlockCodecFactory.createDataBlockCodec(compression);
-	}
-
 	private interface DataBlockFactory {
 
 		DataBlock<?> createDataBlock(final int[] blockSize, final long[] gridPosition, final int numElements);

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

@@ -28,7 +28,9 @@
 import java.io.Serializable;
 import java.util.Arrays;
 import java.util.HashMap;
+
 import org.janelia.saalfeldlab.n5.codec.DataBlockCodec;
+import org.janelia.saalfeldlab.n5.codec.N5Codecs;
 
 /**
  * Mandatory dataset attributes:
@@ -58,16 +60,16 @@ public class DatasetAttributes implements Serializable {
 	private final long[] dimensions;
 	private final int[] blockSize;
 	private final DataType dataType;
-	private final Compression compression;
 	private final DataBlockCodec<?> dataBlockCodec;
+	private final Compression compression;
 
 	public DatasetAttributes(
 			final long[] dimensions,
 			final int[] blockSize,
 			final DataType dataType,
 			final Compression compression) {
 
-		this(dimensions, blockSize, dataType, compression, dataType.createDataBlockCodec(compression));
+		this(dimensions, blockSize, dataType, compression, N5Codecs.createDataBlockCodec(dataType, compression));
 	}
 
 	protected DatasetAttributes(
@@ -118,7 +120,7 @@ public DataType getDataType() {
 	 * @return the {@code DataBlockCodec} for this dataset
 	 */
 	public <T> DataBlockCodec<T> getDataBlockCodec() {
-		return (DataBlockCodec<T>) dataBlockCodec;
+		return (DataBlockCodec<T>)dataBlockCodec;
 	}
 
 	public HashMap<String, Object> asMap() {

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

@@ -85,9 +85,9 @@ private InputStream decode(final InputStream in) throws IOException {
 	}
 
 	@Override
-	public ReadData decode(final ReadData readData, final int decodedLength) throws IOException {
-		final InputStream inflater = decode(readData.inputStream());
-		return ReadData.from(inflater, decodedLength);
+	public ReadData decode(final ReadData readData) throws IOException {
+
+		return ReadData.from(decode(readData.inputStream()));
 	}
 
 	@Override

src/main/java/org/janelia/saalfeldlab/n5/Lz4Compression.java

@@ -60,9 +60,9 @@ public boolean equals(final Object other) {
 	}
 
 	@Override
-	public ReadData decode(final ReadData readData, final int decodedLength) throws IOException {
-		final InputStream inflater = new LZ4BlockInputStream(readData.inputStream());
-		return ReadData.from(inflater, decodedLength);
+	public ReadData decode(final ReadData readData) throws IOException {
+
+		return ReadData.from(new LZ4BlockInputStream(readData.inputStream()));
 	}
 
 	@Override

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

@@ -35,10 +35,7 @@ public class RawCompression implements Compression {
 
 	@Override
 	public boolean equals(final Object other) {
-		if (other == null || other.getClass() != RawCompression.class)
-			return false;
-		else
-			return true;
+		return other != null && other.getClass() == RawCompression.class;
 	}
 
 	@Override
@@ -47,7 +44,7 @@ public ReadData encode(final ReadData readData) {
 	}
 
 	@Override
-	public ReadData decode(final ReadData readData, int decodedLength) {
+	public ReadData decode(final ReadData readData) {
 		return readData;
 	}
 }

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

@@ -60,9 +60,9 @@ public boolean equals(final Object other) {
 	}
 
 	@Override
-	public ReadData decode(final ReadData readData, final int decodedLength) throws IOException {
-		final InputStream inflater = new XZCompressorInputStream(readData.inputStream());
-		return ReadData.from(inflater, decodedLength);
+	public ReadData decode(final ReadData readData) throws IOException {
+
+		return ReadData.from(new XZCompressorInputStream(readData.inputStream()));
 	}
 
 	@Override