Merge pull request #94 from minnerbe/feature/vlstring-io

Variable length string array support

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

@@ -102,6 +102,12 @@ public enum DataType {
 					blockSize,
 					gridPosition,
 					new double[numElements])),
+	VLENSTRING(
+			"String(-1)",
+			(blockSize, gridPosition, numElements) -> new VLenStringDataBlock(
+					blockSize,
+					gridPosition,
+					new byte[numElements])),
 	OBJECT(
 			"object",
 			(blockSize, gridPosition, numElements) -> new ByteArrayDataBlock(
@@ -111,9 +117,9 @@ public enum DataType {
 
 	private final String label;
 
-	private DataBlockFactory dataBlockFactory;
+	private final DataBlockFactory dataBlockFactory;
 
-	private DataType(final String label, final DataBlockFactory dataBlockFactory) {
+	DataType(final String label, final DataBlockFactory dataBlockFactory) {
 
 		this.label = label;
 		this.dataBlockFactory = dataBlockFactory;
@@ -165,9 +171,9 @@ public DataBlock<?> createDataBlock(final int[] blockSize, final long[] gridPosi
 		return dataBlockFactory.createDataBlock(blockSize, gridPosition, DataBlock.getNumElements(blockSize));
 	}
 
-	private static interface DataBlockFactory {
+	private interface DataBlockFactory {
 
-		public DataBlock<?> createDataBlock(final int[] blockSize, final long[] gridPosition, final int numElements);
+		DataBlock<?> createDataBlock(final int[] blockSize, final long[] gridPosition, final int numElements);
 	}
 
 	static public class JsonAdapter implements JsonDeserializer<DataType>, JsonSerializer<DataType> {

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

@@ -0,0 +1,87 @@
+/**
+ * Copyright (c) 2017, Stephan Saalfeld
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * 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.
+ * 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 SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.janelia.saalfeldlab.n5;
+
+import java.io.ByteArrayOutputStream;
+import java.nio.ByteBuffer;
+import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
+
+public class VLenStringDataBlock extends AbstractDataBlock<String[]> {
+
+    protected static final Charset ENCODING = StandardCharsets.UTF_8;
+    protected static final String NULLCHAR = "\0";
+    protected byte[] serializedData = null;
+    protected String[] actualData = null;
+
+    public VLenStringDataBlock(final int[] size, final long[] gridPosition, final String[] data) {
+        super(size, gridPosition, new String[0]);
+        actualData = data;
+    }
+
+    public VLenStringDataBlock(final int[] size, final long[] gridPosition, final byte[] data) {
+        super(size, gridPosition, new String[0]);
+        serializedData = data;
+    }
+
+    @Override
+    public ByteBuffer toByteBuffer() {
+        if (serializedData == null)
+            serializedData = serialize(actualData);
+        return ByteBuffer.wrap(serializedData);
+    }
+
+    @Override
+    public void readData(final ByteBuffer buffer) {
+        if (buffer.array() != serializedData)
+            buffer.get(serializedData);
+        actualData = deserialize(buffer.array());
+    }
+
+    protected byte[] serialize(String[] strings) {
+        final String flattenedArray = String.join(NULLCHAR, strings) + NULLCHAR;
+        return flattenedArray.getBytes(ENCODING);
+    }
+
+    protected String[] deserialize(byte[] rawBytes) {
+        final String rawChars = new String(rawBytes, ENCODING);
+        return rawChars.split(NULLCHAR);
+    }
+
+    @Override
+    public int getNumElements() {
+        if (serializedData == null)
+            serializedData = serialize(actualData);
+        return serializedData.length;
+    }
+
+    @Override
+    public String[] getData() {
+        if (actualData == null)
+            actualData = deserialize(serializedData);
+        return actualData;
+    }
+}