Add a DataHandle which operates on a BytesLocation

This was migrated from SCIFIO/Bio-Formats's ByteArrayHandle.

Author: ctrueden

src/main/java/org/scijava/io/BytesHandle.java

@@ -0,0 +1,301 @@
+/*
+ * #%L
+ * SciJava Common shared library for SciJava software.
+ * %%
+ * Copyright (C) 2009 - 2016 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
+ * %%
+ * 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 HOLDERS 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.
+ * #L%
+ */
+
+package org.scijava.io;
+
+import java.io.EOFException;
+import java.io.IOException;
+import java.nio.BufferUnderflowException;
+import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
+
+import org.scijava.plugin.Plugin;
+
+/**
+ * {@link DataHandle} for a {@link BytesLocation}.
+ * 
+ * @author Curtis Rueden
+ * @author Melissa Linkert
+ */
+@Plugin(type = DataHandle.class)
+public class BytesHandle extends AbstractDataHandle<BytesLocation> {
+
+	// -- DataHandle methods --
+
+	@Override
+	public long offset() {
+		return bytes().position();
+	}
+
+	@Override
+	public long length() {
+		return bytes().limit();
+	}
+
+	@Override
+	public void setLength(final long length) throws IOException {
+		if (length > bytes().capacity()) {
+			// NB: We cannot extend the length of a ByteBuffer beyond its capacity.
+			// We have no choice but to allocate a new, higher capacity ByteBuffer,
+			// and copy the contents and state of the old ByteBuffer into it.
+			// This will change the backing ByteBuffer of the BytesLocation!
+
+			// save state of the existing buffer
+			final long off = offset();
+			final ByteOrder order = getOrder();
+
+			// allocate a new, higher capacity buffer
+			final ByteBuffer newBytes = ByteBuffer.allocate((int) (length * 2));
+
+			// copy bytes from the old buffer to the new one
+			seek(0);
+			newBytes.put(bytes());
+
+			// update the backing BytesLocation's backing ByteBuffer
+			get().setByteBuffer(newBytes);
+
+			// restore the previous state (order and offset) to the new buffer
+			setOrder(order);
+			seek(off);
+		}
+
+		// set the length (a.k.a. "limit") of the buffer to match
+		bytes().limit((int) length);
+	}
+
+	@Override
+	public ByteOrder getOrder() {
+		return bytes().order();
+	}
+
+	@Override
+	public void setOrder(final ByteOrder order) {
+		bytes().order(order);
+	}
+
+	@Override
+	public int read(final byte[] b, final int off, int len) throws IOException {
+		if (offset() + len > length()) {
+			len = (int) (length() - offset());
+		}
+		bytes().get(b, off, len);
+		return len;
+	}
+
+	@Override
+	public void seek(final long pos) throws IOException {
+		if (pos > length()) setLength(pos);
+		bytes().position((int) pos);
+	}
+
+	// -- DataInput methods --
+
+	@Override
+	public byte readByte() throws IOException {
+		ensureReadable(1);
+		try {
+			// we need to convert the bytes into the range 0-255
+			return bytes().get();
+		}
+		catch (final BufferUnderflowException e) {
+			throw eofException(e);
+		}
+	}
+
+	@Override
+	public char readChar() throws IOException {
+		ensureReadable(2);
+		try {
+			return bytes().getChar();
+		}
+		catch (final BufferUnderflowException e) {
+			throw eofException(e);
+		}
+	}
+
+	@Override
+	public double readDouble() throws IOException {
+		ensureReadable(8);
+		try {
+			return bytes().getDouble();
+		}
+		catch (final BufferUnderflowException e) {
+			throw eofException(e);
+		}
+	}
+
+	@Override
+	public float readFloat() throws IOException {
+		ensureReadable(4);
+		try {
+			return bytes().getFloat();
+		}
+		catch (final BufferUnderflowException e) {
+			throw eofException(e);
+		}
+	}
+
+	@Override
+	public void readFully(final byte[] b, final int off, final int len)
+		throws IOException
+	{
+		ensureReadable(len);
+		try {
+			bytes().get(b, off, len);
+		}
+		catch (final BufferUnderflowException e) {
+			throw eofException(e);
+		}
+	}
+
+	@Override
+	public int readInt() throws IOException {
+		ensureReadable(4);
+		try {
+			return bytes().getInt();
+		}
+		catch (final BufferUnderflowException e) {
+			throw eofException(e);
+		}
+	}
+
+	@Override
+	public long readLong() throws IOException {
+		ensureReadable(8);
+		try {
+			return bytes().getLong();
+		}
+		catch (final BufferUnderflowException e) {
+			throw eofException(e);
+		}
+	}
+
+	@Override
+	public short readShort() throws IOException {
+		ensureReadable(2);
+		try {
+			return bytes().getShort();
+		}
+		catch (final BufferUnderflowException e) {
+			throw eofException(e);
+		}
+	}
+
+	// -- DataOutput methods --
+
+	@Override
+	public void write(final byte[] b, final int off, final int len)
+		throws IOException
+	{
+		ensureWritable(len);
+		bytes().put(b, off, len);
+	}
+
+	@Override
+	public void write(final int b) throws IOException {
+		ensureWritable(1);
+		bytes().put((byte) b);
+	}
+
+	@Override
+	public void writeChar(final int v) throws IOException {
+		ensureWritable(2);
+		bytes().putChar((char) v);
+	}
+
+	@Override
+	public void writeChars(final String s) throws IOException {
+		final int len = 2 * s.length();
+		ensureWritable(len);
+		final char[] c = s.toCharArray();
+		for (int i = 0; i < c.length; i++) {
+			writeChar(c[i]);
+		}
+	}
+
+	@Override
+	public void writeDouble(final double v) throws IOException {
+		ensureWritable(8);
+		bytes().putDouble(v);
+	}
+
+	@Override
+	public void writeFloat(final float v) throws IOException {
+		ensureWritable(4);
+		bytes().putFloat(v);
+	}
+
+	@Override
+	public void writeInt(final int v) throws IOException {
+		ensureWritable(4);
+		bytes().putInt(v);
+	}
+
+	@Override
+	public void writeLong(final long v) throws IOException {
+		ensureWritable(8);
+		bytes().putLong(v);
+	}
+
+	@Override
+	public void writeShort(final int v) throws IOException {
+		ensureWritable(2);
+		bytes().putShort((short) v);
+	}
+
+	// -- Closeable methods --
+
+	@Override
+	public void close() {
+		// NB: No action needed.
+	}
+
+	// -- Typed methods --
+
+	@Override
+	public Class<BytesLocation> getType() {
+		return BytesLocation.class;
+	}
+
+	// -- Helper methods --
+
+	/** Backing {@link ByteBuffer} accessor, purely for succinctness. */
+	private ByteBuffer bytes() {
+		return get().getByteBuffer();
+	}
+
+	private EOFException eofException(final Throwable cause) {
+		final EOFException eof = new EOFException();
+		eof.initCause(cause);
+		return eof;
+	}
+
+}