//
// BaseCodec.java
//
/*
OME Bio-Formats package for reading and converting biological file formats.
Copyright (C) 2005-@year@ UW-Madison LOCI and Glencoe Software, Inc.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package loci.formats.codec;
import java.io.IOException;
import java.util.Random;
import loci.common.RandomAccessInputStream;
import loci.formats.FormatException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* BaseCodec contains default implementation and testing for classes
* implementing the Codec interface, and acts as a base class for any
* of the compression classes.
* Base 1D compression and decompression methods are not implemented here, and
* are left as abstract. 2D methods do simple concatenation and call to the 1D
* methods
*
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/bio-formats/src/loci/formats/codec/BaseCodec.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/codec/BaseCodec.java;hb=HEAD">Gitweb</a></dd></dl>
*
* @author Eric Kjellman egkjellman at wisc.edu
*/
public abstract class BaseCodec implements Codec {
// -- Constants --
protected static final Logger LOGGER =
LoggerFactory.getLogger(BaseCodec.class);
// -- BaseCodec API methods --
/**
* Main testing method default implementation.
*
* This method tests whether the data is the same after compressing and
* decompressing, as well as doing a basic test of the 2D methods.
*
* @throws FormatException Can only occur if there is a bug in the
* compress method.
*/
public void test() throws FormatException {
byte[] testdata = new byte[50000];
Random r = new Random();
LOGGER.info("Testing {}", this.getClass().getName());
LOGGER.info("Generating random data");
r.nextBytes(testdata);
LOGGER.info("Compressing data");
byte[] compressed = compress(testdata, null);
LOGGER.info("Compressed size: {}", compressed.length);
LOGGER.info("Decompressing data");
byte[] decompressed = decompress(compressed);
LOGGER.info("Comparing data...");
if (testdata.length != decompressed.length) {
LOGGER.info("Test data differs in length from uncompressed data");
LOGGER.info("Exiting...");
System.exit(-1);
}
else {
boolean equalsFlag = true;
for (int i = 0; i < testdata.length; i++) {
if (testdata[i] != decompressed[i]) {
LOGGER.info("Test data and uncompressed data differ at byte {}", i);
equalsFlag = false;
}
}
if (!equalsFlag) {
LOGGER.info("Comparison failed. Exiting...");
System.exit(-1);
}
}
LOGGER.info("Success.");
LOGGER.info("Generating 2D byte array test");
byte[][] twoDtest = new byte[100][500];
for (int i = 0; i < 100; i++) {
System.arraycopy(testdata, 500*i, twoDtest[i], 0, 500);
}
byte[] twoDcompressed = compress(twoDtest, null);
LOGGER.info("Comparing compressed data...");
if (twoDcompressed.length != compressed.length) {
LOGGER.info("1D and 2D compressed data not same length");
LOGGER.info("Exiting...");
System.exit(-1);
}
boolean equalsFlag = true;
for (int i = 0; i < twoDcompressed.length; i++) {
if (twoDcompressed[i] != compressed[i]) {
LOGGER.info("1D data and 2D compressed data differs at byte {}", i);
equalsFlag = false;
}
if (!equalsFlag) {
LOGGER.info("Comparison failed. Exiting...");
System.exit(-1);
}
}
LOGGER.info("Success.");
LOGGER.info("Test complete.");
}
// -- Codec API methods --
/**
* 2D data block encoding default implementation.
* This method simply concatenates data[0] + data[1] + ... + data[i] into
* a 1D block of data, then calls the 1D version of compress.
*
* @param data The data to be compressed.
* @param options Options to be used during compression, if appropriate.
* @return The compressed data.
* @throws FormatException If input is not a compressed data block of the
* appropriate type.
*/
public byte[] compress(byte[][] data, CodecOptions options)
throws FormatException
{
int len = 0;
for (int i = 0; i < data.length; i++) {
len += data[i].length;
}
byte[] toCompress = new byte[len];
int curPos = 0;
for (int i = 0; i < data.length; i++) {
System.arraycopy(data[i], 0, toCompress, curPos, data[i].length);
curPos += data[i].length;
}
return compress(toCompress, options);
}
/* @see Codec#decompress(byte[]) */
public byte[] decompress(byte[] data) throws FormatException {
return decompress(data, null);
}
/* @see Codec#decompress(byte[][]) */
public byte[] decompress(byte[][] data) throws FormatException {
return decompress(data, null);
}
/* @see Codec#decompress(byte[], CodecOptions) */
public byte[] decompress(byte[] data, CodecOptions options)
throws FormatException
{
try {
RandomAccessInputStream r = new RandomAccessInputStream(data);
byte[] t = decompress(r, options);
r.close();
return t;
}
catch (IOException e) {
throw new FormatException(e);
}
}
/* @see Codec#decompress(RandomAccessInputStream, CodecOptions) */
public abstract byte[] decompress(RandomAccessInputStream in,
CodecOptions options) throws FormatException, IOException;
/**
* 2D data block decoding default implementation.
* This method simply concatenates data[0] + data[1] + ... + data[i] into
* a 1D block of data, then calls the 1D version of decompress.
*
* @param data The data to be decompressed.
* @return The decompressed data.
* @throws FormatException If input is not a compressed data block of the
* appropriate type.
*/
public byte[] decompress(byte[][] data, CodecOptions options)
throws FormatException
{
if (data == null)
throw new IllegalArgumentException("No data to decompress.");
int len = 0;
for (int i = 0; i < data.length; i++) {
len += data[i].length;
}
byte[] toDecompress = new byte[len];
int curPos = 0;
for (int i = 0; i < data.length; i++) {
System.arraycopy(data[i], 0, toDecompress, curPos, data[i].length);
curPos += data[i].length;
}
return decompress(toDecompress, options);
}
}