ome.codecs

Class BaseCodec

java.lang.Object

ome.codecs.BaseCodec

All Implemented Interfaces:

Codec

Direct Known Subclasses:

Base64Codec, HuffmanCodec, JPEG2000Codec, JPEGCodec, LosslessJPEGCodec, LZ4Codec, LZOCodec, LZWCodec, MJPBCodec, MSRLECodec, MSVideoCodec, PackbitsCodec, PassthroughCodec, QTRLECodec, RPZACodec, ZlibCodec, ZstdCodec

public abstract class BaseCodec
extends Object
implements Codec

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

Author:

Eric Kjellman egkjellman at wisc.edu

Field Summary

Fields

Modifier and Type	Field and Description
protected static org.slf4j.Logger	LOGGER

Constructor Summary

Constructors

Constructor and Description
BaseCodec()

Method Summary

Modifier and Type	Method and Description
byte[]	compress(byte[][] data, CodecOptions options) 2D data block encoding default implementation.
ByteBuffer	compress(ByteBuffer target, byte[] data, CodecOptions options) Compress using ByteBuffers.
byte[]	decompress(byte[] data) Decompresses a block of data.
byte[]	decompress(byte[][] data) Decompresses a block of data.
byte[]	decompress(byte[][] data, CodecOptions options) 2D data block decoding default implementation.
byte[]	decompress(byte[] data, CodecOptions options) Decompresses a block of data.
abstract byte[]	decompress(loci.common.RandomAccessInputStream in, CodecOptions options) Decompresses data from the given RandomAccessInputStream.
void	test() Main testing method default implementation.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface ome.codecs.Codec

compress

Field Detail

LOGGER

protected static final org.slf4j.Logger LOGGER

Constructor Detail

BaseCodec

public BaseCodec()

Method Detail

test

public void test()
          throws CodecException

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:

CodecException - Can only occur if there is a bug in the compress method.

compress

public byte[] compress(byte[][] data,
                       CodecOptions options)
                throws CodecException

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.

Specified by:

compress in interface Codec

Parameters:

data - The data to be compressed.

options - Options to be used during compression, if appropriate.

Returns:

The compressed data.

Throws:

CodecException - If input is not a compressed data block of the appropriate type.

compress

public ByteBuffer compress(ByteBuffer target,
                           byte[] data,
                           CodecOptions options)
                    throws CodecException

Compress using ByteBuffers. This implementation just calls the byte array based compression method and wraps the result properly.

Specified by:

compress in interface Codec

Parameters:

target - A preallocated ByteBuffer that may be used for the compressed data. This may be null to force the compressor to allocate a fresh buffer.

data - The data to be compressed.

options - Options to be used during compression, if appropriate.

Returns:

The ByteBuffer holding the compressed data.

Throws:

CodecException - If input cannot be processed.

See Also:

Codec.compress(ByteBuffer, byte[], CodecOptions)

decompress

public byte[] decompress(byte[] data)
                  throws CodecException

Description copied from interface: Codec

Decompresses a block of data.

Specified by:

decompress in interface Codec

Parameters:

data - the data to be decompressed.

Returns:

The decompressed data.

Throws:

CodecException - If data is not valid compressed data for this decompressor.

decompress

public byte[] decompress(byte[][] data)
                  throws CodecException

Description copied from interface: Codec

Decompresses a block of data.

Specified by:

decompress in interface Codec

Parameters:

data - The data to be decompressed.

Returns:

The decompressed data.

Throws:

CodecException - If data is not valid compressed data for this decompressor.

decompress

public byte[] decompress(byte[] data,
                         CodecOptions options)
                  throws CodecException

Description copied from interface: Codec

Decompresses a block of data.

Specified by:

decompress in interface Codec

Parameters:

data - the data to be decompressed

options - Options to be used during decompression.

Returns:

the decompressed data.

Throws:

CodecException - If data is not valid.

decompress

public abstract byte[] decompress(loci.common.RandomAccessInputStream in,
                                  CodecOptions options)
                           throws CodecException,
                                  IOException

Description copied from interface: Codec

Decompresses data from the given RandomAccessInputStream.

Specified by:

decompress in interface Codec

Parameters:

in - The stream from which to read compressed data.

options - Options to be used during decompression.

Returns:

The decompressed data.

Throws:

CodecException - If data is not valid compressed data for this decompressor.

IOException

decompress

public byte[] decompress(byte[][] data,
                         CodecOptions options)
                  throws CodecException

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.

Specified by:

decompress in interface Codec

Parameters:

data - The data to be decompressed.

options - Options to be used during decompression.

Returns:

The decompressed data.

Throws:

CodecException - If input is not a compressed data block of the appropriate type.