Package gov.nih.mipav.model.file

Class FileRawChunk

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FileRawChunk

public class FileRawChunk
extends FileBase

The class reads and writes raw files of all data types: boolean, byte, short, int, long, float, and double. For the read process an offset can be passed as a parameter to identify the location in the file where the data starts. A number of file formats while not "raw" have data at a specific location after a fixed length but unknown header and therefore can be treated as raw.

Version:

0.1 Sept 2, 1997

Author:

Matthew J. McAuliffe, Ph.D.

See Also:

• FileRaw

Field Summary

Fields

Modifier and Type	Field	Description
private int	bitsAllocated
private int	bitsStored
private BitSet	bufferBitSet	DOCUMENT ME!
private byte[]	bufferByte	DOCUMENT ME!
private double[]	bufferDouble	DOCUMENT ME!
private float[]	bufferFloat	DOCUMENT ME!
private int[]	bufferInt	DOCUMENT ME!
private long[]	bufferLong	DOCUMENT ME!
private short[]	bufferShort	DOCUMENT ME!
private int	bufferSize	DOCUMENT ME!
private int	compressionType	DOCUMENT ME!
private DeflaterOutputStream	deflaterStream	DOCUMENT ME!
private FileInfoBase	fileInfo	DOCUMENT ME!
private int	highBit
private InflaterInputStream	inflaterStream	DOCUMENT ME!
private int	minimumBitsMinus1	Used in reading and writing boolean
private int	numChannels
private int	planarConfig	DOCUMENT ME!
static final int	RGB	DOCUMENT ME!
private boolean	RGBAOrder
static final int	RRRGGGBBB	DOCUMENT ME!
private int	shiftToDivide	Used in reading and writing boolean
private boolean	threeByteInteger
private int	type	DOCUMENT ME!

Fields inherited from class gov.nih.mipav.model.file.FileBase

BIG_ENDIAN, bitsPerPixel, fileNames, LITTLE_ENDIAN, pBarVisible, raFile, READ, READ_WRITE

Constructor Summary

Constructors

Constructor	Description
FileRawChunk(RandomAccessFile file, FileInfoBase fInfo)	Raw reader/writer constructor.
FileRawChunk(String fileName, FileInfoBase fInfo, int rwFlag, int compress)	Compressed raw reader/writer constructor.

Method Summary

Modifier and Type	Method	Description
final void	close()	Closes the file.
void	finalize()	Prepares this class for cleanup.
BitSet	getBitSetBuffer()	Gets the Bitset buffer (binary image).
byte[]	getByteBuffer()	Gets the byte buffer (image).
double[]	getDoubleBuffer()	Gets the double buffer (image).
float[]	getFloatBuffer()	Gets the float buffer (image).
int[]	getIntBuffer()	gGets the integer buffer (image).
long[]	getLongBuffer()	Gets the long buffer (image).
short[]	getShortBuffer()	Gets the short buffer (image).
void	readImage(int type, long start, int length)	This method reads a raw chunk from a file.
void	setBitsAllocated(int bitsAllocated)
void	setBitsStored(int bitsStored)
void	setHighBit(int highBit)
void	setImageFile(RandomAccessFile file, FileInfoBase fInfo)	Sets the classes file handle to the past in the method.
void	setMinimumBitsMinus1(int minimumBitsMinus1)	Used in reading and writing boolean
void	setNumChannels(int numChannels)	Sets the number of channels used in RGB files.
void	setPlanarConfig(int _planarConfig)	Sets the planar configuration for RGB images.
void	setRGBAOrder(boolean RGBAOrder)	DOCUMENT ME!
void	setShiftToDivide(int shiftToDivide)	Used in reading and writing boolean
void	setThreeByteInteger(boolean threeByteInteger)
void	writeBufferByte(byte[] buffer, int start, int end)	This method writes a raw byte buffer to a file.
void	writeBufferDouble(double[] buffer, int start, int end, boolean endianess)	This method writes a double buffer to a file.
void	writeBufferFloat(float[] buffer, int start, int end, boolean endianess)	This method writes a float buffer to a file.
void	writeBufferInt(int[] buffer, int start, int end, boolean endianess)	This method writes a int buffer to a file.
void	writeBufferLong(long[] buffer, int start, int end, boolean endianess)	This method writes a int buffer to a file.
void	writeBufferRGB(int[] buffer, int start, int end)	This method writes a RGB buffer to a file.
void	writeBufferRGB_USHORT(int[] buffer, int start, int end, boolean endianess)	This method writes a RGB_USHORT buffer to a file.
void	writeBufferShort(short[] buffer, int start, int end, boolean endianess)	This method writes a raw short buffer to a file.
void	writeBufferUByte(short[] buffer, int start, int end)	This method writes a raw unsigned byte buffer to a file.
void	writeBufferUInt(long[] buffer, int start, int end, boolean endianess)	This method writes an unisgned int buffer to a file.
void	writeBufferUShort(int[] buffer, int start, int end, boolean endianess)	This method writes a raw unsigned short buffer to a file.
void	writeImage(ModelImage image, int start, int end)	This method writes a raw image file (1D-5D).

Methods inherited from class gov.nih.mipav.model.file.FileBase

addProgressChangeListener, bytesToDouble, bytesToFloat, bytesToInt, bytesToShort, doubleToBytes, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, floatToBytes, getBufferDouble, getBufferFloat, getBufferInt, getBufferLong, getBufferShort, getBufferUShort, getDataType, getDouble, getFloat, getInt, getLong, getProgressChangeListeners, getRaFile, getSignedShort, getString, getUInt, getUnsignedByte, getUnsignedShort, intToBytes, isBigEndian, isProgressBarVisible, linkProgress, longToBytes, readDouble, readFloat, readInt, readLong, readShort, readString, readUnsignedShort, removeProgressChangeListener, setBigEndian, setBufferFloat, setBufferInt, setBufferLong, setBufferShort, setBufferString, setDataType, setEndianess, shortToBytes, writeBytes, writeDouble, writeFloat, writeInt, writeLong, writeShort

Methods inherited from class java.lang.Object

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

Field Details

RGB

public static final int RGB

DOCUMENT ME!

See Also:

• Constant Field Values

RRRGGGBBB

public static final int RRRGGGBBB

DOCUMENT ME!

See Also:

• Constant Field Values

bufferBitSet

private BitSet bufferBitSet

DOCUMENT ME!

bufferByte

private byte[] bufferByte

DOCUMENT ME!

bufferDouble

private double[] bufferDouble

DOCUMENT ME!

bufferFloat

private float[] bufferFloat

DOCUMENT ME!

bufferInt

private int[] bufferInt

DOCUMENT ME!

bufferLong

private long[] bufferLong

DOCUMENT ME!

bufferShort

private short[] bufferShort

DOCUMENT ME!

bufferSize

private int bufferSize

DOCUMENT ME!

compressionType

private int compressionType

DOCUMENT ME!

deflaterStream

private DeflaterOutputStream deflaterStream

DOCUMENT ME!

fileInfo

private FileInfoBase fileInfo

DOCUMENT ME!

inflaterStream

private InflaterInputStream inflaterStream

DOCUMENT ME!

numChannels

private int numChannels

planarConfig

private int planarConfig

DOCUMENT ME!

RGBAOrder

private boolean RGBAOrder

type

private int type

DOCUMENT ME!

minimumBitsMinus1

private int minimumBitsMinus1

Used in reading and writing boolean

shiftToDivide

private int shiftToDivide

Used in reading and writing boolean

threeByteInteger

private boolean threeByteInteger

bitsAllocated

private int bitsAllocated

bitsStored

private int bitsStored

highBit

private int highBit

Constructor Details

FileRawChunk

public FileRawChunk(RandomAccessFile file,
 FileInfoBase fInfo)

Raw reader/writer constructor.

Parameters:

file - random access file pointer

fInfo - information that describes the image

FileRawChunk

public FileRawChunk(String fileName,
 FileInfoBase fInfo,
 int rwFlag,
 int compress)

Compressed raw reader/writer constructor.

Parameters:

fileName - the name of the file to read/write

fInfo - information that describes the image

rwFlag - whether we are reading or writing the file (READ or WRITE)

compress - the compression method to use (should not be none)

Method Details

close

public final void close()
                 throws IOException

Closes the file.

Throws:

IOException - DOCUMENT ME!

finalize

public void finalize()

Prepares this class for cleanup.

Overrides:

finalize in class FileBase

setMinimumBitsMinus1

public void setMinimumBitsMinus1(int minimumBitsMinus1)

Used in reading and writing boolean

Parameters:

minimumBitsMinus1 -

setThreeByteInteger

public void setThreeByteInteger(boolean threeByteInteger)

setBitsAllocated

public void setBitsAllocated(int bitsAllocated)

setBitsStored

public void setBitsStored(int bitsStored)

setHighBit

public void setHighBit(int highBit)

setShiftToDivide

public void setShiftToDivide(int shiftToDivide)

Used in reading and writing boolean

Parameters:

shiftToDivide -

getBitSetBuffer

public BitSet getBitSetBuffer()

Gets the Bitset buffer (binary image).

Returns:

the buffer

getByteBuffer

public byte[] getByteBuffer()

Gets the byte buffer (image).

Returns:

the buffer

getDoubleBuffer

public double[] getDoubleBuffer()

Gets the double buffer (image).

Returns:

the buffer

getFloatBuffer

public float[] getFloatBuffer()

Gets the float buffer (image).

Returns:

the buffer

getIntBuffer

public int[] getIntBuffer()

gGets the integer buffer (image).

Returns:

the buffer

getLongBuffer

public long[] getLongBuffer()

Gets the long buffer (image).

Returns:

the buffer

getShortBuffer

public short[] getShortBuffer()

Gets the short buffer (image).

Returns:

the buffer

readImage

public void readImage(int type,
 long start,
 int length)
               throws IOException

This method reads a raw chunk from a file.

Parameters:

type - type of data that is to be read

start - points to where the data of the image is located.

length - number of pixels to be read

Throws:

IOException - if there is an error reading the file

setImageFile

public void setImageFile(RandomAccessFile file,
 FileInfoBase fInfo)

Sets the classes file handle to the past in the method.

Parameters:

file - random access file pointer

fInfo - information that describes the image

setNumChannels

public void setNumChannels(int numChannels)

Sets the number of channels used in RGB files.

Parameters:

numChannels - DOCUMENT ME!

setPlanarConfig

public void setPlanarConfig(int _planarConfig)

Sets the planar configuration for RGB images.

Parameters:

_planarConfig - 0 indicates pixels are RGB, RGB chunky 1 indicates pixels are RRR, GGG, BBB planar

setRGBAOrder

public void setRGBAOrder(boolean RGBAOrder)

DOCUMENT ME!

Parameters:

RGBAOrder - DOCUMENT ME!

writeBufferByte

public void writeBufferByte(byte[] buffer,
 int start,
 int end)
                     throws IOException

This method writes a raw byte buffer to a file.

Parameters:

buffer - the image data buffer

start - start of data in the read image file in units of extents[0]*extents[1]

end - end of data in the read image file in units of extents[0]*extents[1]

Throws:

IOException - DOCUMENT ME!

writeBufferDouble

public void writeBufferDouble(double[] buffer,
 int start,
 int end,
 boolean endianess)
                       throws IOException

This method writes a double buffer to a file.

Parameters:

buffer - the image data buffer

start - start of data in the read image file in units of extents[0]*extents[1]

end - end of data in the read image file in units of extents[0]*extents[1]

endianess - the endianess of the data

Throws:

IOException - DOCUMENT ME!

writeBufferFloat

public void writeBufferFloat(float[] buffer,
 int start,
 int end,
 boolean endianess)
                      throws IOException

This method writes a float buffer to a file.

Parameters:

buffer - the image data buffer

start - start of data in the read image file in units of extents[0]*extents[1]

end - end of data in the read image file in units of extents[0]*extents[1]

endianess - the endianess of the data

Throws:

IOException - DOCUMENT ME!

writeBufferInt

public void writeBufferInt(int[] buffer,
 int start,
 int end,
 boolean endianess)
                    throws IOException

This method writes a int buffer to a file.

Parameters:

buffer - the image data buffer

start - start of data in the read image file in units of extents[0]*extents[1]

end - end of data in the read image file in units of extents[0]*extents[1]

endianess - the endianess of the data

Throws:

IOException - DOCUMENT ME!

writeBufferLong

public void writeBufferLong(long[] buffer,
 int start,
 int end,
 boolean endianess)
                     throws IOException

This method writes a int buffer to a file.

Parameters:

buffer - the image data buffer

start - start of data in the read image file in units of extents[0]*extents[1]

end - end of data in the read image file in units of extents[0]*extents[1]

endianess - the endianess of the data

Throws:

IOException - DOCUMENT ME!

writeBufferRGB

public void writeBufferRGB(int[] buffer,
 int start,
 int end)
                    throws IOException

This method writes a RGB buffer to a file.

Parameters:

buffer - the image data buffer

start - start of data in the read image file in units of extents[0]*extents[1]

end - end of data in the read image file in units of extents[0]*extents[1]

Throws:

IOException - DOCUMENT ME!

writeBufferRGB_USHORT

public void writeBufferRGB_USHORT(int[] buffer,
 int start,
 int end,
 boolean endianess)
                           throws IOException

This method writes a RGB_USHORT buffer to a file.

Parameters:

buffer - the image data buffer

start - start of data in the read image file in units of extents[0]*extents[1]

end - end of data in the read image file in units of extents[0]*extents[1]

endianess - the endianess of the data

Throws:

IOException - DOCUMENT ME!

writeBufferShort

public void writeBufferShort(short[] buffer,
 int start,
 int end,
 boolean endianess)
                      throws IOException

This method writes a raw short buffer to a file.

Parameters:

buffer - the image data buffer

start - start of data in the read image file in units of extents[0]*extents[1]

end - end of data in the read image file in units of extents[0]*extents[1]

endianess - the endianess of the data

Throws:

IOException - DOCUMENT ME!

writeBufferUByte

public void writeBufferUByte(short[] buffer,
 int start,
 int end)
                      throws IOException

This method writes a raw unsigned byte buffer to a file.

Parameters:

buffer - image data buffer

start - start of data in the read image file in units of extents[0]*extents[1]

end - end of data in the read image file in units of extents[0]*extents[1]

Throws:

IOException - DOCUMENT ME!

writeBufferUInt

public void writeBufferUInt(long[] buffer,
 int start,
 int end,
 boolean endianess)
                     throws IOException

This method writes an unisgned int buffer to a file.

Parameters:

buffer - the image data buffer

start - start of data in the read image file in units of extents[0]*extents[1]

end - end of data in the read image file in units of extents[0]*extents[1]

endianess - the endianess of the data

Throws:

IOException - DOCUMENT ME!

writeBufferUShort

public void writeBufferUShort(int[] buffer,
 int start,
 int end,
 boolean endianess)
                       throws IOException

This method writes a raw unsigned short buffer to a file.

Parameters:

buffer - the image data buffer

start - start of data in the read image file in units of extents[0]*extents[1]

end - end of data in the read image file in units of extents[0]*extents[1]

endianess - the endianess of the data

Throws:

IOException - DOCUMENT ME!

writeImage

public void writeImage(ModelImage image,
 int start,
 int end)
                throws IOException

This method writes a raw image file (1D-5D).

Parameters:

image - image model from which the data will be read.

start - start of data in the read image file in units of extents[0]*extents[1]

end - end of data in the read image file in units of extents[0]*extents[1]

Throws:

IOException - DOCUMENT ME!