Package gov.nih.mipav.model.file

Class FilePackBit

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FilePackBit

public class FilePackBit
extends FileBase

The class reads and writes packed bit files for tiff formatted images (including STK).

Field Summary

Fields

Modifier and Type	Field	Description
private byte[]	bufferByte	Buffer used to store image of type byte.
private byte[]	bufferByte2	Second buffer used to store image of type byte.
private short[]	bufferShort	Buffer used to store image of type short or unsigned byte.
private int	bufferSize	Size of buffer to be allocated.
private byte[]	litArray	Temporary buffer.
private byte[]	repArray	Temporary buffer.
private int	type	Image type ID.

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
FilePackBit(java.io.RandomAccessFile file)	Packbitconstructor.

Method Summary

Modifier and Type	Method	Description
void	finalize()	Prepares this class for cleanup.
byte[]	getByteBuffer()	Gets the byte buffer of the image data.
short[]	getShortBuffer()	Gets the short buffer of the image.
int	getStripSize(ModelImage image, int start, int end)	This method returns the packed bit strip size.
void	setImageFile(java.io.RandomAccessFile file)	Sets the image file.
void	writePackBitImage(ModelImage image, int start, int end)	This method writes a packed bit 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 Detail

bufferByte

private byte[] bufferByte

Buffer used to store image of type byte.

bufferByte2

private byte[] bufferByte2

Second buffer used to store image of type byte.

bufferShort

private short[] bufferShort

Buffer used to store image of type short or unsigned byte.

bufferSize

private int bufferSize

Size of buffer to be allocated.

litArray

private byte[] litArray

Temporary buffer.

repArray

private byte[] repArray

Temporary buffer.

type

private int type

Image type ID.

Constructor Detail

FilePackBit

public FilePackBit(java.io.RandomAccessFile file)

Packbitconstructor.

Parameters:

file - random access file pointer

Method Detail

finalize

public void finalize()

Prepares this class for cleanup.

Overrides:

finalize in class FileBase

getByteBuffer

public byte[] getByteBuffer()

Gets the byte buffer of the image data.

Returns:

the buffer

getShortBuffer

public short[] getShortBuffer()

Gets the short buffer of the image.

Returns:

the buffer

getStripSize

public int getStripSize(ModelImage image,
                        int start,
                        int end)
                 throws java.io.IOException

This method returns the packed bit strip size.

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] Note that bufferSize is also in units of extents[0]*extents[1] This method only applies to BYTE or UBYTE data.

Returns:

DOCUMENT ME!

Throws:

java.io.IOException - DOCUMENT ME!

setImageFile

public void setImageFile(java.io.RandomAccessFile file)

Sets the image file.

Parameters:

file - random access file pointer

writePackBitImage

public void writePackBitImage(ModelImage image,
                              int start,
                              int end)
                       throws java.io.IOException

This method writes a packed bit 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] Note that bufferSize is also in units of extents[0]*extents[1] This method only applies to BYTE or UBYTE data.

Throws:

java.io.IOException - DOCUMENT ME!