Package gov.nih.mipav.model.file

Class FileJP2

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FileJP2

All Implemented Interfaces:

ActionListener, EventListener

public class FileJP2
extends FileBase
implements ActionListener

Jpeg2K reader/ writer for 3D images.

Version:

0.1, Mar 2007

Author:

Dzung Nguyen, Nam Nguyen

See Also:

• FileIO
• FileInfoJP2

Field Summary

Fields

Modifier and Type	Field	Description
private JDialog	advDecOptDialog	The height of image
private JRadioButton	cerOff
private JRadioButton	cerOn
private JRadioButton	codeStrInfoOff
private JRadioButton	codeStrInfoOn
private JCheckBox	csIgnoreBox
private JRadioButton	cverberOff
private JRadioButton	cverberOn
private JButton	decCancelBut
private JButton	decDefBut
private JTextField	decFrameEnd
private JTextField	decFrameStart
JButton	decOkBut
private JRadioButton	decParsOff
private JRadioButton	decParsOn
private JTextField	decRateField
private JCheckBox	decResChkBox
private JTextField	decResTf
private boolean	endianess	DOCUMENT ME!
private DecimalFormat	f
private String	fileDir	File directory.
private FileInfoJP2	fileInfo	File Info.
private String	fileName	File name.
private ModelImage	image	Model Image.
private int[]	intBuffer	DOCUMENT ME!
(package private) int	nEndFrameDec
private JRadioButton	noRoiOff
private JRadioButton	noRoiOn
(package private) int	nStartFrameDec
private ViewJProgressBar	progressBar
private JCheckBox	showDecInf

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
FileJP2()	Tiff reader/writer constructor.
FileJP2(String fileName, String fileDir, ViewJProgressBar progressBar)	Tiff reader/writer constructor.

Method Summary

Modifier and Type	Method	Description
void	actionPerformed(ActionEvent e)
private void	createDecGui()
int[]	decodeImageData(byte[] imageData, int imageType)
void	finalize()	Prepares this class for cleanup.
FileInfoBase	getFileInfo()	Accessor that returns the file info.
int[]	getImageBuffer()	Accessor that returns the image buffer.
ModelLUT	getModelLUT()
ModelImage	readImage(boolean multiFile, boolean one)	Reads the JP2 header which indicates the number of slices and each slice's size.
void	setFileDir(String fDir)	Accessor to set the file dir (used when reading TIFF multiFile).
void	setFileName(String fName)	Accessor to set the file name (used when reading TIFF multiFile).
private void	writeHeader()	This function is not used.
void	writeImage(ModelImage image, FileWriteOptions options)

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

endianess

private boolean endianess

DOCUMENT ME!

fileDir

private String fileDir

File directory.

fileInfo

private FileInfoJP2 fileInfo

File Info.

image

private ModelImage image

Model Image.

fileName

private String fileName

File name.

intBuffer

private int[] intBuffer

DOCUMENT ME!

advDecOptDialog

private JDialog advDecOptDialog

The height of image

decRateField

private JTextField decRateField

decOkBut

public JButton decOkBut

decDefBut

private JButton decDefBut

decCancelBut

private JButton decCancelBut

showDecInf

private JCheckBox showDecInf

decResChkBox

private JCheckBox decResChkBox

csIgnoreBox

private JCheckBox csIgnoreBox

decParsOn

private JRadioButton decParsOn

decParsOff

private JRadioButton decParsOff

codeStrInfoOn

private JRadioButton codeStrInfoOn

codeStrInfoOff

private JRadioButton codeStrInfoOff

cerOn

private JRadioButton cerOn

cerOff

private JRadioButton cerOff

cverberOn

private JRadioButton cverberOn

cverberOff

private JRadioButton cverberOff

noRoiOn

private JRadioButton noRoiOn

noRoiOff

private JRadioButton noRoiOff

decResTf

private JTextField decResTf

f

private DecimalFormat f

nStartFrameDec

int nStartFrameDec

nEndFrameDec

int nEndFrameDec

decFrameStart

private JTextField decFrameStart

decFrameEnd

private JTextField decFrameEnd

progressBar

private ViewJProgressBar progressBar

Constructor Details

FileJP2

public FileJP2(String fileName,
 String fileDir,
 ViewJProgressBar progressBar)
        throws IOException

Tiff reader/writer constructor.

Parameters:

fileName - file name

fileDir - file directory

Throws:

IOException - if there is an error making the file

FileJP2

public FileJP2()
        throws IOException

Tiff reader/writer constructor.

Parameters:

fileName - file name

fileDir - file directory

Throws:

IOException - if there is an error making the file

Method Details

finalize

public void finalize()

Prepares this class for cleanup. Calls the finalize method for existing elements, closes any open files and sets other elements to null.

Overrides:

finalize in class FileBase

getFileInfo

public FileInfoBase getFileInfo()

Accessor that returns the file info.

Returns:

FileInfoBase containing the file info

getImageBuffer

public int[] getImageBuffer()

Accessor that returns the image buffer.

Returns:

buffer of image.

decodeImageData

public int[] decodeImageData(byte[] imageData,
 int imageType)

readImage

public ModelImage readImage(boolean multiFile,
 boolean one)
                     throws IOException

Reads the JP2 header which indicates the number of slices and each slice's size. It then reads all the encoded slice. This method then opens a Model of an image and imports the the images one slice at a time. Image slices are separated by an IFD.

Parameters:

multiFile - true if a set of files each containing a separate 2D image is present false if one file with either a 2D image or a stack of 2D images

one - true if only want to read in one image of the 3D set

Returns:

returns the image

Throws:

IOException - if there is an error reading the file

setFileDir

public void setFileDir(String fDir)

Accessor to set the file dir (used when reading TIFF multiFile).

Parameters:

fDir - file dir of image to read.

setFileName

public void setFileName(String fName)

Accessor to set the file name (used when reading TIFF multiFile).

Parameters:

fName - file name of image to read.

writeImage

public void writeImage(ModelImage image,
 FileWriteOptions options)
                throws IOException

Throws:

IOException

writeHeader

private void writeHeader()
                  throws IOException

This function is not used. Instead, use the RAWJP2Header class. Writes JP2 starting file header.

Throws:

IOException - DOCUMENT ME!

getModelLUT

public ModelLUT getModelLUT()

createDecGui

private void createDecGui()

actionPerformed

public void actionPerformed(ActionEvent e)

Specified by:

actionPerformed in interface ActionListener