Package gov.nih.mipav.model.file

Class FileGESigna5X

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FileGESigna5X

public class FileGESigna5X
extends FileBase

Reads both GE Neducak Systems MR 5X and LX. Modify to handle MRGE files from a GE signa-5 with IMGF starting at locating 3228 and image data starting at location 8424. Follows file format thru lenUsrDefData field; then varies from format.

Field Summary

Fields

Modifier and Type	Field	Description
private byte[]	byteBuffer	DOCUMENT ME!
private int	compression	DOCUMENT ME!
private int	depth
private java.lang.String	fileDir	DOCUMENT ME!
private java.io.File	fileHeader	DOCUMENT ME!
private FileInfoGESigna5X	fileInfo	DOCUMENT ME!
private java.lang.String	fileName	DOCUMENT ME!
private int	height	DOCUMENT ME!
private int	imageNumber	DOCUMENT ME!
private int	imagePtr	DOCUMENT ME!
private int	lenExamHdr	DOCUMENT ME!
private int	lenImageHdr	DOCUMENT ME!
private int	lenSeriesHdr	DOCUMENT ME!
private int[]	orient	DOCUMENT ME!
private float[]	start	DOCUMENT ME!
private int	startAdjust	DOCUMENT ME!
private int	width	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
FileGESigna5X(java.lang.String fileName, java.lang.String fileDir)	reader/writer constructor.

Method Summary

Modifier and Type	Method	Description
private boolean	checkMagicNumber()	DOCUMENT ME!
void	finalize()	Prepares this class for cleanup.
FileInfoGESigna5X	getFileInfo()	DOCUMENT ME!
int	getHeight()	DOCUMENT ME!
int	getImageNumber()	DOCUMENT ME!
int	getStartAdjust()	DOCUMENT ME!
int	getWidth()	DOCUMENT ME!
boolean	isGESigna5X()	Looks for the magic number "IMGF" in image header for GE Signa 5.X type file.
private void	readBuffer(float[] buffer)	Reads a slice of data at a time and stores the results in the buffer.
void	readImage(float[] buffer)	reads the Signa 5X file header and data.
int	readImageFileData()	DOCUMENT ME!
void	setFileName(java.lang.String fName)	Accessor that sets the file name and allocates new FileInfo, File and RandomAccess file objects.
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 Detail

byteBuffer

private byte[] byteBuffer

DOCUMENT ME!

compression

private int compression

DOCUMENT ME!

depth

private int depth

fileDir

private java.lang.String fileDir

DOCUMENT ME!

fileHeader

private java.io.File fileHeader

DOCUMENT ME!

fileInfo

private FileInfoGESigna5X fileInfo

DOCUMENT ME!

fileName

private java.lang.String fileName

DOCUMENT ME!

imageNumber

private int imageNumber

DOCUMENT ME!

imagePtr

private int imagePtr

DOCUMENT ME!

lenExamHdr

private int lenExamHdr

DOCUMENT ME!

lenImageHdr

private int lenImageHdr

DOCUMENT ME!

lenSeriesHdr

private int lenSeriesHdr

DOCUMENT ME!

orient

private int[] orient

DOCUMENT ME!

start

private float[] start

DOCUMENT ME!

startAdjust

private int startAdjust

DOCUMENT ME!

width

private int width

DOCUMENT ME!

height

private int height

DOCUMENT ME!

Constructor Detail

FileGESigna5X

public FileGESigna5X(java.lang.String fileName,
                     java.lang.String fileDir)
              throws java.io.IOException

reader/writer constructor.

Parameters:

fileName - file name

fileDir - file directory

Throws:

java.io.IOException - if there is an error making the file

Method Detail

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 FileInfoGESigna5X getFileInfo()

DOCUMENT ME!

Returns:

FileInfoGESigna5X fileInfo

getHeight

public int getHeight()

DOCUMENT ME!

Returns:

int height

getImageNumber

public int getImageNumber()

DOCUMENT ME!

Returns:

int image number

getStartAdjust

public int getStartAdjust()

DOCUMENT ME!

Returns:

DOCUMENT ME!

getWidth

public int getWidth()

DOCUMENT ME!

Returns:

int width

readImage

public void readImage(float[] buffer)
               throws java.io.IOException

reads the Signa 5X file header and data.

Parameters:

buffer - DOCUMENT ME!

Throws:

java.io.IOException - if there is an error reading the file

readImageFileData

public int readImageFileData()

DOCUMENT ME!

Returns:

int size of image file data

setFileName

public void setFileName(java.lang.String fName)
                 throws java.io.IOException

Accessor that sets the file name and allocates new FileInfo, File and RandomAccess file objects.

Parameters:

fName - File name.

Throws:

java.io.IOException - if there is an error constructing the files.

isGESigna5X

public boolean isGESigna5X()
                    throws java.io.IOException

Looks for the magic number "IMGF" in image header for GE Signa 5.X type file. If present, the image is GE SIGNA 5.X format.

Returns:

boolean true if the magic number was found in the image header.

Throws:

java.io.IOException - Indicates error reading the file

checkMagicNumber

private boolean checkMagicNumber()

DOCUMENT ME!

Returns:

DOCUMENT ME!

readBuffer

private void readBuffer(float[] buffer)
                 throws java.io.IOException

Reads a slice of data at a time and stores the results in the buffer.

Parameters:

buffer - buffer where the info is stored

Throws:

java.io.IOException - DOCUMENT ME!

writeImage

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

Throws:

java.io.IOException