Package gov.nih.mipav.model.file

Class FileCheshire

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FileCheshire

public class FileCheshire
extends FileBase

The class reads Cheshire file images.

Version:

0.1 Oct 14, 1997

Author:

Matthew J. McAuliffe, Ph.D.

See Also:

FileIO, FileInfoAnalyze, FileRaw

Field Summary

Fields

Modifier and Type	Field	Description
private java.lang.String	fileDir	DOCUMENT ME!
private FileInfoCheshire	fileInfo	DOCUMENT ME!
private FileInfoCheshire	fileInfoCopy
private java.lang.String	fileName	DOCUMENT ME!
private ModelImage	image	DOCUMENT ME!
private long	nBytesPerVoxel	DOCUMENT ME!
private float[]	scaleFactor	DOCUMENT ME!
private long	startFirstImage	DOCUMENT ME!
private long	startSecondImage	DOCUMENT ME!
private long	subLength	DOCUMENT ME!
private int	tDim	DOCUMENT ME!
private float	tRes	DOCUMENT ME!
private int	xDim	DOCUMENT ME!
private float	xRes	DOCUMENT ME!
private int	yDim	DOCUMENT ME!
private float	yRes	DOCUMENT ME!
private int	zDim	DOCUMENT ME!
private float	zRes	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
FileCheshire(java.lang.String fName, java.lang.String fDir, boolean show)	Creates a new FileCheshire object.

Method Summary

Modifier and Type	Method	Description
void	finalize()	Prepares this class for cleanup.
FileInfoCheshire	getFileInfo()	Returns the FileInfoCheshire read from the file.
static boolean	isCheshire(java.lang.String fName, java.lang.String fDir)	Method to test to determine if the image format is Cheshire, so appropriate read method may be called.
boolean	readHeader(java.lang.String imageFileName, java.lang.String fileDir)	Reads the header and stores the information in fileInfo.
ModelImage	readImage()	Reads an Cheshire image file by reading the header then making a FileRaw to read the image for all filenames in the file list.

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

fileDir

private java.lang.String fileDir

DOCUMENT ME!

fileInfo

private FileInfoCheshire fileInfo

DOCUMENT ME!

fileInfoCopy

private FileInfoCheshire fileInfoCopy

fileName

private java.lang.String fileName

DOCUMENT ME!

image

private ModelImage image

DOCUMENT ME!

nBytesPerVoxel

private long nBytesPerVoxel

DOCUMENT ME!

scaleFactor

private float[] scaleFactor

DOCUMENT ME!

startFirstImage

private long startFirstImage

DOCUMENT ME!

startSecondImage

private long startSecondImage

DOCUMENT ME!

subLength

private long subLength

DOCUMENT ME!

xDim

private int xDim

DOCUMENT ME!

yDim

private int yDim

DOCUMENT ME!

zDim

private int zDim

DOCUMENT ME!

tDim

private int tDim

DOCUMENT ME!

xRes

private float xRes

DOCUMENT ME!

yRes

private float yRes

DOCUMENT ME!

zRes

private float zRes

DOCUMENT ME!

tRes

private float tRes

DOCUMENT ME!

Constructor Detail

FileCheshire

public FileCheshire(java.lang.String fName,
                    java.lang.String fDir,
                    boolean show)

Creates a new FileCheshire object.

Parameters:

fName - file name

fDir - file directory

show - boolean for showing the progress bar

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

isCheshire

public static boolean isCheshire(java.lang.String fName,
                                 java.lang.String fDir)

Method to test to determine if the image format is Cheshire, so appropriate read method may be called.

Parameters:

fName - File name of image.

fDir - Directory.

Returns:

true if Cheshire file, false otherwise.

getFileInfo

public FileInfoCheshire getFileInfo()

Returns the FileInfoCheshire read from the file.

Returns:

File info structure read from file, or null if file has not been read.

readHeader

public boolean readHeader(java.lang.String imageFileName,
                          java.lang.String fileDir)
                   throws java.io.IOException

Reads the header and stores the information in fileInfo.

Parameters:

imageFileName - File name of image.

fileDir - Directory.

Returns:

Flag to confirm a successful read.

Throws:

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

See Also:

FileInfoAnalyze

readImage

public ModelImage readImage()
                     throws java.io.IOException,
                            java.lang.OutOfMemoryError

Reads an Cheshire image file by reading the header then making a FileRaw to read the image for all filenames in the file list. Only the one file directory (currently) supported.

Throws:

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

java.lang.OutOfMemoryError

See Also:

FileRaw