Package gov.nih.mipav.model.file

Class FileCheshireVOI

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FileCheshireVOI

public class FileCheshireVOI
extends FileBase

Addresses and lengths are always contained in 4 bytes. The first 4 bytes plus 4 give the location of ascii text saying UserWndLevels, overlays, or sticks if overlays are present. The same region of interest in the same slice may be saved with exactly the same contour using 2 different bounding boxes. The first 90 bytes are header bytes. Location 0x24 may give a location to the start of information for a given slice. The first 4 bytes of this slice information will give the location of the start of information for another slice. This will continue until the first 4 bytes of a slice contains 0x28. 0x28 contains 0. If 0x24 does not point to the start of slice information, then it contains 0x28. However, the code collecting slice information from 0x24 was commented out since it produced a contour in slice 15 in 10080-2-dwi-bo-sw.oly that was not seen in Cheshire. With UserWndLevels 0x8C gives the start of a slice of information and the first 4 bytes of the information slice give the start of another slice until finally 1 slice starts with 0. With overlays and sticks an information slice starts 24 bytes after overlays. This 1 information slice was different from other information slices in that the first 8 bytes had the locations of 2 information slices instead of just 4 bytes for 1 location like the other information slices. Also note that information slices may be fragmentary - they may not contain all the information promised by length bytes. In these cases just ignore the fragments of the information slices.

Field Summary

Fields

Modifier and Type	Field	Description
private VOI[]	addedVOI	DOCUMENT ME!
private Polygon	contourPolygon	DOCUMENT ME!
private short[]	expImgBuffer	DOCUMENT ME!
private File	file	DOCUMENT ME!
private String	fileName	DOCUMENT ME!
private int	fileType	DOCUMENT ME!
private short[]	grayScaleArray	DOCUMENT ME!
private short	grayScaleNumber	DOCUMENT ME!
private ModelImage	image	DOCUMENT ME!
private short[]	imgBuffer	DOCUMENT ME!
private int	it	DOCUMENT ME!
private int	length	DOCUMENT ME!
private BitSet	mask	DOCUMENT ME!
private BitSet	mask2	DOCUMENT ME!
private BitSet	maskAll	DOCUMENT ME!
private BitSet	maskE	DOCUMENT ME!
private BitSet	maskN	DOCUMENT ME!
private BitSet	maskS	DOCUMENT ME!
private BitSet	maskW	DOCUMENT ME!
private int	neighbors	DOCUMENT ME!
private boolean	newGrayScale	DOCUMENT ME!
static final int	OVERLAYS	DOCUMENT ME!
(package private) ViewJProgressBar	progressBar	DOCUMENT ME!
private int	scanPos	DOCUMENT ME!
private int	sliceSize	DOCUMENT ME!
private int	smallPos	DOCUMENT ME!
private int	smallX	DOCUMENT ME!
private int	smallY	DOCUMENT ME!
static final int	STICKS	DOCUMENT ME!
private int	testPos	DOCUMENT ME!
private int	totalSize	DOCUMENT ME!
static final int	USERWNDLEVELS	DOCUMENT ME!
private int	xDim	DOCUMENT ME!
private int	xDimE	DOCUMENT ME!
private int	xt	DOCUMENT ME!
private int	yDim	DOCUMENT ME!
private int	yDimE	DOCUMENT ME!
private int	yt	DOCUMENT ME!
private int	zDim	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
FileCheshireVOI(String fileName, String fileDir, ModelImage image)	FileCheshireVOI - VOI reader/writer constructor.

Method Summary

Modifier and Type	Method	Description
VOI[]	readVOI()	readVOI - reads an Cheshire overlay file by reading the overlay information for each different VOI into a different bitmap.
void	setRegionMask(int xStart, int yStart, short objectValue)	setRegionMask set the mask of all points in the 4 connected region with a gray scale value of objectValue.
void	setRegionMaskAll()	DOCUMENT ME!

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

addProgressChangeListener, bytesToDouble, bytesToFloat, bytesToInt, bytesToShort, doubleToBytes, finalize, 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

USERWNDLEVELS

public static final int USERWNDLEVELS

DOCUMENT ME!

See Also:

• Constant Field Values

OVERLAYS

public static final int OVERLAYS

DOCUMENT ME!

See Also:

• Constant Field Values

STICKS

public static final int STICKS

DOCUMENT ME!

See Also:

• Constant Field Values

progressBar

ViewJProgressBar progressBar

DOCUMENT ME!

addedVOI

private VOI[] addedVOI

DOCUMENT ME!

contourPolygon

private Polygon contourPolygon

DOCUMENT ME!

expImgBuffer

private short[] expImgBuffer

DOCUMENT ME!

file

private File file

DOCUMENT ME!

fileName

private String fileName

DOCUMENT ME!

fileType

private int fileType

DOCUMENT ME!

grayScaleArray

private short[] grayScaleArray

DOCUMENT ME!

grayScaleNumber

private short grayScaleNumber

DOCUMENT ME!

image

private ModelImage image

DOCUMENT ME!

imgBuffer

private short[] imgBuffer

DOCUMENT ME!

length

private int length

DOCUMENT ME!

mask

private BitSet mask

DOCUMENT ME!

mask2

private BitSet mask2

DOCUMENT ME!

maskAll

private BitSet maskAll

DOCUMENT ME!

maskE

private BitSet maskE

DOCUMENT ME!

maskN

private BitSet maskN

DOCUMENT ME!

maskS

private BitSet maskS

DOCUMENT ME!

maskW

private BitSet maskW

DOCUMENT ME!

neighbors

private int neighbors

DOCUMENT ME!

newGrayScale

private boolean newGrayScale

DOCUMENT ME!

scanPos

private int scanPos

DOCUMENT ME!

sliceSize

private int sliceSize

DOCUMENT ME!

smallPos

private int smallPos

DOCUMENT ME!

smallX

private int smallX

DOCUMENT ME!

smallY

private int smallY

DOCUMENT ME!

testPos

private int testPos

DOCUMENT ME!

totalSize

private int totalSize

DOCUMENT ME!

xDim

private int xDim

DOCUMENT ME!

yDim

private int yDim

DOCUMENT ME!

zDim

private int zDim

DOCUMENT ME!

xDimE

private int xDimE

DOCUMENT ME!

xt

private int xt

DOCUMENT ME!

yt

private int yt

DOCUMENT ME!

it

private int it

DOCUMENT ME!

yDimE

private int yDimE

DOCUMENT ME!

Constructor Details

FileCheshireVOI

public FileCheshireVOI(String fileName,
 String fileDir,
 ModelImage image)
                throws IOException

FileCheshireVOI - VOI reader/writer constructor.

Parameters:

fileName - file name

fileDir - file directory

image - image model: needed during the read process to ensure the VOI "fits" in the image space.

Throws:

IOException - if there is an error making the files

Method Details

readVOI

public VOI[] readVOI()
              throws IOException,
OutOfMemoryError

readVOI - reads an Cheshire overlay file by reading the overlay information for each different VOI into a different bitmap.

Returns:

DOCUMENT ME!

Throws:

IOException - if there is an error reading the file

OutOfMemoryError - DOCUMENT ME!

setRegionMask

public void setRegionMask(int xStart,
 int yStart,
 short objectValue)

setRegionMask set the mask of all points in the 4 connected region with a gray scale value of objectValue.

Parameters:

xStart - the x coordinate of the starting point

yStart - the y coordinate of the starting point

objectValue - the gray scale value of the object

setRegionMaskAll

public void setRegionMaskAll()

DOCUMENT ME!