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 java.awt.Polygon`	`contourPolygon`	DOCUMENT ME!
`private short[]`	`expImgBuffer`	DOCUMENT ME!
`private java.io.File`	`file`	DOCUMENT ME!
`private java.lang.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 java.util.BitSet`	`mask`	DOCUMENT ME!
`private java.util.BitSet`	`mask2`	DOCUMENT ME!
`private java.util.BitSet`	`maskAll`	DOCUMENT ME!
`private java.util.BitSet`	`maskE`	DOCUMENT ME!
`private java.util.BitSet`	`maskN`	DOCUMENT ME!
`private java.util.BitSet`	`maskS`	DOCUMENT ME!
`private java.util.BitSet`	`maskW`	DOCUMENT ME!
`private int`	`neighbors`	DOCUMENT ME!
`private boolean`	`newGrayScale`	DOCUMENT ME!
`static 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 int`	`STICKS`	DOCUMENT ME!
`private int`	`testPos`	DOCUMENT ME!
`private int`	`totalSize`	DOCUMENT ME!
`static 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(java.lang.String fileName, java.lang.String fileDir, ModelImage image)`	FileCheshireVOI - VOI reader/writer constructor.

Method Summary

All Methods Instance Methods Concrete Methods
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 Detail
  - 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 java.awt.Polygon contourPolygon
```
    DOCUMENT ME!
  - expImgBuffer
```
private short[] expImgBuffer
```
    DOCUMENT ME!
  - file
```
private java.io.File file
```
    DOCUMENT ME!
  - fileName
```
private java.lang.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 java.util.BitSet mask
```
    DOCUMENT ME!
  - mask2
```
private java.util.BitSet mask2
```
    DOCUMENT ME!
  - maskAll
```
private java.util.BitSet maskAll
```
    DOCUMENT ME!
  - maskE
```
private java.util.BitSet maskE
```
    DOCUMENT ME!
  - maskN
```
private java.util.BitSet maskN
```
    DOCUMENT ME!
  - maskS
```
private java.util.BitSet maskS
```
    DOCUMENT ME!
  - maskW
```
private java.util.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 Detail
  - FileCheshireVOI
```
public FileCheshireVOI(java.lang.String fileName,
                       java.lang.String fileDir,
                       ModelImage image)
                throws java.io.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:
    
    java.io.IOException - if there is an error making the files
- Method Detail
  - readVOI
```
public VOI[] readVOI()
              throws java.io.IOException,
                     java.lang.OutOfMemoryError
```
    readVOI - reads an Cheshire overlay file by reading the overlay information for each different VOI into a different bitmap.
    
    Returns:
    
    DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
    
    java.lang.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!

Class FileCheshireVOI

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

USERWNDLEVELS

OVERLAYS

STICKS

progressBar

addedVOI

contourPolygon

expImgBuffer

file

fileName

fileType

grayScaleArray

grayScaleNumber

image

imgBuffer

length

mask

mask2

maskAll

maskE

maskN

maskS

maskW

neighbors

newGrayScale

scanPos

sliceSize

smallPos

smallX

smallY

testPos

totalSize

xDim

yDim

zDim

xDimE

xt

yt

it

yDimE

Constructor Detail

FileCheshireVOI

Method Detail

readVOI

setRegionMask

setRegionMaskAll