java.lang.Object
- gov.nih.mipav.model.file.FileBase
- - gov.nih.mipav.model.file.FileLIFF

```
public class FileLIFF
extends FileBase
```

Field Summary

Fields
Modifier and Type	Field	Description
`private static short`	`Clip`
`private static int`	`DEEP_GREY_10`
`private static int`	`DEEP_GREY_16`
`private static int`	`DEEP_GREY_9`
`private static short`	`DefHilite`
`private static short`	`DHDVText`
`private static short`	`DirectBitsRect`
`private static short`	`eraseRect`
`private java.io.File`	`file`	DOCUMENT ME!
`private java.lang.String`	`fileDir`	DOCUMENT ME!
`private FileInfoLIFF`	`fileInfo`	DOCUMENT ME!
`private java.lang.String`	`fileName`	DOCUMENT ME!
`private static short`	`FillPat`
`private static short`	`fontName`
`private static short`	`glyphState`
`private static short`	`HeaderOp`
`private ModelImage`	`image`	DOCUMENT ME!
`private int[]`	`imageExtents`	DOCUMENT ME!
`private float[]`	`imgBuffer`	DOCUMENT ME!
`private float[]`	`imgResols`	DOCUMENT ME!
`private static short`	`kAnnotationLayer`
`private static short`	`kBinaryLayer`
`private static short`	`kBlackChannelLayer`
`private static short`	`kBlueChannelLayer`
`private static short`	`kBrightFieldLayer`
`private static short`	`kCyanChannelLayer`
`private static short`	`kDarkFieldLayer`
`private static short`	`kDeepMaskLayer`
`private static short`	`kGeneralImageLayer`
`private static short`	`kGreenChannelLayer`
`private static short`	`kLuminosityLayer`
`private static short`	`kMagentaChannelLayer`
`private static short`	`kMaskLayer`
`private static short`	`kMasterImageLayer`
`private static short`	`kMovieLayer`
`private static short`	`kRedChannelLayer`
`private static short`	`kRGBChannelLayer`
`private static short`	`kUnitsOther`
`private static short`	`kYellowChannelLayer`
`private static short`	`lineJustify`
`private static short`	`LongComment`
`private ModelLUT`	`LUT`	DOCUMENT ME!
`private static int`	`MAC_1_BIT`
`private static int`	`MAC_16_BIT_COLOR`
`private static int`	`MAC_16_COLORS`
`private static int`	`MAC_16_GREYS`
`private static int`	`MAC_24_BIT_COLOR`
`private static int`	`MAC_256_COLORS`
`private static int`	`MAC_256_GREYS`
`private static int`	`MAC_4_GREYS`
`private static short`	`NOP`
`private static short`	`OpEndPic`
`private static short`	`PackBitsRect`
`private static short`	`TxFont`
`private static short`	`TxSize`
`private static int`	`UNKNOWN`

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

FileLIFF(java.lang.String fileName, java.lang.String fileDir)
LIFF reader/writer constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`finalize()`	Prepares this class for cleanup.
`FileInfoBase`	`getFileInfo()`	Accessor that returns the file info.
`float[]`	`getImageBuffer()`	Accessor that returns the image buffer.
`ModelLUT`	`getModelLUT()`	Rreturns LUT if defined.
`private java.lang.String`	`readCString()`
`ModelImage`	`readImage(boolean multiFile, boolean one)`	Reads the LIFF header which indicates endianess, the TIFF magic number, and the offset in bytes of the first IFD.
`void`	`setFileName(java.lang.String fName)`	Accessor to set the file name (used for reading COR multiFile).

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
  - kMasterImageLayer
```
private static final short kMasterImageLayer
```
    See Also:
    
    Constant Field Values
  - kGeneralImageLayer
```
private static final short kGeneralImageLayer
```
    See Also:
    
    Constant Field Values
  - kBinaryLayer
```
private static final short kBinaryLayer
```
    See Also:
    
    Constant Field Values
  - kRGBChannelLayer
```
private static final short kRGBChannelLayer
```
    See Also:
    
    Constant Field Values
  - kRedChannelLayer
```
private static final short kRedChannelLayer
```
    See Also:
    
    Constant Field Values
  - kGreenChannelLayer
```
private static final short kGreenChannelLayer
```
    See Also:
    
    Constant Field Values
  - kBlueChannelLayer
```
private static final short kBlueChannelLayer
```
    See Also:
    
    Constant Field Values
  - kCyanChannelLayer
```
private static final short kCyanChannelLayer
```
    See Also:
    
    Constant Field Values
  - kMagentaChannelLayer
```
private static final short kMagentaChannelLayer
```
    See Also:
    
    Constant Field Values
  - kYellowChannelLayer
```
private static final short kYellowChannelLayer
```
    See Also:
    
    Constant Field Values
  - kBlackChannelLayer
```
private static final short kBlackChannelLayer
```
    See Also:
    
    Constant Field Values
  - kLuminosityLayer
```
private static final short kLuminosityLayer
```
    See Also:
    
    Constant Field Values
  - kMaskLayer
```
private static final short kMaskLayer
```
    See Also:
    
    Constant Field Values
  - kDeepMaskLayer
```
private static final short kDeepMaskLayer
```
    See Also:
    
    Constant Field Values
  - kAnnotationLayer
```
private static final short kAnnotationLayer
```
    See Also:
    
    Constant Field Values
  - kMovieLayer
```
private static final short kMovieLayer
```
    See Also:
    
    Constant Field Values
  - kDarkFieldLayer
```
private static final short kDarkFieldLayer
```
    See Also:
    
    Constant Field Values
  - kBrightFieldLayer
```
private static final short kBrightFieldLayer
```
    See Also:
    
    Constant Field Values
  - UNKNOWN
```
private static final int UNKNOWN
```
    See Also:
    
    Constant Field Values
  - MAC_1_BIT
```
private static final int MAC_1_BIT
```
    See Also:
    
    Constant Field Values
  - MAC_4_GREYS
```
private static final int MAC_4_GREYS
```
    See Also:
    
    Constant Field Values
  - MAC_16_GREYS
```
private static final int MAC_16_GREYS
```
    See Also:
    
    Constant Field Values
  - MAC_16_COLORS
```
private static final int MAC_16_COLORS
```
    See Also:
    
    Constant Field Values
  - MAC_256_GREYS
```
private static final int MAC_256_GREYS
```
    See Also:
    
    Constant Field Values
  - MAC_256_COLORS
```
private static final int MAC_256_COLORS
```
    See Also:
    
    Constant Field Values
  - MAC_16_BIT_COLOR
```
private static final int MAC_16_BIT_COLOR
```
    See Also:
    
    Constant Field Values
  - MAC_24_BIT_COLOR
```
private static final int MAC_24_BIT_COLOR
```
    See Also:
    
    Constant Field Values
  - DEEP_GREY_9
```
private static final int DEEP_GREY_9
```
    See Also:
    
    Constant Field Values
  - DEEP_GREY_10
```
private static final int DEEP_GREY_10
```
    See Also:
    
    Constant Field Values
  - DEEP_GREY_16
```
private static final int DEEP_GREY_16
```
    See Also:
    
    Constant Field Values
  - kUnitsOther
```
private static final short kUnitsOther
```
    See Also:
    
    Constant Field Values
  - NOP
```
private static final short NOP
```
    See Also:
    
    Constant Field Values
  - Clip
```
private static final short Clip
```
    See Also:
    
    Constant Field Values
  - TxFont
```
private static final short TxFont
```
    See Also:
    
    Constant Field Values
  - FillPat
```
private static final short FillPat
```
    See Also:
    
    Constant Field Values
  - TxSize
```
private static final short TxSize
```
    See Also:
    
    Constant Field Values
  - DefHilite
```
private static final short DefHilite
```
    See Also:
    
    Constant Field Values
  - DHDVText
```
private static final short DHDVText
```
    See Also:
    
    Constant Field Values
  - fontName
```
private static final short fontName
```
    See Also:
    
    Constant Field Values
  - lineJustify
```
private static final short lineJustify
```
    See Also:
    
    Constant Field Values
  - glyphState
```
private static final short glyphState
```
    See Also:
    
    Constant Field Values
  - eraseRect
```
private static final short eraseRect
```
    See Also:
    
    Constant Field Values
  - PackBitsRect
```
private static final short PackBitsRect
```
    See Also:
    
    Constant Field Values
  - DirectBitsRect
```
private static final short DirectBitsRect
```
    See Also:
    
    Constant Field Values
  - LongComment
```
private static final short LongComment
```
    See Also:
    
    Constant Field Values
  - OpEndPic
```
private static final short OpEndPic
```
    See Also:
    
    Constant Field Values
  - HeaderOp
```
private static final short HeaderOp
```
    See Also:
    
    Constant Field Values
  - file
```
private java.io.File file
```
    DOCUMENT ME!
  - fileDir
```
private java.lang.String fileDir
```
    DOCUMENT ME!
  - fileInfo
```
private FileInfoLIFF fileInfo
```
    DOCUMENT ME!
  - fileName
```
private java.lang.String fileName
```
    DOCUMENT ME!
  - image
```
private ModelImage image
```
    DOCUMENT ME!
  - imageExtents
```
private int[] imageExtents
```
    DOCUMENT ME!
  - imgBuffer
```
private float[] imgBuffer
```
    DOCUMENT ME!
  - imgResols
```
private float[] imgResols
```
    DOCUMENT ME!
  - LUT
```
private ModelLUT LUT
```
    DOCUMENT ME!
- Constructor Detail
  - FileLIFF
```
public FileLIFF(java.lang.String fileName,
                java.lang.String fileDir)
         throws java.io.IOException
```
    LIFF 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 FileInfoBase getFileInfo()
```
    Accessor that returns the file info.
    
    Returns:
    
    FileInfoBase containing the file info
  - getImageBuffer
```
public float[] getImageBuffer()
```
    Accessor that returns the image buffer.
    
    Returns:
    
    buffer of image.
  - getModelLUT
```
public ModelLUT getModelLUT()
```
    Rreturns LUT if defined.
    
    Returns:
    
    the LUT if defined else it is null
  - readImage
```
public ModelImage readImage(boolean multiFile,
                            boolean one)
                     throws java.io.IOException
```
    Reads the LIFF header which indicates endianess, the TIFF magic number, and the offset in bytes of the first IFD. It then reads all the IFDs. 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:
    
    java.io.IOException - if there is an error reading the file
  - readCString
```
private java.lang.String readCString()
                              throws java.io.IOException
```
    Throws:
    
    java.io.IOException
  - setFileName
```
public void setFileName(java.lang.String fName)
```
    Accessor to set the file name (used for reading COR multiFile).
    
    Parameters:
    
    fName - file name of image to read.

Class FileLIFF

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

kMasterImageLayer

kGeneralImageLayer

kBinaryLayer

kRGBChannelLayer

kRedChannelLayer

kGreenChannelLayer

kBlueChannelLayer

kCyanChannelLayer

kMagentaChannelLayer

kYellowChannelLayer

kBlackChannelLayer

kLuminosityLayer

kMaskLayer

kDeepMaskLayer

kAnnotationLayer

kMovieLayer

kDarkFieldLayer

kBrightFieldLayer

UNKNOWN

MAC_1_BIT

MAC_4_GREYS

MAC_16_GREYS

MAC_16_COLORS

MAC_256_GREYS

MAC_256_COLORS

MAC_16_BIT_COLOR

MAC_24_BIT_COLOR

DEEP_GREY_9

DEEP_GREY_10

DEEP_GREY_16

kUnitsOther

NOP

Clip

TxFont

FillPat

TxSize

DefHilite

DHDVText

fontName

lineJustify

glyphState

eraseRect

PackBitsRect

DirectBitsRect

LongComment

OpEndPic

HeaderOp

file

fileDir

fileInfo

fileName

image

imageExtents

imgBuffer

imgResols

LUT

Constructor Detail

FileLIFF

Method Detail

finalize

getFileInfo

getImageBuffer

getModelLUT

readImage

readCString

setFileName