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

```
public class FileHistoLUT
extends FileBase
```
HistoLUT reader/writer. This classes incorporates the ability to write/read ModelLUT and ModelRGB information in two ways. The first saves the LUT arrays (not available with ModelRGB), and the second saves the transfer and RGB functions. The LUT transfer Line is saved by default (and likewise opened) when the saveLUT method is called.
NOTE: Reading a LUT does not return a ModelLUT. Rather, it updates the arrays and transfer functions in a provided ModelLUT.

Version:

May 14, 2002

Author:

Lynne M. Pusanik

See Also:

ModelLUT, ModelRGB, JFrameHistogram

Field Summary

Fields
Modifier and Type	Field	Description
`private static java.lang.String`	`endTag`	Tag marking the end of a LUT or transfer file.
`private java.lang.String`	`fileDir`	The file directory containing the data files.
`private java.lang.String`	`funcFileName`	The file name of the transfer function data file.
`private static java.lang.String`	`funcTag`	Tag marking the beginning of a transfer function file.
`private ModelImage`	`img`	ModelImage to use for reference
`private ModelLUT`	`lut`	The (grayscale) LUT to save.
`private java.lang.String`	`lutFileName`	The file name of the LUT data file.
`private static java.lang.String`	`lutTag`	Tag marking the beginning of a LUT data file.
`private TransferFunction`	`opacityFunction`	The opacity transfer function, saved if non-null.
`private ModelRGB`	`rgb`	The color image histogram data to save.
`private boolean`	`useLUT`	Whether to use the LUT or the RGB model.

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
`FileHistoLUT(java.lang.String fileName, java.lang.String fileDir)`	LUT reader/writer constructor.
`FileHistoLUT(java.lang.String fileName, java.lang.String fileDir, ModelImage image, ModelLUT lut)`	LUT reader/writer constructor.
`FileHistoLUT(java.lang.String fileName, java.lang.String fileDir, ModelImage image, ModelRGB rgb)`	RGB reader/writer constructor.
`FileHistoLUT(java.lang.String fileName, java.lang.String fileDir, ModelImage image, ModelStorageBase lut)`	LUT reader/writer constructor.
`FileHistoLUT(java.lang.String fileName, java.lang.String fileDir, ModelLUT lut)`	LUT reader/writer constructor.
`FileHistoLUT(java.lang.String fileName, java.lang.String fileDir, ModelRGB rgb)`	RGB reader/writer constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private static float[]`	`parseString(java.lang.String s, int len)`	Parses a string and returns an array of floats.
`void`	`readFunctions()`	This method reads the transfer and RGB functions associated with a LUT.
`void`	`readFunctions(ModelLUT lut)`	This method reads the transfer for a grayscale image and the RGB functions that define the LUT.
`void`	`readFunctions(ModelRGB rgb)`	This method reads the transfers for a RGB image.
`private static java.lang.String`	`readLine(java.io.RandomAccessFile file)`	Reads a line of the file and strips comments indicated by the # symbol.
`void`	`readLUTandTransferFunction(boolean quietMode)`	This method reads a LUT file and its associated transfer function.
`void`	`readLUTandTransferFunction(ModelLUT lut, boolean quietMode)`	This method reads a LUT file and its associated transfer function.
`private void`	`readTransferFunction(java.io.RandomAccessFile file, TransferFunction funct, java.lang.String functName)`	Reads in a transfer function from a file.
`void`	`setImg(ModelImage img)`
`void`	`setLUT(ModelLUT lut)`	Accessor to set the LUT.
`void`	`setOpacityFunction(TransferFunction opacFunction)`	Sets the opacity function, which indicates that we want it to be saved / read in with the rest of the transfer functions.
`void`	`setRGB(ModelRGB rgb)`	Accessor to set the RGB.
`void`	`write()`	Writes the default ModelLUT or ModelRGB to a file.
`void`	`writeAll()`	Writes the default ModelLUT or ModelRGB to a file.
`void`	`writeFunctions()`	Writes the transfer and RGB functions to a file.
`void`	`writeLUT(ModelLUT lut)`	Writes a ModelLUT to a file.
`void`	`writeLUTandTransferFunction()`	Writes the default ModelLUT or ModelRGB to a file.
`void`	`writeTransferFunction(java.io.RandomAccessFile file, TransferFunction funct, java.lang.String name)`	Write out a transfer function to a file.

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
  - lutTag
```
private static final java.lang.String lutTag
```
    Tag marking the beginning of a LUT data file.
    
    See Also:
    
    Constant Field Values
  - funcTag
```
private static final java.lang.String funcTag
```
    Tag marking the beginning of a transfer function file.
    
    See Also:
    
    Constant Field Values
  - endTag
```
private static final java.lang.String endTag
```
    Tag marking the end of a LUT or transfer file.
    
    See Also:
    
    Constant Field Values
  - fileDir
```
private java.lang.String fileDir
```
    The file directory containing the data files.
  - funcFileName
```
private java.lang.String funcFileName
```
    The file name of the transfer function data file.
  - lut
```
private ModelLUT lut
```
    The (grayscale) LUT to save.
  - lutFileName
```
private java.lang.String lutFileName
```
    The file name of the LUT data file.
  - opacityFunction
```
private TransferFunction opacityFunction
```
    The opacity transfer function, saved if non-null.
  - rgb
```
private ModelRGB rgb
```
    The color image histogram data to save.
  - useLUT
```
private boolean useLUT
```
    Whether to use the LUT or the RGB model.
  - img
```
private ModelImage img
```
    ModelImage to use for reference
- Constructor Detail
  - FileHistoLUT
```
public FileHistoLUT(java.lang.String fileName,
                    java.lang.String fileDir)
             throws java.io.IOException
```
    LUT reader/writer constructor.
    
    Parameters:
    
    fileName - file name
    
    fileDir - file directory
    
    Throws:
    
    java.io.IOException - if there is an error making the files
  - FileHistoLUT
```
public FileHistoLUT(java.lang.String fileName,
                    java.lang.String fileDir,
                    ModelLUT lut)
             throws java.io.IOException
```
    LUT reader/writer constructor.
    
    Parameters:
    
    fileName - file name
    
    fileDir - file directory
    
    lut - the ModelLUT
    
    Throws:
    
    java.io.IOException - if there is an error making the files, or if lut is null
  - FileHistoLUT
```
public FileHistoLUT(java.lang.String fileName,
                    java.lang.String fileDir,
                    ModelImage image,
                    ModelLUT lut)
             throws java.io.IOException
```
    LUT reader/writer constructor.
    
    Parameters:
    
    fileName - file name
    
    fileDir - file directory
    
    lut - the ModelLUT
    
    Throws:
    
    java.io.IOException - if there is an error making the files, or if lut is null
  - FileHistoLUT
```
public FileHistoLUT(java.lang.String fileName,
                    java.lang.String fileDir,
                    ModelImage image,
                    ModelStorageBase lut)
             throws java.io.IOException
```
    LUT reader/writer constructor.
    
    Parameters:
    
    fileName - file name
    
    fileDir - file directory
    
    lut - the ModelLUT
    
    Throws:
    
    java.io.IOException - if there is an error making the files, or if lut is null
  - FileHistoLUT
```
public FileHistoLUT(java.lang.String fileName,
                    java.lang.String fileDir,
                    ModelRGB rgb)
             throws java.io.IOException
```
    RGB reader/writer constructor.
    
    Parameters:
    
    fileName - file name
    
    fileDir - file directory
    
    rgb - the ModelRGB
    
    Throws:
    
    java.io.IOException - if there is an error making the files, or if rgb is null
  - FileHistoLUT
```
public FileHistoLUT(java.lang.String fileName,
                    java.lang.String fileDir,
                    ModelImage image,
                    ModelRGB rgb)
             throws java.io.IOException
```
    RGB reader/writer constructor.
    
    Parameters:
    
    fileName - file name
    
    fileDir - file directory
    
    rgb - the ModelRGB
    
    Throws:
    
    java.io.IOException - if there is an error making the files, or if rgb is null
- Method Detail
  - readFunctions
```
public void readFunctions()
                   throws java.io.IOException
```
    This method reads the transfer and RGB functions associated with a LUT.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readFunctions
```
public void readFunctions(ModelLUT lut)
                   throws java.io.IOException
```
    This method reads the transfer for a grayscale image and the RGB functions that define the LUT.
    
    Parameters:
    
    lut - The ModelLUT that these functions are read to
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readFunctions
```
public void readFunctions(ModelRGB rgb)
                   throws java.io.IOException
```
    This method reads the transfers for a RGB image.
    
    Parameters:
    
    rgb - The ModelRGB that these functions are read to
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readLUTandTransferFunction
```
public void readLUTandTransferFunction(boolean quietMode)
                                throws java.io.IOException
```
    This method reads a LUT file and its associated transfer function.
    
    Parameters:
    
    quietMode - if true indicates that warnings should not be displayed.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readLUTandTransferFunction
```
public void readLUTandTransferFunction(ModelLUT lut,
                                       boolean quietMode)
                                throws java.io.IOException
```
    This method reads a LUT file and its associated transfer function.
    
    Parameters:
    
    lut - The ModelLUT that the LUT data gets applied to
    
    quietMode - if true indicates that warnings should not be displayed.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readTransferFunction
```
private void readTransferFunction(java.io.RandomAccessFile file,
                                  TransferFunction funct,
                                  java.lang.String functName)
                           throws java.io.IOException
```
    Reads in a transfer function from a file.
    
    Parameters:
    
    file - the file to read from
    
    funct - the function to add points to
    
    functName - the transfer function name
    
    Throws:
    
    java.io.IOException - if there is a problem reading from the file
  - setLUT
```
public void setLUT(ModelLUT lut)
            throws java.io.IOException
```
    Accessor to set the LUT.
    
    Parameters:
    
    lut - the ModelLUT
    
    Throws:
    
    java.io.IOException - if lut is null
  - setImg
```
public void setImg(ModelImage img)
```
    Parameters:
    
    img - the img to set
  - setOpacityFunction
```
public void setOpacityFunction(TransferFunction opacFunction)
```
    Sets the opacity function, which indicates that we want it to be saved / read in with the rest of the transfer functions.
    
    Parameters:
    
    opacFunction - the (grayscale) opacity function
  - setRGB
```
public void setRGB(ModelRGB rgb)
            throws java.io.IOException
```
    Accessor to set the RGB.
    
    Parameters:
    
    rgb - the ModelRGB
    
    Throws:
    
    java.io.IOException - if rgb is null
  - write
```
public void write()
           throws java.io.IOException
```
    Writes the default ModelLUT or ModelRGB to a file.
    
    Throws:
    
    java.io.IOException - if there is an error writing the file
  - writeAll
```
public void writeAll()
              throws java.io.IOException
```
    Writes the default ModelLUT or ModelRGB to a file. Also writes the functions for a ModelLUT.
    
    Throws:
    
    java.io.IOException - if there is an error writing the file
  - writeFunctions
```
public void writeFunctions()
                    throws java.io.IOException
```
    Writes the transfer and RGB functions to a file.
    
    Throws:
    
    java.io.IOException - if there is an error writing the file
  - writeLUTandTransferFunction
```
public void writeLUTandTransferFunction()
                                 throws java.io.IOException
```
    Writes the default ModelLUT or ModelRGB to a file. Also writes the functions for a ModelLUT.
    
    Throws:
    
    java.io.IOException - if there is an error writing the file
  - writeLUT
```
public void writeLUT(ModelLUT lut)
              throws java.io.IOException
```
    Writes a ModelLUT to a file.
    
    Parameters:
    
    lut - ModelLUT to write
    
    Throws:
    
    java.io.IOException - if there is an error writing the file
  - writeTransferFunction
```
public void writeTransferFunction(java.io.RandomAccessFile file,
                                  TransferFunction funct,
                                  java.lang.String name)
                           throws java.io.IOException
```
    Write out a transfer function to a file.
    
    Parameters:
    
    file - the file to write the function to
    
    funct - the transfer function
    
    name - the label to apply to the function data
    
    Throws:
    
    java.io.IOException - if there is a problem writing out to the file
  - parseString
```
private static float[] parseString(java.lang.String s,
                                   int len)
                            throws java.lang.Exception
```
    Parses a string and returns an array of floats.
    
    Parameters:
    
    s - string to be parsed
    
    len - length of desired array
    
    Returns:
    
    array of floats
    
    Throws:
    
    java.lang.Exception - if there is a problem reading in the float values
  - readLine
```
private static java.lang.String readLine(java.io.RandomAccessFile file)
                                  throws java.io.IOException
```
    Reads a line of the file and strips comments indicated by the # symbol.
    
    Parameters:
    
    file - the file to read from
    
    Returns:
    
    the line read in
    
    Throws:
    
    java.io.IOException - if there is an error reading the file

Class FileHistoLUT

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

lutTag

funcTag

endTag

fileDir

funcFileName

lut

lutFileName

opacityFunction

rgb

useLUT

img

Constructor Detail

FileHistoLUT

FileHistoLUT

FileHistoLUT

FileHistoLUT

FileHistoLUT

FileHistoLUT

Method Detail

readFunctions

readFunctions

readFunctions

readLUTandTransferFunction

readLUTandTransferFunction

readTransferFunction

setLUT

setImg

setOpacityFunction

setRGB

write

writeAll

writeFunctions

writeLUTandTransferFunction

writeLUT

writeTransferFunction

parseString

readLine