Package gov.nih.mipav.model.file

Class FileHistoLUT

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

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