Package gov.nih.mipav.model.file

Class FileRaw

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FileRaw

public class FileRaw
extends FileBase

The class reads and writes raw files of all data types: boolean, byte, short, int, long, float, and double. For the read process an offset can be pass as a parameter to identify the location in the file where the data starts. A number of file formats while not "raw" have data at a specific location after a fixed length but unknown header and therefore can be treated as raw.

Version:

0.1 Sept 2, 1997

See Also:

FileIO, FileInfoXML, FileRawChunk

Field Summary

Fields

Modifier and Type	Field	Description
private int	bitsAllocated
private int	bitsStored
private int	compressionType	DOCUMENT ME!
private java.lang.String[]	dataFileName
private java.io.File	file	DOCUMENT ME!
private FileInfoBase	fileInfo	DOCUMENT ME!
private java.lang.String	fileName
private FileRawChunk	fileRW	DOCUMENT ME!
private int	highBit
private int	minimumBitsMinus1	Used in reading and writing boolean
private int	nImages	DOCUMENT ME!
private int	nTimePeriods	DOCUMENT ME!
private int	numChannels
private int	planarConfig	DOCUMENT ME!
private boolean	RGBAOrder	Allow reading from 4 color files with RGBA order
private int	shiftToDivide	Used in reading and writing boolean
private long	startPosition	DOCUMENT ME!
private boolean	threeByteInteger
private boolean	YBR_FULL_422
private boolean	zeroLengthFlag	flag that indicates if raFile should first be set to length of 0

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
FileRaw(FileInfoBase fInfo)	Constructor for Raw Files that will be used to write from 4D to 3D or from 3D to 2D.
FileRaw(java.lang.String fileName, FileInfoBase fInfo, int rwFlag)	Raw reader/writer constructor.
FileRaw(java.lang.String fileName, java.lang.String fileDir, FileInfoBase fInfo, int rwFlag)	Raw reader/writer constructor..

Method Summary

Modifier and Type	Method	Description
void	close()	Closes random access file associated with this object.
void	finalize()	Prepares this class for cleanup.
java.lang.String[]	getDataFileName()	Accessor that returns the array of data file names
int	getNImages()	Accessor that returns the number of image slices saved.
int	getNTimePeriods()	Accessor that returns the number of time periods saved.
void	readFloatImage(ModelImage image, int originalDataType, float[] scaleFactor, float[] offsetAdjustment, long offset)	This method reads a raw image file (1D - 5D).
void	readImage(double[] buffer, long offset)	This method reads a file and puts the data in the buffer.
void	readImage(float[] buffer, long offset, int imageType)	This method reads a file and puts the data in the buffer.
void	readImage(int[] buffer, long offset, int imageType)	This method reads a file and puts the data in the buffer.
void	readImage(short[] buffer, long offset, int imageType)	This method reads a file and puts the data in the buffer.
void	readImage(ModelImage image, long offset)	This method reads a raw image file (1D - 5D).
void	setBitsAllocated(int bitsAllocated)
void	setBitsStored(int bitsStored)
void	setHighBit(int highBit)
void	setImageFile(java.lang.String fileName, java.lang.String fileDir, FileInfoBase fInfo, int rwFlag)	Sets the name and directory to new values opens the file.
void	setMinimumBitsMinus1(int minimumBitsMinus1)	Used in reading and writing boolean
void	setNumChannels(int numChannels)	Sets the number of channels used in RGB files
void	setPlanarConfig(int _planarConfig)	Sets the planar configuration for RGB images.
void	setRGBAOrder(boolean RGBAOrder)
void	setShiftToDivide(int shiftToDivide)	Used in reading and writing boolean
void	setStartPosition(long startPosition)	DOCUMENT ME!
void	setThreeByteInteger(boolean threeByteInteger)
void	setYBR_FULL_422(boolean YBR_FULL_422)
void	setZeroLengthFlag(boolean zeroLengthFlag)	setZeroLengthFlag
void	writeImage(ModelImage image, int beginSlice, int endSlice, int beginTimePeriod, int endTimePeriod)	This method writes a raw image file.
void	writeImage(ModelImage image, FileWriteOptions options)	This method writes a raw image file.
void	writeImage3DTo2D(ModelImage image, FileWriteOptions options, java.lang.String suffix)	Method to save 3D images to an array of 2D images.
void	writeImage3DTo2D(ModelImage image, FileWriteOptions options, java.lang.String suffix, long[] finalHeaderPosition)	Method to save 3D images to an array of 2D images.
void	writeImage4DTo3D(ModelImage image, FileWriteOptions options, java.lang.String suffix)	Method to write 4D images to an array of 3D image files. the files will be named sequentially with the given # of digits and given starting #.
void	writeImage4DTo3D(ModelImage image, FileWriteOptions options, java.lang.String suffix, long[] finalHeaderPosition)	Method to write 4D images to an array of 3D image files. the files will be named sequentially with the given # of digits and given starting #.

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

compressionType

private int compressionType

DOCUMENT ME!

file

private java.io.File file

DOCUMENT ME!

fileInfo

private FileInfoBase fileInfo

DOCUMENT ME!

fileName

private java.lang.String fileName

fileRW

private FileRawChunk fileRW

DOCUMENT ME!

nImages

private int nImages

DOCUMENT ME!

nTimePeriods

private int nTimePeriods

DOCUMENT ME!

planarConfig

private int planarConfig

DOCUMENT ME!

YBR_FULL_422

private boolean YBR_FULL_422

startPosition

private long startPosition

DOCUMENT ME!

numChannels

private int numChannels

RGBAOrder

private boolean RGBAOrder

Allow reading from 4 color files with RGBA order

zeroLengthFlag

private boolean zeroLengthFlag

flag that indicates if raFile should first be set to length of 0

dataFileName

private java.lang.String[] dataFileName

minimumBitsMinus1

private int minimumBitsMinus1

Used in reading and writing boolean

shiftToDivide

private int shiftToDivide

Used in reading and writing boolean

threeByteInteger

private boolean threeByteInteger

bitsAllocated

private int bitsAllocated

bitsStored

private int bitsStored

highBit

private int highBit

Constructor Detail

FileRaw

public FileRaw(FileInfoBase fInfo)

Constructor for Raw Files that will be used to write from 4D to 3D or from 3D to 2D.

Parameters:

fInfo - fileinfo

FileRaw

public FileRaw(java.lang.String fileName,
               FileInfoBase fInfo,
               int rwFlag)
        throws java.io.IOException

Raw reader/writer constructor.

Parameters:

fileName - Complete file name

fInfo - Information that describes the image.

rwFlag - Read/write flag.

Throws:

java.io.IOException - if there is an error making the files

FileRaw

public FileRaw(java.lang.String fileName,
               java.lang.String fileDir,
               FileInfoBase fInfo,
               int rwFlag)
        throws java.io.IOException

Raw reader/writer constructor..

Parameters:

fileName - File name (no path)

fileDir - File directory (with trailing file separator).

fInfo - Information that describes the image.

showProgressBar - Boolean indicating if progess bar should be displayed.

rwFlag - Read/write flag.

Throws:

java.io.IOException - if there is an error making the files

Method Detail

close

public void close()
           throws java.io.IOException

Closes random access file associated with this object.

Throws:

java.io.IOException - DOCUMENT ME!

finalize

public void finalize()

Prepares this class for cleanup.

Overrides:

finalize in class FileBase

setThreeByteInteger

public void setThreeByteInteger(boolean threeByteInteger)

setBitsAllocated

public void setBitsAllocated(int bitsAllocated)

setBitsStored

public void setBitsStored(int bitsStored)

setHighBit

public void setHighBit(int highBit)

setMinimumBitsMinus1

public void setMinimumBitsMinus1(int minimumBitsMinus1)

Used in reading and writing boolean

Parameters:

minimumBitsMinus1 -

setShiftToDivide

public void setShiftToDivide(int shiftToDivide)

Used in reading and writing boolean

Parameters:

shiftToDivide -

setYBR_FULL_422

public void setYBR_FULL_422(boolean YBR_FULL_422)

getNImages

public int getNImages()

Accessor that returns the number of image slices saved.

Returns:

The number of images.

getNTimePeriods

public int getNTimePeriods()

Accessor that returns the number of time periods saved.

Returns:

The number of time periods.

getDataFileName

public java.lang.String[] getDataFileName()

Accessor that returns the array of data file names

Returns:

readImage

public void readImage(ModelImage image,
                      long offset)
               throws java.io.IOException

This method reads a raw image file (1D - 5D).

Parameters:

image - Image model where the data will be stored.

offset - Points to where the data of the image is located. It is equal to the header length.

Throws:

java.io.IOException - if there is an error reading the file

See Also:

FileInfoXML, FileRawChunk

readFloatImage

public void readFloatImage(ModelImage image,
                           int originalDataType,
                           float[] scaleFactor,
                           float[] offsetAdjustment,
                           long offset)
                    throws java.io.IOException

This method reads a raw image file (1D - 5D). Then multiplies raw data by a scaleFactor[k] and adds an offsetAdjustment[k], where k is the slice index

Parameters:

image - Image model where the data will be stored. Either a ModelStorageBase.FLOAT or a ModelStorageBase.ARGB_FLOAT.

originalDataType -

scaleFactor - array with a multiplicative factor for each slice

offsetAdjustment - array with an additive offset adjustment for each slice

offset - Points to where the data of the image is located. It is equal to the header length.

Throws:

java.io.IOException - if there is an error reading the file

See Also:

FileInfoXML, FileRawChunk

readImage

public void readImage(float[] buffer,
                      long offset,
                      int imageType)
               throws java.io.IOException

This method reads a file and puts the data in the buffer.

Parameters:

buffer - float buffer where the data will be stored.

offset - points to where the data of the image is located. It is equal to the header length.

imageType - ModelImage type (i.e. boolean, byte ...);

Throws:

java.io.IOException - if there is an error reading the file

See Also:

FileInfoXML, FileRawChunk

readImage

public void readImage(double[] buffer,
                      long offset)
               throws java.io.IOException

This method reads a file and puts the data in the buffer.

Parameters:

buffer - double buffer where the data will be stored.

offset - points to where the data of the image is located. It is equal to the header length.

Throws:

java.io.IOException - if there is an error reading the file

See Also:

FileInfoXML, FileRawChunk

readImage

public void readImage(short[] buffer,
                      long offset,
                      int imageType)
               throws java.io.IOException

This method reads a file and puts the data in the buffer. Added here to help speed the reading of DICOM images

Parameters:

buffer - float buffer where the data will be stored.

offset - points to where the data of the image is located. It is equal to the header length.

imageType - ModelImage type (i.e. boolean, byte ...);

Throws:

java.io.IOException - if there is an error reading the file

See Also:

FileInfoXML, FileRawChunk

readImage

public void readImage(int[] buffer,
                      long offset,
                      int imageType)
               throws java.io.IOException

This method reads a file and puts the data in the buffer. Added here to help speed the reading of DICOM images

Parameters:

buffer - float buffer where the data will be stored.

offset - points to where the data of the image is located. It is equal to the header length.

imageType - ModelImage type (i.e. boolean, byte ...);

Throws:

java.io.IOException - if there is an error reading the file

See Also:

FileInfoXML, FileRawChunk

setImageFile

public void setImageFile(java.lang.String fileName,
                         java.lang.String fileDir,
                         FileInfoBase fInfo,
                         int rwFlag)
                  throws java.io.IOException

Sets the name and directory to new values opens the file.

Parameters:

fileName - DOCUMENT ME!

fileDir - File directory.

fInfo - Information that describes the image.

rwFlag - Read/write flag.

Throws:

java.io.IOException - if there is an error making the files

setPlanarConfig

public void setPlanarConfig(int _planarConfig)

Sets the planar configuration for RGB images.

Parameters:

_planarConfig - 0 indicates pixels are RGB, RGB chunky
1 indicates pixels are RRR, GGG, BBB planar

setNumChannels

public void setNumChannels(int numChannels)

Sets the number of channels used in RGB files

Parameters:

numChannels -

setRGBAOrder

public void setRGBAOrder(boolean RGBAOrder)

setStartPosition

public void setStartPosition(long startPosition)

DOCUMENT ME!

Parameters:

startPosition - starting byte position for writing data

writeImage

public void writeImage(ModelImage image,
                       FileWriteOptions options)
                throws java.io.IOException

This method writes a raw image file.

Parameters:

image - image model where the data is stored.

options - DOCUMENT ME!

Throws:

java.io.IOException - if there is an error writing the file

writeImage

public void writeImage(ModelImage image,
                       int beginSlice,
                       int endSlice,
                       int beginTimePeriod,
                       int endTimePeriod)
                throws java.io.IOException

This method writes a raw image file.

Parameters:

image - image model where the data is stored.

beginSlice -

endSlice -

beginTimePeriod -

endTimePeriod -

Throws:

java.io.IOException - if there is an error writing the file

writeImage3DTo2D

public void writeImage3DTo2D(ModelImage image,
                             FileWriteOptions options,
                             java.lang.String suffix)
                      throws java.io.IOException

Method to save 3D images to an array of 2D images. Images will be name sequentially with the given start # and # of digits

Parameters:

image - Image to be saved (broken down into 2D images)

options - File Write options

suffix - Suffix for file names. Example: ".xml", ".img"

Throws:

java.io.IOException - DOCUMENT ME!

writeImage3DTo2D

public void writeImage3DTo2D(ModelImage image,
                             FileWriteOptions options,
                             java.lang.String suffix,
                             long[] finalHeaderPosition)
                      throws java.io.IOException

Method to save 3D images to an array of 2D images. Images will be name sequentially with the given start # and # of digits

Parameters:

image - Image to be saved (broken down into 2D images)

options - File Write options

suffix - Suffix for file names. Example: ".xml", ".img"

finalHeaderPosition - starting locations

Throws:

java.io.IOException - DOCUMENT ME!

writeImage4DTo3D

public void writeImage4DTo3D(ModelImage image,
                             FileWriteOptions options,
                             java.lang.String suffix)
                      throws java.io.IOException

Method to write 4D images to an array of 3D image files. the files will be named sequentially with the given # of digits and given starting #. This method will save ALL slices and the files will be split up by time-period

Parameters:

image - Image that is to be saved

options - File write options

suffix - file suffix for saving name-convention example ".raw", ".img"

Throws:

java.io.IOException - DOCUMENT ME!

writeImage4DTo3D

public void writeImage4DTo3D(ModelImage image,
                             FileWriteOptions options,
                             java.lang.String suffix,
                             long[] finalHeaderPosition)
                      throws java.io.IOException

Method to write 4D images to an array of 3D image files. the files will be named sequentially with the given # of digits and given starting #. This method will save ALL slices and the files will be split up by time-period

Parameters:

image - Image that is to be saved

options - File write options

suffix - file suffix for saving name-convention example ".raw", ".img"

finalHeaderPosition - starting positions

Throws:

java.io.IOException - DOCUMENT ME!

setZeroLengthFlag

public void setZeroLengthFlag(boolean zeroLengthFlag)

setZeroLengthFlag

Parameters:

zeroLengthFlag -