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

All Methods Instance Methods Concrete Methods
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 -

Class FileRaw

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

compressionType

file

fileInfo

fileName

fileRW

nImages

nTimePeriods

planarConfig

YBR_FULL_422

startPosition

numChannels

RGBAOrder

zeroLengthFlag

dataFileName

minimumBitsMinus1

shiftToDivide

threeByteInteger

bitsAllocated

bitsStored

highBit

Constructor Detail

FileRaw

FileRaw

FileRaw

Method Detail

close

finalize

setThreeByteInteger

setBitsAllocated

setBitsStored

setHighBit

setMinimumBitsMinus1

setShiftToDivide

setYBR_FULL_422

getNImages

getNTimePeriods

getDataFileName

readImage

readFloatImage

readImage

readImage

readImage

readImage

setImageFile

setPlanarConfig

setNumChannels

setRGBAOrder

setStartPosition

writeImage

writeImage

writeImage3DTo2D

writeImage3DTo2D

writeImage4DTo3D

writeImage4DTo3D

setZeroLengthFlag