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

```
public class FileRawChunk
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 passed 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

Author:

Matthew J. McAuliffe, Ph.D.

See Also:

FileRaw

Field Summary

Fields
Modifier and Type	Field	Description
`private int`	`bitsAllocated`
`private int`	`bitsStored`
`private java.util.BitSet`	`bufferBitSet`	DOCUMENT ME!
`private byte[]`	`bufferByte`	DOCUMENT ME!
`private double[]`	`bufferDouble`	DOCUMENT ME!
`private float[]`	`bufferFloat`	DOCUMENT ME!
`private int[]`	`bufferInt`	DOCUMENT ME!
`private long[]`	`bufferLong`	DOCUMENT ME!
`private short[]`	`bufferShort`	DOCUMENT ME!
`private int`	`bufferSize`	DOCUMENT ME!
`private int`	`compressionType`	DOCUMENT ME!
`private java.util.zip.DeflaterOutputStream`	`deflaterStream`	DOCUMENT ME!
`private FileInfoBase`	`fileInfo`	DOCUMENT ME!
`private int`	`highBit`
`private java.util.zip.InflaterInputStream`	`inflaterStream`	DOCUMENT ME!
`private int`	`minimumBitsMinus1`	Used in reading and writing boolean
`private int`	`numChannels`
`private int`	`planarConfig`	DOCUMENT ME!
`static int`	`RGB`	DOCUMENT ME!
`private boolean`	`RGBAOrder`
`static int`	`RRRGGGBBB`	DOCUMENT ME!
`private int`	`shiftToDivide`	Used in reading and writing boolean
`private boolean`	`threeByteInteger`
`private int`	`type`	DOCUMENT ME!

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
`FileRawChunk(java.io.RandomAccessFile file, FileInfoBase fInfo)`	Raw reader/writer constructor.
`FileRawChunk(java.lang.String fileName, FileInfoBase fInfo, int rwFlag, int compress)`	Compressed raw reader/writer constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`close()`	Closes the file.
`void`	`finalize()`	Prepares this class for cleanup.
`java.util.BitSet`	`getBitSetBuffer()`	Gets the Bitset buffer (binary image).
`byte[]`	`getByteBuffer()`	Gets the byte buffer (image).
`double[]`	`getDoubleBuffer()`	Gets the double buffer (image).
`float[]`	`getFloatBuffer()`	Gets the float buffer (image).
`int[]`	`getIntBuffer()`	gGets the integer buffer (image).
`long[]`	`getLongBuffer()`	Gets the long buffer (image).
`short[]`	`getShortBuffer()`	Gets the short buffer (image).
`void`	`readImage(int type, long start, int length)`	This method reads a raw chunk from a file.
`void`	`setBitsAllocated(int bitsAllocated)`
`void`	`setBitsStored(int bitsStored)`
`void`	`setHighBit(int highBit)`
`void`	`setImageFile(java.io.RandomAccessFile file, FileInfoBase fInfo)`	Sets the classes file handle to the past in the method.
`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)`	DOCUMENT ME!
`void`	`setShiftToDivide(int shiftToDivide)`	Used in reading and writing boolean
`void`	`setThreeByteInteger(boolean threeByteInteger)`
`void`	`writeBufferByte(byte[] buffer, int start, int end)`	This method writes a raw byte buffer to a file.
`void`	`writeBufferDouble(double[] buffer, int start, int end, boolean endianess)`	This method writes a double buffer to a file.
`void`	`writeBufferFloat(float[] buffer, int start, int end, boolean endianess)`	This method writes a float buffer to a file.
`void`	`writeBufferInt(int[] buffer, int start, int end, boolean endianess)`	This method writes a int buffer to a file.
`void`	`writeBufferLong(long[] buffer, int start, int end, boolean endianess)`	This method writes a int buffer to a file.
`void`	`writeBufferRGB(int[] buffer, int start, int end)`	This method writes a RGB buffer to a file.
`void`	`writeBufferRGB_USHORT(int[] buffer, int start, int end, boolean endianess)`	This method writes a RGB_USHORT buffer to a file.
`void`	`writeBufferShort(short[] buffer, int start, int end, boolean endianess)`	This method writes a raw short buffer to a file.
`void`	`writeBufferUByte(short[] buffer, int start, int end)`	This method writes a raw unsigned byte buffer to a file.
`void`	`writeBufferUInt(long[] buffer, int start, int end, boolean endianess)`	This method writes an unisgned int buffer to a file.
`void`	`writeBufferUShort(int[] buffer, int start, int end, boolean endianess)`	This method writes a raw unsigned short buffer to a file.
`void`	`writeImage(ModelImage image, int start, int end)`	This method writes a raw image file (1D-5D).

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
  - RGB
```
public static final int RGB
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - RRRGGGBBB
```
public static final int RRRGGGBBB
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - bufferBitSet
```
private java.util.BitSet bufferBitSet
```
    DOCUMENT ME!
  - bufferByte
```
private byte[] bufferByte
```
    DOCUMENT ME!
  - bufferDouble
```
private double[] bufferDouble
```
    DOCUMENT ME!
  - bufferFloat
```
private float[] bufferFloat
```
    DOCUMENT ME!
  - bufferInt
```
private int[] bufferInt
```
    DOCUMENT ME!
  - bufferLong
```
private long[] bufferLong
```
    DOCUMENT ME!
  - bufferShort
```
private short[] bufferShort
```
    DOCUMENT ME!
  - bufferSize
```
private int bufferSize
```
    DOCUMENT ME!
  - compressionType
```
private int compressionType
```
    DOCUMENT ME!
  - deflaterStream
```
private java.util.zip.DeflaterOutputStream deflaterStream
```
    DOCUMENT ME!
  - fileInfo
```
private FileInfoBase fileInfo
```
    DOCUMENT ME!
  - inflaterStream
```
private java.util.zip.InflaterInputStream inflaterStream
```
    DOCUMENT ME!
  - numChannels
```
private int numChannels
```
  - planarConfig
```
private int planarConfig
```
    DOCUMENT ME!
  - RGBAOrder
```
private boolean RGBAOrder
```
  - type
```
private int type
```
    DOCUMENT ME!
  - 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
  - FileRawChunk
```
public FileRawChunk(java.io.RandomAccessFile file,
                    FileInfoBase fInfo)
```
    Raw reader/writer constructor.
    
    Parameters:
    
    file - random access file pointer
    
    fInfo - information that describes the image
  - FileRawChunk
```
public FileRawChunk(java.lang.String fileName,
                    FileInfoBase fInfo,
                    int rwFlag,
                    int compress)
```
    Compressed raw reader/writer constructor.
    
    Parameters:
    
    fileName - the name of the file to read/write
    
    fInfo - information that describes the image
    
    rwFlag - whether we are reading or writing the file (READ or WRITE)
    
    compress - the compression method to use (should not be none)
- Method Detail
  - close
```
public final void close()
                 throws java.io.IOException
```
    Closes the file.
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - finalize
```
public void finalize()
```
    Prepares this class for cleanup.
    
    Overrides:
    
    finalize in class FileBase
  - setMinimumBitsMinus1
```
public void setMinimumBitsMinus1(int minimumBitsMinus1)
```
    Used in reading and writing boolean
    
    Parameters:
    
    minimumBitsMinus1 -
  - setThreeByteInteger
```
public void setThreeByteInteger(boolean threeByteInteger)
```
  - setBitsAllocated
```
public void setBitsAllocated(int bitsAllocated)
```
  - setBitsStored
```
public void setBitsStored(int bitsStored)
```
  - setHighBit
```
public void setHighBit(int highBit)
```
  - setShiftToDivide
```
public void setShiftToDivide(int shiftToDivide)
```
    Used in reading and writing boolean
    
    Parameters:
    
    shiftToDivide -
  - getBitSetBuffer
```
public java.util.BitSet getBitSetBuffer()
```
    Gets the Bitset buffer (binary image).
    
    Returns:
    
    the buffer
  - getByteBuffer
```
public byte[] getByteBuffer()
```
    Gets the byte buffer (image).
    
    Returns:
    
    the buffer
  - getDoubleBuffer
```
public double[] getDoubleBuffer()
```
    Gets the double buffer (image).
    
    Returns:
    
    the buffer
  - getFloatBuffer
```
public float[] getFloatBuffer()
```
    Gets the float buffer (image).
    
    Returns:
    
    the buffer
  - getIntBuffer
```
public int[] getIntBuffer()
```
    gGets the integer buffer (image).
    
    Returns:
    
    the buffer
  - getLongBuffer
```
public long[] getLongBuffer()
```
    Gets the long buffer (image).
    
    Returns:
    
    the buffer
  - getShortBuffer
```
public short[] getShortBuffer()
```
    Gets the short buffer (image).
    
    Returns:
    
    the buffer
  - readImage
```
public void readImage(int type,
                      long start,
                      int length)
               throws java.io.IOException
```
    This method reads a raw chunk from a file.
    
    Parameters:
    
    type - type of data that is to be read
    
    start - points to where the data of the image is located.
    
    length - number of pixels to be read
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - setImageFile
```
public void setImageFile(java.io.RandomAccessFile file,
                         FileInfoBase fInfo)
```
    Sets the classes file handle to the past in the method.
    
    Parameters:
    
    file - random access file pointer
    
    fInfo - information that describes the image
  - setNumChannels
```
public void setNumChannels(int numChannels)
```
    Sets the number of channels used in RGB files.
    
    Parameters:
    
    numChannels - DOCUMENT ME!
  - 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
  - setRGBAOrder
```
public void setRGBAOrder(boolean RGBAOrder)
```
    DOCUMENT ME!
    
    Parameters:
    
    RGBAOrder - DOCUMENT ME!
  - writeBufferByte
```
public void writeBufferByte(byte[] buffer,
                            int start,
                            int end)
                     throws java.io.IOException
```
    This method writes a raw byte buffer to a file.
    
    Parameters:
    
    buffer - the image data buffer
    
    start - start of data in the read image file in units of extents[0]*extents[1]
    
    end - end of data in the read image file in units of extents[0]*extents[1]
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - writeBufferDouble
```
public void writeBufferDouble(double[] buffer,
                              int start,
                              int end,
                              boolean endianess)
                       throws java.io.IOException
```
    This method writes a double buffer to a file.
    
    Parameters:
    
    buffer - the image data buffer
    
    start - start of data in the read image file in units of extents[0]*extents[1]
    
    end - end of data in the read image file in units of extents[0]*extents[1]
    
    endianess - the endianess of the data
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - writeBufferFloat
```
public void writeBufferFloat(float[] buffer,
                             int start,
                             int end,
                             boolean endianess)
                      throws java.io.IOException
```
    This method writes a float buffer to a file.
    
    Parameters:
    
    buffer - the image data buffer
    
    start - start of data in the read image file in units of extents[0]*extents[1]
    
    end - end of data in the read image file in units of extents[0]*extents[1]
    
    endianess - the endianess of the data
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - writeBufferInt
```
public void writeBufferInt(int[] buffer,
                           int start,
                           int end,
                           boolean endianess)
                    throws java.io.IOException
```
    This method writes a int buffer to a file.
    
    Parameters:
    
    buffer - the image data buffer
    
    start - start of data in the read image file in units of extents[0]*extents[1]
    
    end - end of data in the read image file in units of extents[0]*extents[1]
    
    endianess - the endianess of the data
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - writeBufferLong
```
public void writeBufferLong(long[] buffer,
                            int start,
                            int end,
                            boolean endianess)
                     throws java.io.IOException
```
    This method writes a int buffer to a file.
    
    Parameters:
    
    buffer - the image data buffer
    
    start - start of data in the read image file in units of extents[0]*extents[1]
    
    end - end of data in the read image file in units of extents[0]*extents[1]
    
    endianess - the endianess of the data
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - writeBufferRGB
```
public void writeBufferRGB(int[] buffer,
                           int start,
                           int end)
                    throws java.io.IOException
```
    This method writes a RGB buffer to a file.
    
    Parameters:
    
    buffer - the image data buffer
    
    start - start of data in the read image file in units of extents[0]*extents[1]
    
    end - end of data in the read image file in units of extents[0]*extents[1]
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - writeBufferRGB_USHORT
```
public void writeBufferRGB_USHORT(int[] buffer,
                                  int start,
                                  int end,
                                  boolean endianess)
                           throws java.io.IOException
```
    This method writes a RGB_USHORT buffer to a file.
    
    Parameters:
    
    buffer - the image data buffer
    
    start - start of data in the read image file in units of extents[0]*extents[1]
    
    end - end of data in the read image file in units of extents[0]*extents[1]
    
    endianess - the endianess of the data
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - writeBufferShort
```
public void writeBufferShort(short[] buffer,
                             int start,
                             int end,
                             boolean endianess)
                      throws java.io.IOException
```
    This method writes a raw short buffer to a file.
    
    Parameters:
    
    buffer - the image data buffer
    
    start - start of data in the read image file in units of extents[0]*extents[1]
    
    end - end of data in the read image file in units of extents[0]*extents[1]
    
    endianess - the endianess of the data
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - writeBufferUByte
```
public void writeBufferUByte(short[] buffer,
                             int start,
                             int end)
                      throws java.io.IOException
```
    This method writes a raw unsigned byte buffer to a file.
    
    Parameters:
    
    buffer - image data buffer
    
    start - start of data in the read image file in units of extents[0]*extents[1]
    
    end - end of data in the read image file in units of extents[0]*extents[1]
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - writeBufferUInt
```
public void writeBufferUInt(long[] buffer,
                            int start,
                            int end,
                            boolean endianess)
                     throws java.io.IOException
```
    This method writes an unisgned int buffer to a file.
    
    Parameters:
    
    buffer - the image data buffer
    
    start - start of data in the read image file in units of extents[0]*extents[1]
    
    end - end of data in the read image file in units of extents[0]*extents[1]
    
    endianess - the endianess of the data
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - writeBufferUShort
```
public void writeBufferUShort(int[] buffer,
                              int start,
                              int end,
                              boolean endianess)
                       throws java.io.IOException
```
    This method writes a raw unsigned short buffer to a file.
    
    Parameters:
    
    buffer - the image data buffer
    
    start - start of data in the read image file in units of extents[0]*extents[1]
    
    end - end of data in the read image file in units of extents[0]*extents[1]
    
    endianess - the endianess of the data
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - writeImage
```
public void writeImage(ModelImage image,
                       int start,
                       int end)
                throws java.io.IOException
```
    This method writes a raw image file (1D-5D).
    
    Parameters:
    
    image - image model from which the data will be read.
    
    start - start of data in the read image file in units of extents[0]*extents[1]
    
    end - end of data in the read image file in units of extents[0]*extents[1]
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!

Class FileRawChunk

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

RGB

RRRGGGBBB

bufferBitSet

bufferByte

bufferDouble

bufferFloat

bufferInt

bufferLong

bufferShort

bufferSize

compressionType

deflaterStream

fileInfo

inflaterStream

numChannels

planarConfig

RGBAOrder

type

minimumBitsMinus1

shiftToDivide

threeByteInteger

bitsAllocated

bitsStored

highBit

Constructor Detail

FileRawChunk

FileRawChunk

Method Detail

close

finalize

setMinimumBitsMinus1

setThreeByteInteger

setBitsAllocated

setBitsStored

setHighBit

setShiftToDivide

getBitSetBuffer

getByteBuffer

getDoubleBuffer

getFloatBuffer

getIntBuffer

getLongBuffer

getShortBuffer

readImage

setImageFile

setNumChannels

setPlanarConfig

setRGBAOrder

writeBufferByte

writeBufferDouble

writeBufferFloat

writeBufferInt

writeBufferLong

writeBufferRGB

writeBufferRGB_USHORT

writeBufferShort

writeBufferUByte

writeBufferUInt

writeBufferUShort

writeImage