java.lang.Object
- jj2000.j2k.image.input.ImgReader
- - gov.nih.mipav.model.file.rawjp2.ImgReaderRAW

All Implemented Interfaces:

jj2000.j2k.image.BlkImgDataSrc, jj2000.j2k.image.ImgData
```
public class ImgReaderRAW
extends jj2000.j2k.image.input.ImgReader
```
This class implements the ImgData interface for reading 16 bit unsigned data from a binary RAW file.
After being read the coefficients are level shifted by subtracting 2^(nominal bit range-1)

The TransferType (see ImgData) of this class is TYPE_INT.

NOTE: This class is not thread safe, for reasons of internal buffering.

See Also:

ImgData

Field Summary

Fields
Modifier and Type	Field	Description
`private byte[]`	`buf`	The line buffer.
`static int`	`DC_OFFSET`	DC offset value used when reading image
`private ModelImage`	`image`	image store
`private java.io.RandomAccessFile`	`in`	Where to read the data from
`private jj2000.j2k.image.DataBlkInt`	`intBlk`	Temporary DataBlkInt object (needed when encoder uses floating-point filters).
`private int`	`numSlice`	Number of slices in 3D image
`private int`	`offset`	The offset of the raw pixel data in the RAW file
`private int`	`rb`	The number of bits that determine the nominal dynamic range

Fields inherited from class jj2000.j2k.image.input.ImgReader
h, nc, w

Constructor Summary

Constructors
Constructor	Description
`ImgReaderRAW(ModelImage image)`
`ImgReaderRAW(java.io.File file)`	Creates a new PGM file reader from the specified file.
`ImgReaderRAW(java.io.RandomAccessFile in)`	Creates a new PGM file reader from the specified RandomAccessFile object.
`ImgReaderRAW(java.lang.String fname)`	Creates a new PGM file reader from the specified file name.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`close()`	Closes the underlying RandomAccessFile from where the image data is being read.
`private void`	`confirmFileType()`	Checks that the RandomAccessIO begins with 'P5'
`private byte`	`countedByteRead()`	Returns a byte read from the RandomAccessIO.
`jj2000.j2k.image.DataBlk`	`getCompData(jj2000.j2k.image.DataBlk blk, int c)`	Returns, in the blk argument, a block of image data containing the specifed rectangular area, in the specified component.
`int`	`getFixedPoint(int c)`	Returns the position of the fixed point in the specified component (i.e. the number of fractional bits), which is always 0 for this ImgReader.
`jj2000.j2k.image.DataBlk`	`getInternCompData(jj2000.j2k.image.DataBlk blk, int c)`	Returns, in the blk argument, the block of image data containing the specifed rectangular area, in the specified component.
`int`	`getNomRangeBits(int c)`	Returns the number of bits corresponding to the nominal range of the data in the specified component.
`boolean`	`isOrigSigned(int c)`	Returns true if the data read was originally signed in the specified component, false if not.
`private int`	`readHeaderInt()`	Returns an int read from the header of the PGM file.
`private void`	`skipCommentAndWhiteSpace()`	Skips any line in the header starting with '#' and any space, tab, line feed or carriage return.
`java.lang.String`	`toString()`	Returns a string of information about the object, more than 1 line long.

Methods inherited from class jj2000.j2k.image.input.ImgReader
getCompImgHeight, getCompImgWidth, getCompSubsX, getCompSubsY, getCompULX, getCompULY, getImgHeight, getImgULX, getImgULY, getImgWidth, getNomTileHeight, getNomTileWidth, getNumComps, getNumTiles, getNumTiles, getTile, getTileCompHeight, getTileCompWidth, getTileHeight, getTileIdx, getTilePartULX, getTilePartULY, getTileWidth, nextTile, setTile

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - DC_OFFSET
```
public static int DC_OFFSET
```
    DC offset value used when reading image
  - in
```
private java.io.RandomAccessFile in
```
    Where to read the data from
  - offset
```
private int offset
```
    The offset of the raw pixel data in the RAW file
  - rb
```
private int rb
```
    The number of bits that determine the nominal dynamic range
  - buf
```
private byte[] buf
```
    The line buffer.
  - intBlk
```
private jj2000.j2k.image.DataBlkInt intBlk
```
    Temporary DataBlkInt object (needed when encoder uses floating-point filters). This avoid allocating new DataBlk at each time
  - image
```
private ModelImage image
```
    image store
  - numSlice
```
private int numSlice
```
    Number of slices in 3D image
- Constructor Detail
  - ImgReaderRAW
```
public ImgReaderRAW(java.io.File file)
             throws java.io.IOException
```
    Creates a new PGM file reader from the specified file.
    
    Parameters:
    
    file - The input file.
    
    Throws:
    
    java.io.IOException - If an error occurs while opening the file.
  - ImgReaderRAW
```
public ImgReaderRAW(java.lang.String fname)
             throws java.io.IOException
```
    Creates a new PGM file reader from the specified file name.
    
    Parameters:
    
    fname - The input file name.
    
    Throws:
    
    java.io.IOException - If an error occurs while opening the file.
  - ImgReaderRAW
```
public ImgReaderRAW(java.io.RandomAccessFile in)
             throws java.io.EOFException,
                    java.io.IOException
```
    Creates a new PGM file reader from the specified RandomAccessFile object. The file header is read to acquire the image size.
    
    Parameters:
    
    in - From where to read the data
    
    Throws:
    
    java.io.EOFException - if an EOF is read
    
    java.io.IOException - if an error occurs when opening the file
  - ImgReaderRAW
```
public ImgReaderRAW(ModelImage image)
```
- Method Detail
  - close
```
public void close()
           throws java.io.IOException
```
    Closes the underlying RandomAccessFile from where the image data is being read. No operations are possible after a call to this method.
    
    Specified by:
    
    close in class jj2000.j2k.image.input.ImgReader
    
    Throws:
    
    java.io.IOException - If an I/O error occurs.
  - getNomRangeBits
```
public int getNomRangeBits(int c)
```
    Returns the number of bits corresponding to the nominal range of the data in the specified component. This is the value rb (range bits) that was specified in the constructor, which normally is 8 for non bilevel data, and 1 for bilevel data.
    If this number is b then the nominal range is between -2^(b-1) and 2^(b-1)-1, since unsigned data is level shifted to have a nominal average of 0.
    
    Parameters:
    
    c - The index of the component.
    
    Returns:
    
    The number of bits corresponding to the nominal range of the data. Fro floating-point data this value is not applicable and the return value is undefined.
  - getFixedPoint
```
public int getFixedPoint(int c)
```
    Returns the position of the fixed point in the specified component (i.e. the number of fractional bits), which is always 0 for this ImgReader.
    
    Parameters:
    
    c - The index of the component.
    
    Returns:
    
    The position of the fixed-point (i.e. the number of fractional bits). Always 0 for this ImgReader.
  - getInternCompData
```
public final jj2000.j2k.image.DataBlk getInternCompData(jj2000.j2k.image.DataBlk blk,
                                                        int c)
```
    Returns, in the blk argument, the block of image data containing the specifed rectangular area, in the specified component. The data is returned, as a reference to the internal data, if any, instead of as a copy, therefore the returned data should not be modified.
    After being read the coefficients are level shifted by subtracting 2^(nominal bit range - 1)
    The rectangular area to return is specified by the 'ulx', 'uly', 'w' and 'h' members of the 'blk' argument, relative to the current tile. These members are not modified by this method. The 'offset' and 'scanw' of the returned data can be arbitrary. See the 'DataBlk' class.
    If the data array in blk is null, then a new one is created if necessary. The implementation of this interface may choose to return the same array or a new one, depending on what is more efficient. Therefore, the data array in blk prior to the method call should not be considered to contain the returned data, a new array may have been created. Instead, get the array from blk after the method has returned.
    The returned data always has its 'progressive' attribute unset (i.e. false).
    When an I/O exception is encountered the JJ2KExceptionHandler is used. The exception is passed to its handleException method. The action that is taken depends on the action that has been registered in JJ2KExceptionHandler. See JJ2KExceptionHandler for details.
    
    Parameters:
    
    blk - Its coordinates and dimensions specify the area to return. Some fields in this object are modified to return the data.
    
    c - The index of the component from which to get the data. Only 0 is valid.
    
    Returns:
    
    The requested DataBlk
    
    See Also:
    
    getCompData(jj2000.j2k.image.DataBlk, int), JJ2KExceptionHandler
  - getCompData
```
public jj2000.j2k.image.DataBlk getCompData(jj2000.j2k.image.DataBlk blk,
                                            int c)
```
    Returns, in the blk argument, a block of image data containing the specifed rectangular area, in the specified component. The data is returned, as a copy of the internal data, therefore the returned data can be modified "in place".
    After being read the coefficients are level shifted by subtracting 2^(nominal bit range - 1)
    The rectangular area to return is specified by the 'ulx', 'uly', 'w' and 'h' members of the 'blk' argument, relative to the current tile. These members are not modified by this method. The 'offset' of the returned data is 0, and the 'scanw' is the same as the block's width. See the 'DataBlk' class.
    If the data array in 'blk' is 'null', then a new one is created. If the data array is not 'null' then it is reused, and it must be large enough to contain the block's data. Otherwise an 'ArrayStoreException' or an 'IndexOutOfBoundsException' is thrown by the Java system.
    The returned data has its 'progressive' attribute unset (i.e. false).
    This method just calls 'getInternCompData(blk, n)'.
    When an I/O exception is encountered the JJ2KExceptionHandler is used. The exception is passed to its handleException method. The action that is taken depends on the action that has been registered in JJ2KExceptionHandler. See JJ2KExceptionHandler for details.
    
    Parameters:
    
    blk - Its coordinates and dimensions specify the area to return. If it contains a non-null data array, then it must have the correct dimensions. If it contains a null data array a new one is created. The fields in this object are modified to return the data.
    
    c - The index of the component from which to get the data. Only 0 is valid.
    
    Returns:
    
    The requested DataBlk
    
    See Also:
    
    getInternCompData(jj2000.j2k.image.DataBlk, int), JJ2KExceptionHandler
  - countedByteRead
```
private byte countedByteRead()
                      throws java.io.IOException,
                             java.io.EOFException
```
    Returns a byte read from the RandomAccessIO. The number of read byted are counted to keep track of the offset of the pixel data in the PGM file
    
    Returns:
    
    One byte read from the header of the PGM file.
    
    Throws:
    
    java.io.IOException - If an I/O error occurs.
    
    java.io.EOFException - If an EOF is read
  - confirmFileType
```
private void confirmFileType()
                      throws java.io.IOException,
                             java.io.EOFException
```
    Checks that the RandomAccessIO begins with 'P5'
    
    Throws:
    
    java.io.IOException - If an I/O error occurs.
    
    java.io.EOFException - If an EOF is read
  - skipCommentAndWhiteSpace
```
private void skipCommentAndWhiteSpace()
                               throws java.io.IOException,
                                      java.io.EOFException
```
    Skips any line in the header starting with '#' and any space, tab, line feed or carriage return.
    
    Throws:
    
    java.io.IOException - If an I/O error occurs.
    
    java.io.EOFException - if an EOF is read
  - readHeaderInt
```
private int readHeaderInt()
                   throws java.io.IOException,
                          java.io.EOFException
```
    Returns an int read from the header of the PGM file.
    
    Returns:
    
    One int read from the header of the PGM file.
    
    Throws:
    
    java.io.IOException - If an I/O error occurs.
    
    java.io.EOFException - If an EOF is read
  - isOrigSigned
```
public boolean isOrigSigned(int c)
```
    Returns true if the data read was originally signed in the specified component, false if not. This method returns always false since PGM data is always unsigned.
    
    Specified by:
    
    isOrigSigned in class jj2000.j2k.image.input.ImgReader
    
    Parameters:
    
    c - The index of the component, from 0 to N-1.
    
    Returns:
    
    always false, since PGM data is always unsigned.
  - toString
```
public java.lang.String toString()
```
    Returns a string of information about the object, more than 1 line long. The information string includes information from the underlying RandomAccessIO (its toString() method is called in turn).
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    A string of information about the object.

Class ImgReaderRAW

Field Summary

Fields inherited from class jj2000.j2k.image.input.ImgReader

Constructor Summary

Method Summary

Methods inherited from class jj2000.j2k.image.input.ImgReader

Methods inherited from class java.lang.Object

Field Detail

DC_OFFSET

in

offset

rb

buf

intBlk

image

numSlice

Constructor Detail

ImgReaderRAW

ImgReaderRAW

ImgReaderRAW

ImgReaderRAW

Method Detail

close

getNomRangeBits

getFixedPoint

getInternCompData

getCompData

countedByteRead

confirmFileType

skipCommentAndWhiteSpace

readHeaderInt

isOrigSigned

toString