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

All Implemented Interfaces:

jj2000.j2k.image.BlkImgDataSrc, jj2000.j2k.image.ImgData

Direct Known Subclasses:

ImgReaderRAWColorSlice
```
public class ImgReaderRAWSlice
extends jj2000.j2k.image.input.ImgReader
```
This class implements the ImgData interface for reading slices of 16 bit unsigned data from a 3D RAW image 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 int`	`blah`
`private byte[]`	`buf`	The line buffer.
`static int`	`DC_OFFSET`	DC offset value used when reading image
`protected java.lang.String`	`fName`
`protected ModelImage`	`image`	image store
`protected java.io.RandomAccessFile`	`in`	Where to read the data from
`protected jj2000.j2k.image.DataBlkInt`	`intBlk`	Temporary DataBlkInt object (needed when encoder uses floating-point filters).
`private int`	`offset`	The offset of the raw pixel data in the RAW file
`protected int`	`rb`	The number of bits that determine the nominal dynamic range
`private boolean`	`savingAsEncJP2`
`protected boolean`	`useModImg`

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

Constructor Summary

Constructors
Constructor	Description
`ImgReaderRAWSlice(ModelImage image, int si, boolean savingAsEncJP2)`
`ImgReaderRAWSlice(ModelImage image, int si, int ti, boolean savingAsEncJP2)`
`ImgReaderRAWSlice(java.io.File file, int si)`	Creates a new PGM file reader from the specified file.
`ImgReaderRAWSlice(java.io.RandomAccessFile in, int si)`	Creates a new PGM file reader from the specified RandomAccessFile object.
`ImgReaderRAWSlice(java.lang.String fname, int si)`	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.
`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.
`void`	`setSliceIndex(int si, boolean useModImg)`
`void`	`setSliceIndex(int si, int ti, boolean useModImg)`
`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
```
protected 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
  - image
```
protected ModelImage image
```
    image store
  - rb
```
protected int rb
```
    The number of bits that determine the nominal dynamic range
  - buf
```
private byte[] buf
```
    The line buffer.
  - intBlk
```
protected jj2000.j2k.image.DataBlkInt intBlk
```
    Temporary DataBlkInt object (needed when encoder uses floating-point filters). This avoid allocating new DataBlk at each time
  - useModImg
```
protected boolean useModImg
```
  - fName
```
protected java.lang.String fName
```
  - savingAsEncJP2
```
private boolean savingAsEncJP2
```
  - blah
```
private int blah
```
- Constructor Detail
  - ImgReaderRAWSlice
```
public ImgReaderRAWSlice(java.io.File file,
                         int si)
                  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.
  - ImgReaderRAWSlice
```
public ImgReaderRAWSlice(java.lang.String fname,
                         int si)
                  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.
  - ImgReaderRAWSlice
```
public ImgReaderRAWSlice(java.io.RandomAccessFile in,
                         int si)
                  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
  - ImgReaderRAWSlice
```
public ImgReaderRAWSlice(ModelImage image,
                         int si,
                         boolean savingAsEncJP2)
```
  - ImgReaderRAWSlice
```
public ImgReaderRAWSlice(ModelImage image,
                         int si,
                         int ti,
                         boolean savingAsEncJP2)
```
- 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 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
  
  setSliceIndex
  
  public void setSliceIndex(int si, boolean useModImg) throws java.io.IOException
  
  Throws:
  
  java.io.IOException
  
  setSliceIndex
  
  public void setSliceIndex(int si, int ti, boolean useModImg) throws java.io.IOException
  
  Throws:
  
  java.io.IOException
  
  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 ImgReaderRAWSlice

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

image

rb

buf

intBlk

useModImg

fName

savingAsEncJP2

blah

Constructor Detail

ImgReaderRAWSlice

ImgReaderRAWSlice

ImgReaderRAWSlice

ImgReaderRAWSlice

ImgReaderRAWSlice

Method Detail

close

getNomRangeBits

getFixedPoint

getInternCompData

getCompData

setSliceIndex

setSliceIndex

isOrigSigned

toString