java.lang.Object
- gov.nih.mipav.model.file.FileDicomJPEG

public class FileDicomJPEG
extends java.lang.Object

Class that reads a lossless compressed JPEG file. These are sometimes encapsulated in DICOM. The lossless decoder uses a Huffman table to interpret values. For color images this file will have to be modified. Some code for color is here but it isn't universal. There is a private class within this file that does the bit reading and packing. For more information see the comments in front of that class. This code was ported from Huang and Smith's Cornell software.

 Copyright (c) 1993 Cornell University, Kongji Huang
 All rights reserved.
 
 Permission to use, copy, modify, and distribute this software and its
 documentation for research purposes, without fee, and without written
 agreement is hereby granted, provided that the above copyright notice
 and the following two paragraphs appear in all copies of this
 software.
 
 IN NO EVENT SHALL THE CORNELL UNIVERSITY BE LIABLE TO ANY PARTY FOR
 DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING
 OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF THE
 UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
 DAMAGE.
 
 THE CORNELL UNIVERSITY SPECIFICALLY DISCLAIMS ANY WARRANTIES,
 INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
 MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE SOFTWARE
 PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF
 CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES,
 ENHANCEMENTS, OR MODIFICATIONS.

 Copyright (c) 1993 The Regents of the University of California, Brian
 C. Smith All rights reserved.
 
 Permission to use, copy, modify, and distribute this software and its
 documentation for any purpose, without fee, and without written
 agreement is hereby granted, provided that the above copyright notice
 and the following two paragraphs appear in all copies of this
 software.
 
 IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY
 FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
 ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF
 THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF
 SUCH DAMAGE.
 
 THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES,
 INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
 MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE SOFTWARE
 PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF
 CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES,
 ENHANCEMENTS, OR MODIFICATIONS.

 IJG Copyright
 
 The authors make NO WARRANTY or representation, either express or
 implied, with respect to this software, its quality, accuracy,
 merchantability, or fitness for a particular purpose.  This software is
 provided "AS IS", and you, its user, assume the entire risk as to its
 quality and accuracy.
 
 This software is copyright (C) 1991, 1992, Thomas G. Lane.  All Rights
 Reserved except as specified below.
 
 Permission is hereby granted to use, copy, modify, and distribute this
 software (or portions thereof) for any purpose, without fee, subject to
 these conditions:  (1) If any part of the source code for this software
 is distributed, then this README file must be included, with this
 copyright and no-warranty notice unaltered; and any additions,
 deletions, or changes to the original files must be clearly indicated
 in accompanying documentation.  (2) If only executable code is
 distributed, then the accompanying documentation must state that "this
 software is based in part on the work of the Independent JPEG Group".
 (3) Permission for use of this software is granted only if the user
 accepts full responsibility for any undesirable consequences; the
 authors accept NO LIABILITY for damages of any kind.
 
 Permission is NOT granted for the use of any IJG author's name or
 company name in advertising or publicity relating to this software or
 products derived from it.  This software may be referred to only as
 "the Independent JPEG Group's software".
 
 We specifically permit and encourage the use of this software as the
 basis of commercial products, provided that all warranty or liability
 claims are assumed by the product vendor.

Version:: 1.0 May 14, 2002
Author:: Neva Cherniavsky

Nested Class Summary

Nested Classes
Modifier and Type Class Description

(package private) class FileDicomJPEG.HuffTable
This class reads and packs the bits appropriately for interpreting the huffman codes.

Field Summary

Fields
Modifier and Type	Field	Description
`private int[]`	`bitMask`	Useful bit mask for getting appropriate bits out of number.
`private byte[][]`	`bits`	Read in DHT header.
`private int[]`	`componentId`	Needed for color images.
`private short[]`	`componentIndex`	Needed for color images.
`private int`	`compsInScan`	Number of components in scan; 1 for black and white, 4 for color.
`private byte`	`dataPrecision`	Data precision.
`private int`	`dicomH`	Height read in from DICOM file; only use if imageHeight isn't defined.
`private int`	`dicomW`	Width read in from DICOM file; only use if imageWidth isn't defined.
`private static int[]`	`extendOffset`	Entry n is (-1 << n) + 1; used to make a number negative.
`private static int[]`	`extendTest`	Entry n is 2**(n-1); used to test whether we need to make a number negative.
`private int[]`	`hSampFactor`	Horizontal sample factor.
`private byte[][]`	`huffval`	Read in DHT header.
`private byte[]`	`image`	Image data we're reading.
`private int`	`imageHeight`	Image height.
`private int`	`imageWidth`	Image width.
`private static byte`	`M_APP0`	Required marker in this standard.
`private static byte`	`M_DHT`	DOCUMENT ME!
`private static byte`	`M_DQT`	DOCUMENT ME!
`private static byte`	`M_DRI`	DOCUMENT ME!
`private static byte`	`M_EOI`	DOCUMENT ME!
`private static byte`	`M_JPG`	DOCUMENT ME!
`private static byte`	`M_RST0`	DOCUMENT ME!
`private static byte`	`M_RST1`	DOCUMENT ME!
`private static byte`	`M_RST2`	DOCUMENT ME!
`private static byte`	`M_RST3`	DOCUMENT ME!
`private static byte`	`M_RST4`	DOCUMENT ME!
`private static byte`	`M_RST5`	DOCUMENT ME!
`private static byte`	`M_RST6`	DOCUMENT ME!
`private static byte`	`M_RST7`	DOCUMENT ME!
`private static byte`	`M_SOF0`	Marker tags in JPEG header.
`private static byte`	`M_SOF1`	DOCUMENT ME!
`private static byte`	`M_SOF10`	DOCUMENT ME!
`private static byte`	`M_SOF11`	DOCUMENT ME!
`private static byte`	`M_SOF13`	DOCUMENT ME!
`private static byte`	`M_SOF14`	DOCUMENT ME!
`private static byte`	`M_SOF15`	DOCUMENT ME!
`private static byte`	`M_SOF2`	DOCUMENT ME!
`private static byte`	`M_SOF3`	DOCUMENT ME!
`private static byte`	`M_SOF5`	DOCUMENT ME!
`private static byte`	`M_SOF6`	DOCUMENT ME!
`private static byte`	`M_SOF7`	DOCUMENT ME!
`private static byte`	`M_SOF9`	DOCUMENT ME!
`private static byte`	`M_SOI`	DOCUMENT ME!
`private static byte`	`M_SOS`	DOCUMENT ME!
`private static byte`	`M_TEM`	DOCUMENT ME!
`private int[][]`	`maxcode`	mincode[index] = minimum legal code at that index.
`private short[][]`	`mincode`	mincode[index] = minimum legal code at that index.
`private int`	`nextRestartNum`	Numbers needed for restart.
`private int[][]`	`numbits`	number of bits needed for code at index.
`private int`	`numComponents`	Number of components - 1 for black and white, 4 for color.
`private int`	`Pt`	Shift by this when putting into int buffer.
`private int`	`restartInRows`	Numbers needed for restart.
`private int`	`restartInterval`	Restart interval.
`private int`	`restartRowsToGo`	Numbers needed for restart.
`private byte`	`Ss`	Byte indicating which location to use as the predictor.
`private int[]`	`tableNo`	Table number - always 0 for non-color images.
`private java.util.Vector<byte[]>`	`v`
`private java.util.Vector<int[]>`	`v2`
`private short[][]`	`valptr`	valptr[index] = pointer to where legal code values start.
`private int[][]`	`value`	huffman value for code.
`private int`	`vIndex`
`private int[]`	`vSampFactor`	Vertical sample factor.

Constructor Summary

Constructors
Constructor	Description
`FileDicomJPEG(byte[] imageBuffer, int width, int height)`	Assigns image buffer and creates the other arrays needed to read in image.
`FileDicomJPEG(java.util.Vector<byte[]> v, java.util.Vector<int[]> v2, int width, int height)`	Assigns image buffer and creates the other arrays needed to read in image.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`decodeFirstRow(FileDicomJPEG.HuffTable table, short[][] curRowBuf)`	Decode the first raster line of samples at the start of the scan and at the beginning of each restart interval.
`private int[]`	`decodeImage(int index)`	Decode the input stream.
`int[]`	`extractJPEGImage()`	Extracts the JPEG image by processing the byte image array.
`void`	`extractMultiJPEGImage()`
`private void`	`fixHuffmanTable(int tableNum)`	Sets up Huffman table based on values read in header.
`private int`	`getAPPO(int index)`	Get APPO part of header.
`private int`	`getDHT(int index)`	Get the Huffman table.
`private int`	`getDRI(int index)`	Get DRI part of header.
`private int`	`getSOF(int index)`	Get the SOF part of header.
`private int`	`getSOS(int index)`	Get the SOS part of header.
`private int`	`nextMarker(int index)`	Gets the next marker in the header.
`private int`	`processRestart(int index)`	Check for a restart marker & resynchronize decoder.
`private int`	`processTables(int index)`	Process the header markers.
`private int`	`skipVariable(int index)`	Skip this variable.

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

- Field Detail
  - M_SOF0
```
private static final byte M_SOF0
```
    Marker tags in JPEG header.
    
    See Also:
    
    Constant Field Values
  - M_SOF1
```
private static final byte M_SOF1
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_SOF2
```
private static final byte M_SOF2
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_SOF3
```
private static final byte M_SOF3
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_SOF5
```
private static final byte M_SOF5
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_SOF6
```
private static final byte M_SOF6
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_SOF7
```
private static final byte M_SOF7
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_JPG
```
private static final byte M_JPG
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_SOF9
```
private static final byte M_SOF9
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_SOF10
```
private static final byte M_SOF10
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_SOF11
```
private static final byte M_SOF11
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_SOF13
```
private static final byte M_SOF13
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_SOF14
```
private static final byte M_SOF14
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_SOF15
```
private static final byte M_SOF15
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_DHT
```
private static final byte M_DHT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_RST0
```
private static final byte M_RST0
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_RST1
```
private static final byte M_RST1
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_RST2
```
private static final byte M_RST2
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_RST3
```
private static final byte M_RST3
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_RST4
```
private static final byte M_RST4
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_RST5
```
private static final byte M_RST5
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_RST6
```
private static final byte M_RST6
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_RST7
```
private static final byte M_RST7
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_SOI
```
private static final byte M_SOI
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_EOI
```
private static final byte M_EOI
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_SOS
```
private static final byte M_SOS
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_DQT
```
private static final byte M_DQT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_DRI
```
private static final byte M_DRI
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - M_APP0
```
private static final byte M_APP0
```
    Required marker in this standard.
    
    See Also:
    
    Constant Field Values
  - M_TEM
```
private static final byte M_TEM
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - extendTest
```
private static int[] extendTest
```
    Entry n is 2**(n-1); used to test whether we need to make a number negative.
  - extendOffset
```
private static int[] extendOffset
```
    Entry n is (-1 << n) + 1; used to make a number negative.
  - bitMask
```
private final int[] bitMask
```
    Useful bit mask for getting appropriate bits out of number.
  - bits
```
private final byte[][] bits
```
    Read in DHT header. Number of codes with bitlength of index. Thus, bits[2] = 1 means one code represented by 2 bits. bits[3] = 4 means four codes represented by 3 bits. 2D array necessary in case of color image - component #.
  - componentId
```
private final int[] componentId
```
    Needed for color images.
  - componentIndex
```
private final short[] componentIndex
```
    Needed for color images.
  - compsInScan
```
private int compsInScan
```
    Number of components in scan; 1 for black and white, 4 for color.
  - dataPrecision
```
private byte dataPrecision
```
    Data precision.
  - dicomH
```
private final int dicomH
```
    Height read in from DICOM file; only use if imageHeight isn't defined.
  - dicomW
```
private final int dicomW
```
    Width read in from DICOM file; only use if imageWidth isn't defined.
  - hSampFactor
```
private final int[] hSampFactor
```
    Horizontal sample factor.
  - huffval
```
private final byte[][] huffval
```
    Read in DHT header. Huffman code values, used to determine Huffman table (value array). Also directly accessed when numbits > 8, since fast lookup is not possible.
  - image
```
private byte[] image
```
    Image data we're reading.
  - imageHeight
```
private int imageHeight
```
    Image height.
  - imageWidth
```
private int imageWidth
```
    Image width.
  - maxcode
```
private final int[][] maxcode
```
    mincode[index] = minimum legal code at that index.
  - mincode
```
private final short[][] mincode
```
    mincode[index] = minimum legal code at that index.
  - nextRestartNum
```
private int nextRestartNum
```
    Numbers needed for restart. Hasn't been tested!
  - numbits
```
private final int[][] numbits
```
    number of bits needed for code at index.
  - numComponents
```
private int numComponents
```
    Number of components - 1 for black and white, 4 for color.
  - Pt
```
private int Pt
```
    Shift by this when putting into int buffer.
  - restartInRows
```
private int restartInRows
```
    Numbers needed for restart. Hasn't been tested!
  - restartInterval
```
private int restartInterval
```
    Restart interval.
  - restartRowsToGo
```
private int restartRowsToGo
```
    Numbers needed for restart. Hasn't been tested!
  - Ss
```
private byte Ss
```
    Byte indicating which location to use as the predictor.
  - tableNo
```
private final int[] tableNo
```
    Table number - always 0 for non-color images.
  - valptr
```
private final short[][] valptr
```
    valptr[index] = pointer to where legal code values start.
  - value
```
private final int[][] value
```
    huffman value for code.
  - vSampFactor
```
private final int[] vSampFactor
```
    Vertical sample factor.
  - v
```
private java.util.Vector<byte[]> v
```
  - vIndex
```
private int vIndex
```
  - v2
```
private java.util.Vector<int[]> v2
```
- Constructor Detail
  - FileDicomJPEG
```
public FileDicomJPEG(byte[] imageBuffer,
                     int width,
                     int height)
```
    Assigns image buffer and creates the other arrays needed to read in image.
    
    Parameters:
    
    imageBuffer - Image buffer.
    
    width - DOCUMENT ME!
    
    height - DOCUMENT ME!
  - FileDicomJPEG
```
public FileDicomJPEG(java.util.Vector<byte[]> v,
                     java.util.Vector<int[]> v2,
                     int width,
                     int height)
```
    Assigns image buffer and creates the other arrays needed to read in image.
    
    Parameters:
    
    imageBuffer - Image buffer.
    
    width - DOCUMENT ME!
    
    height - DOCUMENT ME!
- Method Detail
  - extractMultiJPEGImage
```
public void extractMultiJPEGImage()
                           throws java.io.IOException
```
    Throws:
    
    java.io.IOException
  - extractJPEGImage
```
public int[] extractJPEGImage()
                       throws java.io.IOException
```
    Extracts the JPEG image by processing the byte image array.
    
    Returns:
    
    image buffer - the JPEG image
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - decodeFirstRow
```
private void decodeFirstRow(FileDicomJPEG.HuffTable table,
                            short[][] curRowBuf)
```
    Decode the first raster line of samples at the start of the scan and at the beginning of each restart interval. This includes modifying the component value so the real value, not the difference is returned.
    
    Parameters:
    
    table - Huffman table.
    
    curRowBuf - Current row buffer; 2D because if image is color, there are 4 components.
  - decodeImage
```
private int[] decodeImage(int index)
```
    Decode the input stream. This includes modifying the component value so the real value, not the difference is returned.
    
    Parameters:
    
    index - Index where we currently are in the image.
    
    Returns:
    
    Buffer holding decompressed image.
  - fixHuffmanTable
```
private void fixHuffmanTable(int tableNum)
```
    Sets up Huffman table based on values read in header.
    
    Parameters:
    
    tableNum - Usually 0, haven't tested when it isn't.
  - getAPPO
```
private int getAPPO(int index)
```
    Get APPO part of header.
    
    Parameters:
    
    index - Index we're at in the image array.
    
    Returns:
    
    Last accessed index.
  - getDHT
```
private int getDHT(int index)
```
    Get the Huffman table.
    
    Parameters:
    
    index - Index we're at in the image array.
    
    Returns:
    
    Last accessed index.
  - getDRI
```
private int getDRI(int index)
```
    Get DRI part of header.
    
    Parameters:
    
    index - Index we're at in the image array.
    
    Returns:
    
    Last accessed index.
  - getSOF
```
private int getSOF(int index)
```
    Get the SOF part of header.
    
    Parameters:
    
    index - Index we're at in the image array.
    
    Returns:
    
    Last accessed index.
  - getSOS
```
private int getSOS(int index)
```
    Get the SOS part of header.
    
    Parameters:
    
    index - Index we're at in the image array.
    
    Returns:
    
    Last accessed index.
  - nextMarker
```
private int nextMarker(int index)
```
    Gets the next marker in the header.
    
    Parameters:
    
    index - Index that we're at in the image array.
    
    Returns:
    
    Last accessed index.
  - processRestart
```
private int processRestart(int index)
```
    Check for a restart marker & resynchronize decoder. Haven't tested this at all.
    
    Parameters:
    
    index - Index we're at in the image array.
    
    Returns:
    
    Last accessed index.
  - processTables
```
private int processTables(int index)
```
    Process the header markers.
    
    Parameters:
    
    index - Index we're at in the image array.
    
    Returns:
    
    Last accessed index.
  - skipVariable
```
private int skipVariable(int index)
```
    Skip this variable.
    
    Parameters:
    
    index - Index we're at in the image array.
    
    Returns:
    
    Last accessed index.

Class FileDicomJPEG

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

M_SOF0

M_SOF1

M_SOF2

M_SOF3

M_SOF5

M_SOF6

M_SOF7

M_JPG

M_SOF9

M_SOF10

M_SOF11

M_SOF13

M_SOF14

M_SOF15

M_DHT

M_RST0

M_RST1

M_RST2

M_RST3

M_RST4

M_RST5

M_RST6

M_RST7

M_SOI

M_EOI

M_SOS

M_DQT

M_DRI

M_APP0

M_TEM

extendTest

extendOffset

bitMask

bits

componentId

componentIndex

compsInScan

dataPrecision

dicomH

dicomW

hSampFactor

huffval

image

imageHeight

imageWidth

maxcode

mincode

nextRestartNum

numbits

numComponents

Pt

restartInRows

restartInterval

restartRowsToGo

Ss

tableNo

valptr

value

vSampFactor

v

vIndex

v2

Constructor Detail

FileDicomJPEG

FileDicomJPEG

Method Detail

extractMultiJPEGImage

extractJPEGImage

decodeFirstRow

decodeImage

fixHuffmanTable

getAPPO

getDHT