com.pixelmed.dicom

Class EncapsulatedInputStream

java.lang.Object

java.io.InputStream

com.pixelmed.dicom.EncapsulatedInputStream

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable

public class EncapsulatedInputStream
extends java.io.InputStream

A class that extends InputStream by adding a mechanism for unencapsulating an undefined length DICOM attribute, such as is used for compressed Pixel Data.

The read methods hide the fact that the data is encapsulated by removing the Items and Item and Sequence delimiter tags, as well as skipping any Basic Offset Table that may be present in the first Item.

Since an individual frame may be fragmented and padded beyond the JPEG EOI marker (0xffd9), and since the codec used for decoding may be "reading ahead" this class also removes any padding bytes at the end of any fragment, back as far as the EOI marker. Note that this means that theoretically frames could span fragments as long as there was no padding between them.

Constructor Summary

Constructors

Constructor and Description
EncapsulatedInputStream(BinaryInputStream i) Construct a byte ordered stream from the supplied stream.
EncapsulatedInputStream(BinaryInputStream i, boolean jpegEOIDetection, boolean oneFragmentPerFrame) Construct a byte ordered stream from the supplied stream.

Method Summary

Modifier and Type	Method and Description
boolean	framesAreSeparated() Are frames separated (seperable)?
long[]	getByteOffsetsOfItemsForCurrentFrame(long startOfPixelData)
protected long	getBytesRead()
long[]	getItemLengthsForCurrentFrame()
int	getOffsetOfNextByteToReadFromStartOfFragment()
void	nextFrame() Skip to the start of the first fragment for a frame, if not already there.
int	read() Extracts the next byte of data from the current or subsequent fragments.
int	read(byte[] b) Extracts byte.length bytes of data from the current or subsequent fragments.
int	read(byte[] b, int off, int len) Extracts len bytes of data from the current or subsequent fragments.
void	readSequenceDelimiter()
void	readUnsigned16(short[] w, int offset, int len) Read an array of unsigned integer 16 bit values.
long	readUnsigned32LittleEndian() Read an unsigned integer 32 bit values little endian regardless of endianness of stream.
void	readUnsigned32LittleEndian(long[] w, int offset, int len) Read an array of unsigned integer 32 bit values little endian regardless of endianness of stream.
void	skipInsistently(long length) Skip as many bytes as requested, unless an exception occurs.

Methods inherited from class java.io.InputStream

available, close, mark, markSupported, reset, skip

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

EncapsulatedInputStream

public EncapsulatedInputStream(BinaryInputStream i)

Construct a byte ordered stream from the supplied stream.

The byte order may be changed later.

JPEG EOI detection is enabled, to allow frames to span fragments.

Do not use for RLE encapsulated data, since it will assume all fragments are in one frame, rather than one fragment per frame.

Parameters:

i - the input stream to read from

EncapsulatedInputStream

public EncapsulatedInputStream(BinaryInputStream i,
                               boolean jpegEOIDetection,
                               boolean oneFragmentPerFrame)

Construct a byte ordered stream from the supplied stream.

The byte order may be changed later.

Parameters:

i - the input stream to read from

jpegEOIDetection - whether or not to detect JPEG EOI, to allow frames to span fragments

oneFragmentPerFrame - if not using jpegEOIDetection, whether or not to assume one fragment per frame (e.g., for RLE), rather than all fragments in one frame (e.g., for MPEG)

Method Detail

framesAreSeparated

public boolean framesAreSeparated()

Are frames separated (seperable)?

This will be either because the stream contains recognizable end of frame markers (e.g., JPEG) or the Transfer Syntax specifies one fragment per frame (e.g., RLE).

Returns:

true if frames are separated rather than being lumped together in one byte stream/array

getByteOffsetsOfItemsForCurrentFrame

public long[] getByteOffsetsOfItemsForCurrentFrame(long startOfPixelData)

getBytesRead

protected long getBytesRead()

getItemLengthsForCurrentFrame

public long[] getItemLengthsForCurrentFrame()

getOffsetOfNextByteToReadFromStartOfFragment

public int getOffsetOfNextByteToReadFromStartOfFragment()

nextFrame

public void nextFrame()

Skip to the start of the first fragment for a frame, if not already there.

read

public final int read()
               throws java.io.IOException

Extracts the next byte of data from the current or subsequent fragments.

Specified by:

read in class java.io.InputStream

Returns:

the next byte of data, or -1 if there is no more data because the end of the stream has been reached.

Throws:

java.io.IOException - if an I/O error occurs.

read

public final int read(byte[] b)
               throws java.io.IOException

Extracts byte.length bytes of data from the current or subsequent fragments.

This method simply performs the call read(b, 0, b.length) and returns the result.

Overrides:

read in class java.io.InputStream

Parameters:

b - the buffer into which the data is read.

Returns:

the total number of bytes read into the buffer (always whatever was asked for), or -1 if there is no more data because the end of the stream has been reached.

Throws:

java.io.IOException - if an I/O error occurs.

See Also:

read(byte[], int, int)

read

public final int read(byte[] b,
                      int off,
                      int len)
               throws java.io.IOException

Extracts len bytes of data from the current or subsequent fragments.

Overrides:

read in class java.io.InputStream

Parameters:

b - the buffer into which the data is read.

off - the start offset of the data.

len - the number of bytes read.

Returns:

the total number of bytes read into the buffer (always whatever was asked for), or -1 if there is no more data because the end of a frame has been reached.

Throws:

java.io.IOException - if an I/O error occurs.

readSequenceDelimiter

public void readSequenceDelimiter()
                           throws java.io.IOException

Throws:

java.io.IOException - if an I/O error occurs

readUnsigned16

public final void readUnsigned16(short[] w,
                                 int offset,
                                 int len)
                          throws java.io.IOException

Read an array of unsigned integer 16 bit values.

Parameters:

w - an array of sufficient size in which to return the values read

offset - the offset in the array at which to begin storing values

len - the number of 16 bit values to read

Throws:

java.io.IOException - if an I/O error occurs

readUnsigned32LittleEndian

public final long readUnsigned32LittleEndian()
                                      throws java.io.IOException

Read an unsigned integer 32 bit values little endian regardless of endianness of stream.

Returns:

the value read

Throws:

java.io.IOException - if an I/O error occurs

readUnsigned32LittleEndian

public final void readUnsigned32LittleEndian(long[] w,
                                             int offset,
                                             int len)
                                      throws java.io.IOException

Read an array of unsigned integer 32 bit values little endian regardless of endianness of stream.

Parameters:

w - an array of sufficient size in which to return the values read

offset - the offset in the array at which to begin storing values

len - the number of 32 bit values to read

Throws:

java.io.IOException - if an I/O error occurs

skipInsistently

public void skipInsistently(long length)
                     throws java.io.IOException

Skip as many bytes as requested, unless an exception occurs.

Parameters:

length - number of bytes to read (no more and no less)

Throws:

java.io.IOException - if an I/O error occurs