Package gov.nih.mipav.model.dicomcomm

Class DICOM_Comms

java.lang.Object
gov.nih.mipav.model.dicomcomm.DICOM_Comms
Direct Known Subclasses:
DICOM_CommsLink, DICOM_FileIO, DICOM_PDUService
public class DICOM_Comms extends Object
This class is used as a base class for all DICOM file and network I/O.
This DICOM communication package was originally based on the Java Dicom Package, whose license is below: 
 Java Dicom Package (com.zmed.dicom)
 
  Copyright (c) 1996-1997 Z Medical Imaging Systems, Inc.
 
  This software is provided, as is, for non-commercial educational
  purposes only.   Use or incorporation of this software or derivative
  works in commercial applications requires written consent from
  Z Medical Imaging Systems, Inc.
 
  Z MEDICAL IMAGING SYSTEMS MAKES NO REPRESENTATIONS OR WARRANTIES ABOUT
  THE SUITABILITY OF THE SOFTWARE, EITHER EXPRESS OR IMPLIED, INCLUDING
  BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS
  FOR A PARTICULAR PURPOSE, NON-INFRINGEMENT, OR CONFORMANCE TO ANY
  SPECIFICATION OR STANDARD.  Z MEDICAL IMAGING SYSTEMS SHALL NOT BE
  LIABLE FOR ANY DAMAGES SUFFERED BY LICENSEE AS A RESULT OF USING OR
  MODIFYING THIS SOFTWARE OR ITS DERIVATIVES.
 
  =============================================================================
 
  This software package is implemented similarly to the UC Davis public
  domain C++ DICOM implementation which contains the following copyright
  notice:
 
  Copyright (C) 1995, University of California, Davis
 
  THIS SOFTWARE IS MADE AVAILABLE, AS IS, AND THE UNIVERSITY
  OF CALIFORNIA DOES NOT MAKE ANY WARRANTY ABOUT THE SOFTWARE, ITS
  PERFORMANCE, ITS MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR
  USE, FREEDOM FROM ANY COMPUTER DISEASES OR ITS CONFORMITY TO ANY
  SPECIFICATION. THE ENTIRE RISK AS TO QUALITY AND PERFORMANCE OF
  THE SOFTWARE IS WITH THE USER.
 
  Copyright of the software and supporting documentation is
  owned by the University of California, and free access
  is hereby granted as a license to use this software, copy this
  software and prepare derivative works based upon this software.
  However, any distribution of this software source code or
  supporting documentation or derivative works (source code and
  supporting documentation) must include this copyright notice.
 
  The UC Davis C++ source code is publicly available from the following
  anonymous ftp site:
 
  ftp://imrad.ucdmc.ucdavis.edu/pub/dicom/UCDMC/

  • Nested Class Summary

    Nested Classes
    Modifier and Type
    Class
    Description
    protected class 
    DICOM_Comms.ByteBuffer
    Simple inner class to facilitate the memory allocation of of a byte buffer used in DICOM_Comms to support I/O.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    BIG_ENDIAN
    Flag used to indicate Big Endianess.
    protected int
    breakSize
    Defaults to the maximum buffer size in streaming.
    private byte[]
    byteArray1
    One byte array allocated once to speed process and reduced the need to reallocate memory.
    private byte[]
    byteArray2
    Two byte array allocated once to speed process and reduced the need to reallocate memory.
    private byte[]
    byteArray4
    Four byte array allocated once to speed process and reduced the need to reallocate memory.
    private boolean
    debugFlag
    Debug flag.
    private boolean
    havePeeked
    Flag indicating whether the first byte has been looked at.
    protected int
    inBuffersLength
    Length of the total input data (Not buffer size but total length of data ).
    protected Vector<DICOM_Comms.ByteBuffer>
    incomingBuffers
    Vector of ByteBuffer's of incoming data.
    private int
    inEndianess
    Endianess of the input stream.
    static final int
    LITTLE_ENDIAN
    Flag used to indicate Little Endianess.
    static final int
    MAX_READ_LENGTH
    The maximum read buffer size.
    protected int
    outBuffersLength
    Length of the total output data (Not buffer size but total length of data ).
    private int
    outEndianess
    Endianess of the output stream.
    protected Vector<DICOM_Comms.ByteBuffer>
    outgoingBuffers
    Vector of ByteBuffer's of outgoing data.
    private byte
    peekedByte
    Storage for the first byte (i.e. the PDU type )
    private byte[]
    srcByteArray
    Source byte array allocated ONCE used in reading from the stream.

  • Constructor Summary

    Constructors
    Constructor
    Description
    DICOM_Comms()
    Constructor for DICOM network I/O class.

  • Method Summary

    Modifier and Type
    Method
    Description
    static final int
    bufferToInt16(byte[] buffer, int index, int endianess)
    Copies a 2 byte array into a 16 bit integer of proper endianess.
    static final int
    bufferToInt32(byte[] buffer, int index, int endianess)
    Copies a 4 byte array into a 32 bit integer of proper endianess.
    protected void
    finalize()
    Prepares this class for destruction.
    void
    flush()
    Sends all byte buffers of the outgoing buffer vector out the port. see DICOM PDUService.sendBinary and DICOMSocket
    void
    flush(int nBytes)
    Sends specified number of bytes out the port. see DICOM PDUService.sendBinary and DICOMSocket
    int
    getIncomingEndian()
    Returns constant indicating endianess of incoming data.
    int
    getIncomingSize()
    Returns the incoming data size.
    int
    getOutgoingEndian()
    Returns constant indicating endianess of outgoing data.
    int
    getOutgoingSize()
    Returns the outgoing data size.
    static final void
    int16ToBuffer(byte[] buffer, int index, int value, int endianess)
    Copies a 16 bit (2 bytes) integer into the specified portion of the byte array of proper endianess.
    static final void
    int32ToBuffer(byte[] buffer, int index, int value, int endianess)
    Copies a 32 bit (4 bytes) integer into the specified portion of the byte array of proper endianess.
    byte
    peekFirstByte()
    Typically used to determine the PDUTYPE (i.e.
    int
    peekForEndOfSequence()
    DOCUMENT ME!
    void
    read(byte[] data)
    Simple method that take a byte array and call read with two parameters: byte array and array length.
    void
    read(byte[] data, int nBytes)
    Reads a specified number of bytes into the byte data buffer.
    int
    readBinary(byte[] data, int nbytes)
    Dummy method and should be overloaded by DICOMPDUService.
    private void
    readBlock(int useBreakSize)
    This is the method that actually reads in the data from the socket or IO stream.
    final byte
    readByte()
    Reads a single byte from the data stream.
    final byte[]
    readBytes(int length)
    Allocates and.
    void
    readFill(int nBytes)
    Reads in a nBytes and puts them in a ByteBuffer and puts the byte buffer in the vector of incomingBuffers.
    final int
    readInt32()
    Reads a 4 byte integer (otherwise known as an int).
    final int
    readShort16()
    Reads a 2 byte integer (otherwise known as a short).
    void
    seekToEndOfGroupTwoTags()
    Strips preamble and group 2 tags from ioBuffer if present.
    void
    sendBinary(byte[] data, int startIndex, int nbytes)
    Dummy method and should be overloaded by DICOMPDUService.
    void
    setIncomingEndianess(int endianess)
    Sets the endianess for the incoming data.
    void
    setOutgoingEndianess(int endianess)
    Sets the endianess for the outgoing data.
    final void
    write(byte[] byteArray)
    Writes a byte arrary to the outgoing buffers.
    void
    write(byte[] data, int dataOffset, int nBytes)
    Writes a specified number of bytes from the byte buffer into outGoing ByteBuffer list of byte buffers.
    final void
    writeByte(byte value)
    Writes a byte to the outgoing buffers.
    final void
    writeByteIn(byte value, DICOM_FileIO ioBuffer)
    Writes a byte to the incoming buffers.
    void
    writeIn(byte[] data, int dataOffset, int nBytes, DICOM_FileIO ioBuffer)
    Writes a specified number of bytes from the byte buffer into incomming ByteBuffer list of byte buffers.
    final void
    writeInt32(int value)
    Writes a 32 (4 byte) integer to the outgoing buffers.
    final void
    writeInt32In(int value, DICOM_FileIO ioBuffer)
    Writes a 32 (4 byte) integer to the incoming buffers.
    final void
    writeShort16(int value)
    Writes a 16 (2 byte) integer to the outgoing buffers.
    final void
    writeShort16In(int value, DICOM_FileIO ioBuffer)
    Writes a 16 (2 byte) integer to the incomming buffers.

    Methods inherited from class java.lang.Object

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

  • Field Details

    • BIG_ENDIAN

      public static final int BIG_ENDIAN
      Flag used to indicate Big Endianess.
      See Also:

    • LITTLE_ENDIAN

      public static final int LITTLE_ENDIAN
      Flag used to indicate Little Endianess.
      See Also:

    • MAX_READ_LENGTH

      public static final int MAX_READ_LENGTH
      The maximum read buffer size.
      See Also:

    • breakSize

      protected int breakSize
      Defaults to the maximum buffer size in streaming.

    • inBuffersLength

      protected int inBuffersLength
      Length of the total input data (Not buffer size but total length of data ).

    • incomingBuffers

      protected Vector<DICOM_Comms.ByteBuffer> incomingBuffers
      Vector of ByteBuffer's of incoming data.

    • outBuffersLength

      protected int outBuffersLength
      Length of the total output data (Not buffer size but total length of data ).

    • outgoingBuffers

      protected Vector<DICOM_Comms.ByteBuffer> outgoingBuffers
      Vector of ByteBuffer's of outgoing data.

    • byteArray1

      private byte[] byteArray1
      One byte array allocated once to speed process and reduced the need to reallocate memory.

    • byteArray2

      private byte[] byteArray2
      Two byte array allocated once to speed process and reduced the need to reallocate memory.

    • byteArray4

      private byte[] byteArray4
      Four byte array allocated once to speed process and reduced the need to reallocate memory.

    • debugFlag

      private boolean debugFlag
      Debug flag.

    • havePeeked

      private boolean havePeeked
      Flag indicating whether the first byte has been looked at.

    • inEndianess

      private int inEndianess
      Endianess of the input stream.

    • outEndianess

      private int outEndianess
      Endianess of the output stream.

    • peekedByte

      private byte peekedByte
      Storage for the first byte (i.e. the PDU type )

    • srcByteArray

      private byte[] srcByteArray
      Source byte array allocated ONCE used in reading from the stream.

  • Constructor Details

    • DICOM_Comms

      public DICOM_Comms()
      Constructor for DICOM network I/O class. Sets byte ordering for read and write to big endian.

  • Method Details

    • bufferToInt16

      public static final int bufferToInt16(byte[] buffer, int index, int endianess)
      Copies a 2 byte array into a 16 bit integer of proper endianess.
      Parameters:
      buffer - source byte array
      index - index into buffer
      endianess - Byte ordering as defined above.
      Returns:
      16 bit integer value

    • bufferToInt32

      public static final int bufferToInt32(byte[] buffer, int index, int endianess)
      Copies a 4 byte array into a 32 bit integer of proper endianess.
      Parameters:
      buffer - source byte array
      index - index into buffer
      endianess - endianess
      Returns:
      32 bit integer value

    • int16ToBuffer

      public static final void int16ToBuffer(byte[] buffer, int index, int value, int endianess)
      Copies a 16 bit (2 bytes) integer into the specified portion of the byte array of proper endianess.
      Parameters:
      buffer - destination byte array
      index - index into buffer
      value - 16 bit integer value
      endianess - endianess

    • int32ToBuffer

      public static final void int32ToBuffer(byte[] buffer, int index, int value, int endianess)
      Copies a 32 bit (4 bytes) integer into the specified portion of the byte array of proper endianess.
      Parameters:
      buffer - destination byte array
      index - index into buffer
      value - 16 bit integer value
      endianess - endianess

    • flush

      public void flush() throws DICOM_Exception
      Sends all byte buffers of the outgoing buffer vector out the port. see DICOM PDUService.sendBinary and DICOMSocket
      Throws:
      DICOM_Exception - DOCUMENT ME!

    • flush

      public void flush(int nBytes) throws DICOM_Exception
      Sends specified number of bytes out the port. see DICOM PDUService.sendBinary and DICOMSocket
      Parameters:
      nBytes - number of bytes to flush
      Throws:
      DICOM_Exception - Throws an error when attempting to flush more bytes than are present!

    • getIncomingEndian

      public int getIncomingEndian()
      Returns constant indicating endianess of incoming data.
      Returns:
      the endianess of the incoming data

    • getIncomingSize

      public int getIncomingSize()
      Returns the incoming data size.
      Returns:
      the number of bytes in the incoming data

    • getOutgoingEndian

      public int getOutgoingEndian()
      Returns constant indicating endianess of outgoing data.
      Returns:
      the endianess of the outgoing data

    • getOutgoingSize

      public int getOutgoingSize()
      Returns the outgoing data size.
      Returns:
      the number of bytes in the outgoing data

    • peekFirstByte

      public byte peekFirstByte() throws DICOM_Exception
      Typically used to determine the PDUTYPE (i.e. PDUTYPE_PresentationContextAccept)
      Returns:
      the PDU type identifier
      Throws:
      DICOM_Exception - DOCUMENT ME!

    • peekForEndOfSequence

      public int peekForEndOfSequence() throws DICOM_Exception
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!
      Throws:
      DICOM_Exception - DOCUMENT ME!

    • read

      public void read(byte[] data) throws DICOM_Exception
      Simple method that take a byte array and call read with two parameters: byte array and array length.
      Parameters:
      data - byte buffer in which to store the data
      Throws:
      DICOM_Exception - DOCUMENT ME!

    • read

      public void read(byte[] data, int nBytes) throws DICOM_Exception
      Reads a specified number of bytes into the byte data buffer.
      Parameters:
      data - byte data array ( destination )
      nBytes - the number of bytes to read into the buffer
      Throws:
      DICOM_Exception - Throws error if there is an error reading data from the port.

    • readBinary

      public int readBinary(byte[] data, int nbytes) throws DICOM_Exception
      Dummy method and should be overloaded by DICOMPDUService.
      Parameters:
      data - Buffer to store the data.
      nbytes - Number of bytes to be read.
      Returns:
      The actual number of bytes read.
      Throws:
      DICOM_Exception - Throws error if method is not overwritten!

    • readByte

      public final byte readByte() throws DICOM_Exception
      Reads a single byte from the data stream.
      Returns:
      a single byte of data
      Throws:
      DICOM_Exception - Throws error if there is an error reading data from the port.

    • readBytes

      public final byte[] readBytes(int length) throws DICOM_Exception
      Allocates and.
      Parameters:
      length - DOCUMENT ME!
      Returns:
      DOCUMENT ME!
      Throws:
      DICOM_Exception - DOCUMENT ME!

    • readFill

      public void readFill(int nBytes) throws DICOM_Exception
      Reads in a nBytes and puts them in a ByteBuffer and puts the byte buffer in the vector of incomingBuffers.
      Parameters:
      nBytes - number of bytes to read
      Throws:
      DICOM_Exception - DOCUMENT ME!

    • readInt32

      public final int readInt32() throws DICOM_Exception
      Reads a 4 byte integer (otherwise known as an int).
      Returns:
      an integer
      Throws:
      DICOM_Exception - DOCUMENT ME!

    • readShort16

      public final int readShort16() throws DICOM_Exception
      Reads a 2 byte integer (otherwise known as a short).
      Returns:
      an integer of the 2 byte data.
      Throws:
      DICOM_Exception - DOCUMENT ME!

    • seekToEndOfGroupTwoTags

      public void seekToEndOfGroupTwoTags()
      Strips preamble and group 2 tags from ioBuffer if present.

    • sendBinary

      public void sendBinary(byte[] data, int startIndex, int nbytes) throws DICOM_Exception
      Dummy method and should be overloaded by DICOMPDUService.
      Parameters:
      data - Buffer of data send out the port (connection).
      startIndex - starting offset
      nbytes - Number of bytes to be sent.
      Throws:
      DICOM_Exception - DOCUMENT ME!

    • setIncomingEndianess

      public void setIncomingEndianess(int endianess)
      Sets the endianess for the incoming data.
      Parameters:
      endianess - the byte ordering (endianess) of the incoming data

    • setOutgoingEndianess

      public void setOutgoingEndianess(int endianess)
      Sets the endianess for the outgoing data.
      Parameters:
      endianess - the byte ordering (endianess) of the outgoing data

    • write

      public final void write(byte[] byteArray)
      Writes a byte arrary to the outgoing buffers.
      Parameters:
      byteArray - the array of data.

    • write

      public void write(byte[] data, int dataOffset, int nBytes)
      Writes a specified number of bytes from the byte buffer into outGoing ByteBuffer list of byte buffers.
      Parameters:
      data - byte buffer
      dataOffset - DOCUMENT ME!
      nBytes - number of bytes to write

    • writeIn

      public void writeIn(byte[] data, int dataOffset, int nBytes, DICOM_FileIO ioBuffer)
      Writes a specified number of bytes from the byte buffer into incomming ByteBuffer list of byte buffers.
      Parameters:
      data - byte buffer
      dataOffset - DOCUMENT ME!
      nBytes - number of bytes to write
      ioBuffer -

    • writeByte

      public final void writeByte(byte value)
      Writes a byte to the outgoing buffers.
      Parameters:
      value - byte value

    • writeByteIn

      public final void writeByteIn(byte value, DICOM_FileIO ioBuffer)
      Writes a byte to the incoming buffers.
      Parameters:
      value - byte value
      ioBuffer -

    • writeInt32

      public final void writeInt32(int value)
      Writes a 32 (4 byte) integer to the outgoing buffers.
      Parameters:
      value - the value to be sent. The value is put into a 4 byte "byte" buffer in the order indicated by the specified endianess of this class.

    • writeInt32In

      public final void writeInt32In(int value, DICOM_FileIO ioBuffer)
      Writes a 32 (4 byte) integer to the incoming buffers.
      Parameters:
      value - the value to be sent. The value is put into a 4 byte "byte" buffer in the order indicated by the specified endianess of this class.
      ioBuffer -

    • writeShort16

      public final void writeShort16(int value)
      Writes a 16 (2 byte) integer to the outgoing buffers.
      Parameters:
      value - the value to be sent. The value is put into a 2 byte "byte" buffer in the order indicated by the specified endianess of this class.

    • writeShort16In

      public final void writeShort16In(int value, DICOM_FileIO ioBuffer)
      Writes a 16 (2 byte) integer to the incomming buffers.
      Parameters:
      value - the value to be sent. The value is put into a 2 byte "byte" buffer in the order indicated by the specified endianess of this class.
      ioBuffer -

    • finalize

      protected void finalize()
      Prepares this class for destruction.
      Overrides:
      finalize in class Object

    • readBlock

      private void readBlock(int useBreakSize) throws DICOM_Exception
      This is the method that actually reads in the data from the socket or IO stream.
      Parameters:
      useBreakSize - the recommended size of the read buffer
      Throws:
      DICOM_Exception - Throws error if there is an error reading data from the port.