Provided by: dcmtk_3.6.0-15_amd64 bug

NAME

       dcmcjpls - Encode DICOM file to JPEG-LS transfer syntax

SYNOPSIS

       dcmcjpls [options] dcmfile-in dcmfile-out

DESCRIPTION

       The  dcmcjpls  utility  reads an uncompressed DICOM image (dcmfile-in), performs a JPEG-LS
       compression (i. e. conversion to an encapsulated DICOM transfer  syntax)  and  writes  the
       converted image to an output file (dcmfile-out).

PARAMETERS

       dcmfile-in   DICOM input filename to be converted

       dcmfile-out  DICOM output filename

OPTIONS

   general options
         -h   --help
                print this help text and exit

              --version
                print version information and exit

              --arguments
                print expanded command line arguments

         -q   --quiet
                quiet mode, print no warnings and errors

         -v   --verbose
                verbose mode, print processing details

         -d   --debug
                debug mode, print debug information

         -ll  --log-level  [l]evel: string constant
                (fatal, error, warn, info, debug, trace)
                use level l for the logger

         -lc  --log-config  [f]ilename: string
                use config file f for the logger

   input options
       input file format:

         +f   --read-file
                read file format or data set (default)

         +fo  --read-file-only
                read file format only

         -f   --read-dataset
                read data set without file meta information

       input transfer syntax:

         -t=  --read-xfer-auto
                use TS recognition (default)

         -td  --read-xfer-detect
                ignore TS specified in the file meta header

         -te  --read-xfer-little
                read with explicit VR little endian TS

         -tb  --read-xfer-big
                read with explicit VR big endian TS

         -ti  --read-xfer-implicit
                read with implicit VR little endian TS

   JPEG-LS encoding options
       JPEG-LS process:

         +el  --encode-lossless
                encode JPEG-LS lossless only TS (default)

         # This options selects the JPEG-LS lossless only transfer syntax
         # and performs a lossless compression.

         +en  --encode-nearlossless
                encode JPEG-LS near-lossless TS (NEAR: 2)

         # This options selects the JPEG-LS lossy transfer syntax
         # and performs a near-lossless compression.

       JPEG-LS bit rate (near-lossless only):

         +md  --max-deviation  [d]eviation: integer (default: 2)
                defines maximum deviation for an encoded pixel

         # This option specifies the maximum deviation for a single pixel from
         # the original pixel value.

       lossless compression:

         +pr  --prefer-raw
                prefer raw encoder mode (default)

         # This option enables the raw encoder. The raw encoder encodes the
         # complete pixel cell as it was read from the source image without
         # performing any modifications.

         +pc  --prefer-cooked
                prefer cooked encoder mode

         # This option enables the cooked encoder. The cooked encoder moves
         # overlay data to separate tags (60xx,3000) and only encodes the
         # stored bits in each pixel.

       JPEG-LS compression:

         +t1  --threshold1  [t]hreshhold: integer (default for 8 bpp: 3)
                set JPEG-LS encoding parameter threshold 1

         +t2  --threshold2  [t]hreshhold: integer (default for 8 bpp: 7)
                set JPEG-LS encoding parameter threshold 2

         +t3  --threshold3  [t]hreshhold: integer (default for 8 bpp: 21)
                set JPEG-LS encoding parameter threshold 3

         +rs  --reset  [r]eset: integer (default: 64)
                set JPEG-LS encoding parameter reset

         +lm  --limit  [l]imit: integer (default: 0)
                set JPEG-LS encoding parameter limit

       JPEG-LS interleave:

         +il  --interleave-line
                force line-interleaved JPEG-LS images (default)

         # This flag forces line-interleaved mode for the resulting image.
         # In line-interleave mode each line from the source image is
         # compressed separately for each component and then the next line
         # is encoded.

         +is  --interleave-sample
                force sample-interleaved JPEG-LS images

         # This flag forces sample-interleaved mode for the resulting image.
         # In sample-interleave mode each pixel's components are encoded before
         # the next pixe is encoded.

         +in  --interleave-none
                force uninterleaved JPEG-LS images

         # This flag forces uninterleaved mode for the resulting image.
         # In this mode, each of the image's components are completely encoded
         # before the next component is handled.

         +iv  --interleave-default
                use the fastest possible interleave mode

         # This flag selects an interleave mode based on the source image's mode.
         # If possible, the image is not converted to a different interleave mode.

   encapsulated pixel data encoding options
       encapsulated pixel data fragmentation:

         +ff  --fragment-per-frame
                encode each frame as one fragment (default)

         # This option causes the creation of one compressed fragment for each
         # frame (recommended).

         +fs  --fragment-size  [s]ize: integer
                limit fragment size to s kbytes

         # This option limits the fragment size which may cause the creation of
         # multiple fragments per frame.

       basic offset table encoding:

         +ot  --offset-table-create
                create offset table (default)

         # This option causes the creation of a valid offset table for the
         # compressed JPEG fragments.

         -ot  --offset-table-empty
                leave offset table empty

         # This option causes the creation of an empty offset table
         # for the compressed JPEG fragments.

       SOP Class UID:

         +cd  --class-default
                keep SOP Class UID (default)

         # Keep the SOP Class UID of the source image.

         +cs  --class-sc
                convert to Secondary Capture Image (implies --uid-always)

         # Convert the image to Secondary Capture.  In addition to the SOP Class
         # UID, all attributes required for a valid secondary capture image are
         # added. A new SOP instance UID is always assigned.

       SOP Instance UID:

         +ud  --uid-default
                assign new UID if lossy compression (default)

         # Assigns a new SOP instance UID if the compression is lossy JPEG.

         +ua  --uid-always
                always assign new UID

         # Unconditionally assigns a new SOP instance UID.

         +un  --uid-never
                never assign new UID

         # Never assigns a new SOP instance UID.

   output options
       post-1993 value representations:

         +u   --enable-new-vr
                enable support for new VRs (UN/UT) (default)

         -u   --disable-new-vr
                disable support for new VRs, convert to OB

       group length encoding:

         +g=  --group-length-recalc
                recalculate group lengths if present (default)

         +g   --group-length-create
                always write with group length elements

         -g   --group-length-remove
                always write without group length elements

       length encoding in sequences and items:

         +e   --length-explicit
                write with explicit lengths (default)

         -e   --length-undefined
                write with undefined lengths

       data set trailing padding:

         -p=  --padding-retain
                do not change padding (default)

         -p   --padding-off
                no padding

         +p   --padding-create  [f]ile-pad [i]tem-pad: integer
                align file on multiple of f bytes
                and items on multiple of i bytes

NOTES

       The  dcmcjpls  utility  compresses DICOM images of all SOP classes. However, dcmcjpls does
       not attempt to ensure that the compressed image still complies with  all  restrictions  of
       the object's IOD.

       The  user  is  responsible  for  making  sure  that  the  compressed images he creates are
       compliant with the DICOM standard. If in question, the dcmcjpls utility allows to  convert
       an  image  to  secondary  capture  - this SOP class does not pose restrictions as the ones
       mentioned above.

TRANSFER SYNTAXES

       dcmcjpls supports the following transfer syntaxes for input (dcmfile-in):

       LittleEndianImplicitTransferSyntax             1.2.840.10008.1.2
       LittleEndianExplicitTransferSyntax             1.2.840.10008.1.2.1
       DeflatedExplicitVRLittleEndianTransferSyntax   1.2.840.10008.1.2.1.99 (*)
       BigEndianExplicitTransferSyntax                1.2.840.10008.1.2.2

       (*) if compiled with zlib support enabled

       dcmcjpls supports the following transfer syntaxes for output (dcmfile-out):

       JPEGLSLosslessTransferSyntax                   1.2.840.10008.1.2.4.80
       JPEGLSLossyTransferSyntax                      1.2.840.10008.1.2.4.81

LOGGING

       The level of logging output of the various command line tools and underlying libraries can
       be specified by the user. By default, only errors and warnings are written to the standard
       error stream. Using option --verbose also informational messages like  processing  details
       are  reported.  Option  --debug  can be used to get more details on the internal activity,
       e.g. for debugging purposes. Other logging levels can  be  selected  using  option  --log-
       level.  In  --quiet mode only fatal errors are reported. In such very severe error events,
       the application will usually terminate. For more details on the different logging  levels,
       see documentation of module 'oflog'.

       In  case  the logging output should be written to file (optionally with logfile rotation),
       to syslog (Unix) or the  event  log  (Windows)  option  --log-config  can  be  used.  This
       configuration  file also allows for directing only certain messages to a particular output
       stream and for filtering certain messages based on the module or  application  where  they
       are generated. An example configuration file is provided in <etcdir>/logger.cfg).

COMMAND LINE

       All  command line tools use the following notation for parameters: square brackets enclose
       optional values (0-1), three trailing dots  indicate  that  multiple  values  are  allowed
       (1-n), a combination of both means 0 to n values.

       Command  line  options  are  distinguished  from  parameters by a leading '+' or '-' sign,
       respectively. Usually, order and position of command line options are arbitrary (i.e. they
       can  appear anywhere). However, if options are mutually exclusive the rightmost appearance
       is used. This behaviour conforms to the standard evaluation rules of common Unix shells.

       In addition, one or more command files can be specified using an '@' sign as a  prefix  to
       the  filename  (e.g.  @command.txt). Such a command argument is replaced by the content of
       the corresponding text file (multiple whitespaces are treated as a single separator unless
       they appear between two quotation marks) prior to any further evaluation. Please note that
       a command file cannot contain another command file. This  simple  but  effective  approach
       allows  to  summarize  common  combinations  of  options/parameters and avoids longish and
       confusing command lines (an example is provided in file <datadir>/dumppat.txt).

ENVIRONMENT

       The dcmcjpls utility will attempt  to  load  DICOM  data  dictionaries  specified  in  the
       DCMDICTPATH environment variable. By default, i.e. if the DCMDICTPATH environment variable
       is not set, the file <datadir>/dicom.dic will be loaded unless  the  dictionary  is  built
       into the application (default for Windows).

       The  default  behaviour  should be preferred and the DCMDICTPATH environment variable only
       used when alternative data dictionaries are required. The DCMDICTPATH environment variable
       has  the  same  format  as  the  Unix  shell PATH variable in that a colon (':') separates
       entries. On Windows systems, a semicolon (';') is used as a separator. The data dictionary
       code  will attempt to load each file specified in the DCMDICTPATH environment variable. It
       is an error if no data dictionary can be loaded.

SEE ALSO

       dcmdjpls(1)

COPYRIGHT

       Copyright (C) 2009-2010 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.