NAME

dcmdjpls - Decode JPEG-LS compressed DICOM file

SYNOPSIS

dcmdjpls [options] dcmfile-in dcmfile-out

DESCRIPTION

The dcmdjpls utility reads a JPEG-ls compressed DICOM image (dcmfile-in), decompresses the JPEG-LS data (i. e. conversion to a native 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
  # This option allows one to decompress JPEG-LS compressed DICOM objects that have
  # been stored as dataset without meta-header. Such a thing should not exist
  # since the transfer syntax cannot be reliably determined without meta-header,
  # but unfortunately it does.

processing options

planar configuration:
  +pr  --planar-restore
         restore original planar configuration (default)
  # If the compressed image is a color image, restore the planar
  # configuration as described in the Planar Configuration attribute.
  +pa  --planar-auto
         automatically determine planar configuration
         from SOP class and color space
  # If the compressed image is a color image, store in color-by-plane
  # planar configuration if required by the SOP class and photometric
  # interpretation. Hardcopy Color images are always stored color-by-
  # plane, and the revised Ultrasound image objects are stored color-by-
  # plane if the color model is YBR_FULL.  Everything else is stored
  # color-by-pixel.
  +px  --color-by-pixel
         always store color-by-pixel
  # If the compressed image is a color image, store in color-by-pixel
  # planar configuration.
  +pl  --color-by-plane
         always store color-by-plane
  # If the compressed image is a color image, store in color-by-plane
  # planar configuration.
SOP Instance UID:
  +ud  --uid-default
         keep same SOP Instance UID (default)
  #  Never assigns a new SOP instance UID.
  +ua  --uid-always
         always assign new UID
  # Always assigns a new SOP instance UID.
workaround options for incorrect JPEG-LS encodings:
  +wi  --workaround-incpl
         enable workaround for incomplete JPEG-LS data
other processing options:
  +io  --ignore-offsettable
         ignore offset table when decompressing

output options

output file format:
  +F   --write-file
         write file format (default)
  -F   --write-dataset
         write data set without file meta information
output transfer syntax:
  +te  --write-xfer-little
         write with explicit VR little endian (default)
  +tb  --write-xfer-big
         write with explicit VR big endian TS
  +ti  --write-xfer-implicit
         write with implicit VR little endian TS
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 (not with --write-dataset):
  -p=  --padding-retain
         do not change padding (default if not --write-dataset)
  -p   --padding-off
         no padding (implicit if --write-dataset)
  +p   --padding-create  [f]ile-pad [i]tem-pad: integer
         align file on multiple of f bytes
         and items on multiple of i bytes

TRANSFER SYNTAXES

dcmdjpls 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
JPEGLSLosslessTransferSyntax                   1.2.840.10008.1.2.4.80
JPEGLSLossyTransferSyntax                      1.2.840.10008.1.2.4.81

(*) if compiled with zlib support enabled

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

LittleEndianImplicitTransferSyntax             1.2.840.10008.1.2
LittleEndianExplicitTransferSyntax             1.2.840.10008.1.2.1
BigEndianExplicitTransferSyntax                1.2.840.10008.1.2.2

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 behavior 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 one 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 dcmdjpls 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 behavior 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.