man dcmcrle (1): Encode DICOM file to RLE transfer syntax

SYNOPSIS

dcmcrle [options] dcmfile-in dcmfile-out

DESCRIPTION

The dcmcrle utility reads an uncompressed DICOM image (dcmfile-in), performs RLE 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

encapsulated pixel data encoding options

pixel data fragmentation:
  +ff  --fragment-per-frame
         encode each frame as one fragment (default)
  +fs  --fragment-size  [s]ize: integer
         limit fragment size to s kbytes (non-standard)
basic offset table encoding:
  +ot  --offset-table-create
         create offset table (default)
  -ot  --offset-table-empty
         leave offset table empty
SOP Class UID:
  +cd  --class-default
         keep SOP Class UID (default)
  +cs  --class-sc
         convert to Secondary Capture Image (implies --uid-always)
SOP Instance UID:
  +un  --uid-never
         never assign new UID (default)
  +ua  --uid-always
         always assign new 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

Please note that the DICOM standard does not allow for storing the pixel data with multiple fragments per frame (when RLE compression is used). So limiting the fragment size with option --fragment-size (or +fs) may result in a non-standard conformant DICOM image.

TRANSFER SYNTAXES

dcmcrle 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

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

RLELosslessTransferSyntax                      1.2.840.10008.1.2.5

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 dcmcrle 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.