NAME

cda2dcm - Encapsulate CDA file into DICOM file format

SYNOPSIS

cda2dcm [options] cdafile-in dcmfile-out

DESCRIPTION

The cda2dcm utility reads a CDA file (cdafile-in), converts it to a DICOM Encapsulated CDA Storage SOP instance and stores the converted data to an output file (dcmfile-out).

PARAMETERS

cdafile-in   CDA input filename to be encapsulated
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

DICOM document options

document title:
  +t   --title  [t]itle: string (default: empty)
         document title
  +cn  --concept-name  [CSD] [CV] [CM]: string (default: empty)
         coded representation of document title defined by coding
         scheme designator CSD, code value CV and code meaning CM
patient data:
  +pn  --patient-name  [n]ame: string
         patient's name in DICOM PN syntax
  +pi  --patient-id  [i]d: string
         patient identifier
  +pb  --patient-birthdate  [d]ate: string (YYYYMMDD)
         patient's birth date
  +ps  --patient-sex  [s]ex: string (M, F or O)
         patient's sex
study and series:
  +sg  --generate
         generate new study and series UIDs (default)
  +st  --study-from  [f]ilename: string
         read patient/study data from DICOM file
  +se  --series-from  [f]ilename: string
         read patient/study/series data from DICOM file
instance number:
  +i1  --instance-one
         use instance number 1 (default, not with +se)
  +ii  --instance-inc
         increment instance number (only with +se)
  +is  --instance-set [i]nstance number: integer
         use instance number i
burned-in annotation:
  +an  --annotation-yes
         document contains patient identifying data (default)
  -an  --annotation-no
         document does not contain patient identifying data
override CDA file data:
  -ov  --no-override
         CDA patient and document data must match study,
         series or manually entered information (default)
  +ov  --override
         data obtained from the CDA file will be overwritten
         by study, series, or manually entered information

processing options

other processing options:
  -k   --key  [k]ey: gggg,eeee="str", path or dictionary name="str"
         add further attribute

output options

output file format:
  +F   --write-file
         write file format (default)
  -F   --write-dataset
         write data set without file meta information
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-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

NOTES

Attribute Sources

The application may be fed with some additional input for filling mandatory (and optional) attributes in the new DICOM file like patient, study and series information:

•: The --key option can be used to add further attributes to the DICOM output file.

•: It is also possible to specify sequences, items and nested attributes using the --key option. In these cases, a special 'path' notation has to be used. Details on this path notation can be found in the documentation of dcmodify.

•: The --key option can be present more than once.

•: The value part (after the '=') may be absent causing the attribute to be set with zero length.

•: Please be advised that the --key option is applied at the very end, just before saving the DICOM file, so there is no value checking whatsoever.

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).

EXIT CODES

The cda2dcm utility uses the following exit codes when terminating. This enables the user to check for the reason why the application terminated.

general

EXITCODE_NO_ERROR                 0
EXITCODE_COMMANDLINE_SYNTAX_ERROR 1
EXITCODE_MEMORY_EXHAUSTED         4

input file errors

EXITCODE_CANNOT_READ_INPUT_FILE   20
EXITCODE_NO_INPUT_FILES           21
EXITCODE_INVALID_INPUT_FILE       22

output file errors

EXITCODE_CANNOT_WRITE_OUTPUT_FILE 40

ENVIRONMENT

The cda2dcm 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.