table of contents
| cda2dcm(1) | OFFIS DCMTK | cda2dcm(1) |
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.
COPYRIGHT¶
Copyright (C) 2018-2022 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.
| Fri Apr 22 2022 | Version 3.6.7 |