xenial (1) dcmgpdir.1.gz

Provided by: dcmtk_3.6.1~20150924-5_amd64 bug

NAME

       dcmgpdir - Create a general purpose DICOMDIR

SYNOPSIS

       dcmgpdir [options] [dcmfile-in...]

DESCRIPTION

       The  dcmgpdir  utility creates a DICOMDIR file from the specified referenced DICOM files according to the
       DICOM Part 11 Media Storage Application Profiles.

       Currently, the following profiles are supported:

       • General Purpose CD-R Interchange (STD-GEN-CD)
       • General Purpose Interchange on DVD-RAM Media (STD-GEN-DVD-RAM)
       dcmmkdir is an extended version of this tool which also supports other Media Storage Application Profiles
       than the general purpose one (e.g. both cardio profiles requiring the use of icon images).

PARAMETERS

       dcmfile-in  referenced DICOM file (or directory to be scanned)

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
       DICOMDIR identifiers:

         +F    --fileset-id  [i]d: string
                 use specific file-set ID
                 (default: DCMTK_MEDIA_DEMO, "" for none)

         +R    --descriptor  [f]ilename: string
                 add a file-set descriptor file ID
                 (e.g. README, default: no descriptor)

         +C    --char-set  [c]harset: string
                 add a specific character set for descriptor
                 (default: "ISO_IR 100" if descriptor present)

       reading:

         +id   --input-directory  [d]irectory: string
                 read referenced DICOM files from directory d
                 (default for --recurse: current directory)

         -m    --keep-filenames
                 expect filenames to be in DICOM format (default)

         +m    --map-filenames
                 map to DICOM filenames (lowercase->uppercase,
                 and remove trailing period)

         -r    --no-recurse
                 do not recurse within directories (default)

         +r    --recurse
                 recurse within filesystem directories

         +p    --pattern  [p]attern: string (only with --recurse)
                 pattern for filename matching (wildcards)

                 # possibly not available on all systems
   processing options
       consistency check:

         -W    --no-consistency-check
                 do not check files for consistency

         +W    --warn-inconsist-files
                 warn about inconsistent files (default)

         -a    --abort-inconsist-file
                 abort on first inconsistent file

       type 1 attributes:

         -I    --strict
                 exit with error if DICOMDIR type 1 attributes
                 are missing in DICOM file (default)

         +I    --invent
                 invent DICOMDIR type 1 attributes if missing in DICOM file

         +Ipi  --invent-patient-id
                 invent new PatientID in case of inconsistent
                 PatientName attributes

       other checks:

         +Nrs  --allow-retired-sop
                 allow retired SOP classes defined in previous editions
                 of the DICOM standard

         -Nxc  --no-xfer-check
                 do not reject images with non-standard transfer syntax
                 (just warn)
   output options
       DICOMDIR file:

         +D    --output-file  [f]ilename: string
                 generate specific DICOMDIR file
                 (default: DICOMDIR in current directory)

       writing:

         -A    --replace
                 replace existing DICOMDIR (default)

         +A    --append
                 append to existing DICOMDIR

         +U    --update
                 update existing DICOMDIR

         -w    --discard
                 do not write out DICOMDIR

       backup:

               --create-backup
                 create a backup of existing DICOMDIR (default)

         -nb   --no-backup
                 do not create a backup of existing DICOMDIR

       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-remove
                 write without group length elements (default)

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

       length encoding in sequences and items:

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

         -e    --length-undefined
                 write with undefined lengths

NOTES

       All  files  specified  on  the  command  line  (or  discovered  by  recursively examining the contents of
       directories with the +r option) are first evaluated for their compatibility with the General Purpose CD-R
       Image  Interchange  Profile  (Supplement 19). Only appropriate files encoded using the Explicit VR Little
       Endian Uncompressed Transfer Syntax will be accepted. Files having invalid  filenames  will  be  rejected
       (the  rules can be relaxed via the +m option). Files missing required attributes will be rejected (the +I
       option can relax this behavior).
       A DICOMDIR file will only be constructed if all files have passed initial tests.
       The dcmgpdir utility also allows one to append new entries  to  and  to  update  existing  entries  in  a
       DICOMDIR  file. Using option +A new entries are only appended to the DICOMDIR, i.e. existing records like
       the ones for PATIENT information are not updated. Using option  +U  also  existing  records  are  updated
       according  to  the  information found in the referenced DICOM files. Please note that this update process
       might be slower than just appending new entries. However, it makes sure that additional information  that
       is required for the selected application profile is also added to existing records.
   Scanning Directories
       Adding  files  from  directories  is  possible  by  using  option  --recurse.  If no further command line
       parameters are given, the directory specified by option --input-directory (default: current directory) is
       scanned  for  files. If parameters are given, they can either specify a file or directory name; the input
       directory is always prepended. If the files in the provided directories should be selected according to a
       specific  name  pattern (e.g. using wildcard matching), option --pattern has to be used. Please note that
       this file pattern only applies to the files within the scanned directories, and, if  any  other  patterns
       are  specified  on the command line outside the --input-directory option (e.g. in order to select further
       files), these do not apply to the specified directories.

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 dcmgpdir 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.

SEE ALSO

       dcmmkdir(1)
       Copyright (C) 1996-2014 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.