dcmmkdir man page

dcmmkdir — Create a DICOMDIR file

Synopsis

dcmmkdir [options] [dcmfile-in...]

Description

The dcmmkdir 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 (others might be added later):

·
General Purpose CD-R Interchange (STD-GEN-CD)
·
General Purpose Interchange on DVD-RAM Media (STD-GEN-DVD-RAM)
·
General Purpose DVD Interchange with JPEG (STD-GEN-DVD-JPEG)
·
General Purpose DVD Interchange with JPEG 2000 (STD-GEN-DVD-J2K)
·
General Purpose BD Interchange with JPEG (STD-GEN-BD-JPEG)
·
General Purpose BD Interchange with JPEG 2000 (STD-GEN-BD-J2K)
·
General Purpose BD Interchange with MPEG2 MP@ML (STD-GEN-BD-MPEG2-MPML)
·
General Purpose BD Interchange with MPEG2 MP@HL (STD-GEN-BD-MPEG2-MPHL)
·
General Purpose BD Interchange with MPEG-4 AVC/H.264 HiP@Level4.1 (STD-GEN-BD-MPEG4-HPLV41)
·
General Purpose BD Interchange with MPEG-4 AVC/H.264 BD-Compatible HiP@Level4.1 (STD-GEN-BD-MPEG4-HPLV41BD)
·
General Purpose USB and Flash Memory Interchange with JPEG (STD-GEN-USB/MMC/CF/SD-JPEG)
·
General Purpose USB and Flash Memory Interchange with JPEG 2000 (STD-GEN-USB/MMC/CF/SD-J2K)
·
General Purpose MIME Interchange (STD-GEN-MIME)
·
DVD Interchange with MPEG2 MP@ML (STD-DVD-MPEG2-MPML)
·
Basic Cardiac X-Ray Angiographic Studies on CD-R Media (STD-XABC-CD)
·
1024 X-Ray Angiographic Studies on CD-R Media (STD-XA1K-CD)
·
1024 X-Ray Angiographic Studies on DVD Media (STD-XA1K-DVD)
·
Dental Radiograph Interchange (STD-DEN-CD)
·
CT/MR Studies on various Media (STD-CTMR-xxxx)
·
Ultrasound Single Frame for Image Display (STD-US-ID-SF-xxxx)
·
Ultrasound Single Frame with Spatial Calibration (STD-US-SC-SF-xxxx)
·
Ultrasound Single Frame with Combined Calibration (STD-US-CC-SF-xxxx)
·
Ultrasound Single & Multi-Frame for Image Display (STD-US-ID-MF-xxxx)
·
Ultrasound Single & Multi-Frame with Spatial Calibration (STD-US-SC-MF-xxxx)
·
Ultrasound Single & Multi-Frame with Combined Calibration (STD-US-CC-MF-xxxx)
·
12-lead ECG Interchange on Diskette (STD-WVFM-ECG-FD)
·
Hemodynamic Waveform Interchange on Diskette (STD-WVFM-HD-FD)

This tool extends dcmgpdir which can only create General Purpose DICOMDIR files. The default behavior of dcmmkdir (with --general-purpose) is equivalent to that of dcmgpdir.

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)

  -Nec  --no-encoding-check
          do not reject images with non-standard pixel encoding
          (just warn)

  -Nrc  --no-resolution-check
          do not reject images with non-standard spatial resolution
          (just warn)

icon images:

  +X    --add-icon-image
          add monochrome icon image on IMAGE level
          (default for cardiac profiles)

  -Xs   --icon-image-size  [s]ize: integer (1..128)
          width and height of the icon image (in pixel)
          (fixed: 128 for XA, 64 for CT/MR profile)

  -Xi   --icon-file-prefix  [p]refix: string
          use PGM image 'prefix'+'dcmfile-in' as icon
          (default: create icon from DICOM image)

  -Xd   --default-icon  [f]ilename: string
          use specified PGM image if icon cannot be
          created automatically (default: black image)

output options

DICOMDIR file:

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

profiles:

  -Pgp  --general-purpose
          General Purpose Interchange on CD-R or DVD-RAM Media
          (STD-GEN-CD/DVD-RAM, default)

  -Pdv  --general-dvd-jpeg
          General Purpose DVD Interchange with JPEG
          (STD-GEN-DVD-JPEG)

  -Pd2  --general-dvd-j2k
          General Purpose DVD Interchange with JPEG 2000
          (STD-GEN-DVD-J2K)

  -Pbd  --general-bd-jpeg
          General Purpose BD Interchange with JPEG
          (STD-GEN-BD-JPEG)

  -Pb2  --general-bd-j2k
          General Purpose BD Interchange with JPEG 2000
          (STD-GEN-BD-J2K)

  -Pbm  --general-bd-mpeg2-mpml
          General Purpose BD Interchange with MPEG2 MP@ML
          (STD-GEN-BD-MPEG2-MPML)

  -Pbh  --general-bd-mpeg2-mphl
          General Purpose BD Interchange with MPEG2 MP@HL
          (STD-GEN-BD-MPEG2-MPHL)

  -Pba  --general-bd-mpeg4-hp
          General Purpose BD Interchange with MPEG-4 AVC/H.264
          HiP@Level4.1 (STD-GEN-BD-MPEG4-HPLV41)

  -Pbb  --general-bd-mpeg4-hpbd
          General Purpose BD Interchange with MPEG-4 AVC/H.264
          BD-Compatible HiP@Level4.1 (STD-GEN-BD-MPEG4-HPLV41BD)

  -Pfl  --usb-and-flash-jpeg
          General Purpose USB/Flash Memory Interchange with JPEG
          (STD-GEN-USB/MMC/CF/SD-JPEG)

  -Pf2  --usb-and-flash-j2k
          General Purpose USB/Flash Memory Interchange with JPEG 2000
          (STD-GEN-USB/MMC/CF/SD-J2K)

  -Pmi  --general-mime
          General Purpose MIME Interchange (STD-GEN-MIME)

  -Pmp  --mpeg2-mpml-dvd
          DVD Interchange with MPEG2 Main Profile @ Main Level
          (STD-DVD-MPEG2-MPML)

  -Pbc  --basic-cardiac
          Basic Cardiac X-Ray Angiographic Studies on CD-R Media
          (STD-XABC-CD)

  -Pxa  --xray-angiographic
          1024 X-Ray Angiographic Studies on CD-R Media
          (STD-XA1K-CD)

  -Pxd  --xray-angiographic-dvd
          1024 X-Ray Angiographic Studies on DVD Media
          (STD-XA1K-DVD)

  -Pde  --dental-radiograph
          Dental Radiograph Interchange (STD-DEN-CD)

  -Pcm  --ct-and-mr
          CT/MR Studies (STD-CTMR-xxxx)

  -Pus  --ultrasound-id-sf
          Ultrasound Single Frame for Image Display
          (STD-US-ID-SF-xxxx)

        --ultrasound-sc-sf
          Ultrasound Single Frame with Spatial Calibration
          (STD-US-SC-SF-xxxx)

        --ultrasound-cc-sf
          Ultrasound Single Frame with Combined Calibration
          (STD-US-CC-SF-xxxx)

  -Pum  --ultrasound-id-mf
          Ultrasound Single & Multi-Frame for Image Display
          (STD-US-ID-MF-xxxx)

        --ultrasound-sc-mf
          Ultrasound Single & Multi-Frame with Spatial Calibration
          (STD-UD-SC-MF-xxxx)

        --ultrasound-cc-mf
          Ultrasound Single & Multi-Frame with Combined Calibration
          (STD-UD-CC-MF-xxxx)

  -Pec  --12-lead-ecg
          12-lead ECG Interchange on Diskette
          (STD-WVFM-ECG-FD)

  -Phd  --hemodynamic-waveform
          Hemodynamic Waveform Interchange on Diskette
          (STD-WVFM-HD-FD)

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 specified Media Storage Application Profile (Part 11). Only appropriate files encoded using one of the allowed Transfer Syntaxes 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 dcmmkdir 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.

The support for icon images is currently restricted to monochrome images. This might change in the future. Till then, color images are automatically converted to grayscale mode. The icon size is 128*128 pixels for the cardiac profiles (as required by the DICOM standard) and 64*64 for all others.

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 dcmmkdir 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

dcmgpdir(1)

Referenced By

dcmftest(1), dcmgpdir(1).

Tue Jun 17 2014 Version 3.6.1 OFFIS DCMTK