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|
.TH "dcmmkdir" 1 "Fri Apr 22 2022" "Version 3.6.7" "OFFIS DCMTK" \" -*- nroff -*-
.nh
.SH NAME
dcmmkdir \- Create a DICOMDIR file
.SH "SYNOPSIS"
.PP
.PP
.nf
dcmmkdir [options] [dcmfile-in...]
.fi
.PP
.SH "DESCRIPTION"
.PP
The \fBdcmmkdir\fP utility creates a \fIDICOMDIR\fP file from the specified referenced DICOM files according to the DICOM Part 11 Media Storage Application Profiles\&.
.PP
Currently the following profiles are supported (others might be added later):
.PP
.PD 0
.IP "\(bu" 2
General Purpose CD-R Interchange (STD-GEN-CD)
.IP "\(bu" 2
General Purpose Interchange on DVD-RAM Media (STD-GEN-DVD-RAM)
.IP "\(bu" 2
General Purpose DVD Interchange with JPEG (STD-GEN-DVD-JPEG)
.IP "\(bu" 2
General Purpose DVD Interchange with JPEG 2000 (STD-GEN-DVD-J2K)
.IP "\(bu" 2
General Purpose BD Interchange with JPEG (STD-GEN-BD-JPEG)
.IP "\(bu" 2
General Purpose BD Interchange with JPEG 2000 (STD-GEN-BD-J2K)
.IP "\(bu" 2
General Purpose BD Interchange with MPEG2 MP@ML (STD-GEN-BD-MPEG2-MPML)
.IP "\(bu" 2
General Purpose BD Interchange with MPEG2 MP@HL (STD-GEN-BD-MPEG2-MPHL)
.IP "\(bu" 2
General Purpose BD Interchange with MPEG-4 AVC/H\&.264 HiP@Level4\&.1 (STD-GEN-BD-MPEG4-HPLV41)
.IP "\(bu" 2
General Purpose BD Interchange with MPEG-4 AVC/H\&.264 BD-Compatible HiP@Level4\&.1 (STD-GEN-BD-MPEG4-HPLV41BD)
.IP "\(bu" 2
General Purpose BD Interchange with MPEG-4 AVC/H\&.264 HiP@Level4\&.2 for 2D video (STD-GEN-BD-MPEG4-HPLV42-2D)
.IP "\(bu" 2
General Purpose BD Interchange with MPEG-4 AVC/H\&.264 HiP@Level4\&.2 for 3D video (STD-GEN-BD-MPEG4-HPLV42-3D)
.IP "\(bu" 2
General Purpose BD Interchange with MPEG-4 AVC/H\&.264 Stereo HiP@Level4\&.2 (STD-GEN-BD-MPEG4-SHPLV42)
.IP "\(bu" 2
General Purpose USB and Flash Memory Interchange with JPEG (STD-GEN-USB/MMC/CF/SD-JPEG)
.IP "\(bu" 2
General Purpose USB and Flash Memory Interchange with JPEG 2000 (STD-GEN-USB/MMC/CF/SD-J2K)
.IP "\(bu" 2
General Purpose MIME Interchange (STD-GEN-MIME)
.IP "\(bu" 2
DVD Interchange with MPEG2 MP@ML (STD-DVD-MPEG2-MPML)
.IP "\(bu" 2
Basic Cardiac X-Ray Angiographic Studies on CD-R Media (STD-XABC-CD)
.IP "\(bu" 2
1024 X-Ray Angiographic Studies on CD-R Media (STD-XA1K-CD)
.IP "\(bu" 2
1024 X-Ray Angiographic Studies on DVD Media (STD-XA1K-DVD)
.IP "\(bu" 2
Dental Radiograph Interchange (STD-DEN-CD)
.IP "\(bu" 2
CT/MR Studies on various Media (STD-CTMR-xxxx)
.IP "\(bu" 2
Ultrasound Single Frame for Image Display (STD-US-ID-SF-xxxx)
.IP "\(bu" 2
Ultrasound Single Frame with Spatial Calibration (STD-US-SC-SF-xxxx)
.IP "\(bu" 2
Ultrasound Single Frame with Combined Calibration (STD-US-CC-SF-xxxx)
.IP "\(bu" 2
Ultrasound Single & Multi-Frame for Image Display (STD-US-ID-MF-xxxx)
.IP "\(bu" 2
Ultrasound Single & Multi-Frame with Spatial Calibration (STD-US-SC-MF-xxxx)
.IP "\(bu" 2
Ultrasound Single & Multi-Frame with Combined Calibration (STD-US-CC-MF-xxxx)
.IP "\(bu" 2
12-lead ECG Interchange on Diskette (STD-WVFM-ECG-FD)
.IP "\(bu" 2
Hemodynamic Waveform Interchange on Diskette (STD-WVFM-HD-FD)
.PP
This tool extends \fBdcmgpdir\fP which can only create General Purpose \fIDICOMDIR\fP files\&. The default behavior of \fBdcmmkdir\fP (with \fI--general-purpose\fP) is equivalent to that of \fBdcmgpdir\fP\&.
.SH "PARAMETERS"
.PP
.PP
.nf
dcmfile-in referenced DICOM file (or directory to be scanned)
.fi
.PP
.SH "OPTIONS"
.PP
.SS "general options"
.PP
.nf
-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
.fi
.PP
.SS "input options"
.PP
.nf
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
.fi
.PP
.SS "processing options"
.PP
.nf
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)
.fi
.PP
.SS "output options"
.PP
.nf
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)
--general-bd-mpeg4-hp2d
General Purpose BD Interchange with MPEG-4 AVC/H.264
HiP@Level4.2 for 2D video (STD-GEN-BD-MPEG4-HPLV42-2D)
--general-bd-mpeg4-hp3d
General Purpose BD Interchange with MPEG-4 AVC/H.264
HiP@Level4.2 for 3D video (STD-GEN-BD-MPEG4-HPLV42-3D)
--general-bd-mpeg4-hpst
General Purpose BD Interchange with MPEG-4 AVC/H.264
Stereo HiP@Level4.2 (STD-GEN-BD-MPEG4-SHPLV42)
-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
.fi
.PP
.SH "NOTES"
.PP
All files specified on the command line (or discovered by recursively examining the contents of directories with the \fI+r\fP 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 \fI+m\fP option)\&. Files missing required attributes will be rejected (the \fI+I\fP option can relax this behavior)\&.
.PP
A \fIDICOMDIR\fP file will only be constructed if all files have passed initial tests\&.
.PP
The \fBdcmmkdir\fP utility also allows one to append new entries to and to update existing entries in a \fIDICOMDIR\fP file\&. Using option \fI+A\fP new entries are only appended to the DICOMDIR, i\&.e\&. existing records like the ones for PATIENT information are not updated\&. Using option \fI+U\fP 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\&.
.PP
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\&.
.SS "Scanning Directories"
Adding files from directories is possible by using option \fI--recurse\fP\&. If no further command line parameters are given, the directory specified by option \fI--input-directory\fP (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 \fI--pattern\fP 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 \fI--input-directory\fP option (e\&.g\&. in order to select further files), these do not apply to the specified directories\&.
.SH "LOGGING"
.PP
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 \fI--verbose\fP also informational messages like processing details are reported\&. Option \fI--debug\fP can be used to get more details on the internal activity, e\&.g\&. for debugging purposes\&. Other logging levels can be selected using option \fI--log-level\fP\&. In \fI--quiet\fP 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'\&.
.PP
In case the logging output should be written to file (optionally with logfile rotation), to syslog (Unix) or the event log (Windows) option \fI--log-config\fP 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 \fI<etcdir>/logger\&.cfg\fP\&.
.SH "COMMAND LINE"
.PP
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\&.
.PP
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\&.
.PP
In addition, one or more command files can be specified using an '@' sign as a prefix to the filename (e\&.g\&. \fI@command\&.txt\fP)\&. 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 \fI<datadir>/dumppat\&.txt\fP)\&.
.SH "ENVIRONMENT"
.PP
The \fBdcmmkdir\fP utility will attempt to load DICOM data dictionaries specified in the \fIDCMDICTPATH\fP environment variable\&. By default, i\&.e\&. if the \fIDCMDICTPATH\fP environment variable is not set, the file \fI<datadir>/dicom\&.dic\fP will be loaded unless the dictionary is built into the application (default for Windows)\&.
.PP
The default behavior should be preferred and the \fIDCMDICTPATH\fP environment variable only used when alternative data dictionaries are required\&. The \fIDCMDICTPATH\fP environment variable has the same format as the Unix shell \fIPATH\fP 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 \fIDCMDICTPATH\fP environment variable\&. It is an error if no data dictionary can be loaded\&.
.SH "SEE ALSO"
.PP
\fBdcmgpdir\fP(1)
.SH "COPYRIGHT"
.PP
Copyright (C) 2001-2022 by OFFIS e\&.V\&., Escherweg 2, 26121 Oldenburg, Germany\&.
|
