OFFIS DCMTK  Version 3.6.0
dcmmkdir.man
1 /*!
2 
3 \if MANPAGES
4 \page dcmmkdir Create a DICOMDIR file
5 \else
6 \page dcmmkdir dcmmkdir: Create a DICOMDIR file
7 \endif
8 
9 \section synopsis SYNOPSIS
10 
11 \verbatim
12 dcmmkdir [options] [dcmfile-in...]
13 \endverbatim
14 
15 \section description DESCRIPTION
16 
17 The \b dcmmkdir utility creates a \e DICOMDIR file from the specified
18 referenced DICOM files according to the DICOM Part 11 Media Storage Application
19 Profiles.
20 
21 Currently the following profiles are supported (others might be added later):
22 
23 \li General Purpose CD-R Interchange (STD-GEN-CD)
24 \li General Purpose Interchange on DVD-RAM Media (STD-GEN-DVD-RAM)
25 \li General Purpose DVD with Compression Interchange (STD-GEN-DVD-JPEG/J2K)
26 \li General Purpose MIME Interchange (STD-GEN-MIME)
27 \li General Purpose USB and Flash Memory with Compression Interchange
28  (STD-GEN-USB/MMC/CF/SD-JPEG/J2K)
29 \li DVD Interchange with MPEG2 MP\@ML (STD-DVD-MPEG2-MPML)
30 \li Basic Cardiac X-Ray Angiographic Studies on CD-R Media (STD-XABC-CD)
31 \li 1024 X-Ray Angiographic Studies on CD-R Media (STD-XA1K-CD)
32 \li 1024 X-Ray Angiographic Studies on DVD Media (STD-XA1K-DVD)
33 \li Dental Radiograph Interchange (STD-DEN-CD)
34 \li CT/MR Studies on various Media (STD-CTMR-xxxx)
35 \li Ultrasound Single Frame for Image Display (STD-US-ID-SF-xxxx)
36 \li Ultrasound Single Frame with Spatial Calibration (STD-US-SC-SF-xxxx)
37 \li Ultrasound Single Frame with Combined Calibration (STD-US-CC-SF-xxxx)
38 \li Ultrasound Single & Multi-Frame for Image Display (STD-US-ID-MF-xxxx)
39 \li Ultrasound Single & Multi-Frame with Spatial Calibration
40  (STD-US-SC-MF-xxxx)
41 \li Ultrasound Single & Multi-Frame with Combined Calibration
42  (STD-US-CC-MF-xxxx)
43 \li 12-lead ECG Interchange on Diskette (STD-WVFM-ECG-FD)
44 \li Hemodynamic Waveform Interchange on Diskette (STD-WVFM-HD-FD)
45 
46 This tool extends \b dcmgpdir which can only create General Purpose \e DICOMDIR
47 files. The default behaviour of \b dcmmkdir (with \e --general-purpose) is
48 equivalent to that of \b dcmgpdir.
49 
50 \section parameters PARAMETERS
51 
52 \verbatim
53 dcmfile-in referenced DICOM file
54 \endverbatim
55 
56 \section options OPTIONS
57 \subsection general_options general options
58 \verbatim
59  -h --help
60  print this help text and exit
61 
62  --version
63  print version information and exit
64 
65  --arguments
66  print expanded command line arguments
67 
68  -q --quiet
69  quiet mode, print no warnings and errors
70 
71  -v --verbose
72  verbose mode, print processing details
73 
74  -d --debug
75  debug mode, print debug information
76 
77  -ll --log-level [l]evel: string constant
78  (fatal, error, warn, info, debug, trace)
79  use level l for the logger
80 
81  -lc --log-config [f]ilename: string
82  use config file f for the logger
83 \endverbatim
84 
85 \subsection input_options input options
86 \verbatim
87 DICOMDIR identifiers:
88 
89  +D --output-file [f]ilename: string
90  generate specific DICOMDIR file
91  (default: DICOMDIR in current directory)
92 
93  +F --fileset-id [i]d: string (default: DCMTK_MEDIA_DEMO)
94  use specific file set ID
95 
96  +R --descriptor [f]ilename: string
97  add a file set descriptor file ID
98  (e.g. README, default: no descriptor)
99 
100  +C --char-set [c]harset: string
101  add a specific character set for descriptor
102  (default: "ISO_IR 100" if descriptor present)
103 
104 reading:
105 
106  +id --input-directory [d]irectory: string
107  read referenced DICOM files from directory d
108  (default for --recurse: current directory)
109 
110  -m --keep-filenames
111  expect filenames to be in DICOM format (default)
112 
113  +m --map-filenames
114  map to DICOM filenames (lowercase->uppercase,
115  and remove trailing period)
116 
117  -r --no-recurse
118  do not recurse within directories (default)
119 
120  +r --recurse
121  recurse within filesystem directories
122 
123  +p --pattern [p]attern: string (only with --recurse)
124  pattern for filename matching (wildcards)
125 
126  # possibly not available on all systems
127 \endverbatim
128 
129 \subsection processing_options processing options
130 \verbatim
131 consistency check:
132 
133  -W --no-consistency-check
134  do not check files for consistency
135 
136  +W --warn-inconsist-files
137  warn about inconsistent files (default)
138 
139  -a --abort-inconsist-file
140  abort on first inconsistent file
141 
142 type 1 attributes:
143 
144  -I --strict
145  exit with error if DICOMDIR type 1 attributes
146  are missing in DICOM file (default)
147 
148  +I --invent
149  invent DICOMDIR type 1 attributes if missing in DICOM file
150 
151  +Ipi --invent-patient-id
152  invent new PatientID in case of inconsistent
153  PatientName attributes
154 
155 other checks:
156 
157  +Nrs --allow-retired-sop
158  allow retired SOP classes defined in previous editions
159  of the DICOM standard
160 
161  -Nxc --no-xfer-check
162  do not reject images with non-standard transfer syntax
163  (just warn)
164 
165  -Nec --no-encoding-check
166  do not reject images with non-standard pixel encoding
167  (just warn)
168 
169  -Nrc --no-resolution-check
170  do not reject images with non-standard spatial resolution
171  (just warn)
172 
173 icon images:
174 
175  +X --add-icon-image
176  add monochrome icon image on IMAGE level
177  (default for cardiac profiles)
178 
179  -Xs --icon-image-size [s]ize: integer (1..128)
180  width and height of the icon image (in pixel)
181  (fixed: 128 for XA, 64 for CT/MR profile)
182 
183  -Xi --icon-file-prefix [p]refix: string
184  use PGM image 'prefix'+'dcmfile-in' as icon
185  (default: create icon from DICOM image)
186 
187  -Xd --default-icon [f]ilename: string
188  use specified PGM image if icon cannot be
189  created automatically (default: black image)
190 \endverbatim
191 
192 \subsection output_options output options
193 \verbatim
194 profiles:
195 
196  -Pgp --general-purpose
197  General Purpose Interchange on CD-R or
198  DVD-RAM Media (STD-GEN-CD/DVD-RAM, default)
199 
200  -Pdv --general-purpose-dvd
201  General Purpose DVD with Compression Interchange
202  (STD-GEN-DVD-JPEG/J2K)
203 
204  -Pmi --general-purpose-mime
205  General Purpose MIME Interchange (STD-GEN-MIME)
206 
207  -Pfl --usb-and-flash
208  General Purpose USB/Flash Memory with Compression
209  Interchange (STD-GEN-USB/MMC/CF/SD-JPEG/J2K)
210 
211  -Pmp --mpeg2-mpml-dvd
212  DVD Interchange with MPEG2 Main Profile @ Main
213  Level (STD-DVD-MPEG2-MPML)
214 
215  -Pbc --basic-cardiac
216  Basic Cardiac X-Ray Angiographic Studies on
217  CD-R Media (STD-XABC-CD)
218 
219  -Pxa --xray-angiographic
220  1024 X-Ray Angiographic Studies on CD-R Media
221  (STD-XA1K-CD)
222 
223  -Pxd --xray-angiographic-dvd
224  1024 X-Ray Angiographic Studies on DVD Media
225  (STD-XA1K-DVD)
226 
227  -Pde --dental-radiograph
228  Dental Radiograph Interchange (STD-DEN-CD)
229 
230  -Pcm --ct-and-mr
231  CT/MR Studies (STD-CTMR-xxxx)
232 
233  -Pus --ultrasound-id-sf
234  Ultrasound Single Frame for Image Display
235  (STD-US-ID-SF-xxxx)
236 
237  --ultrasound-sc-sf
238  Ultrasound Single Frame with Spatial
239  Calibration (STD-US-SC-SF-xxxx)
240 
241  --ultrasound-cc-sf
242  Ultrasound Single Frame with Combined
243  Calibration (STD-US-CC-SF-xxxx)
244 
245  -Pum --ultrasound-id-mf
246  Ultrasound Single & Multi-Frame for Image
247  Display (STD-US-ID-MF-xxxx)
248 
249  --ultrasound-sc-mf
250  Ultrasound Single & Multi-Frame with Spatial
251  Calibration (STD-UD-SC-MF-xxxx)
252 
253  --ultrasound-cc-mf
254  Ultrasound Single & Multi-Frame with Combined
255  Calibration (STD-UD-CC-MF-xxxx)
256 
257  -Pec --12-lead-ecg
258  12-lead ECG Interchange on Diskette
259  (STD-WVFM-ECG-FD)
260 
261  -Phd --hemodynamic-waveform
262  Hemodynamic Waveform Interchange on Diskette
263  (STD-WVFM-HD-FD)
264 
265 writing:
266 
267  -A --replace
268  replace existing DICOMDIR (default)
269 
270  +A --append
271  append to existing DICOMDIR
272 
273  +U --update
274  update existing DICOMDIR
275 
276  -w --discard
277  do not write out DICOMDIR
278 
279  -nb --no-backup
280  do not create a backup of existing DICOMDIR
281 
282 post-1993 value representations:
283 
284  +u --enable-new-vr
285  enable support for new VRs (UN/UT) (default)
286 
287  -u --disable-new-vr
288  disable support for new VRs, convert to OB
289 
290 group length encoding:
291 
292  -g --group-length-remove
293  write without group length elements (default)
294 
295  +g --group-length-create
296  write with group length elements
297 
298 length encoding in sequences and items:
299 
300  +e --length-explicit
301  write with explicit lengths (default)
302 
303  -e --length-undefined
304  write with undefined lengths
305 \endverbatim
306 
307 \section notes NOTES
308 
309 All files specified on the command line (or discovered by recursivly examining
310 the contents of directories with the \e +r option) are first evaluated for
311 their compatibility with the specified Media Storage Application Profile (Part
312 11). Only appropriate files encoded using one of the allowed Transfer Syntaxes
313 will be accepted. Files having invalid filenames will be rejected (the rules
314 can be relaxed via the \e +m option). Files missing required attributes will
315 be rejected (the \e +I option can relax this behaviour).
316 
317 A \e DICOMDIR file will only be constructed if all files have passed initial
318 tests.
319 
320 The \b dcmmkdir utility also allows to append new entries to and to update
321 existing entries in a \e DICOMDIR file. Using option \e +A new entries are
322 only appended to the DICOMDIR, i.e. existing records like the ones for PATIENT
323 information are not updated. Using option \e +U also existing records are
324 updated according to the information found in the referenced DICOM files.
325 Please note that this update process might be slower than just appending new
326 entries. However, it makes sure that additional information that is required
327 for the selected application profile is also added to existing records.
328 
329 The support for icon images is currently restricted to monochrome images.
330 This might change in the future. Till then, color images are automatically
331 converted to grayscale mode. The icon size is 128*128 pixels for the cardiac
332 profiles (as required by the DICOM standard) and 64*64 for all others.
333 
334 \section logging LOGGING
335 
336 The level of logging output of the various command line tools and underlying
337 libraries can be specified by the user. By default, only errors and warnings
338 are written to the standard error stream. Using option \e --verbose also
339 informational messages like processing details are reported. Option
340 \e --debug can be used to get more details on the internal activity, e.g. for
341 debugging purposes. Other logging levels can be selected using option
342 \e --log-level. In \e --quiet mode only fatal errors are reported. In such
343 very severe error events, the application will usually terminate. For more
344 details on the different logging levels, see documentation of module "oflog".
345 
346 In case the logging output should be written to file (optionally with logfile
347 rotation), to syslog (Unix) or the event log (Windows) option \e --log-config
348 can be used. This configuration file also allows for directing only certain
349 messages to a particular output stream and for filtering certain messages
350 based on the module or application where they are generated. An example
351 configuration file is provided in <em><etcdir>/logger.cfg</em>).
352 
353 \section command_line COMMAND LINE
354 
355 All command line tools use the following notation for parameters: square
356 brackets enclose optional values (0-1), three trailing dots indicate that
357 multiple values are allowed (1-n), a combination of both means 0 to n values.
358 
359 Command line options are distinguished from parameters by a leading '+' or '-'
360 sign, respectively. Usually, order and position of command line options are
361 arbitrary (i.e. they can appear anywhere). However, if options are mutually
362 exclusive the rightmost appearance is used. This behaviour conforms to the
363 standard evaluation rules of common Unix shells.
364 
365 In addition, one or more command files can be specified using an '@' sign as a
366 prefix to the filename (e.g. <em>\@command.txt</em>). Such a command argument
367 is replaced by the content of the corresponding text file (multiple
368 whitespaces are treated as a single separator unless they appear between two
369 quotation marks) prior to any further evaluation. Please note that a command
370 file cannot contain another command file. This simple but effective approach
371 allows to summarize common combinations of options/parameters and avoids
372 longish and confusing command lines (an example is provided in file
373 <em><datadir>/dumppat.txt</em>).
374 
375 \section environment ENVIRONMENT
376 
377 The \b dcmmkdir utility will attempt to load DICOM data dictionaries specified
378 in the \e DCMDICTPATH environment variable. By default, i.e. if the
379 \e DCMDICTPATH environment variable is not set, the file
380 <em><datadir>/dicom.dic</em> will be loaded unless the dictionary is built
381 into the application (default for Windows).
382 
383 The default behaviour should be preferred and the \e DCMDICTPATH environment
384 variable only used when alternative data dictionaries are required. The
385 \e DCMDICTPATH environment variable has the same format as the Unix shell
386 \e PATH variable in that a colon (":") separates entries. On Windows systems,
387 a semicolon (";") is used as a separator. The data dictionary code will
388 attempt to load each file specified in the \e DCMDICTPATH environment variable.
389 It is an error if no data dictionary can be loaded.
390 
391 \section see_also SEE ALSO
392 
393 <b>dcmgpdir</b>(1)
394 
395 \section copyright COPYRIGHT
396 
397 Copyright (C) 2001-2010 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.
398 
399 */


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