OFFIS DCMTK  Version 3.6.0
dcmdjpeg.man
1 /*!
2 
3 \if MANPAGES
4 \page dcmdjpeg Decode JPEG-compressed DICOM file
5 \else
6 \page dcmdjpeg dcmdjpeg: Decode JPEG-compressed DICOM file
7 \endif
8 
9 \section synopsis SYNOPSIS
10 
11 \verbatim
12 dcmdjpeg [options] dcmfile-in dcmfile-out
13 \endverbatim
14 
15 \section description DESCRIPTION
16 
17 The \b dcmdjpeg utility reads a JPEG-compressed DICOM image (\e dcmfile-in),
18 decompresses the JPEG data (i. e. conversion to a native DICOM transfer syntax)
19 and writes the converted image to an output file (\e dcmfile-out).
20 
21 \section parameters PARAMETERS
22 
23 \verbatim
24 dcmfile-in DICOM input filename to be converted
25 
26 dcmfile-out DICOM output filename
27 \endverbatim
28 
29 \section options OPTIONS
30 
31 \subsection general_options general options
32 \verbatim
33  -h --help
34  print this help text and exit
35 
36  --version
37  print version information and exit
38 
39  --arguments
40  print expanded command line arguments
41 
42  -q --quiet
43  quiet mode, print no warnings and errors
44 
45  -v --verbose
46  verbose mode, print processing details
47 
48  -d --debug
49  debug mode, print debug information
50 
51  -ll --log-level [l]evel: string constant
52  (fatal, error, warn, info, debug, trace)
53  use level l for the logger
54 
55  -lc --log-config [f]ilename: string
56  use config file f for the logger
57 \endverbatim
58 
59 \subsection input_options input options
60 
61 \verbatim
62 input file format:
63 
64  +f --read-file
65  read file format or data set (default)
66 
67  +fo --read-file-only
68  read file format only
69 
70  -f --read-dataset
71  read data set without file meta information
72 
73  # This option allows to decompress JPEG compressed DICOM objects that
74  # have been stored as dataset without meta-header. Such a thing should
75  # not exist since the transfer syntax cannot be reliably determined,
76  # without meta-header but unfortunately it does.
77 \endverbatim
78 
79 \subsection processing_options processing options
80 
81 \verbatim
82 color space conversion:
83 
84  +cp --conv-photometric
85  convert if YCbCr photometric interpretation (default)
86 
87  # If the compressed image uses YBR_FULL or YBR_FULL_422 photometric
88  # interpretation, convert to RGB during decompression.
89 
90  +cl --conv-lossy
91  convert YCbCr to RGB if lossy JPEG
92 
93  # If the compressed image is encoded in lossy JPEG, assume YCbCr
94  # color model and convert to RGB.
95 
96  +cg --conv-guess
97  convert to RGB if YCbCr is guessed by library
98 
99  # If the underlying JPEG library "guesses" the color space of the
100  # compressed image to be YCbCr, convert to RGB.
101 
102  +cgl --conv-guess-lossy
103  convert to RGB if lossy JPEG and YCbCr is
104  guessed by the underlying JPEG library
105 
106  # If the compressed image is encoded in lossy JPEG and the underlying
107  # JPEG library "guesses" the color space to be YCbCr, convert to RGB.
108 
109  +ca --conv-always
110  always convert YCbCr to RGB
111 
112  # If the compressed image is a color image, assume YCbCr color model
113  # and convert to RGB.
114 
115  +cn --conv-never
116  never convert color space
117 
118  # Never convert color space during decompression.
119 
120 planar configuration:
121 
122  +pa --planar-auto
123  automatically determine planar configuration
124  from SOP class and color space (default)
125 
126  # If the compressed image is a color image, store in color-by-plane
127  # planar configuration if required by the SOP class and photometric
128  # interpretation. Hardcopy Color images are always stored color-by-
129  # plane, and the revised Ultrasound image objects are stored color-by-
130  # plane if the color model is YBR_FULL. Everything else is stored
131  # color-by-pixel.
132 
133  +px --color-by-pixel
134  always store color-by-pixel
135 
136  # If the compressed image is a color image, store in color-by-pixel
137  # planar configuration.
138 
139  +pl --color-by-plane
140  always store color-by-plane
141 
142  # If the compressed image is a color image, store in color-by-plane
143  # planar configuration.
144 
145 SOP Instance UID:
146 
147  +ud --uid-default
148  keep same SOP Instance UID (default)
149 
150  # Never assigns a new SOP instance UID.
151 
152  +ua --uid-always
153  always assign new UID
154 
155  # Always assigns a new SOP instance UID.
156 
157 workaround options for incorrect JPEG encodings:
158 
159  +w6 --workaround-pred6
160  enable workaround for JPEG lossless images
161  with overflow in predictor 6
162 
163  # DICOM images with 16 bits/pixel have been observed "in the wild"
164  # that are compressed with lossless JPEG and need special handling
165  # because the encoder produced an 16-bit integer overflow in predictor
166  # 6, which needs to be compensated (reproduced) during decompression.
167  # This flag enables a correct decompression of such faulty images, but
168  # at the same time will cause an incorrect decompression of correctly
169  # compressed images. Use with care.
170 \endverbatim
171 
172 \subsection output_options output options
173 
174 \verbatim
175 output file format:
176 
177  +F --write-file
178  write file format (default)
179 
180  -F --write-dataset
181  write data set without file meta information
182 
183 output transfer syntax:
184 
185  +te --write-xfer-little
186  write with explicit VR little endian (default)
187 
188  +tb --write-xfer-big
189  write with explicit VR big endian TS
190 
191  +ti --write-xfer-implicit
192  write with implicit VR little endian TS
193 
194 post-1993 value representations:
195 
196  +u --enable-new-vr
197  enable support for new VRs (UN/UT) (default)
198 
199  -u --disable-new-vr
200  disable support for new VRs, convert to OB
201 
202 group length encoding:
203 
204  +g= --group-length-recalc
205  recalculate group lengths if present (default)
206 
207  +g --group-length-create
208  always write with group length elements
209 
210  -g --group-length-remove
211  always write without group length elements
212 
213 length encoding in sequences and items:
214 
215  +e --length-explicit
216  write with explicit lengths (default)
217 
218  -e --length-undefined
219  write with undefined lengths
220 
221 data set trailing padding (not with --write-dataset):
222 
223  -p= --padding-retain
224  do not change padding (default if not --write-dataset)
225 
226  -p --padding-off
227  no padding (implicit if --write-dataset)
228 
229  +p --padding-create [f]ile-pad [i]tem-pad: integer
230  align file on multiple of f bytes
231  and items on multiple of i bytes
232 \endverbatim
233 
234 \section transfer_syntaxes TRANSFER SYNTAXES
235 
236 \b dcmdjpeg supports the following transfer syntaxes for input
237 (\e dcmfile-in):
238 
239 \verbatim
240 LittleEndianImplicitTransferSyntax 1.2.840.10008.1.2
241 LittleEndianExplicitTransferSyntax 1.2.840.10008.1.2.1
242 DeflatedExplicitVRLittleEndianTransferSyntax 1.2.840.10008.1.2.1.99 (*)
243 BigEndianExplicitTransferSyntax 1.2.840.10008.1.2.2
244 JPEGProcess1TransferSyntax 1.2.840.10008.1.2.4.50
245 JPEGProcess2_4TransferSyntax 1.2.840.10008.1.2.4.51
246 JPEGProcess6_8TransferSyntax 1.2.840.10008.1.2.4.53
247 JPEGProcess10_12TransferSyntax 1.2.840.10008.1.2.4.55
248 JPEGProcess14TransferSyntax 1.2.840.10008.1.2.4.57
249 JPEGProcess14SV1TransferSyntax 1.2.840.10008.1.2.4.70
250 \endverbatim
251 
252 (*) if compiled with zlib support enabled
253 
254 \b dcmdjpeg supports the following transfer syntaxes for output
255 (\e dcmfile-out):
256 
257 \verbatim
258 LittleEndianImplicitTransferSyntax 1.2.840.10008.1.2
259 LittleEndianExplicitTransferSyntax 1.2.840.10008.1.2.1
260 BigEndianExplicitTransferSyntax 1.2.840.10008.1.2.2
261 \endverbatim
262 
263 \section logging LOGGING
264 
265 The level of logging output of the various command line tools and underlying
266 libraries can be specified by the user. By default, only errors and warnings
267 are written to the standard error stream. Using option \e --verbose also
268 informational messages like processing details are reported. Option
269 \e --debug can be used to get more details on the internal activity, e.g. for
270 debugging purposes. Other logging levels can be selected using option
271 \e --log-level. In \e --quiet mode only fatal errors are reported. In such
272 very severe error events, the application will usually terminate. For more
273 details on the different logging levels, see documentation of module "oflog".
274 
275 In case the logging output should be written to file (optionally with logfile
276 rotation), to syslog (Unix) or the event log (Windows) option \e --log-config
277 can be used. This configuration file also allows for directing only certain
278 messages to a particular output stream and for filtering certain messages
279 based on the module or application where they are generated. An example
280 configuration file is provided in <em><etcdir>/logger.cfg</em>).
281 
282 \section command_line COMMAND LINE
283 
284 All command line tools use the following notation for parameters: square
285 brackets enclose optional values (0-1), three trailing dots indicate that
286 multiple values are allowed (1-n), a combination of both means 0 to n values.
287 
288 Command line options are distinguished from parameters by a leading '+' or '-'
289 sign, respectively. Usually, order and position of command line options are
290 arbitrary (i.e. they can appear anywhere). However, if options are mutually
291 exclusive the rightmost appearance is used. This behaviour conforms to the
292 standard evaluation rules of common Unix shells.
293 
294 In addition, one or more command files can be specified using an '@' sign as a
295 prefix to the filename (e.g. <em>\@command.txt</em>). Such a command argument
296 is replaced by the content of the corresponding text file (multiple
297 whitespaces are treated as a single separator unless they appear between two
298 quotation marks) prior to any further evaluation. Please note that a command
299 file cannot contain another command file. This simple but effective approach
300 allows to summarize common combinations of options/parameters and avoids
301 longish and confusing command lines (an example is provided in file
302 <em><datadir>/dumppat.txt</em>).
303 
304 \section environment ENVIRONMENT
305 
306 The \b dcmdjpeg utility will attempt to load DICOM data dictionaries specified
307 in the \e DCMDICTPATH environment variable. By default, i.e. if the
308 \e DCMDICTPATH environment variable is not set, the file
309 <em><datadir>/dicom.dic</em> will be loaded unless the dictionary is built
310 into the application (default for Windows).
311 
312 The default behaviour should be preferred and the \e DCMDICTPATH environment
313 variable only used when alternative data dictionaries are required. The
314 \e DCMDICTPATH environment variable has the same format as the Unix shell
315 \e PATH variable in that a colon (":") separates entries. On Windows systems,
316 a semicolon (";") is used as a separator. The data dictionary code will
317 attempt to load each file specified in the \e DCMDICTPATH environment variable.
318 It is an error if no data dictionary can be loaded.
319 
320 \section see_also SEE ALSO
321 
322 <b>dcmcjpeg</b>(1)
323 
324 \section copyright COPYRIGHT
325 
326 Copyright (C) 2001-2010 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.
327 
328 */


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