1dcmdjpeg(1) OFFIS DCMTK dcmdjpeg(1)
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6 dcmdjpeg - Decode JPEG-compressed DICOM file
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10 dcmdjpeg [options] dcmfile-in dcmfile-out
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13 The dcmdjpeg utility reads a JPEG-compressed DICOM image (dcmfile-in),
14 decompresses the JPEG data (i. e. conversion to a native DICOM transfer
15 syntax) and writes the converted image to an output file (dcmfile-out).
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18 dcmfile-in DICOM input filename to be converted
19 dcmfile-out DICOM output filename
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23 general options
24 -h --help
25 print this help text and exit
26 --version
28 print version information and exit
29 --arguments
31 print expanded command line arguments
32 -q --quiet
34 quiet mode, print no warnings and errors
35 -v --verbose
37 verbose mode, print processing details
38 -d --debug
40 debug mode, print debug information
41 -ll --log-level [l]evel: string constant
43 (fatal, error, warn, info, debug, trace)
44 use level l for the logger
45 -lc --log-config [f]ilename: string
47 use config file f for the logger
48 input options
50 input file format:
51 +f --read-file
53 read file format or data set (default)
54 +fo --read-file-only
56 read file format only
57 -f --read-dataset
59 read data set without file meta information
60 # This option allows one to decompress JPEG compressed DICOM objects that
62 # have been stored as dataset without meta-header. Such a thing should
63 # not exist since the transfer syntax cannot be reliably determined,
64 # without meta-header but unfortunately it does.
65 processing options
67 color space conversion:
68 +cp --conv-photometric
70 convert if YCbCr photometric interpretation (default)
71 # If the compressed image uses YBR_FULL or YBR_FULL_422 photometric
73 # interpretation, convert to RGB during decompression.
74 +cl --conv-lossy
76 convert YCbCr to RGB if lossy JPEG
77 # If the compressed image is encoded in lossy JPEG, assume YCbCr
79 # color model and convert to RGB.
80 +cg --conv-guess
82 convert to RGB if YCbCr is guessed by library
83 # If the underlying JPEG library "guesses" the color space of the
85 # compressed image to be YCbCr, convert to RGB.
86 +cgl --conv-guess-lossy
88 convert to RGB if lossy JPEG and YCbCr is
89 guessed by the underlying JPEG library
90 # If the compressed image is encoded in lossy JPEG and the underlying
92 # JPEG library "guesses" the color space to be YCbCr, convert to RGB.
93 +ca --conv-always
95 always convert YCbCr to RGB
96 # If the compressed image is a color image, assume YCbCr color model
98 # and convert to RGB.
99 +cn --conv-never
101 never convert color space
102 # Never convert color space during decompression.
104 planar configuration:
106 +pa --planar-auto
108 automatically determine planar configuration
109 from SOP class and color space (default)
110 # If the compressed image is a color image, store in color-by-plane
112 # planar configuration if required by the SOP class and photometric
113 # interpretation. Hardcopy Color images are always stored color-by-
114 # plane, and the revised Ultrasound image objects are stored color-by-
115 # plane if the color model is YBR_FULL. Everything else is stored
116 # color-by-pixel.
117 +px --color-by-pixel
119 always store color-by-pixel
120 # If the compressed image is a color image, store in color-by-pixel
122 # planar configuration.
123 +pl --color-by-plane
125 always store color-by-plane
126 # If the compressed image is a color image, store in color-by-plane
128 # planar configuration.
129 SOP Instance UID:
131 +ud --uid-default
133 keep same SOP Instance UID (default)
134 # Never assigns a new SOP instance UID.
136 +ua --uid-always
138 always assign new UID
139 # Always assigns a new SOP instance UID.
141 workaround options for incorrect JPEG encodings:
143 +w6 --workaround-pred6
145 enable workaround for JPEG lossless images
146 with overflow in predictor 6
147 # DICOM images with 16 bits/pixel have been observed "in the wild"
149 # that are compressed with lossless JPEG and need special handling
150 # because the encoder produced an 16-bit integer overflow in predictor
151 # 6, which needs to be compensated (reproduced) during decompression.
152 # This flag enables a correct decompression of such faulty images, but
153 # at the same time will cause an incorrect decompression of correctly
154 # compressed images. Use with care.
155 +wi --workaround-incpl
157 enable workaround for incomplete JPEG data
158 # This option causes dcmjpeg to ignore incomplete JPEG data
160 # at the end of a compressed fragment and to start decompressing
161 # the next frame from the next fragment (if any). This permits
162 # images with incomplete JPEG data to be decoded.
163 +wc --workaround-cornell
165 enable workaround for 16-bit JPEG lossless
166 Cornell images with Huffman table overflow
167 # One of the first open-source implementations of lossless JPEG
169 # compression, the "Cornell" library, has a well-known bug that leads
170 # to invalid values in the Huffmann table when images with 16 bit/sample
171 # are compressed. This flag enables a workaround that permits such
172 # images to be decoded correctly..fi
173 output options
175 output file format:
176 +F --write-file
178 write file format (default)
179 -F --write-dataset
181 write data set without file meta information
182 output transfer syntax:
184 +te --write-xfer-little
186 write with explicit VR little endian (default)
187 +tb --write-xfer-big
189 write with explicit VR big endian TS
190 +ti --write-xfer-implicit
192 write with implicit VR little endian TS
193 post-1993 value representations:
195 +u --enable-new-vr
197 enable support for new VRs (UN/UT) (default)
198 -u --disable-new-vr
200 disable support for new VRs, convert to OB
201 group length encoding:
203 +g= --group-length-recalc
205 recalculate group lengths if present (default)
206 +g --group-length-create
208 always write with group length elements
209 -g --group-length-remove
211 always write without group length elements
212 length encoding in sequences and items:
214 +e --length-explicit
216 write with explicit lengths (default)
217 -e --length-undefined
219 write with undefined lengths
220 data set trailing padding (not with --write-dataset):
222 -p= --padding-retain
224 do not change padding (default if not --write-dataset)
225 -p --padding-off
227 no padding (implicit if --write-dataset)
228 +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
234 dcmdjpeg supports the following transfer syntaxes for input (dcmfile-
235 in):
236 LittleEndianImplicitTransferSyntax 1.2.840.10008.1.2
238 LittleEndianExplicitTransferSyntax 1.2.840.10008.1.2.1
239 DeflatedExplicitVRLittleEndianTransferSyntax 1.2.840.10008.1.2.1.99 (*)
240 BigEndianExplicitTransferSyntax 1.2.840.10008.1.2.2
241 JPEGProcess1TransferSyntax 1.2.840.10008.1.2.4.50
242 JPEGProcess2_4TransferSyntax 1.2.840.10008.1.2.4.51
243 JPEGProcess6_8TransferSyntax 1.2.840.10008.1.2.4.53
244 JPEGProcess10_12TransferSyntax 1.2.840.10008.1.2.4.55
245 JPEGProcess14TransferSyntax 1.2.840.10008.1.2.4.57
246 JPEGProcess14SV1TransferSyntax 1.2.840.10008.1.2.4.70
247 (*) if compiled with zlib support enabled
249 dcmdjpeg supports the following transfer syntaxes for output (dcmfile-
251 out):
252 LittleEndianImplicitTransferSyntax 1.2.840.10008.1.2
254 LittleEndianExplicitTransferSyntax 1.2.840.10008.1.2.1
255 BigEndianExplicitTransferSyntax 1.2.840.10008.1.2.2
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258 The level of logging output of the various command line tools and
259 underlying libraries can be specified by the user. By default, only
260 errors and warnings are written to the standard error stream. Using
261 option --verbose also informational messages like processing details
262 are reported. Option --debug can be used to get more details on the
263 internal activity, e.g. for debugging purposes. Other logging levels
264 can be selected using option --log-level. In --quiet mode only fatal
265 errors are reported. In such very severe error events, the application
266 will usually terminate. For more details on the different logging
267 levels, see documentation of module 'oflog'.
268 In case the logging output should be written to file (optionally with
270 logfile rotation), to syslog (Unix) or the event log (Windows) option
271 --log-config can be used. This configuration file also allows for
272 directing only certain messages to a particular output stream and for
273 filtering certain messages based on the module or application where
274 they are generated. An example configuration file is provided in
275 <etcdir>/logger.cfg.
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278 All command line tools use the following notation for parameters:
279 square brackets enclose optional values (0-1), three trailing dots
280 indicate that multiple values are allowed (1-n), a combination of both
281 means 0 to n values.
282 Command line options are distinguished from parameters by a leading '+'
284 or '-' sign, respectively. Usually, order and position of command line
285 options are arbitrary (i.e. they can appear anywhere). However, if
286 options are mutually exclusive the rightmost appearance is used. This
287 behavior conforms to the standard evaluation rules of common Unix
288 shells.
289 In addition, one or more command files can be specified using an '@'
291 sign as a prefix to the filename (e.g. @command.txt). Such a command
292 argument is replaced by the content of the corresponding text file
293 (multiple whitespaces are treated as a single separator unless they
294 appear between two quotation marks) prior to any further evaluation.
295 Please note that a command file cannot contain another command file.
296 This simple but effective approach allows one to summarize common
297 combinations of options/parameters and avoids longish and confusing
298 command lines (an example is provided in file <datadir>/dumppat.txt).
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301 The dcmdjpeg utility will attempt to load DICOM data dictionaries
302 specified in the DCMDICTPATH environment variable. By default, i.e. if
303 the DCMDICTPATH environment variable is not set, the file
304 <datadir>/dicom.dic will be loaded unless the dictionary is built into
305 the application (default for Windows).
306 The default behavior should be preferred and the DCMDICTPATH
308 environment variable only used when alternative data dictionaries are
309 required. The DCMDICTPATH environment variable has the same format as
310 the Unix shell PATH variable in that a colon (':') separates entries.
311 On Windows systems, a semicolon (';') is used as a separator. The data
312 dictionary code will attempt to load each file specified in the
313 DCMDICTPATH environment variable. It is an error if no data dictionary
314 can be loaded.
315
317 dcmcjpeg(1)
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320 Copyright (C) 2001-2018 by OFFIS e.V., Escherweg 2, 26121 Oldenburg,
321 Germany.
322Version 3.6.4 Thu Nov 29 2018 dcmdjpeg(1)