OFFIS DCMTK  Version 3.6.0
dcmcjpls.man
1 /*!
2 
3 \if MANPAGES
4 \page dcmcjpls Encode DICOM file to JPEG-LS transfer syntax
5 \else
6 \page dcmcjpls dcmcjpls: Encode DICOM file to JPEG-LS transfer syntax
7 \endif
8 
9 \section synopsis SYNOPSIS
10 
11 \verbatim
12 dcmcjpls [options] dcmfile-in dcmfile-out
13 \endverbatim
14 
15 \section description DESCRIPTION
16 
17 The \b dcmcjpls utility reads an uncompressed DICOM image (\e dcmfile-in),
18 performs a JPEG-LS compression (i. e. conversion to an encapsulated DICOM
19 transfer syntax) and writes the converted image to an output file
20 (\e dcmfile-out).
21 
22 \section parameters PARAMETERS
23 
24 \verbatim
25 dcmfile-in DICOM input filename to be converted
26 
27 dcmfile-out DICOM output filename
28 \endverbatim
29 
30 \section options OPTIONS
31 
32 \subsection general_options general options
33 \verbatim
34  -h --help
35  print this help text and exit
36 
37  --version
38  print version information and exit
39 
40  --arguments
41  print expanded command line arguments
42 
43  -q --quiet
44  quiet mode, print no warnings and errors
45 
46  -v --verbose
47  verbose mode, print processing details
48 
49  -d --debug
50  debug mode, print debug information
51 
52  -ll --log-level [l]evel: string constant
53  (fatal, error, warn, info, debug, trace)
54  use level l for the logger
55 
56  -lc --log-config [f]ilename: string
57  use config file f for the logger
58 \endverbatim
59 
60 \subsection input_options input options
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 input transfer syntax:
74 
75  -t= --read-xfer-auto
76  use TS recognition (default)
77 
78  -td --read-xfer-detect
79  ignore TS specified in the file meta header
80 
81  -te --read-xfer-little
82  read with explicit VR little endian TS
83 
84  -tb --read-xfer-big
85  read with explicit VR big endian TS
86 
87  -ti --read-xfer-implicit
88  read with implicit VR little endian TS
89 \endverbatim
90 
91 \subsection JPEG_LS_encoding_options JPEG-LS encoding options
92 \verbatim
93 JPEG-LS process:
94 
95  +el --encode-lossless
96  encode JPEG-LS lossless only TS (default)
97 
98  # This options selects the JPEG-LS lossless only transfer syntax
99  # and performs a lossless compression.
100 
101  +en --encode-nearlossless
102  encode JPEG-LS near-lossless TS (NEAR: 2)
103 
104  # This options selects the JPEG-LS lossy transfer syntax
105  # and performs a near-lossless compression.
106 
107 JPEG-LS bit rate (near-lossless only):
108 
109  +md --max-deviation [d]eviation: integer (default: 2)
110  defines maximum deviation for an encoded pixel
111 
112  # This option specifies the maximum deviation for a single pixel from
113  # the original pixel value.
114 
115 lossless compression:
116 
117  +pr --prefer-raw
118  prefer raw encoder mode (default)
119 
120  # This option enables the raw encoder. The raw encoder encodes the
121  # complete pixel cell as it was read from the source image without
122  # performing any modifications.
123 
124  +pc --prefer-cooked
125  prefer cooked encoder mode
126 
127  # This option enables the cooked encoder. The cooked encoder moves
128  # overlay data to separate tags (60xx,3000) and only encodes the
129  # stored bits in each pixel.
130 
131 JPEG-LS compression:
132 
133  +t1 --threshold1 [t]hreshhold: integer (default for 8 bpp: 3)
134  set JPEG-LS encoding parameter threshold 1
135 
136  +t2 --threshold2 [t]hreshhold: integer (default for 8 bpp: 7)
137  set JPEG-LS encoding parameter threshold 2
138 
139  +t3 --threshold3 [t]hreshhold: integer (default for 8 bpp: 21)
140  set JPEG-LS encoding parameter threshold 3
141 
142  +rs --reset [r]eset: integer (default: 64)
143  set JPEG-LS encoding parameter reset
144 
145  +lm --limit [l]imit: integer (default: 0)
146  set JPEG-LS encoding parameter limit
147 
148 JPEG-LS interleave:
149 
150  +il --interleave-line
151  force line-interleaved JPEG-LS images (default)
152 
153  # This flag forces line-interleaved mode for the resulting image.
154  # In line-interleave mode each line from the source image is
155  # compressed separately for each component and then the next line
156  # is encoded.
157 
158  +is --interleave-sample
159  force sample-interleaved JPEG-LS images
160 
161  # This flag forces sample-interleaved mode for the resulting image.
162  # In sample-interleave mode each pixel's components are encoded before
163  # the next pixe is encoded.
164 
165  +in --interleave-none
166  force uninterleaved JPEG-LS images
167 
168  # This flag forces uninterleaved mode for the resulting image.
169  # In this mode, each of the image's components are completely encoded
170  # before the next component is handled.
171 
172  +iv --interleave-default
173  use the fastest possible interleave mode
174 
175  # This flag selects an interleave mode based on the source image's mode.
176  # If possible, the image is not converted to a different interleave mode.
177 \endverbatim
178 
179 \subsection enc_pix_data_encoding_opt encapsulated pixel data encoding options
180 \verbatim
181 encapsulated pixel data fragmentation:
182 
183  +ff --fragment-per-frame
184  encode each frame as one fragment (default)
185 
186  # This option causes the creation of one compressed fragment for each
187  # frame (recommended).
188 
189  +fs --fragment-size [s]ize: integer
190  limit fragment size to s kbytes
191 
192  # This option limits the fragment size which may cause the creation of
193  # multiple fragments per frame.
194 
195 basic offset table encoding:
196 
197  +ot --offset-table-create
198  create offset table (default)
199 
200  # This option causes the creation of a valid offset table for the
201  # compressed JPEG fragments.
202 
203  -ot --offset-table-empty
204  leave offset table empty
205 
206  # This option causes the creation of an empty offset table
207  # for the compressed JPEG fragments.
208 
209 SOP Class UID:
210 
211  +cd --class-default
212  keep SOP Class UID (default)
213 
214  # Keep the SOP Class UID of the source image.
215 
216  +cs --class-sc
217  convert to Secondary Capture Image (implies --uid-always)
218 
219  # Convert the image to Secondary Capture. In addition to the SOP Class
220  # UID, all attributes required for a valid secondary capture image are
221  # added. A new SOP instance UID is always assigned.
222 
223 SOP Instance UID:
224 
225  +ud --uid-default
226  assign new UID if lossy compression (default)
227 
228  # Assigns a new SOP instance UID if the compression is lossy JPEG.
229 
230  +ua --uid-always
231  always assign new UID
232 
233  # Unconditionally assigns a new SOP instance UID.
234 
235  +un --uid-never
236  never assign new UID
237 
238  # Never assigns a new SOP instance UID.
239 \endverbatim
240 
241 \subsection output_options output options
242 \verbatim
243 post-1993 value representations:
244 
245  +u --enable-new-vr
246  enable support for new VRs (UN/UT) (default)
247 
248  -u --disable-new-vr
249  disable support for new VRs, convert to OB
250 
251 group length encoding:
252 
253  +g= --group-length-recalc
254  recalculate group lengths if present (default)
255 
256  +g --group-length-create
257  always write with group length elements
258 
259  -g --group-length-remove
260  always write without group length elements
261 
262 length encoding in sequences and items:
263 
264  +e --length-explicit
265  write with explicit lengths (default)
266 
267  -e --length-undefined
268  write with undefined lengths
269 
270 data set trailing padding:
271 
272  -p= --padding-retain
273  do not change padding (default)
274 
275  -p --padding-off
276  no padding
277 
278  +p --padding-create [f]ile-pad [i]tem-pad: integer
279  align file on multiple of f bytes
280  and items on multiple of i bytes
281 \endverbatim
282 
283 \section notes NOTES
284 
285 The \b dcmcjpls utility compresses DICOM images of all SOP classes. However,
286 \b dcmcjpls does not attempt to ensure that the compressed image still
287 complies with all restrictions of the object's IOD.
288 
289 The user is responsible for making sure that the compressed images he creates
290 are compliant with the DICOM standard. If in question, the \b dcmcjpls utility
291 allows to convert an image to secondary capture - this SOP class does not pose
292 restrictions as the ones mentioned above.
293 
294 \section transfer_syntaxes TRANSFER SYNTAXES
295 
296 \b dcmcjpls supports the following transfer syntaxes for input
297 (\e dcmfile-in):
298 
299 \verbatim
300 LittleEndianImplicitTransferSyntax 1.2.840.10008.1.2
301 LittleEndianExplicitTransferSyntax 1.2.840.10008.1.2.1
302 DeflatedExplicitVRLittleEndianTransferSyntax 1.2.840.10008.1.2.1.99 (*)
303 BigEndianExplicitTransferSyntax 1.2.840.10008.1.2.2
304 \endverbatim
305 
306 (*) if compiled with zlib support enabled
307 
308 \b dcmcjpls supports the following transfer syntaxes for output
309 (\e dcmfile-out):
310 
311 \verbatim
312 JPEGLSLosslessTransferSyntax 1.2.840.10008.1.2.4.80
313 JPEGLSLossyTransferSyntax 1.2.840.10008.1.2.4.81
314 \endverbatim
315 
316 \section logging LOGGING
317 
318 The level of logging output of the various command line tools and underlying
319 libraries can be specified by the user. By default, only errors and warnings
320 are written to the standard error stream. Using option \e --verbose also
321 informational messages like processing details are reported. Option
322 \e --debug can be used to get more details on the internal activity, e.g. for
323 debugging purposes. Other logging levels can be selected using option
324 \e --log-level. In \e --quiet mode only fatal errors are reported. In such
325 very severe error events, the application will usually terminate. For more
326 details on the different logging levels, see documentation of module "oflog".
327 
328 In case the logging output should be written to file (optionally with logfile
329 rotation), to syslog (Unix) or the event log (Windows) option \e --log-config
330 can be used. This configuration file also allows for directing only certain
331 messages to a particular output stream and for filtering certain messages
332 based on the module or application where they are generated. An example
333 configuration file is provided in <em><etcdir>/logger.cfg</em>).
334 
335 \section command_line COMMAND LINE
336 
337 All command line tools use the following notation for parameters: square
338 brackets enclose optional values (0-1), three trailing dots indicate that
339 multiple values are allowed (1-n), a combination of both means 0 to n values.
340 
341 Command line options are distinguished from parameters by a leading '+' or '-'
342 sign, respectively. Usually, order and position of command line options are
343 arbitrary (i.e. they can appear anywhere). However, if options are mutually
344 exclusive the rightmost appearance is used. This behaviour conforms to the
345 standard evaluation rules of common Unix shells.
346 
347 In addition, one or more command files can be specified using an '@' sign as a
348 prefix to the filename (e.g. <em>\@command.txt</em>). Such a command argument
349 is replaced by the content of the corresponding text file (multiple
350 whitespaces are treated as a single separator unless they appear between two
351 quotation marks) prior to any further evaluation. Please note that a command
352 file cannot contain another command file. This simple but effective approach
353 allows to summarize common combinations of options/parameters and avoids
354 longish and confusing command lines (an example is provided in file
355 <em><datadir>/dumppat.txt</em>).
356 
357 \section environment ENVIRONMENT
358 
359 The \b dcmcjpls utility will attempt to load DICOM data dictionaries specified
360 in the \e DCMDICTPATH environment variable. By default, i.e. if the
361 \e DCMDICTPATH environment variable is not set, the file
362 <em><datadir>/dicom.dic</em> will be loaded unless the dictionary is built
363 into the application (default for Windows).
364 
365 The default behaviour should be preferred and the \e DCMDICTPATH environment
366 variable only used when alternative data dictionaries are required. The
367 \e DCMDICTPATH environment variable has the same format as the Unix shell
368 \e PATH variable in that a colon (":") separates entries. On Windows systems,
369 a semicolon (";") is used as a separator. The data dictionary code will
370 attempt to load each file specified in the \e DCMDICTPATH environment variable.
371 It is an error if no data dictionary can be loaded.
372 
373 \section see_also SEE ALSO
374 
375 <b>dcmdjpls</b>(1)
376 
377 \section copyright COPYRIGHT
378 
379 Copyright (C) 2009-2010 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.
380 
381 */


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