1dcmcjpls(1) OFFIS DCMTK dcmcjpls(1)
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6 dcmcjpls - Encode DICOM file to JPEG-LS transfer syntax
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10 dcmcjpls [options] dcmfile-in dcmfile-out
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13 The dcmcjpls utility reads an uncompressed DICOM image (dcmfile-in),
14 performs a JPEG-LS compression (i. e. conversion to an encapsulated
15 DICOM transfer syntax) and writes the converted image to an output file
16 (dcmfile-out).
17
19 dcmfile-in DICOM input filename to be converted
20 dcmfile-out DICOM output filename
22
24 general options
25 -h --help
26 print this help text and exit
27 --version
29 print version information and exit
30 --arguments
32 print expanded command line arguments
33 -q --quiet
35 quiet mode, print no warnings and errors
36 -v --verbose
38 verbose mode, print processing details
39 -d --debug
41 debug mode, print debug information
42 -ll --log-level [l]evel: string constant
44 (fatal, error, warn, info, debug, trace)
45 use level l for the logger
46 -lc --log-config [f]ilename: string
48 use config file f for the logger
49 input options
51 input file format:
52 +f --read-file
54 read file format or data set (default)
55 +fo --read-file-only
57 read file format only
58 -f --read-dataset
60 read data set without file meta information
61 input transfer syntax:
63 -t= --read-xfer-auto
65 use TS recognition (default)
66 -td --read-xfer-detect
68 ignore TS specified in the file meta header
69 -te --read-xfer-little
71 read with explicit VR little endian TS
72 -tb --read-xfer-big
74 read with explicit VR big endian TS
75 -ti --read-xfer-implicit
77 read with implicit VR little endian TS
78 JPEG-LS encoding options
80 JPEG-LS process:
81 +el --encode-lossless
83 encode JPEG-LS lossless only TS (default)
84 # This options selects the JPEG-LS lossless only transfer syntax
86 # and performs a lossless compression.
87 +en --encode-nearlossless
89 encode JPEG-LS near-lossless TS (NEAR: 2)
90 # This options selects the JPEG-LS lossy transfer syntax
92 # and performs a near-lossless compression.
93 JPEG-LS bit rate (near-lossless only):
95 +md --max-deviation [d]eviation: integer (default: 2)
97 defines maximum deviation for an encoded pixel
98 # This option specifies the maximum deviation for a single pixel from
100 # the original pixel value.
101 lossless compression:
103 +pr --prefer-raw
105 prefer raw encoder mode (default)
106 # This option enables the raw encoder. The raw encoder encodes the
108 # complete pixel cell as it was read from the source image without
109 # performing any modifications.
110 +pc --prefer-cooked
112 prefer cooked encoder mode
113 # This option enables the cooked encoder. The cooked encoder moves
115 # overlay data to separate tags (60xx,3000) and only encodes the
116 # stored bits in each pixel.
117 JPEG-LS compression:
119 +t1 --threshold1 [t]hreshhold: integer (default for 8 bpp: 3)
121 set JPEG-LS encoding parameter threshold 1
122 +t2 --threshold2 [t]hreshhold: integer (default for 8 bpp: 7)
124 set JPEG-LS encoding parameter threshold 2
125 +t3 --threshold3 [t]hreshhold: integer (default for 8 bpp: 21)
127 set JPEG-LS encoding parameter threshold 3
128 +rs --reset [r]eset: integer (default: 64)
130 set JPEG-LS encoding parameter reset
131 +lm --limit [l]imit: integer (default: 0)
133 set JPEG-LS encoding parameter limit
134 JPEG-LS interleave:
136 +il --interleave-line
138 force line-interleaved JPEG-LS images (default)
139 # This flag forces line-interleaved mode for the resulting image.
141 # In line-interleave mode each line from the source image is
142 # compressed separately for each component and then the next line
143 # is encoded.
144 +is --interleave-sample
146 force sample-interleaved JPEG-LS images
147 # This flag forces sample-interleaved mode for the resulting image.
149 # In sample-interleave mode each pixel's components are encoded before
150 # the next pixel is encoded.
151 +in --interleave-none
153 force uninterleaved JPEG-LS images
154 # This flag forces uninterleaved mode for the resulting image.
156 # In this mode, each of the image's components are completely encoded
157 # before the next component is handled.
158 +iv --interleave-default
160 use the fastest possible interleave mode
161 # This flag selects an interleave mode based on the source image's mode.
163 # If possible, the image is not converted to a different interleave mode.
164 encapsulated pixel data encoding options
166 encapsulated pixel data fragmentation:
167 +ff --fragment-per-frame
169 encode each frame as one fragment (default)
170 # This option causes the creation of one compressed fragment for each
172 # frame (recommended).
173 +fs --fragment-size [s]ize: integer
175 limit fragment size to s kbytes
176 # This option limits the fragment size which may cause the creation of
178 # multiple fragments per frame.
179 basic offset table encoding:
181 +ot --offset-table-create
183 create offset table (default)
184 # This option causes the creation of a valid offset table for the
186 # compressed JPEG fragments.
187 -ot --offset-table-empty
189 leave offset table empty
190 # This option causes the creation of an empty offset table
192 # for the compressed JPEG fragments.
193 SOP Class UID:
195 +cd --class-default
197 keep SOP Class UID (default)
198 # Keep the SOP Class UID of the source image.
200 +cs --class-sc
202 convert to Secondary Capture Image (implies --uid-always)
203 # Convert the image to Secondary Capture. In addition to the SOP Class
205 # UID, all attributes required for a valid secondary capture image are
206 # added. A new SOP instance UID is always assigned.
207 SOP Instance UID:
209 +ud --uid-default
211 assign new UID if lossy compression (default)
212 # Assigns a new SOP instance UID if the compression is lossy JPEG.
214 +ua --uid-always
216 always assign new UID
217 # Unconditionally assigns a new SOP instance UID.
219 +un --uid-never
221 never assign new UID
222 # Never assigns a new SOP instance UID.
224 output options
226 post-1993 value representations:
227 +u --enable-new-vr
229 enable support for new VRs (UN/UT) (default)
230 -u --disable-new-vr
232 disable support for new VRs, convert to OB
233 group length encoding:
235 +g= --group-length-recalc
237 recalculate group lengths if present (default)
238 +g --group-length-create
240 always write with group length elements
241 -g --group-length-remove
243 always write without group length elements
244 length encoding in sequences and items:
246 +e --length-explicit
248 write with explicit lengths (default)
249 -e --length-undefined
251 write with undefined lengths
252 data set trailing padding:
254 -p= --padding-retain
256 do not change padding (default)
257 -p --padding-off
259 no padding
260 +p --padding-create [f]ile-pad [i]tem-pad: integer
262 align file on multiple of f bytes
263 and items on multiple of i bytes
264
266 The dcmcjpls utility compresses DICOM images of all SOP classes. It
267 processes all Pixel Data (7fe0,0010) elements in the dataset, i.e.
268 compression is also performed on an icon image. However, dcmcjpls does
269 not attempt to ensure that the compressed image still complies with all
270 restrictions of the object's IOD.
271 The user is responsible for making sure that the compressed images he
273 creates are compliant with the DICOM standard. If in question, the
274 dcmcjpls utility allows one to convert an image to secondary capture -
275 this SOP class does not pose restrictions as the ones mentioned above.
276
278 dcmcjpls supports the following transfer syntaxes for input (dcmfile-
279 in):
280 LittleEndianImplicitTransferSyntax 1.2.840.10008.1.2
282 LittleEndianExplicitTransferSyntax 1.2.840.10008.1.2.1
283 DeflatedExplicitVRLittleEndianTransferSyntax 1.2.840.10008.1.2.1.99 (*)
284 BigEndianExplicitTransferSyntax 1.2.840.10008.1.2.2
285 (*) if compiled with zlib support enabled
287 dcmcjpls supports the following transfer syntaxes for output (dcmfile-
289 out):
290 JPEGLSLosslessTransferSyntax 1.2.840.10008.1.2.4.80
292 JPEGLSLossyTransferSyntax 1.2.840.10008.1.2.4.81
293
295 The level of logging output of the various command line tools and
296 underlying libraries can be specified by the user. By default, only
297 errors and warnings are written to the standard error stream. Using
298 option --verbose also informational messages like processing details
299 are reported. Option --debug can be used to get more details on the
300 internal activity, e.g. for debugging purposes. Other logging levels
301 can be selected using option --log-level. In --quiet mode only fatal
302 errors are reported. In such very severe error events, the application
303 will usually terminate. For more details on the different logging
304 levels, see documentation of module 'oflog'.
305 In case the logging output should be written to file (optionally with
307 logfile rotation), to syslog (Unix) or the event log (Windows) option
308 --log-config can be used. This configuration file also allows for
309 directing only certain messages to a particular output stream and for
310 filtering certain messages based on the module or application where
311 they are generated. An example configuration file is provided in
312 <etcdir>/logger.cfg.
313
315 All command line tools use the following notation for parameters:
316 square brackets enclose optional values (0-1), three trailing dots
317 indicate that multiple values are allowed (1-n), a combination of both
318 means 0 to n values.
319 Command line options are distinguished from parameters by a leading '+'
321 or '-' sign, respectively. Usually, order and position of command line
322 options are arbitrary (i.e. they can appear anywhere). However, if
323 options are mutually exclusive the rightmost appearance is used. This
324 behavior conforms to the standard evaluation rules of common Unix
325 shells.
326 In addition, one or more command files can be specified using an '@'
328 sign as a prefix to the filename (e.g. @command.txt). Such a command
329 argument is replaced by the content of the corresponding text file
330 (multiple whitespaces are treated as a single separator unless they
331 appear between two quotation marks) prior to any further evaluation.
332 Please note that a command file cannot contain another command file.
333 This simple but effective approach allows one to summarize common
334 combinations of options/parameters and avoids longish and confusing
335 command lines (an example is provided in file <datadir>/dumppat.txt).
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338 The dcmcjpls utility will attempt to load DICOM data dictionaries
339 specified in the DCMDICTPATH environment variable. By default, i.e. if
340 the DCMDICTPATH environment variable is not set, the file
341 <datadir>/dicom.dic will be loaded unless the dictionary is built into
342 the application (default for Windows).
343 The default behavior should be preferred and the DCMDICTPATH
345 environment variable only used when alternative data dictionaries are
346 required. The DCMDICTPATH environment variable has the same format as
347 the Unix shell PATH variable in that a colon (':') separates entries.
348 On Windows systems, a semicolon (';') is used as a separator. The data
349 dictionary code will attempt to load each file specified in the
350 DCMDICTPATH environment variable. It is an error if no data dictionary
351 can be loaded.
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354 dcmdjpls(1)
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357 Copyright (C) 2009-2018 by OFFIS e.V., Escherweg 2, 26121 Oldenburg,
358 Germany.
359Version 3.6.4 Thu Nov 29 2018 dcmcjpls(1)