1dcmj2pnm(1) OFFIS DCMTK dcmj2pnm(1)
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6 dcmj2pnm - Convert DICOM images to PGM/PPM, PNG, TIFF, JPEG or BMP
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9 dcmj2pnm [options] dcmfile-in [bitmap-out]
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12 The dcmj2pnm utility reads a DICOM image, converts the pixel data
13 according to the selected image processing options and writes back an
14 image in the well-known PGM/PPM (portable gray map / portable pix map),
15 PNG, TIFF, JPEG (Joint Photographic Experts Group) or Windows BMP
16 format. This utility supports uncompressed as well as JPEG and RLE
17 compressed DICOM images.
18
20 dcmfile-in DICOM input filename to be converted
21 bitmap-out output filename to be written (default: stdout)
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25 general options
26 -h --help
27 print this help text and exit
28 --version
30 print version information and exit
31 --arguments
33 print expanded command line arguments
34 -q --quiet
36 quiet mode, print no warnings and errors
37 -v --verbose
39 verbose mode, print processing details
40 -d --debug
42 debug mode, print debug information
43 -ll --log-level [l]evel: string constant
45 (fatal, error, warn, info, debug, trace)
46 use level l for the logger
47 -lc --log-config [f]ilename: string
49 use config file f for the logger
50 input options
52 input file format:
53 +f --read-file
55 read file format or data set (default)
56 +fo --read-file-only
58 read file format only
59 -f --read-dataset
61 read data set without file meta information
62 input transfer syntax:
64 -t= --read-xfer-auto
66 use TS recognition (default)
67 -td --read-xfer-detect
69 ignore TS specified in the file meta header
70 -te --read-xfer-little
72 read with explicit VR little endian TS
73 -tb --read-xfer-big
75 read with explicit VR big endian TS
76 -ti --read-xfer-implicit
78 read with implicit VR little endian TS
79 image processing options
81 frame selection:
82 +F --frame [n]umber: integer
84 select specified frame (default: 1)
85 +Fr --frame-range [n]umber [c]ount: integer
87 select c frames beginning with frame n
88 +Fa --all-frames
90 select all frames
91 rotation:
93 +Rl --rotate-left
95 rotate image left (-90 degrees)
96 +Rr --rotate-right
98 rotate image right (+90 degrees)
99 +Rtd --rotate-top-down
101 rotate image top-down (180 degrees)
102 flipping:
104 +Lh --flip-horizontally
106 flip image horizontally
107 +Lv --flip-vertically
109 flip image vertically
110 +Lhv --flip-both-axes
112 flip image horizontally and vertically
113 scaling:
115 +a --recognize-aspect
117 recognize pixel aspect ratio (default)
118 -a --ignore-aspect
120 ignore pixel aspect ratio when scaling
121 +i --interpolate [n]umber of algorithm: integer
123 use interpolation when scaling (1..4, default: 1)
124 -i --no-interpolation
126 no interpolation when scaling
127 -S --no-scaling
129 no scaling, ignore pixel aspect ratio (default)
130 +Sxf --scale-x-factor [f]actor: float
132 scale x axis by factor, auto-compute y axis
133 +Syf --scale-y-factor [f]actor: float
135 scale y axis by factor, auto-compute x axis
136 +Sxv --scale-x-size [n]umber: integer
138 scale x axis to n pixels, auto-compute y axis
139 +Syv --scale-y-size [n]umber: integer
141 scale y axis to n pixels, auto-compute x axis
142 color space conversion (compressed images only):
144 +cp --conv-photometric
146 convert if YCbCr photometric interpretation (default)
147 +cl --conv-lossy
149 convert YCbCr to RGB if lossy JPEG
150 +cg --conv-guess
152 convert to RGB if YCbCr is guessed by library
153 +cgl --conv-guess-lossy
155 convert to RGB if lossy JPEG and YCbCr is
156 guessed by the underlying JPEG library
157 +ca --conv-always
159 always convert YCbCr to RGB
160 +cn --conv-never
162 never convert color space
163 modality LUT transformation:
165 -M --no-modality
167 ignore stored modality LUT transformation
168 +M --use-modality
170 use modality LUT transformation (default)
171 VOI LUT transformation:
173 -W --no-windowing
175 no VOI windowing (default)
176 +Wi --use-window [n]umber: integer
178 use the n-th VOI window from image file
179 +Wl --use-voi-lut [n]umber: integer
181 use the n-th VOI look up table from image file
182 +Wm --min-max-window
184 compute VOI window using min-max algorithm
185 +Wn --min-max-window-n
187 compute VOI window using min-max algorithm,
188 ignoring extreme values
189 +Wr --roi-min-max-window [l]eft [t]op [w]idth [h]eight: integer
191 compute ROI window using min-max algorithm,
192 region of interest is specified by l,t,w,h
193 +Wh --histogram-window [n]umber: integer
195 compute VOI window using Histogram algorithm,
196 ignoring n percent
197 +Ww --set-window [c]enter [w]idth: float
199 compute VOI window using center c and width w
200 +Wfl --linear-function
202 set VOI LUT function to LINEAR
203 +Wfs --sigmoid-function
205 set VOI LUT function to SIGMOID
206 presentation LUT transformation:
208 +Pid --identity-shape
210 set presentation LUT shape to IDENTITY
211 +Piv --inverse-shape
213 set presentation LUT shape to INVERSE
214 +Pod --lin-od-shape
216 set presentation LUT shape to LIN OD
217 overlay:
219 -O --no-overlays
221 do not display overlays
222 +O --display-overlay [n]umber: integer
224 display overlay n (0..16, 0=all, default: +O 0)
225 +Omr --ovl-replace
227 use overlay mode "Replace"
228 (default for Graphic overlays)
229 +Omt --ovl-threshold
231 use overlay mode "Threshold Replace"
232 +Omc --ovl-complement
234 use overlay mode "Complement"
235 +Omv --ovl-invert
237 use overlay mode "Invert Bitmap"
238 +Omi --ovl-roi
240 use overlay mode "Region of Interest"
241 (default for ROI overlays)
242 +Osf --set-foreground [d]ensity: float
244 set overlay foreground density (0..1, default: 1)
245 +Ost --set-threshold [d]ensity: float
247 set overlay threshold density (0..1, default: 0.5)
248 display LUT transformation:
250 +Dm --monitor-file [f]ilename: string
252 calibrate output according to monitor characteristics
253 defined in f
254 +Dp --printer-file [f]ilename: string
256 calibrate output according to printer characteristics
257 defined in f
258 +Da --ambient-light [a]mbient light: float
260 ambient light value (cd/m^2, default: file f)
261 +Di --illumination [i]llumination: float
263 illumination value (cd/m^2, default: file f)
264 +Dn --min-density [m]inimum optical density: float
266 Dmin value (default: off, only with +Dp)
267 +Dx --max-density [m]aximum optical density: float
269 Dmax value (default: off, only with +Dp)
270 +Dg --gsd-function
272 use GSDF for calibration (default for +Dm/+Dp)
273 +Dc --cielab-function
275 use CIELAB function for calibration
276 compatibility:
278 +Ma --accept-acr-nema
280 accept ACR-NEMA images without photometric
281 interpretation
282 +Mp --accept-palettes
284 accept incorrect palette attribute tags
285 (0028,111x) and (0028,121x)
286 +Mc --check-lut-depth
288 check 3rd value of the LUT descriptor, compare
289 with expected bit depth based on LUT data
290 +Mm --ignore-mlut-depth
292 ignore 3rd value of the modality LUT descriptor,
293 determine bits per table entry automatically
294 +Mv --ignore-vlut-depth
296 ignore 3rd value of the VOI LUT descriptor,
297 determine bits per table entry automatically
298 TIFF format:
300 +Tl --compr-lzw
302 LZW compression (default)
303 +Tr --compr-rle
305 RLE compression
306 +Tn --compr-none
308 uncompressed
309 +Pd --predictor-default
311 no LZW predictor (default)
312 +Pn --predictor-none
314 LZW predictor 1 (no prediction)
315 +Ph --predictor-horz
317 LZW predictor 2 (horizontal differencing)
318 +Rs --rows-per-strip [r]ows: integer (default: 0)
320 rows per strip, default 8K per strip
321 PNG format:
323 +il --interlace
325 create interlaced file (default)
326 -il --nointerlace
328 create non-interlaced file
329 +mf --meta-file
331 create PNG file meta information (default)
332 -mf --meta-none
334 no PNG file meta information
335 JPEG format:
337 +Jq --compr-quality [q]uality: integer (0..100, default: 90)
339 quality value for compression (in percent)
340 +Js4 --sample-444
342 4:4:4 sampling (no subsampling)
343 +Js2 --sample-422
345 4:2:2 subsampling (horizontal subsampling of
346 chroma components, default)
347 +Js1 --sample-411
349 4:1:1 subsampling (horizontal and vertical
350 subsampling of chroma components)
351 other transformations:
353 +G --grayscale
355 convert to grayscale if necessary
356 +P --change-polarity
358 change polarity (invert pixel output)
359 +C --clip-region [l]eft [t]op [w]idth [h]eight: integer
361 clip image region (l, t, w, h)
362 output options
364 general:
365 -im --image-info
367 print image details (requires verbose mode)
368 -o --no-output
370 do not create any output (useful with -im)
371 image format:
373 +op --write-raw-pnm
375 write 8-bit binary PGM/PPM (default for files)
376 +opb --write-8-bit-pnm
378 write 8-bit ASCII PGM/PPM (default for stdout)
379 +opw --write-16-bit-pnm
381 write 16-bit ASCII PGM/PPM
382 +opn --write-n-bit-pnm [n]umber: integer
384 write n-bit ASCII PGM/PPM (1..32)
385 +ob --write-bmp
387 write 8-bit (monochrome) or 24-bit (color) BMP
388 +obp --write-8-bit-bmp
390 write 8-bit palette BMP (monochrome only)
391 +obt --write-24-bit-bmp
393 write 24-bit truecolor BMP
394 +obr --write-32-bit-bmp
396 write 32-bit truecolor BMP
397 +ot --write-tiff
399 write 8-bit (monochrome) or 24-bit (color) TIFF
400 +on --write-png
402 write 8-bit (monochrome) or 24-bit (color) PNG
403 +oj --write-jpeg
405 write 8-bit lossy JPEG (baseline)
406
408 The following preferred interpolation algorithms can be selected using
409 the --interpolate option:
410 · 1 = free scaling algorithm with interpolation from pbmplus toolkit
412 · 2 = free scaling algorithm with interpolation from c't magazine
413 · 3 = magnification algorithm with bilinear interpolation from Eduard
414 Stanescu
415 · 4 = magnification algorithm with bicubic interpolation from Eduard
416 Stanescu
417 The --write-tiff option is only available when DCMTK has been
418 configured and compiled with support for the external libtiff TIFF
419 library. The availability of the TIFF compression options depends on
420 the libtiff configuration. In particular, the patented LZW algorithm
421 may not be available.
422 The --write-png option is only available when DCMTK has been configured
423 and compiled with support for the external libpng PNG library. Option
424 --interlace enables progressive image view while loading the PNG file.
425 Only a few applications take care of the meta info (TEXT) in a PNG
426 file.
428 dcmj2pnm supports the following transfer syntaxes for input (dcmfile-
429 in):
430 LittleEndianImplicitTransferSyntax 1.2.840.10008.1.2
431 LittleEndianExplicitTransferSyntax 1.2.840.10008.1.2.1
432 DeflatedExplicitVRLittleEndianTransferSyntax 1.2.840.10008.1.2.1.99 (*)
433 BigEndianExplicitTransferSyntax 1.2.840.10008.1.2.2
434 JPEGProcess1TransferSyntax 1.2.840.10008.1.2.4.50
435 JPEGProcess2_4TransferSyntax 1.2.840.10008.1.2.4.51
436 JPEGProcess6_8TransferSyntax 1.2.840.10008.1.2.4.53
437 JPEGProcess10_12TransferSyntax 1.2.840.10008.1.2.4.55
438 JPEGProcess14TransferSyntax 1.2.840.10008.1.2.4.57
439 JPEGProcess14SV1TransferSyntax 1.2.840.10008.1.2.4.70
440 RLELosslessTransferSyntax 1.2.840.10008.1.2.5
441 (*) if compiled with zlib support enabled
443 The level of logging output of the various command line tools and
444 underlying libraries can be specified by the user. By default, only
445 errors and warnings are written to the standard error stream. Using
446 option --verbose also informational messages like processing details
447 are reported. Option --debug can be used to get more details on the
448 internal activity, e.g. for debugging purposes. Other logging levels
449 can be selected using option --log-level. In --quiet mode only fatal
450 errors are reported. In such very severe error events, the application
451 will usually terminate. For more details on the different logging
452 levels, see documentation of module 'oflog'.
453 In case the logging output should be written to file (optionally with
454 logfile rotation), to syslog (Unix) or the event log (Windows) option
455 --log-config can be used. This configuration file also allows for
456 directing only certain messages to a particular output stream and for
457 filtering certain messages based on the module or application where
458 they are generated. An example configuration file is provided in
459 <etcdir>/logger.cfg).
461 All command line tools use the following notation for parameters:
462 square brackets enclose optional values (0-1), three trailing dots
463 indicate that multiple values are allowed (1-n), a combination of both
464 means 0 to n values.
465 Command line options are distinguished from parameters by a leading '+'
466 or '-' sign, respectively. Usually, order and position of command line
467 options are arbitrary (i.e. they can appear anywhere). However, if
468 options are mutually exclusive the rightmost appearance is used. This
469 behaviour conforms to the standard evaluation rules of common Unix
470 shells.
471 In addition, one or more command files can be specified using an '@'
472 sign as a prefix to the filename (e.g. @command.txt). Such a command
473 argument is replaced by the content of the corresponding text file
474 (multiple whitespaces are treated as a single separator unless they
475 appear between two quotation marks) prior to any further evaluation.
476 Please note that a command file cannot contain another command file.
477 This simple but effective approach allows to summarize common
478 combinations of options/parameters and avoids longish and confusing
479 command lines (an example is provided in file <datadir>/dumppat.txt).
481 The dcmj2pnm utility will attempt to load DICOM data dictionaries
482 specified in the DCMDICTPATH environment variable. By default, i.e. if
483 the DCMDICTPATH environment variable is not set, the file
484 <datadir>/dicom.dic will be loaded unless the dictionary is built into
485 the application (default for Windows).
486 The default behaviour should be preferred and the DCMDICTPATH
487 environment variable only used when alternative data dictionaries are
488 required. The DCMDICTPATH environment variable has the same format as
489 the Unix shell PATH variable in that a colon (':') separates entries.
490 On Windows systems, a semicolon (';') is used as a separator. The data
491 dictionary code will attempt to load each file specified in the
492 DCMDICTPATH environment variable. It is an error if no data dictionary
493 can be loaded.
495 <datadir>/camera.lut - sample characteristics file of a camera
496 <datadir>/monitor.lut - sample characteristics file of a monitor
497 <datadir>/printer.lut - sample characteristics file of a printer
498 <datadir>/scanner.lut - sample characteristics file of a scanner
500 dcm2pnm(1), img2dcm(1)
502 Copyright (C) 2001-2010 by OFFIS e.V., Escherweg 2, 26121 Oldenburg,
503 Germany.
504Version 3.6.0 6 Jan 2011 dcmj2pnm(1)