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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10 dcmj2pnm [options] dcmfile-in [bitmap-out]
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13 The dcmj2pnm utility reads a DICOM image, converts the pixel data
14 according to the selected image processing options and writes back an
15 image in the well-known PGM/PPM (portable gray map / portable pix map),
16 PNG, TIFF, JPEG (Joint Photographic Experts Group) or Windows BMP
17 format. This utility supports uncompressed as well as JPEG and RLE
18 compressed DICOM images.
19
21 dcmfile-in DICOM input filename to be converted
22 bitmap-out output filename to be written (default: stdout)
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26 general options
27 -h --help
28 print this help text and exit
29 --version
31 print version information and exit
32 --arguments
34 print expanded command line arguments
35 -q --quiet
37 quiet mode, print no warnings and errors
38 -v --verbose
40 verbose mode, print processing details
41 -d --debug
43 debug mode, print debug information
44 -ll --log-level [l]evel: string constant
46 (fatal, error, warn, info, debug, trace)
47 use level l for the logger
48 -lc --log-config [f]ilename: string
50 use config file f for the logger
51 input options
53 input file format:
54 +f --read-file
56 read file format or data set (default)
57 +fo --read-file-only
59 read file format only
60 -f --read-dataset
62 read data set without file meta information
63 input transfer syntax:
65 -t= --read-xfer-auto
67 use TS recognition (default)
68 -td --read-xfer-detect
70 ignore TS specified in the file meta header
71 -te --read-xfer-little
73 read with explicit VR little endian TS
74 -tb --read-xfer-big
76 read with explicit VR big endian TS
77 -ti --read-xfer-implicit
79 read with implicit VR little endian TS
80 image processing options
82 frame selection:
83 +F --frame [n]umber: integer
85 select specified frame (default: 1)
86 +Fr --frame-range [n]umber [c]ount: integer
88 select c frames beginning with frame n
89 +Fa --all-frames
91 select all frames
92 rotation:
94 +Rl --rotate-left
96 rotate image left (-90 degrees)
97 +Rr --rotate-right
99 rotate image right (+90 degrees)
100 +Rtd --rotate-top-down
102 rotate image top-down (180 degrees)
103 flipping:
105 +Lh --flip-horizontally
107 flip image horizontally
108 +Lv --flip-vertically
110 flip image vertically
111 +Lhv --flip-both-axes
113 flip image horizontally and vertically
114 scaling:
116 +a --recognize-aspect
118 recognize pixel aspect ratio (default)
119 -a --ignore-aspect
121 ignore pixel aspect ratio when scaling
122 +i --interpolate [n]umber of algorithm: integer
124 use interpolation when scaling (1..4, default: 1)
125 -i --no-interpolation
127 no interpolation when scaling
128 -S --no-scaling
130 no scaling, ignore pixel aspect ratio (default)
131 +Sxf --scale-x-factor [f]actor: float
133 scale x axis by factor, auto-compute y axis
134 +Syf --scale-y-factor [f]actor: float
136 scale y axis by factor, auto-compute x axis
137 +Sxv --scale-x-size [n]umber: integer
139 scale x axis to n pixels, auto-compute y axis
140 +Syv --scale-y-size [n]umber: integer
142 scale y axis to n pixels, auto-compute x axis
143 color space conversion (compressed images only):
145 +cp --conv-photometric
147 convert if YCbCr photometric interpretation (default)
148 +cl --conv-lossy
150 convert YCbCr to RGB if lossy JPEG
151 +cg --conv-guess
153 convert to RGB if YCbCr is guessed by library
154 +cgl --conv-guess-lossy
156 convert to RGB if lossy JPEG and YCbCr is
157 guessed by the underlying JPEG library
158 +ca --conv-always
160 always convert YCbCr to RGB
161 +cn --conv-never
163 never convert color space
164 modality LUT transformation:
166 -M --no-modality
168 ignore stored modality LUT transformation
169 +M --use-modality
171 use modality LUT transformation (default)
172 VOI LUT transformation:
174 -W --no-windowing
176 no VOI windowing (default)
177 +Wi --use-window [n]umber: integer
179 use the n-th VOI window from image file
180 +Wl --use-voi-lut [n]umber: integer
182 use the n-th VOI look up table from image file
183 +Wm --min-max-window
185 compute VOI window using min-max algorithm
186 +Wn --min-max-window-n
188 compute VOI window using min-max algorithm,
189 ignoring extreme values
190 +Wr --roi-min-max-window [l]eft [t]op [w]idth [h]eight: integer
192 compute ROI window using min-max algorithm,
193 region of interest is specified by l,t,w,h
194 +Wh --histogram-window [n]umber: integer
196 compute VOI window using Histogram algorithm,
197 ignoring n percent
198 +Ww --set-window [c]enter [w]idth: float
200 compute VOI window using center c and width w
201 +Wfl --linear-function
203 set VOI LUT function to LINEAR
204 +Wfs --sigmoid-function
206 set VOI LUT function to SIGMOID
207 presentation LUT transformation:
209 +Pid --identity-shape
211 set presentation LUT shape to IDENTITY
212 +Piv --inverse-shape
214 set presentation LUT shape to INVERSE
215 +Pod --lin-od-shape
217 set presentation LUT shape to LIN OD
218 overlay:
220 -O --no-overlays
222 do not display overlays
223 +O --display-overlay [n]umber: integer
225 display overlay n (0..16, 0=all, default: +O 0)
226 +Omr --ovl-replace
228 use overlay mode "Replace"
229 (default for Graphic overlays)
230 +Omt --ovl-threshold
232 use overlay mode "Threshold Replace"
233 +Omc --ovl-complement
235 use overlay mode "Complement"
236 +Omv --ovl-invert
238 use overlay mode "Invert Bitmap"
239 +Omi --ovl-roi
241 use overlay mode "Region of Interest"
242 (default for ROI overlays)
243 +Osf --set-foreground [d]ensity: float
245 set overlay foreground density (0..1, default: 1)
246 +Ost --set-threshold [d]ensity: float
248 set overlay threshold density (0..1, default: 0.5)
249 display LUT transformation:
251 +Dm --monitor-file [f]ilename: string
253 calibrate output according to monitor characteristics
254 defined in f
255 +Dp --printer-file [f]ilename: string
257 calibrate output according to printer characteristics
258 defined in f
259 +Da --ambient-light [a]mbient light: float
261 ambient light value (cd/m^2, default: file f)
262 +Di --illumination [i]llumination: float
264 illumination value (cd/m^2, default: file f)
265 +Dn --min-density [m]inimum optical density: float
267 Dmin value (default: off, only with +Dp)
268 +Dx --max-density [m]aximum optical density: float
270 Dmax value (default: off, only with +Dp)
271 +Dg --gsd-function
273 use GSDF for calibration (default for +Dm/+Dp)
274 +Dc --cielab-function
276 use CIELAB function for calibration
277 compatibility:
279 +Ma --accept-acr-nema
281 accept ACR-NEMA images without photometric
282 interpretation
283 +Mp --accept-palettes
285 accept incorrect palette attribute tags
286 (0028,111x) and (0028,121x)
287 +Mc --check-lut-depth
289 check 3rd value of the LUT descriptor, compare
290 with expected bit depth based on LUT data
291 +Mm --ignore-mlut-depth
293 ignore 3rd value of the modality LUT descriptor,
294 determine bits per table entry automatically
295 +Mv --ignore-vlut-depth
297 ignore 3rd value of the VOI LUT descriptor,
298 determine bits per table entry automatically
299 TIFF format:
301 +Tl --compr-lzw
303 LZW compression (default)
304 +Tr --compr-rle
306 RLE compression
307 +Tn --compr-none
309 uncompressed
310 +Pd --predictor-default
312 no LZW predictor (default)
313 +Pn --predictor-none
315 LZW predictor 1 (no prediction)
316 +Ph --predictor-horz
318 LZW predictor 2 (horizontal differencing)
319 +Rs --rows-per-strip [r]ows: integer (default: 0)
321 rows per strip, default 8K per strip
322 PNG format:
324 +il --interlace
326 create interlaced file (default)
327 -il --nointerlace
329 create non-interlaced file
330 +mf --meta-file
332 create PNG file meta information (default)
333 -mf --meta-none
335 no PNG file meta information
336 JPEG format:
338 +Jq --compr-quality [q]uality: integer (0..100, default: 90)
340 quality value for compression (in percent)
341 +Js4 --sample-444
343 4:4:4 sampling (no subsampling)
344 +Js2 --sample-422
346 4:2:2 subsampling (horizontal subsampling of
347 chroma components, default)
348 +Js1 --sample-411
350 4:1:1 subsampling (horizontal and vertical
351 subsampling of chroma components)
352 other transformations:
354 +G --grayscale
356 convert to grayscale if necessary
357 +P --change-polarity
359 change polarity (invert pixel output)
360 +C --clip-region [l]eft [t]op [w]idth [h]eight: integer
362 clip image region (l, t, w, h)
363 output options
365 general:
366 -im --image-info
368 print image details (requires verbose mode)
369 -o --no-output
371 do not create any output (useful with -im)
372 filename generation (only with --frame-range or --all-frames):
374 +Fc --use-frame-counter
376 use 0-based counter for filenames (default)
377 +Fn --use-frame-number
379 use absolute frame number for filenames
380 image format:
382 +op --write-raw-pnm
384 write 8-bit binary PGM/PPM (default for files)
385 +opb --write-8-bit-pnm
387 write 8-bit ASCII PGM/PPM (default for stdout)
388 +opw --write-16-bit-pnm
390 write 16-bit ASCII PGM/PPM
391 +opn --write-n-bit-pnm [n]umber: integer
393 write n-bit ASCII PGM/PPM (1..32)
394 +ob --write-bmp
396 write 8-bit (monochrome) or 24-bit (color) BMP
397 +obp --write-8-bit-bmp
399 write 8-bit palette BMP (monochrome only)
400 +obt --write-24-bit-bmp
402 write 24-bit truecolor BMP
403 +obr --write-32-bit-bmp
405 write 32-bit truecolor BMP
406 +ot --write-tiff
408 write 8-bit (monochrome) or 24-bit (color) TIFF
409 +on --write-png
411 write 8-bit (monochrome) or 24-bit (color) PNG
412 +on2 --write-16-bit-png
414 write 16-bit (monochrome) or 48-bit (color) PNG
415 +oj --write-jpeg
417 write 8-bit lossy JPEG (baseline)
418
420 The following preferred interpolation algorithms can be selected using
421 the --interpolate option:
422 · 1 = free scaling algorithm with interpolation from pbmplus toolkit
424 · 2 = free scaling algorithm with interpolation from c't magazine
425 · 3 = magnification algorithm with bilinear interpolation from Eduard
426 Stanescu
427 · 4 = magnification algorithm with bicubic interpolation from Eduard
428 Stanescu
429 The --write-tiff option is only available when DCMTK has been
430 configured and compiled with support for the external libtiff TIFF
431 library. The availability of the TIFF compression options depends on
432 the libtiff configuration. In particular, the patented LZW algorithm
433 may not be available.
434 The --write-png option is only available when DCMTK has been configured
435 and compiled with support for the external libpng PNG library. Option
436 --interlace enables progressive image view while loading the PNG file.
437 Only a few applications take care of the meta info (TEXT) in a PNG
438 file.
440 dcmj2pnm supports the following transfer syntaxes for input (dcmfile-
441 in):
442 LittleEndianImplicitTransferSyntax 1.2.840.10008.1.2
443 LittleEndianExplicitTransferSyntax 1.2.840.10008.1.2.1
444 DeflatedExplicitVRLittleEndianTransferSyntax 1.2.840.10008.1.2.1.99 (*)
445 BigEndianExplicitTransferSyntax 1.2.840.10008.1.2.2
446 JPEGProcess1TransferSyntax 1.2.840.10008.1.2.4.50
447 JPEGProcess2_4TransferSyntax 1.2.840.10008.1.2.4.51
448 JPEGProcess6_8TransferSyntax 1.2.840.10008.1.2.4.53
449 JPEGProcess10_12TransferSyntax 1.2.840.10008.1.2.4.55
450 JPEGProcess14TransferSyntax 1.2.840.10008.1.2.4.57
451 JPEGProcess14SV1TransferSyntax 1.2.840.10008.1.2.4.70
452 RLELosslessTransferSyntax 1.2.840.10008.1.2.5
453 (*) if compiled with zlib support enabled
455 The level of logging output of the various command line tools and
456 underlying libraries can be specified by the user. By default, only
457 errors and warnings are written to the standard error stream. Using
458 option --verbose also informational messages like processing details
459 are reported. Option --debug can be used to get more details on the
460 internal activity, e.g. for debugging purposes. Other logging levels
461 can be selected using option --log-level. In --quiet mode only fatal
462 errors are reported. In such very severe error events, the application
463 will usually terminate. For more details on the different logging
464 levels, see documentation of module 'oflog'.
465 In case the logging output should be written to file (optionally with
466 logfile rotation), to syslog (Unix) or the event log (Windows) option
467 --log-config can be used. This configuration file also allows for
468 directing only certain messages to a particular output stream and for
469 filtering certain messages based on the module or application where
470 they are generated. An example configuration file is provided in
471 <etcdir>/logger.cfg.
473 All command line tools use the following notation for parameters:
474 square brackets enclose optional values (0-1), three trailing dots
475 indicate that multiple values are allowed (1-n), a combination of both
476 means 0 to n values.
477 Command line options are distinguished from parameters by a leading '+'
478 or '-' sign, respectively. Usually, order and position of command line
479 options are arbitrary (i.e. they can appear anywhere). However, if
480 options are mutually exclusive the rightmost appearance is used. This
481 behavior conforms to the standard evaluation rules of common Unix
482 shells.
483 In addition, one or more command files can be specified using an '@'
484 sign as a prefix to the filename (e.g. @command.txt). Such a command
485 argument is replaced by the content of the corresponding text file
486 (multiple whitespaces are treated as a single separator unless they
487 appear between two quotation marks) prior to any further evaluation.
488 Please note that a command file cannot contain another command file.
489 This simple but effective approach allows one to summarize common
490 combinations of options/parameters and avoids longish and confusing
491 command lines (an example is provided in file <datadir>/dumppat.txt).
493 The dcmj2pnm utility will attempt to load DICOM data dictionaries
494 specified in the DCMDICTPATH environment variable. By default, i.e. if
495 the DCMDICTPATH environment variable is not set, the file
496 <datadir>/dicom.dic will be loaded unless the dictionary is built into
497 the application (default for Windows).
498 The default behavior should be preferred and the DCMDICTPATH
499 environment variable only used when alternative data dictionaries are
500 required. The DCMDICTPATH environment variable has the same format as
501 the Unix shell PATH variable in that a colon (':') separates entries.
502 On Windows systems, a semicolon (';') is used as a separator. The data
503 dictionary code will attempt to load each file specified in the
504 DCMDICTPATH environment variable. It is an error if no data dictionary
505 can be loaded.
507 <datadir>/camera.lut - sample characteristics file of a camera
508 <datadir>/monitor.lut - sample characteristics file of a monitor
509 <datadir>/printer.lut - sample characteristics file of a printer
510 <datadir>/scanner.lut - sample characteristics file of a scanner
512 dcm2pnm(1), img2dcm(1)
514 Copyright (C) 2001-2014 by OFFIS e.V., Escherweg 2, 26121 Oldenburg,
515 Germany.
516Version 3.6.2 Fri Jul 14 2017 dcmj2pnm(1)