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 (JPEG 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 workaround options for incorrect encodings (JPEG compressed images only):
166 +w6 --workaround-pred6
168 enable workaround for JPEG lossless images
169 with overflow in predictor 6
170 # DICOM images with 16 bits/pixel have been observed "in the wild"
172 # that are compressed with lossless JPEG and need special handling
173 # because the encoder produced an 16-bit integer overflow in predictor
174 # 6, which needs to be compensated (reproduced) during decompression.
175 # This flag enables a correct decompression of such faulty images, but
176 # at the same time will cause an incorrect decompression of correctly
177 # compressed images. Use with care.
178 +wi --workaround-incpl
180 enable workaround for incomplete JPEG data
181 # This option causes dcmj2pnm to ignore incomplete JPEG data
183 # at the end of a compressed fragment and to start decompressing
184 # the next frame from the next fragment (if any). This permits
185 # images with incomplete JPEG data to be decoded.
186 +wc --workaround-cornell
188 enable workaround for 16-bit JPEG lossless
189 Cornell images with Huffman table overflow
190 # One of the first open-source implementations of lossless JPEG
192 # compression, the "Cornell" library, has a well-known bug that leads
193 # to invalid values in the Huffmann table when images with 16 bit/sample
194 # are compressed. This flag enables a workaround that permits such
195 # images to be decoded correctly.
196 modality LUT transformation:
198 -M --no-modality
200 ignore stored modality LUT transformation
201 +M --use-modality
203 use modality LUT transformation (default)
204 VOI LUT transformation:
206 -W --no-windowing
208 no VOI windowing (default)
209 +Wi --use-window [n]umber: integer
211 use the n-th VOI window from image file
212 +Wl --use-voi-lut [n]umber: integer
214 use the n-th VOI look up table from image file
215 +Wm --min-max-window
217 compute VOI window using min-max algorithm
218 +Wn --min-max-window-n
220 compute VOI window using min-max algorithm,
221 ignoring extreme values
222 +Wr --roi-min-max-window [l]eft [t]op [w]idth [h]eight: integer
224 compute ROI window using min-max algorithm,
225 region of interest is specified by l,t,w,h
226 +Wh --histogram-window [n]umber: integer
228 compute VOI window using Histogram algorithm,
229 ignoring n percent
230 +Ww --set-window [c]enter [w]idth: float
232 compute VOI window using center c and width w
233 +Wfl --linear-function
235 set VOI LUT function to LINEAR
236 +Wfs --sigmoid-function
238 set VOI LUT function to SIGMOID
239 presentation LUT transformation:
241 +Pid --identity-shape
243 set presentation LUT shape to IDENTITY
244 +Piv --inverse-shape
246 set presentation LUT shape to INVERSE
247 +Pod --lin-od-shape
249 set presentation LUT shape to LIN OD
250 overlay:
252 -O --no-overlays
254 do not display overlays
255 +O --display-overlay [n]umber: integer
257 display overlay n (0..16, 0=all, default: +O 0)
258 +Omr --ovl-replace
260 use overlay mode "Replace"
261 (default for Graphic overlays)
262 +Omt --ovl-threshold
264 use overlay mode "Threshold Replace"
265 +Omc --ovl-complement
267 use overlay mode "Complement"
268 +Omv --ovl-invert
270 use overlay mode "Invert Bitmap"
271 +Omi --ovl-roi
273 use overlay mode "Region of Interest"
274 (default for ROI overlays)
275 +Osf --set-foreground [d]ensity: float
277 set overlay foreground density (0..1, default: 1)
278 +Ost --set-threshold [d]ensity: float
280 set overlay threshold density (0..1, default: 0.5)
281 display LUT transformation:
283 +Dm --monitor-file [f]ilename: string
285 calibrate output according to monitor characteristics
286 defined in f
287 +Dp --printer-file [f]ilename: string
289 calibrate output according to printer characteristics
290 defined in f
291 +Da --ambient-light [a]mbient light: float
293 ambient light value (cd/m^2, default: file f)
294 +Di --illumination [i]llumination: float
296 illumination value (cd/m^2, default: file f)
297 +Dn --min-density [m]inimum optical density: float
299 Dmin value (default: off, only with +Dp)
300 +Dx --max-density [m]aximum optical density: float
302 Dmax value (default: off, only with +Dp)
303 +Dg --gsd-function
305 use GSDF for calibration (default for +Dm/+Dp)
306 +Dc --cielab-function
308 use CIELAB function for calibration
309 compatibility:
311 +Ma --accept-acr-nema
313 accept ACR-NEMA images without photometric
314 interpretation
315 +Mp --accept-palettes
317 accept incorrect palette attribute tags
318 (0028,111x) and (0028,121x)
319 +Mc --check-lut-depth
321 check 3rd value of the LUT descriptor, compare
322 with expected bit depth based on LUT data
323 +Mm --ignore-mlut-depth
325 ignore 3rd value of the modality LUT descriptor,
326 determine bits per table entry automatically
327 +Mv --ignore-vlut-depth
329 ignore 3rd value of the VOI LUT descriptor,
330 determine bits per table entry automatically
331 TIFF format:
333 +Tl --compr-lzw
335 LZW compression (default)
336 +Tr --compr-rle
338 RLE compression
339 +Tn --compr-none
341 uncompressed
342 +Pd --predictor-default
344 no LZW predictor (default)
345 +Pn --predictor-none
347 LZW predictor 1 (no prediction)
348 +Ph --predictor-horz
350 LZW predictor 2 (horizontal differencing)
351 +Rs --rows-per-strip [r]ows: integer (default: 0)
353 rows per strip, default 8K per strip
354 PNG format:
356 +il --interlace
358 create interlaced file (default)
359 -il --nointerlace
361 create non-interlaced file
362 +mf --meta-file
364 create PNG file meta information (default)
365 -mf --meta-none
367 no PNG file meta information
368 JPEG format:
370 +Jq --compr-quality [q]uality: integer (0..100, default: 90)
372 quality value for compression (in percent)
373 +Js4 --sample-444
375 4:4:4 sampling (no subsampling)
376 +Js2 --sample-422
378 4:2:2 subsampling (horizontal subsampling of
379 chroma components, default)
380 +Js1 --sample-411
382 4:1:1 subsampling (horizontal and vertical
383 subsampling of chroma components)
384 other transformations:
386 +G --grayscale
388 convert to grayscale if necessary
389 +P --change-polarity
391 change polarity (invert pixel output)
392 +C --clip-region [l]eft [t]op [w]idth [h]eight: integer
394 clip image region (l, t, w, h)
395 output options
397 general:
398 -im --image-info
400 print image details (requires verbose mode)
401 -o --no-output
403 do not create any output (useful with -im)
404 filename generation (only with --frame-range or --all-frames):
406 +Fc --use-frame-counter
408 use 0-based counter for filenames (default)
409 +Fn --use-frame-number
411 use absolute frame number for filenames
412 image format:
414 +op --write-raw-pnm
416 write 8-bit binary PGM/PPM (default for files)
417 +opb --write-8-bit-pnm
419 write 8-bit ASCII PGM/PPM (default for stdout)
420 +opw --write-16-bit-pnm
422 write 16-bit ASCII PGM/PPM
423 +opn --write-n-bit-pnm [n]umber: integer
425 write n-bit ASCII PGM/PPM (1..32)
426 +ob --write-bmp
428 write 8-bit (monochrome) or 24-bit (color) BMP
429 +obp --write-8-bit-bmp
431 write 8-bit palette BMP (monochrome only)
432 +obt --write-24-bit-bmp
434 write 24-bit truecolor BMP
435 +obr --write-32-bit-bmp
437 write 32-bit truecolor BMP
438 +ot --write-tiff
440 write 8-bit (monochrome) or 24-bit (color) TIFF
441 +on --write-png
443 write 8-bit (monochrome) or 24-bit (color) PNG
444 +on2 --write-16-bit-png
446 write 16-bit (monochrome) or 48-bit (color) PNG
447 +oj --write-jpeg
449 write 8-bit lossy JPEG (baseline)
450
452 The following preferred interpolation algorithms can be selected using
453 the --interpolate option:
454 • 1 = free scaling algorithm with interpolation from pbmplus toolkit
456 • 2 = free scaling algorithm with interpolation from c't magazine
457 • 3 = magnification algorithm with bilinear interpolation from Eduard
458 Stanescu
459 • 4 = magnification algorithm with bicubic interpolation from Eduard
460 Stanescu
461 The --write-tiff option is only available when DCMTK has been
462 configured and compiled with support for the external libtiff TIFF
463 library. The availability of the TIFF compression options depends on
464 the libtiff configuration. In particular, the patented LZW algorithm
465 may not be available.
466 The --write-png option is only available when DCMTK has been configured
467 and compiled with support for the external libpng PNG library. Option
468 --interlace enables progressive image view while loading the PNG file.
469 Only a few applications take care of the meta info (TEXT) in a PNG
470 file.
472 dcmj2pnm supports the following transfer syntaxes for input (dcmfile-
473 in):
474 LittleEndianImplicitTransferSyntax 1.2.840.10008.1.2
475 LittleEndianExplicitTransferSyntax 1.2.840.10008.1.2.1
476 DeflatedExplicitVRLittleEndianTransferSyntax 1.2.840.10008.1.2.1.99 (*)
477 BigEndianExplicitTransferSyntax 1.2.840.10008.1.2.2
478 JPEGProcess1TransferSyntax 1.2.840.10008.1.2.4.50
479 JPEGProcess2_4TransferSyntax 1.2.840.10008.1.2.4.51
480 JPEGProcess6_8TransferSyntax 1.2.840.10008.1.2.4.53
481 JPEGProcess10_12TransferSyntax 1.2.840.10008.1.2.4.55
482 JPEGProcess14TransferSyntax 1.2.840.10008.1.2.4.57
483 JPEGProcess14SV1TransferSyntax 1.2.840.10008.1.2.4.70
484 RLELosslessTransferSyntax 1.2.840.10008.1.2.5
485 (*) if compiled with zlib support enabled
487 The level of logging output of the various command line tools and
488 underlying libraries can be specified by the user. By default, only
489 errors and warnings are written to the standard error stream. Using
490 option --verbose also informational messages like processing details
491 are reported. Option --debug can be used to get more details on the
492 internal activity, e.g. for debugging purposes. Other logging levels
493 can be selected using option --log-level. In --quiet mode only fatal
494 errors are reported. In such very severe error events, the application
495 will usually terminate. For more details on the different logging
496 levels, see documentation of module 'oflog'.
497 In case the logging output should be written to file (optionally with
498 logfile rotation), to syslog (Unix) or the event log (Windows) option
499 --log-config can be used. This configuration file also allows for
500 directing only certain messages to a particular output stream and for
501 filtering certain messages based on the module or application where
502 they are generated. An example configuration file is provided in
503 <etcdir>/logger.cfg.
505 All command line tools use the following notation for parameters:
506 square brackets enclose optional values (0-1), three trailing dots
507 indicate that multiple values are allowed (1-n), a combination of both
508 means 0 to n values.
509 Command line options are distinguished from parameters by a leading '+'
510 or '-' sign, respectively. Usually, order and position of command line
511 options are arbitrary (i.e. they can appear anywhere). However, if
512 options are mutually exclusive the rightmost appearance is used. This
513 behavior conforms to the standard evaluation rules of common Unix
514 shells.
515 In addition, one or more command files can be specified using an '@'
516 sign as a prefix to the filename (e.g. @command.txt). Such a command
517 argument is replaced by the content of the corresponding text file
518 (multiple whitespaces are treated as a single separator unless they
519 appear between two quotation marks) prior to any further evaluation.
520 Please note that a command file cannot contain another command file.
521 This simple but effective approach allows one to summarize common
522 combinations of options/parameters and avoids longish and confusing
523 command lines (an example is provided in file <datadir>/dumppat.txt).
525 The dcmj2pnm utility will attempt to load DICOM data dictionaries
526 specified in the DCMDICTPATH environment variable. By default, i.e. if
527 the DCMDICTPATH environment variable is not set, the file
528 <datadir>/dicom.dic will be loaded unless the dictionary is built into
529 the application (default for Windows).
530 The default behavior should be preferred and the DCMDICTPATH
531 environment variable only used when alternative data dictionaries are
532 required. The DCMDICTPATH environment variable has the same format as
533 the Unix shell PATH variable in that a colon (':') separates entries.
534 On Windows systems, a semicolon (';') is used as a separator. The data
535 dictionary code will attempt to load each file specified in the
536 DCMDICTPATH environment variable. It is an error if no data dictionary
537 can be loaded.
539 <datadir>/camera.lut - sample characteristics file of a camera
540 <datadir>/monitor.lut - sample characteristics file of a monitor
541 <datadir>/printer.lut - sample characteristics file of a printer
542 <datadir>/scanner.lut - sample characteristics file of a scanner
544 dcm2pnm(1), img2dcm(1)
546 Copyright (C) 2001-2018 by OFFIS e.V., Escherweg 2, 26121 Oldenburg,
547 Germany.
548Version 3.6.4 Thu Nov 29 2018 dcmj2pnm(1)