dcmj2pnm [options] dcmfile-in [bitmap-out]
The dcmj2pnm utility reads a DICOM image, converts the pixel data according to the selected image processing options and writes back an image in the well-known PGM/PPM (portable gray map / portable pix map), PNG, TIFF, JPEG (Joint Photographic Experts Group) or Windows BMP format. This utility supports uncompressed as well as JPEG and RLE compressed DICOM images.
dcmfile-in DICOM input filename to be converted bitmap-out output filename to be written (default: stdout)
-h --help print this help text and exit --version print version information and exit --arguments print expanded command line arguments -q --quiet quiet mode, print no warnings and errors -v --verbose verbose mode, print processing details -d --debug debug mode, print debug information -ll --log-level [l]evel: string constant (fatal, error, warn, info, debug, trace) use level l for the logger -lc --log-config [f]ilename: string use config file f for the logger
input file format: +f --read-file read file format or data set (default) +fo --read-file-only read file format only -f --read-dataset read data set without file meta information input transfer syntax: -t= --read-xfer-auto use TS recognition (default) -td --read-xfer-detect ignore TS specified in the file meta header -te --read-xfer-little read with explicit VR little endian TS -tb --read-xfer-big read with explicit VR big endian TS -ti --read-xfer-implicit read with implicit VR little endian TS
frame selection: +F --frame [n]umber: integer select specified frame (default: 1) +Fr --frame-range [n]umber [c]ount: integer select c frames beginning with frame n +Fa --all-frames select all frames rotation: +Rl --rotate-left rotate image left (-90 degrees) +Rr --rotate-right rotate image right (+90 degrees) +Rtd --rotate-top-down rotate image top-down (180 degrees) flipping: +Lh --flip-horizontally flip image horizontally +Lv --flip-vertically flip image vertically +Lhv --flip-both-axes flip image horizontally and vertically scaling: +a --recognize-aspect recognize pixel aspect ratio when scaling (default) -a --ignore-aspect ignore pixel aspect ratio when scaling +i --interpolate [n]umber of algorithm: integer use interpolation when scaling (1..4, default: 1) -i --no-interpolation no interpolation when scaling -S --no-scaling no scaling, ignore pixel aspect ratio (default) +Sxf --scale-x-factor [f]actor: float scale x axis by factor, auto-compute y axis +Syf --scale-y-factor [f]actor: float scale y axis by factor, auto-compute x axis +Sxv --scale-x-size [n]umber: integer scale x axis to n pixels, auto-compute y axis +Syv --scale-y-size [n]umber: integer scale y axis to n pixels, auto-compute x axis color space conversion (JPEG compressed images only): +cp --conv-photometric convert if YCbCr photometric interpretation (default) +cl --conv-lossy convert YCbCr to RGB if lossy JPEG +cg --conv-guess convert to RGB if YCbCr is guessed by library +cgl --conv-guess-lossy convert to RGB if lossy JPEG and YCbCr is guessed by the underlying JPEG library +ca --conv-always always convert YCbCr to RGB +cn --conv-never never convert color space workaround options for incorrect encodings (JPEG compressed images only): +w6 --workaround-pred6 enable workaround for JPEG lossless images with overflow in predictor 6 # DICOM images with 16 bits/pixel have been observed "in the wild" # that are compressed with lossless JPEG and need special handling # because the encoder produced an 16-bit integer overflow in predictor # 6, which needs to be compensated (reproduced) during decompression. # This flag enables a correct decompression of such faulty images, but # at the same time will cause an incorrect decompression of correctly # compressed images. Use with care. +wi --workaround-incpl enable workaround for incomplete JPEG data # This option causes dcmj2pnm to ignore incomplete JPEG data # at the end of a compressed fragment and to start decompressing # the next frame from the next fragment (if any). This permits # images with incomplete JPEG data to be decoded. +wc --workaround-cornell enable workaround for 16-bit JPEG lossless Cornell images with Huffman table overflow # One of the first open-source implementations of lossless JPEG # compression, the "Cornell" library, has a well-known bug that leads # to invalid values in the Huffmann table when images with 16 bit/sample # are compressed. This flag enables a workaround that permits such # images to be decoded correctly. modality LUT transformation: -M --no-modality ignore stored modality LUT transformation +M --use-modality use modality LUT transformation (default) VOI LUT transformation: -W --no-windowing no VOI windowing (default) +Wi --use-window [n]umber: integer use the n-th VOI window from image file +Wl --use-voi-lut [n]umber: integer use the n-th VOI look up table from image file +Wm --min-max-window compute VOI window using min-max algorithm +Wn --min-max-window-n compute VOI window using min-max algorithm, ignoring extreme values +Wr --roi-min-max-window [l]eft [t]op [w]idth [h]eight: integer compute ROI window using min-max algorithm, region of interest is specified by l,t,w,h +Wh --histogram-window [n]umber: integer compute VOI window using Histogram algorithm, ignoring n percent +Ww --set-window [c]enter [w]idth: float compute VOI window using center c and width w +Wfl --linear-function set VOI LUT function to LINEAR +Wfs --sigmoid-function set VOI LUT function to SIGMOID presentation LUT transformation: +Pid --identity-shape set presentation LUT shape to IDENTITY +Piv --inverse-shape set presentation LUT shape to INVERSE +Pod --lin-od-shape set presentation LUT shape to LIN OD overlay: -O --no-overlays do not display overlays +O --display-overlay [n]umber: integer display overlay n (0..16, 0=all, default: +O 0) +Omr --ovl-replace use overlay mode "Replace" (default for Graphic overlays) +Omt --ovl-threshold use overlay mode "Threshold Replace" +Omc --ovl-complement use overlay mode "Complement" +Omv --ovl-invert use overlay mode "Invert Bitmap" +Omi --ovl-roi use overlay mode "Region of Interest" (default for ROI overlays) +Osf --set-foreground [d]ensity: float set overlay foreground density (0..1, default: 1) +Ost --set-threshold [d]ensity: float set overlay threshold density (0..1, default: 0.5) display LUT transformation: +Dm --monitor-file [f]ilename: string calibrate output according to monitor characteristics defined in f +Dp --printer-file [f]ilename: string calibrate output according to printer characteristics defined in f +Da --ambient-light [a]mbient light: float ambient light value (cd/m^2, default: file f) +Di --illumination [i]llumination: float illumination value (cd/m^2, default: file f) +Dn --min-density [m]inimum optical density: float Dmin value (default: off, only with +Dp) +Dx --max-density [m]aximum optical density: float Dmax value (default: off, only with +Dp) +Dg --gsd-function use GSDF for calibration (default for +Dm/+Dp) +Dc --cielab-function use CIELAB function for calibration compatibility: +Ma --accept-acr-nema accept ACR-NEMA images without photometric interpretation +Mp --accept-palettes accept incorrect palette attribute tags (0028,111x) and (0028,121x) +Mc --check-lut-depth check 3rd value of the LUT descriptor, compare with expected bit depth based on LUT data +Mm --ignore-mlut-depth ignore 3rd value of the modality LUT descriptor, determine bits per table entry automatically +Mv --ignore-vlut-depth ignore 3rd value of the VOI LUT descriptor, determine bits per table entry automatically TIFF format: +Tl --compr-lzw LZW compression (default) +Tr --compr-rle RLE compression +Tn --compr-none uncompressed +Pd --predictor-default no LZW predictor (default) +Pn --predictor-none LZW predictor 1 (no prediction) +Ph --predictor-horz LZW predictor 2 (horizontal differencing) +Rs --rows-per-strip [r]ows: integer (default: 0) rows per strip, default 8K per strip PNG format: +il --interlace create interlaced file (default) -il --nointerlace create non-interlaced file +mf --meta-file create PNG file meta information (default) -mf --meta-none no PNG file meta information JPEG format: +Jq --compr-quality [q]uality: integer (0..100, default: 90) quality value for compression (in percent) +Js4 --sample-444 4:4:4 sampling (no subsampling) +Js2 --sample-422 4:2:2 subsampling (horizontal subsampling of chroma components, default) +Js1 --sample-411 4:1:1 subsampling (horizontal and vertical subsampling of chroma components) other transformations: +G --grayscale convert color image to grayscale (monochrome) +P --change-polarity change polarity (invert pixel output) +C --clip-region [l]eft [t]op [w]idth [h]eight: integer clip image region (l, t, w, h)
general: -im --image-info print image details (requires verbose mode) -o --no-output do not create any output (useful with -im) filename generation (only with --frame-range or --all-frames): +Fc --use-frame-counter use 0-based counter for filenames (default) +Fn --use-frame-number use absolute frame number for filenames image format: +op --write-raw-pnm write 8-bit binary PGM/PPM (default for files) +opb --write-8-bit-pnm write 8-bit ASCII PGM/PPM (default for stdout) +opw --write-16-bit-pnm write 16-bit ASCII PGM/PPM +opn --write-n-bit-pnm [n]umber: integer write n-bit ASCII PGM/PPM (1..32) +ob --write-bmp write 8-bit (monochrome) or 24-bit (color) BMP +obp --write-8-bit-bmp write 8-bit palette BMP (monochrome only) +obt --write-24-bit-bmp write 24-bit truecolor BMP +obr --write-32-bit-bmp write 32-bit truecolor BMP +ot --write-tiff write 8-bit (monochrome) or 24-bit (color) TIFF +on --write-png write 8-bit (monochrome) or 24-bit (color) PNG +on2 --write-16-bit-png write 16-bit (monochrome) or 48-bit (color) PNG +oj --write-jpeg write 8-bit lossy JPEG (baseline)
The following preferred interpolation algorithms can be selected using the --interpolate option:
0
The --write-tiff option is only available when DCMTK has been configured and compiled with support for the external libtiff TIFF library. The availability of the TIFF compression options depends on the libtiff configuration. In particular, the patented LZW algorithm may not be available.
The --write-png option is only available when DCMTK has been configured and compiled with support for the external libpng PNG library. Option --interlace enables progressive image view while loading the PNG file. Only a few applications take care of the meta info (TEXT) in a PNG file.
dcmj2pnm supports the following transfer syntaxes for input (dcmfile-in):
LittleEndianImplicitTransferSyntax 1.2.840.10008.1.2 LittleEndianExplicitTransferSyntax 1.2.840.10008.1.2.1 DeflatedExplicitVRLittleEndianTransferSyntax 1.2.840.10008.1.2.1.99 (*) BigEndianExplicitTransferSyntax 1.2.840.10008.1.2.2 JPEGProcess1TransferSyntax 1.2.840.10008.1.2.4.50 JPEGProcess2_4TransferSyntax 1.2.840.10008.1.2.4.51 JPEGProcess6_8TransferSyntax 1.2.840.10008.1.2.4.53 JPEGProcess10_12TransferSyntax 1.2.840.10008.1.2.4.55 JPEGProcess14TransferSyntax 1.2.840.10008.1.2.4.57 JPEGProcess14SV1TransferSyntax 1.2.840.10008.1.2.4.70 RLELosslessTransferSyntax 1.2.840.10008.1.2.5
(*) if compiled with zlib support enabled
The level of logging output of the various command line tools and underlying libraries can be specified by the user. By default, only errors and warnings are written to the standard error stream. Using option --verbose also informational messages like processing details are reported. Option --debug can be used to get more details on the internal activity, e.g. for debugging purposes. Other logging levels can be selected using option --log-level. In --quiet mode only fatal errors are reported. In such very severe error events, the application will usually terminate. For more details on the different logging levels, see documentation of module 'oflog'.
In case the logging output should be written to file (optionally with logfile rotation), to syslog (Unix) or the event log (Windows) option --log-config can be used. This configuration file also allows for directing only certain messages to a particular output stream and for filtering certain messages based on the module or application where they are generated. An example configuration file is provided in <etcdir>/logger.cfg.
All command line tools use the following notation for parameters: square brackets enclose optional values (0-1), three trailing dots indicate that multiple values are allowed (1-n), a combination of both means 0 to n values.
Command line options are distinguished from parameters by a leading '+' or '-' sign, respectively. Usually, order and position of command line options are arbitrary (i.e. they can appear anywhere). However, if options are mutually exclusive the rightmost appearance is used. This behavior conforms to the standard evaluation rules of common Unix shells.
In addition, one or more command files can be specified using an '@' sign as a prefix to the filename (e.g. @command.txt). Such a command argument is replaced by the content of the corresponding text file (multiple whitespaces are treated as a single separator unless they appear between two quotation marks) prior to any further evaluation. Please note that a command file cannot contain another command file. This simple but effective approach allows one to summarize common combinations of options/parameters and avoids longish and confusing command lines (an example is provided in file <datadir>/dumppat.txt).
The dcmj2pnm utility will attempt to load DICOM data dictionaries specified in the DCMDICTPATH environment variable. By default, i.e. if the DCMDICTPATH environment variable is not set, the file <datadir>/dicom.dic will be loaded unless the dictionary is built into the application (default for Windows).
The default behavior should be preferred and the DCMDICTPATH environment variable only used when alternative data dictionaries are required. The DCMDICTPATH environment variable has the same format as the Unix shell PATH variable in that a colon (':') separates entries. On Windows systems, a semicolon (';') is used as a separator. The data dictionary code will attempt to load each file specified in the DCMDICTPATH environment variable. It is an error if no data dictionary can be loaded.
<datadir>/camera.lut - sample characteristics file of a camera
<datadir>/monitor.lut - sample characteristics file of a monitor
<datadir>/printer.lut - sample characteristics file of a printer
<datadir>/scanner.lut - sample characteristics file of a scanner
dcm2pnm(1), img2dcm(1)
Copyright (C) 2001-2021 e.V., Escherweg 2, 26121 Oldenburg, Germany.