dcmj2pnm(1)

NAME
dcmj2pnm - Convert DICOM images to PGM/PPM, PNG, TIFF, JPEG or BMP

SYNOPSIS

dcmj2pnm [options] dcmfile-in [bitmap-out]

DESCRIPTION

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.

PARAMETERS

dcmfile-in  DICOM input filename to be converted
bitmap-out  output filename to be written (default: stdout)

OPTIONS

  general options

  -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 options

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

  image processing options

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)

  output options

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)

NOTES

The following preferred interpolation algorithms can be selected using the --interpolate option:

•   1 = free scaling algorithm with interpolation from pbmplus toolkit
•   2 = free scaling algorithm with interpolation from c't magazine
•   3 = magnification algorithm with bilinear interpolation from Eduard Stanescu
•   4 = magnification algorithm with bicubic interpolation from Eduard Stanescu
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.
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.

TRANSFER SYNTAXES
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

LOGGING
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.

COMMAND LINE
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).

ENVIRONMENT
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.

FILES
<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

SEE ALSO
dcm2pnm(1), img2dcm(1)

COPYRIGHT
Copyright (C) 2001-2022 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.