Provided by: dcmtk_3.6.4-2.1_amd64 bug

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 (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 to grayscale if necessary

         +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. 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.

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) 2001-2018 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.