Provided by: dcmtk_3.6.4-2.1_amd64 bug

NAME

       dcmcjpeg - Encode DICOM file to JPEG transfer syntax

SYNOPSIS

       dcmcjpeg [options] dcmfile-in dcmfile-out

DESCRIPTION

       The  dcmcjpeg  utility  reads  an  uncompressed  DICOM image (dcmfile-in), performs a JPEG
       compression (i. e. conversion to an encapsulated DICOM transfer  syntax)  and  writes  the
       converted image to an output file (dcmfile-out).

PARAMETERS

       dcmfile-in   DICOM input filename to be converted

       dcmfile-out  DICOM output filename

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

       compatibility (ignored by +tl):

         +Ma   --accept-acr-nema
                 accept ACR-NEMA images without photometric interpretation

         # Enables compatibility for old ACR-NEMA images without photometric
         # information (only pseudo lossless encoder)

         +Mp   --accept-palettes
                 accept incorrect palette attribute tags (0028,111x) and
                 (0028,121x)

         # If enabled, incorrect palette attribute tags are accepted
         # (only pseudo lossless encoder)

   JPEG encoding options
       JPEG process:

         +e1   --encode-lossless-sv1
                 encode lossless sv1 (default)

         # This option selects the JPEG Lossless, Non-Hierarchical, First-Order
         # Prediction (Process 14 Selection Value 1) Transfer Syntax for
         # Lossless JPEG Image Compression.

         +el   --encode-lossless
                 encode lossless

         # This option selects the JPEG Lossless, Non-Hierarchical (Process 14)
         # Transfer Syntax for Lossless JPEG Image Compression.

         +eb   --encode-baseline
                 encode baseline

         # This option selects the JPEG Baseline (Process 1) Transfer Syntax
         # for Lossy JPEG 8 Bit Image Compression.

         +ee   --encode-extended
                 encode extended sequential

         # This option selects the JPEG Extended (Process 2 & 4) Transfer
         # Syntax for Lossy JPEG Image Compression.

         +es   --encode-spectral
                 encode spectral selection

         # This option selects the JPEG Spectral Selection, Non-Hierarchical
         # (Process 6 & 8) Transfer Syntax for Lossy JPEG Image Compression.

         +ep   --encode-progressive
                 encode progressive

         # This option selects the JPEG Full Progression, Non-Hierarchical
         # (Process 10 & 12) Transfer Syntax for Lossy JPEG Image Compression.

       lossless JPEG codec selection:

         +tl   --true-lossless
                 true lossless codec (default)

         # This option selects an encoder, that guarantees truely lossless
         # image compression. See NOTES for further information.

         +pl   --pseudo-lossless
                 old pseudo-lossless codec

         # Old encoder, that uses lossless compression algorithms, but can
         # cause lossy images because of internal color space transformations
         # etc. Higher compression ratio than --true-lossless in most cases.

       lossless JPEG representation:

         +sv   --selection-value  [sv]: integer (1..7, default: 6)
                 use selection value sv only with --encode-lossless

         # This option selects the selection value for lossless JPEG.

         +pt   --point-transform  [pt]: integer (0..15, default: 0)
                 use point transform pt

         # This option selects the point transform for lossless JPEG.
         # WARNING: Using this option with a value other than zero causes
         # a loss of precision, i. e. makes the compression "lossy".

       lossy JPEG representation:

         +q    --quality  [q]: integer (0..100, default: 90)
                 use quality factor q

         # This option selects the quality factor used to determine the
         # quantization table inside the JPEG compressor, which affects
         # compression ratio and image quality in lossy JPEG.
         # See documentation of the Independent JPEG Group for details.

         +sm   --smooth  [s]: integer (0..100, default: 0)
                 use smoothing factor s

         # This option enables a smoothing (low-pass filter) of the image data
         # prior to compression. Increases the compression ratio at the expense
         # of image quality.

       other JPEG options:

         +ho   --huffman-optimize
                 optimize huffman tables (default)

         # This option enables an optimization of the huffman tables during
         # image compression. It results in a slightly smaller image at a small
         # increase of CPU time. Always on if bits/sample is larger than 8.

         -ho   --huffman-standard
                 use standard huffman tables if 8 bits/sample

         # This option disables an optimization of the huffman tables during
         # image compression.

       compressed bits per sample (always +ba with +tl):

         +ba   --bits-auto
                 choose bits/sample automatically (default)

         +be   --bits-force-8
                 force 8 bits/sample

         +bt   --bits-force-12
                 force 12 bits/sample (not with baseline)

         +bs   --bits-force-16
                 force 16 bits/sample (lossless only)

       compression color space conversion (overridden by +tl):

         +cy   --color-ybr
                 use YCbCr for color images if lossy (default)

         # This option enables a transformation of the color space to YCbCr
         # prior to image compression for color images in lossy JPEG.

         +cr   --color-rgb
                 use RGB for color images if lossy

         # This option prevents the transformation of the color space to YCbCr
         # prior to image compression for color images in lossy JPEG. It causes
         # lossy image compression in the RGB color space which is not
         # recommendable.

         +cm   --monochrome
                 convert color images to monochrome

         # This option forces a conversion of color images to monochrome
         # prior to compression.

       decompression color space conversion
       (if input is compressed; always +cn with +tl):

         +cp   --conv-photometric
                 convert if YCbCr photometric interpretation (default)

         # This option describes the behavior of dcmcjpeg when a compressed
         # image is read and decompressed prior to re-compression.  If the
         # compressed image uses YBR_FULL or YBR_FULL_422 photometric
         # interpretation, it is converted to RGB during decompression.

         +cl   --conv-lossy
                 convert YCbCr to RGB if lossy JPEG

         # If the compressed image is encoded in lossy JPEG, assume YCbCr
         # color model and convert to RGB.

         +cg   --conv-guess
                 convert to RGB if YCbCr is guessed by library

         # If the underlying JPEG library "guesses" the color space of the
         # compressed image to be YCbCr, convert to RGB.

         +cgl  --conv-guess-lossy
                 convert to RGB if lossy JPEG and YCbCr is
                 guessed by the underlying JPEG library

         # If the compressed image is encoded in lossy JPEG and the underlying
         # JPEG library "guesses" the color space to be YCbCr, convert to RGB.

         +ca   --conv-always
                 always convert YCbCr to RGB

         # If the compressed image is a color image, assume YCbCr color model
         # and convert to RGB.

         +cn   --conv-never
                 never convert color space

         # Never convert color space during decompression.

       decompr. workaround options for incorrect encodings (if input is compressed):

         +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 dcmjpeg 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.

       YCbCr component subsampling (lossy JPEG only):

         +s2   --sample-422
                 4:2:2 subsampling with YBR_FULL_422 (default)

         # This option enables a 4:2:2 color component subsampling for
         # compression in the YCbCr color space. The DICOM photometric
         # interpretation is encoded as YBR_FULL_422.

       non-standard YCbCr component subsampling (not with +tl):

         +s4   --nonstd-444
                 4:4:4 sampling with YBR_FULL

         # This option disables color component subsampling for compression in
         # the YCbCr color space. The DICOM photometric interpretation is
         # encoded as YBR_FULL, which violates DICOM rules for lossy JPEG.

         +n2   --nonstd-422-full
                 4:2:2 subsampling with YBR_FULL

         # This option enables a 4:2:2 color component subsampling for
         # compression in the YCbCr color space. The DICOM photometric
         # interpretation is encoded as YBR_FULL, which violates DICOM rules.

         +n1   --nonstd-411-full
                 4:1:1 subsampling with YBR_FULL

         # This option enables a 4:1:1 color component subsampling for
         # compression in the YCbCr color space. The DICOM photometric
         # interpretation is encoded as YBR_FULL, which violates DICOM rules.

         +np   --nonstd-411
                 4:1:1 subsampling with YBR_FULL_422

         # This option enables a 4:1:1 color component subsampling for
         # compression in the YCbCr color space. The DICOM photometric
         # interpretation is encoded as YBR_FULL_422, which violates DICOM rules.

   encapsulated pixel data encoding options:
       encapsulated pixel data fragmentation:

         +ff   --fragment-per-frame
                 encode each frame as one fragment (default)

         # This option causes the creation of one compressed fragment for each
         # frame (recommended).

         +fs   --fragment-size  [s]ize: integer
                 limit fragment size to s kbytes

         # This option limits the fragment size which may cause the creation of
         # multiple fragments per frame.

       basic offset table encoding:

         +ot   --offset-table-create
                 create offset table (default)

         # This option causes the creation of a valid offset table for the
         # compressed JPEG fragments.

         -ot   --offset-table-empty
                 leave offset table empty

         # This option causes the creation of an empty offset table
         # for the compressed JPEG fragments.

       VOI windowing for monochrome images (not with +tl):

         -W    --no-windowing
                 no VOI windowing (default)

         # No window level/width is "burned" into monochrome images prior to
         # compression.  See notes below on pixel scaling and rescale slope
         # and intercept encoding.

         +Wi   --use-window  [n]umber: integer
                 use the n-th VOI window from image file

         # Apply the n-th window center/width encoded in the image data prior
         # to compression.

         +Wl   --use-voi-lut  [n]umber: integer
                 use the n-th VOI look up table from image file

         # Apply the n-th VOI LUT encoded in the image data prior
         # to compression.

         +Wm   --min-max-window
                 compute VOI window using min-max algorithm

         # Compute and apply a window center and width that covers the
         # range from the smallest to the largest occurring pixel value.

         +Wn   --min-max-window-n
                 compute VOI window using min-max algorithm,
                 ignoring extreme values

         # Compute and apply a window center and width that covers the
         # range from the second smallest to the second largest occurring
         # pixel value. This is useful if the background is set to an
         # artificial black (padding value) or if white overlays are burned
         # into the image data which should not be considered for the window
         # computation.

         +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

         # This option works like --min-max-window but only considers the given
         # region of interest inside the image.

         +Wh   --histogram-window  [n]umber: integer
                 compute VOI window using Histogram algorithm,
                 ignoring n percent

         # Compute a histogram of the image data and apply window center
         # and width such than n% of the image data are ignored for the window
         # computation

         +Ww   --set-window  [c]enter [w]idth: float
                 compute VOI window using center c and width w

         # Apply the given window center/width prior to compression.

       pixel scaling for monochrome images (--no-windowing; ignored by +tl):

         +sp   --scaling-pixel
                 scale using min/max pixel value (default)

         # Monochrome image pixel values are always scaled to make use of the
         # pixel range available with the selected JPEG process as good as
         # possible. This option selects a scaling based on the minimum and
         # maximum pixel value occurring in the image.  This often leads to
         # significantly better image quality, but may cause different
         # compressed images within one series to have different values for
         # rescale slope and intercept, which is a problem if a presentation
         # state for one series is to be created.

         +sr   --scaling-range
                 scale using min/max range

         # This options selects a scaling based on the pixel range as defined
         # by the stored bits, pixel representation and modality transform,
         # without consideration of the minimum and maximum value really
         # used within the image.

       rescale slope/intercept encoding for monochrome (-W; ignored by +tl):

         +ri   --rescale-identity
                 encode identity modality rescale (default)
                 Never used for CT images

         # This options prevents the creation of a modality transformation
         # other than an identity transformation (which is required for
         # many DICOM IODs).  Window center/width settings encoded
         # in the image are adapted, VOI LUTs are removed.

         +rm   --rescale-map
                 use modality rescale to scale pixel range
                 Never used for XA/RF/XA Biplane images

         # This option causes the creation of a modality rescale slope and
         # intercept that maps the decompressed image data back to their
         # original range.  This keeps all VOI transformations valid but
         # requires that the DICOM IOD supports a modality rescale slope
         # and intercept transformation other than identity.

       SOP Class UID:

         +cd   --class-default
                 keep SOP Class UID (default)

         # Keep the SOP Class UID of the source image.

         +cs   --class-sc
                 convert to Secondary Capture Image (implies --uid-always)

         # Convert the image to Secondary Capture.  In addition to the SOP
         # Class UID, all attributes required for a valid secondary capture
         # image are added. A new SOP instance UID is always assigned.

       SOP Instance UID:

         +ud   --uid-default
                 assign new UID if lossy compression (default)

         # Assigns a new SOP instance UID if the compression is lossy.

         +ua   --uid-always
                 always assign new UID

         # Unconditionally assigns a new SOP instance UID.

         +un   --uid-never
                 never assign new UID

         # Never assigns a new SOP instance UID.

   output options
       post-1993 value representations:

         +u    --enable-new-vr
                 enable support for new VRs (UN/UT) (default)

         -u    --disable-new-vr
                 disable support for new VRs, convert to OB

       group length encoding:

         +g=   --group-length-recalc
                 recalculate group lengths if present (default)

         +g    --group-length-create
                 always write with group length elements

         -g    --group-length-remove
                 always write without group length elements

       length encoding in sequences and items:

         +e    --length-explicit
                 write with explicit lengths (default)

         -e    --length-undefined
                 write with undefined lengths

       data set trailing padding:

         -p=   --padding-retain
                 do not change padding (default)

         -p    --padding-off
                 no padding

         +p    --padding-create  [f]ile-pad [i]tem-pad: integer
                 align file on multiple of f bytes
                 and items on multiple of i bytes

NOTES

       The  dcmcjpeg  utility  compresses DICOM images of all SOP classes. It processes all Pixel
       Data (7fe0,0010) elements in the dataset, i.e. compression is also performed  on  an  icon
       image.   Special  handling  has  been  implemented  for  CT  images  (where  the  modality
       transformation is required to create Hounsfield units) and the XA/RF/Biplane  SOP  classes
       (where  the  modality transformation has 'inversed' semantics). However, dcmcjpeg does not
       attempt to ensure that the compressed image still complies with all  restrictions  of  the
       object's IOD.

       A few examples:

       · MR images are required to have BitsAllocated=16.
       · NM   Images   can  only  be  encoded  with  MONOCHROME2  or  PALETTE  COLOR  photometric
         interpretation but not with RGB or YBR_FULL (which effectively prevents compression).
       · Hardcopy Color images must have RGB color model which is a problem if lossy  compression
         is to be performed.
       The  user  is  responsible  for  making  sure  that  the  compressed images he creates are
       compliant with the DICOM standard. If in question, the  dcmcjpeg  utility  allows  one  to
       convert  an  image to secondary capture - this SOP class does not pose restrictions as the
       ones mentioned above.
       With version DCMTK 3.5.4 a new encoder for  truly  lossless  JPEG  compression  was  added
       (--true-lossless).  Compared to the old (--pseudo-lossless) encoder, that creates slightly
       lossy images caused from internal color space conversions, windowing  etc.,  there  are  a
       some issues to consider:
       · Only source images with Bits Allocated 8 or 16 are supported
       · Options  for  color  space  conversions,  windowing  or  pixel  scaling  are  ignored or
         overridden
       · Photometric Interpretations  YBR_FULL_422,  YBR_PARTIAL_422,  YBR_PARTIAL_420,  YBR_ICT,
         YBR_RCT are not supported
       · The encoder changes automatically Planar Configuration from 1 to 0 if necessary
       · The compression ratio can be lower than in --pseudo-lossless mode
       However,  when using the new encoder (default), you can be sure, that compression does not
       affect image quality.
       In order to be on the safe side, the Lossy Compression Flag is always set to  '01'  and  a
       new  SOP  instance  UID  is assigned (by default) for the old pseudo-lossless encoder. The
       output of the old and new lossless encoder can also be  distinguished  by  the  Derivation
       Description  in  the  resulting  DICOM  image,  which  contains  the  term  'Lossless JPEG
       compression' for the new and 'Pseudo-Lossless JPEG compression' for the old encoder.

TRANSFER SYNTAXES

       dcmcjpeg 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
       (*) if compiled with zlib support enabled
       dcmcjpeg supports the following transfer syntaxes for output (dcmfile-out):
       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

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 dcmcjpeg 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.

SEE ALSO

       dcmdjpeg(1)

COPYRIGHT

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