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dcmcjpeg(1)			  OFFIS	DCMTK			   dcmcjpeg(1)

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:

       o MR images are required	to have	BitsAllocated=16.
       o NM  Images  can  only	be  encoded  with MONOCHROME2 or PALETTE COLOR
	 photometric interpretation  but  not  with  RGB  or  YBR_FULL	(which
	 effectively prevents compression).
       o 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:
       o Only source images with Bits Allocated	8 or 16	are supported
       o Options  for  color space conversions,	windowing or pixel scaling are
	 ignored or overridden
       o Photometric	Interpretations	    YBR_FULL_422,     YBR_PARTIAL_422,
	 YBR_PARTIAL_420, YBR_ICT, YBR_RCT are not supported
       o The encoder changes automatically Planar Configuration	from 1 to 0 if
	 necessary
       o 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.

Version	3.6.5			Mon Oct	28 2019			   dcmcjpeg(1)

NAME | SYNOPSIS | DESCRIPTION | PARAMETERS | OPTIONS | NOTES | TRANSFER SYNTAXES | LOGGING | COMMAND LINE | ENVIRONMENT | SEE ALSO | COPYRIGHT

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