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dcmcjpls(1)			  OFFIS	DCMTK			   dcmcjpls(1)

NAME
       dcmcjpls	- Encode DICOM file to JPEG-LS transfer	syntax

SYNOPSIS
       dcmcjpls	[options] dcmfile-in dcmfile-out

DESCRIPTION
       The  dcmcjpls  utility  reads an	uncompressed DICOM image (dcmfile-in),
       performs	a JPEG-LS 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

   JPEG-LS encoding options
       JPEG-LS process:

	 +el  --encode-lossless
		encode JPEG-LS lossless	only TS	(default)

	 # This	options	selects	the JPEG-LS lossless only transfer syntax
	 # and performs	a lossless compression.

	 +en  --encode-nearlossless
		encode JPEG-LS near-lossless TS	(NEAR: 2)

	 # This	options	selects	the JPEG-LS lossy transfer syntax
	 # and performs	a near-lossless	compression.

       JPEG-LS bit rate	(near-lossless only):

	 +md  --max-deviation  [d]eviation: integer (default: 2)
		defines	maximum	deviation for an encoded pixel

	 # This	option specifies the maximum deviation for a single pixel from
	 # the original	pixel value.

       lossless	compression:

	 +pr  --prefer-raw
		prefer raw encoder mode	(default)

	 # This	option enables the raw encoder.	The raw	encoder	encodes	the
	 # complete pixel cell as it was read from the source image without
	 # performing any modifications.

	 +pc  --prefer-cooked
		prefer cooked encoder mode

	 # This	option enables the cooked encoder. The cooked encoder moves
	 # overlay data	to separate tags (60xx,3000) and only encodes the
	 # stored bits in each pixel.

       JPEG-LS compression:

	 +t1  --threshold1  [t]hreshhold: integer
		set JPEG-LS encoding parameter threshold 1

	 +t2  --threshold2  [t]hreshhold: integer
		set JPEG-LS encoding parameter threshold 2

	 +t3  --threshold3  [t]hreshhold: integer
		set JPEG-LS encoding parameter threshold 3

	 # By default, the values for T1, T2, T3 are computed based on
	 # the number of bits per sample.

	 +rs  --reset  [r]eset:	integer	(default: 64)
		set JPEG-LS encoding parameter reset

       JPEG-LS interleave:

	 +il  --interleave-line
		force line-interleaved JPEG-LS images (default)

	 # This	flag forces line-interleaved mode for the resulting image.
	 # In line-interleave mode each	line from the source image is
	 # compressed separately for each component and	then the next line
	 # is encoded.

	 +is  --interleave-sample
		force sample-interleaved JPEG-LS images

	 # This	flag forces sample-interleaved mode for	the resulting image.
	 # In sample-interleave	mode each pixel's components are encoded before
	 # the next pixel is encoded.

	 +in  --interleave-none
		force uninterleaved JPEG-LS images

	 # This	flag forces uninterleaved mode for the resulting image.
	 # In this mode, each of the image's components	are completely encoded
	 # before the next component is	handled.

	 +iv  --interleave-default
		use the	fastest	possible interleave mode

	 # This	flag selects an	interleave mode	based on the source image's mode.
	 # If possible,	the image is not converted to a	different interleave mode.

       JPEG-LS padding of odd-length bitstreams:

	 +ps  --padding-standard
		pad with extended EOI marker (default)

	 # Pad odd-length JPEG-LS bitstreams by	writing	an extended end	of image
	 # segment marker FF FF	D9, as required	by the DICOM standard.

	 +pz  --padding-zero
		pad with zero byte (non-standard)

	 # Pad odd-length JPEG-LS bitstreams by	writing	a zero byte after the
	 # end of image	segment	marker,	i.e. FF	D9 00. This is not DICOM conformant
	 # but required	for interoperability with the HP LOCO reference	implementation,
	 # which does not support extended JPEG-LS bitstreams..fi

   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.

       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 JPEG.

	 +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 dcmcjpls 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. However,	dcmcjpls  does
       not attempt to ensure that the compressed image still complies with all
       restrictions of the object's IOD.

       The user	is responsible for making sure that the	compressed  images  he
       creates	are  compliant	with  the  DICOM standard. If in question, the
       dcmcjpls	utility	allows one to convert an image to secondary capture  -
       this SOP	class does not pose restrictions as the	ones mentioned above.

TRANSFER SYNTAXES
       dcmcjpls	 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

       (*) if compiled with zlib support enabled

       dcmcjpls	supports the following transfer	syntaxes for output  (dcmfile-
       out):

       JPEGLSLosslessTransferSyntax		      1.2.840.10008.1.2.4.80
       JPEGLSLossyTransferSyntax		      1.2.840.10008.1.2.4.81

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 dcmcjpls 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
       dcmdjpls(1)

COPYRIGHT
       Copyright  (C)  2009-2019  by OFFIS e.V., Escherweg 2, 26121 Oldenburg,
       Germany.

Version	3.6.5			Mon Oct	28 2019			   dcmcjpls(1)

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

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