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This is the command dcmcjpls that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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 (default for 8 bpp: 3)
set JPEG-LS encoding parameter threshold 1

+t2 --threshold2 [t]hreshhold: integer (default for 8 bpp: 7)
set JPEG-LS encoding parameter threshold 2

+t3 --threshold3 [t]hreshhold: integer (default for 8 bpp: 21)
set JPEG-LS encoding parameter threshold 3

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

+lm --limit [l]imit: integer (default: 0)
set JPEG-LS encoding parameter limit

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 pixe 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.

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. 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.

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