dcmdjpeg - Online in the Cloud

PROGRAM:

NAME

dcmdjpeg - Decode JPEG-compressed DICOM file

SYNOPSIS

dcmdjpeg [options] dcmfile-in dcmfile-out

DESCRIPTION

The dcmdjpeg utility reads a JPEG-compressed DICOM image (dcmfile-in), decompresses the
JPEG data (i. e. conversion to a native 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

# This option allows one to decompress JPEG compressed DICOM objects that
# have been stored as dataset without meta-header. Such a thing should
# not exist since the transfer syntax cannot be reliably determined,
# without meta-header but unfortunately it does.

processing options
color space conversion:

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

# If the compressed image uses YBR_FULL or YBR_FULL_422 photometric
# interpretation, convert 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.

planar configuration:

+pa --planar-auto
automatically determine planar configuration
from SOP class and color space (default)

# If the compressed image is a color image, store in color-by-plane
# planar configuration if required by the SOP class and photometric
# interpretation. Hardcopy Color images are always stored color-by-
# plane, and the revised Ultrasound image objects are stored color-by-
# plane if the color model is YBR_FULL. Everything else is stored
# color-by-pixel.

+px --color-by-pixel
always store color-by-pixel

# If the compressed image is a color image, store in color-by-pixel
# planar configuration.

+pl --color-by-plane
always store color-by-plane

# If the compressed image is a color image, store in color-by-plane
# planar configuration.

SOP Instance UID:

+ud --uid-default
keep same SOP Instance UID (default)

# Never assigns a new SOP instance UID.

+ua --uid-always
always assign new UID

# Always assigns a new SOP instance UID.

workaround options for incorrect JPEG encodings:

+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.

output options
output file format:

+F --write-file
write file format (default)

-F --write-dataset
write data set without file meta information

output transfer syntax:

+te --write-xfer-little
write with explicit VR little endian (default)

+tb --write-xfer-big
write with explicit VR big endian TS

+ti --write-xfer-implicit
write with implicit VR little endian TS

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 (not with --write-dataset):

-p= --padding-retain
do not change padding (default if not --write-dataset)

-p --padding-off
no padding (implicit if --write-dataset)

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

TRANSFER SYNTAXES

dcmdjpeg 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

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

LittleEndianImplicitTransferSyntax 1.2.840.10008.1.2
LittleEndianExplicitTransferSyntax 1.2.840.10008.1.2.1
BigEndianExplicitTransferSyntax 1.2.840.10008.1.2.2

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 dcmdjpeg 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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