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/*!
\page gdcmraw Extract Data Element Value Field.
\section synopsis SYNOPSIS
\verbatim
gdcmraw [options] file-in file-out
\endverbatim
\section description DESCRIPTION
The \b gdcmraw tool is mostly used for development purpose. It is used to
extract a specific binary field from a DICOM DataSet.
\section parameters PARAMETERS
\verbatim
file-in DICOM input filename
file-out output filename
\endverbatim
\section options OPTIONS
\subsection parameters parameters
\verbatim
-i --input Input filename
-o --output Output filename
-t --tag Specify tag to extract value from.
\endverbatim
\subsection options options
\verbatim
-S --split-frags Split fragments into multiple files.
-p --pattern Specify trailing file pattern (see split-frags).
-P --pixel-data Pixel Data trailing 0.
\endverbatim
\subsection general_options general options
\verbatim
-h --help
print this help text and exit
-v --version
print version information and exit
-V --verbose
verbose mode (warning+error).
-W --warning
warning mode, print warning information
-E --error
error mode, print error information
-D --debug
debug mode, print debug information
\endverbatim
\section usage Typical usage
\subsection copy_attribute Copy Attribute Value to file
This will extract the value at Tag (0025,101b):
\verbatim
$ gdcmraw -i GE_MR_0025xx1bProtocolDataBlock.dcm -t 25,101b -o pdb.raw
\endverbatim
\subsection extract_pixeldata Extract Pixel Data
If you do not specify any tag, the Pixel Data element is the default one. So for instance to grab the Pixel Data from an image:
\verbatim
$ gdcmraw -i test.acr -o test.raw
\endverbatim
You can then for example compute the md5sum of this pixel data (very useful):
\verbatim
$ md5sum test.raw
f845c8f283d39a0204c325654493ba53 test.raw
\endverbatim
\subsection encapsulated_syntax Encapsulated Syntax
When the Pixel Data is encapsulated, multiple fragments can be used to store a single slice image:
\verbatim
$ gdcmdump D_CLUNIE_CT1_J2KR.dcm
\endverbatim
\verbatim
\&...
(7fe0,0010) OB # u/l,1 Pixel Data
(fffe,e000) ?? [] # 0,1 Item
(fffe,e000) ?? ff\\4f\\ff\\51\\00\\29\\00\\00\\00\\00\\02\\00\\00\\00\\02\\00\\00\\00\\00\\00\\00\\00\\00\\00\\00\\00\\02\\00\\00\\00\\02\\00 # 65536,1 Item
(fffe,e000) ?? 2c\\b7\\ee\\68\\de\\e3\\93\\2d\\b3\\b8\\ba\\90\\7b\\42\\3e\\f8\\42\\16\\64\\88\\46\\30\\37\\d4\\50\\95\\9b\\b6\\a5\\c7\\38\\9b # 65536,1 Item
(fffe,e000) ?? 48\\3c\\03\\e8\\c4\\3f\\44\\e1\\8a\\5c\\73\\3b\\02\\0a\\ad\\a5\\8f\\e4\\0c\\81\\76\\a2\\d7\\1b\\7f\\b7\\cd\\bc\\30\\c6\\6a\\6a # 43308,1 Item
(fffe,e0dd) 0
\endverbatim
In order to create a J2K image out of it, we need to extract each fragments and concatenate them:
\verbatim
$ gdcmraw -i D_CLUNIE_CT1_J2KR.dcm -o D_CLUNIE_CT1_J2KR.j2k
\endverbatim
This is a valid J2K file, using the Kakadu software package:
\verbatim
$ kdu_expand -i D_CLUNIE_CT1_J2KR.j2k -o D_CLUNIE_CT1_J2KR.tiff -record D_CLUNIE_CT1_J2KR.txt
\endverbatim
\verbatim
$ cat D_CLUNIE_CT1_J2KR.txt
\endverbatim
\verbatim
Sprofile=PROFILE2
Scap=no
Sextensions=0
Ssize={512,512}
Sorigin={0,0}
Stiles={512,512}
Stile_origin={0,0}
Scomponents=1
Ssigned=yes
Sprecision=16
Ssampling={1,1}
Sdims={512,512}
Cycc=no
Cmct=0
Clayers=1
Cuse_sop=no
Cuse_eph=no
Corder=LRCP
Calign_blk_last={no,no}
Clevels=5
Cads=0
Cdfs=0
Cdecomp=B(-:-:-)
Creversible=yes
Ckernels=W5X3
Catk=0
Cuse_precincts=no
Cblk={64,64}
Cmodes=0
Qguard=1
Qabs_ranges=18,19,19,20,19,19,20,19,19,20,19,19,20,19,19,20
>> New attributes for tile 0:
\endverbatim
\subsection extract_fragments Extract fragments as single file
Sometimes each fragments is in fact a single slice, so we would not need to concatenate them:
\verbatim
$ gdcmdump 00191113.dcm
\endverbatim
\verbatim
\&...
(7fe0,0010) OB # u/l,1 Pixel Data
(fffe,e000) ?? 00\\00\\00\\00\\6b\\38\\01\\00\\10\\77\\02\\00\\37\\b6\\03\\00\\a7\\f4\\04\\00 # 20,1 Item
(fffe,e000) ?? ff\\d8\\ff\\c3\\00\\0b\\08\\02\\00\\02\\00\\01\\00\\11\\00\\ff\\c4\\00\\1b\\00\\01\\01\\01\\01\\01\\01\\01\\01\\00\\00\\00\\00 # 79970,1 Item
(fffe,e000) ?? ff\\d8\\ff\\c3\\00\\0b\\08\\02\\00\\02\\00\\01\\00\\11\\00\\ff\\c4\\00\\1b\\00\\01\\01\\01\\01\\01\\01\\01\\01\\00\\00\\00\\00 # 81564,1 Item
(fffe,e000) ?? ff\\d8\\ff\\c3\\00\\0b\\08\\02\\00\\02\\00\\01\\00\\11\\00\\ff\\c4\\00\\1b\\00\\01\\01\\01\\01\\01\\01\\01\\01\\00\\00\\00\\00 # 81694,1 Item
(fffe,e000) ?? ff\\d8\\ff\\c3\\00\\0b\\08\\02\\00\\02\\00\\01\\00\\11\\00\\ff\\c4\\00\\1b\\00\\01\\01\\01\\01\\01\\01\\01\\01\\00\\00\\00\\00 # 81511 (81512),1 Item
(fffe,e0dd) 0
\endverbatim
Let's try to extract those 4 individual Lossless jpeg individually:
\verbatim
$ gdcmraw --split-frags -i 00191113.dcm -o jpeg --pattern %02d.ljpeg
\endverbatim
This will output 4 files:
\verbatim
-rw-r--r-- 1 mathieu mathieu 81512 2008-08-08 22:10 jpeg03.ljpeg
-rw-r--r-- 1 mathieu mathieu 81694 2008-08-08 22:10 jpeg02.ljpeg
-rw-r--r-- 1 mathieu mathieu 81564 2008-08-08 22:10 jpeg01.ljpeg
-rw-r--r-- 1 mathieu mathieu 79970 2008-08-08 22:10 jpeg00.ljpeg
\endverbatim
\section footnote Footnote about JPEG files
It is a common misunderstanding to interchange 'JPEG 8bits lossy' with simply
JPEG file. The JPEG specification is much broader than simply the common lossy
8bits file (as found on internet).
You can have:
\li JPEG Lossy 8bits
\li JPEG Lossy 12bits
\li JPEG Lossless 2-16bits
Those are what is defined in ITU-T T.81, ISO/IEC IS 10918-1.
\section see_also SEE ALSO
<b>gdcmdump</b>(1), <b>gdcmraw</b>(1)
\section copyright COPYRIGHT
Copyright (c) 2006-2011 Mathieu Malaterre
*/
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