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/*!
\if MANPAGES
\page dcm2xml Convert DICOM file and data set to XML
\else
\page dcm2xml dcm2xml: Convert DICOM file and data set to XML
\endif
\section synopsis SYNOPSIS
\verbatim
dcm2xml [options] dcmfile-in [xmlfile-out]
\endverbatim
\section description DESCRIPTION
The \b dcm2xml utility converts the contents of a DICOM file (file format or
raw data set) to XML (Extensible Markup Language). The DTD (Document Type
Definition) is described in the file <em>dcm2xml.dtd</em>.
If \b dcm2xml reads a raw data set (DICOM data without a file format
meta-header) it will attempt to guess the transfer syntax by examining the
first few bytes of the file. It is not always possible to correctly guess the
transfer syntax and it is better to convert a data set to a file format
whenever possible (using the \b dcmconv utility). It is also possible to use
the \e -f and <em>-t[ieb]</em> options to force \b dcm2xml to read a data set
with a particular transfer syntax.
\section parameters PARAMETERS
\verbatim
dcmfile-in DICOM input filename to be converted
xmlfile-out XML output filename (default: stdout)
\endverbatim
\section options OPTIONS
\subsection general_options general options
\verbatim
-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
\endverbatim
\subsection input_options input options
\verbatim
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
long tag values:
+M --load-all
load very long tag values (e.g. pixel data)
-M --load-short
do not load very long values (default)
+R --max-read-length [k]bytes: integer (4..4194302, default: 4)
set threshold for long values to k kbytes
\endverbatim
\subsection processing_options processing options
\verbatim
character set:
+Cr --charset-require
require declaration of extended charset (default)
+Ca --charset-assume [c]harset: string constant
(latin-1 to -5, cyrillic, arabic, greek, hebrew)
assume charset c if no extended charset declared
+Cc --charset-check-all
check all data elements with string values
(default: only PN, LO, LT, SH, ST and UT)
\endverbatim
\subsection output_options output options
\verbatim
XML structure:
+Xd --add-dtd-reference
add reference to document type definition (DTD)
+Xe --embed-dtd-content
embed document type definition into XML document
+Xf --use-dtd-file [f]ilename: string
use specified DTD file (only with +Xe)
(default: /usr/local/share/dcmtk/dcm2xml.dtd)
+Xn --use-xml-namespace
add XML namespace declaration to root element
DICOM data elements:
+Wn --write-element-name
write name of the DICOM data elements (default)
-Wn --no-element-name
do not write name of the DICOM data elements
+Wb --write-binary-data
write binary data of OB and OW elements
(default: off, be careful with --load-all)
+Eh --encode-hex
encode binary data as hex numbers (default)
+Eb --encode-base64
encode binary data as Base64 (RFC 2045, MIME)
\endverbatim
\section notes NOTES
The basic structure of the XML output created from a DICOM image file looks
like the following:
\verbatim
<?xml version="1.0" encoding="ISO-8859-1"?>
<!DOCTYPE file-format SYSTEM "dcm2xml.dtd">
<file-format xmlns="http://dicom.offis.de/dcmtk">
<meta-header xfer="1.2.840.10008.1.2.1" name="LittleEndianExplicit">
<element tag="0002,0000" vr="UL" vm="1" len="4"
name="MetaElementGroupLength">
166
</element>
...
<element tag="0002,0013" vr="SH" vm="1" len="16"
name="ImplementationVersionName">
OFFIS_DCMTK_353
</element>
</meta-header>
<data-set xfer="1.2.840.10008.1.2" name="LittleEndianImplicit">
<element tag="0008,0005" vr="CS" vm="1" len="10"
name="SpecificCharacterSet">
ISO_IR 100
</element>
...
<sequence tag="0028,3010" vr="SQ" card="2" name="VOILUTSequence">
<item card="3">
<element tag="0028,3002" vr="xs" vm="3" len="6"
name="LUTDescriptor">
256\\0\\8
</element>
...
</item>
...
</sequence>
...
<element tag="7fe0,0010" vr="OW" vm="1" len="262144"
name="PixelData" loaded="no" binary="hidden">
</element>
</data-set>
</file-format>
\endverbatim
The "file-format" and "meta-header" tags are absent for DICOM data sets.
\subsection character_encoding Character Encoding
The XML encoding is determined automatically from the DICOM attribute
(0008,0005) "Specific Character Set" (if present) using the following
mapping:
\verbatim
ASCII "ISO_IR 6" => "UTF-8"
UTF-8 "ISO_IR 192" => "UTF-8"
ISO Latin 1 "ISO_IR 100" => "ISO-8859-1"
ISO Latin 2 "ISO_IR 101" => "ISO-8859-2"
ISO Latin 3 "ISO_IR 109" => "ISO-8859-3"
ISO Latin 4 "ISO_IR 110" => "ISO-8859-4"
ISO Latin 5 "ISO_IR 148" => "ISO-8859-9"
Cyrillic "ISO_IR 144" => "ISO-8859-5"
Arabic "ISO_IR 127" => "ISO-8859-6"
Greek "ISO_IR 126" => "ISO-8859-7"
Hebrew "ISO_IR 138" => "ISO-8859-8"
\endverbatim
Multiple character sets are not supported (only the first attribute value is
mapped in case of value multiplicity).
\subsection xml_encoding XML Encoding
Attributes with very large value fields (e.g. pixel data) are not loaded by
default. They can be identified by the additional attribute "loaded" with a
value of "no" (see example above). The command line option \e --load-all
forces to load all value fields including the very long ones.
Furthermore, binary information of OB and OW attributes are not written to the
XML output file by default. These elements can be identified by the
additional attribute "binary" with a value of "hidden" (default is "no"). The
command line option \e --write-binary-data causes also binary value fields to
be printed (attribute value is "yes" or "base64"). But, be careful when using
this option together with \e --load-all because of the large amounts of pixel
data that might be printed to the output.
Multiple values (i.e. where the DICOM value multiplicity is greater than 1)
are separated by a backslash "\" (except for Base64 encoded data). The "len"
attribute indicates the number of bytes for the particular value field as
stored in the DICOM data set, i.e. it might deviate from the XML encoded value
length e.g. because of non-significant padding that has been removed. If this
attribute is missing in "sequence" or "item" start tags, the corresponding
DICOM element has been stored with undefined length.
\section logging 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 \e --verbose also
informational messages like processing details are reported. Option
\e --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
\e --log-level. In \e --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 \e --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 <em>\<etcdir\>/logger.cfg</em>).
\section command_line 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 behaviour 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. <em>\@command.txt</em>). 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 to summarize common combinations of options/parameters and avoids
longish and confusing command lines (an example is provided in file
<em>\<datadir\>/dumppat.txt</em>).
\section environment ENVIRONMENT
The \b dcm2xml utility will attempt to load DICOM data dictionaries specified
in the \e DCMDICTPATH environment variable. By default, i.e. if the
\e DCMDICTPATH environment variable is not set, the file
<em>\<datadir\>/dicom.dic</em> will be loaded unless the dictionary is built
into the application (default for Windows).
The default behaviour should be preferred and the \e DCMDICTPATH environment
variable only used when alternative data dictionaries are required. The
\e DCMDICTPATH environment variable has the same format as the Unix shell
\e 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 \e DCMDICTPATH environment variable.
It is an error if no data dictionary can be loaded.
\section files FILES
<em>\<datadir\>/dcm2xml.dtd</em> - Document Type Definition (DTD) file
\section see_also SEE ALSO
<b>xml2dcm</b>(1), <b>dcmconv</b>(1)
\section copyright COPYRIGHT
Copyright (C) 2002-2010 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.
*/
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