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/*!
\if MANPAGES
\page xml2dcm Convert XML document to DICOM file or data set
\else
\page xml2dcm xml2dcm: Convert XML document to DICOM file or data set
\endif
\section synopsis SYNOPSIS
\verbatim
xml2dcm [options] xmlfile-in dcmfile-out
\endverbatim
\section description DESCRIPTION
The \b xml2dcm utility converts the contents of an XML (Extensible Markup
Language) document to DICOM file or data set. The XML document is expected to
validate against the DTD (Document Type Definition) which is described in file
<em>dcm2xml.dtd</em>. An appropriate XML file can be created using the
\b dcm2xml tool (option \e +Wb recommended to include binary data).
\section parameters PARAMETERS
\verbatim
xmlfile-in XML input filename to be converted (stdin: "-")
dcmfile-out DICOM output filename
\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-meta-info
read meta information if present (default)
-f --ignore-meta-info
ignore file meta information
\endverbatim
\subsection processing_options processing options
\verbatim
validation:
+Vd --validate-document
validate XML document against DTD
+Vn --check-namespace
check XML namespace in document root
unique identifiers:
+Ug --generate-new-uids
generate new Study/Series/SOP Instance UID
-Uo --dont-overwrite-uids
do not overwrite existing UIDs (default)
+Uo --overwrite-uids
overwrite existing UIDs
\endverbatim
\subsection output_options output options
\verbatim
output file format:
+F --write-file
write file format (default)
-F --write-dataset
write data set without file meta information
+Fu --update-meta-info
update particular file meta information
output transfer syntax:
+t= --write-xfer-same
write with same TS as input (default)
+te --write-xfer-little
write with explicit VR little endian TS
+tb --write-xfer-big
write with explicit VR big endian TS
+ti --write-xfer-implicit
write with implicit VR little endian TS
+td --write-xfer-deflated
write with deflated explicit 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
deflate compression level (only with --write-xfer-deflated):
+cl --compression-level [l]evel: integer (default: 6)
0=uncompressed, 1=fastest, 9=best compression
\endverbatim
\section notes NOTES
The basic structure of the XML input expected 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 may be absent for DICOM data sets.
\subsection character_encoding Character Encoding
The DICOM character encoding is determined automatically from the element with
tag "0008,0005" (Specific Character Set) - if present. The following
character sets are currently supported (requires \b libxml2 to include \b iconv
support):
\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 value of the
"Specific Character Set" is used for the character encoding in case of value
multiplicity).
See \b dcm2xml documentation for more details on the XML structure.
\subsection binary_data Binary Data
Binary data can be encoded either as a sequence of hex numbers separated by a
backslash "\" or in Base64 format (binary="base64"). In addition, binary data
can also be read from file (binary="file"). In this case, the filename has to
be specified as the element value, e.g.
\verbatim
<element tag="7fe0,0010" vr="OW" ... binary="file">subdir/pixeldata.raw</element>
\endverbatim
Please note that the contents of the file will be read as is. OW data is
expected to be little endian ordered and will be swapped if necessary. No
checks will be made to ensure that the amount of data is reasonable in terms
of other attributes such as Rows or Columns.
\subsection limitations Limitations
Please note that \b xml2dcm currently does not fully support DICOMDIR files.
Specifically, the value of the various offset data elements is not updated
automatically by this tool.
\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 xml2dcm 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>dcm2xml</b>(1)
\section copyright COPYRIGHT
Copyright (C) 2003-2010 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.
*/
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