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xml2dcm(1) OFFIS DCMTK xml2dcm(1)
NAME
xml2dcm - Convert XML document to DICOM file or data set
SYNOPSIS
xml2dcm [options] xmlfile-in dcmfile-out
DESCRIPTION
The 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 dcm2xml.dtd. An appropriate XML file can be
created using the dcm2xml tool (option +Wb recommended to include
binary data).
PARAMETERS
xmlfile-in XML input filename to be converted (stdin: "-")
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-meta-info
read meta information if present (default)
-f --ignore-meta-info
ignore file meta information
processing options
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
output options
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
NOTES
The basic structure of the XML input expected looks like the following:
<?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>
The 'file-format' and 'meta-header' tags may be absent for DICOM data
sets.
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 libxml2 to
include iconv support):
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)
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 dcm2xml documentation for more details on the XML structure.
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.
<element tag="7fe0,0010" vr="OW" ... binary="file">subdir/pixeldata.raw</element>
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.
Limitations
Please note that xml2dcm currently does not fully support DICOMDIR
files. Specifically, the value of the various offset data elements is
not updated automatically by this tool.
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
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. @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 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 xml2dcm 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 behaviour 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.
FILES
<datadir>/dcm2xml.dtd - Document Type Definition (DTD) file
SEE ALSO
dcm2xml(1)
COPYRIGHT
Copyright (C) 2003-2010 by OFFIS e.V., Escherweg 2, 26121 Oldenburg,
Germany.
Version 3.6.0 6 Jan 2011 xml2dcm(1)