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='Little Endian Explicit'>
<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='Little Endian Implicit'>
<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.
CharacterEncoding
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 libxml to
include iconv support, see --version output):
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)
ISO Latin 9 'ISO_IR 203' (ISO-8859-15)
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.
BinaryData
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.
(*) Please note that currently only OB and OW data is supported, i.e. element values with a VR of OD, OF,
OL and OV are not regarded as 'binary data' and treated as all other VRs.
@subsection xml2dcm_compression Compression
If libxml is compiled with zlib support, the input file (\e xmlfile-in) can also be compressed with ZIP,
which usually results in much smaller files. See output of option \e --version in order to check whether
zlib support is available.
@subsection xml2dcm_limitations Limitations
Different versions of libxml might have different limits for the maximum length of an XML element value.
Therefore, it should be avoided to use very long element values (e.g. for pixel data).
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 xml2dcm_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 xml2dcm_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 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. <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 one 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 xml2dcm_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 behavior 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 DCMDICTPATH environment variable. It is an error if no data dictionary can be loaded.
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