The basic structure of the DCMTK-specific XML output created from a DICOM file 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 are absent for DICOM data sets.
XMLEncoding
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 --load-all forces to load all value fields including the very long ones.
Furthermore, binary data 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 --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 --load-all
because of the large amounts of pixel data that might be printed to the output. Please note that in this
context element values with a VR of OD, OF, OL and OV are not regarded as 'binary data'.
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 dcm2xml_native_format Native DICOM Model Format
The description of the Native DICOM Model format can be found in the DICOM standard, part 19
('Application Hosting').
@subsection dcm2xml_bulk_data Bulk Data
Binary data, i.e. DICOM element values with Value Representations (VR) of OB or OW, as well as OD, OF,
OL, OV and UN values are by default not written to the XML output because of their size. Instead, for
each element, a new Universally Unique Identifier (UUID) is being generated and written as an attribute
of a \<BulkData\> XML element. So far, there is no possibility to write an additional file to hold the
binary data for each of the binary data chunks. This is not required by the standard, however, it might
be useful for implementing an Application Hosting interface; thus this feature may be available in future
versions of \b dcm2xml.
In addition, Supplement 163 (Store Over the Web by Representational State Transfer Services) introduces a
new \<InlineBinary\> XML element that allows for encoding binary data as Base64. Currently, the command
line option \e --encode-base64 enables this encoding for the following VRs: OB, OD, OF, OL, OV, OW and
UN.
@subsection dcm2xml_known_issues Known Issues
In addition to what is written in the above section on 'Bulk Data', there are further known issues with
the current implementation of the Native DICOM Model format. For example, large element values with a VR
other than OB, OD, OF, OL, OV, OW or UN are currently never written as bulk data, although it might be
useful, e.g. for very long text elements (especially UT) or very long numeric fields (of various VRs).
@section dcm2xml_notes NOTES
@subsection dcm2xml_character_encoding Character Encoding
The XML character encoding is determined automatically from the DICOM attribute (0008,0005) 'Specific
Character Set' 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' 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' \endverbatim
If this DICOM attribute is missing in the input file, although needed, option \e --charset-assume can be
used to specify an appropriate character set manually (using one of the DICOM defined terms). For
reasons of backward compatibility with previous versions of this tool, the following terms are also
supported and mapped automatically to the associated DICOM defined terms: latin-1, latin-2, latin-3,
latin-4, latin-5, latin-9, cyrillic, arabic, greek, hebrew.
Multiple character sets using code extension techniques are not supported. If needed, option \e
--convert-to-utf8 can be used to convert the DICOM file or data set to UTF-8 encoding prior to the
conversion to XML format. This is also useful for DICOMDIR files where each directory record can have a
different character set.
If no mapping is defined and option \e --convert-to-utf8 is not used, non-ASCII characters and those
below #32 are stored as '&#nnn;' where 'nnn' refers to the numeric character code. This might lead to
invalid character entity references (such as '' for ESC) and will cause most XML parsers to reject
the document.
@section dcm2xml_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 dcm2xml_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 dcm2xml_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 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.
Depending on the command line options specified, the dcm2xml utility will attempt to load character set
mapping tables. This happens when DCMTK was compiled with the oficonv library (which is the default) and
the mapping tables are not built into the library (default when DCMTK uses shared libraries).
The mapping table files are expected in DCMTK's <datadir>. The DCMICONVPATH environment variable can be
used to specify a different location. If a different location is specified, those mapping tables also
replace any built-in tables.
Install Now
PNG Icons
