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 ("-" for stdin)

dcmfile-out  DICOM output filename ("-" for stdout)

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

error handling:

  -E   --stop-on-error
         do not write if document is invalid (default)

  +E   --ignore-errors
         attempt to write even if document is invalid

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="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.

  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 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.

  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 datacan also be read from file (binary="file"). In this case, the filename has tobe specified as the element value, e.g.@verbatim <element tag="7fe0,0010" vr="OW" ... binary="file">subdir/pixeldata.raw</element>\endverbatimPlease note that the contents of the file will be read as is. OW data isexpected to be little endian ordered and will be swapped if necessary. Nochecks will be made to ensure that the amount of data is reasonable in termsof other attributes such as Rows or Columns.(*) Please note that currently only OB and OW data is supported, i.e. elementvalues with a VR of OD, OF, OL and OV are not regarded as "binary data" andtreated as all other VRs.@subsection xml2dcm_compression CompressionIf libxml is compiled with zlib support, the input file (\e xmlfile-in) canalso be compressed with ZIP, which usually results in much smaller files. Seeoutput of option \e --version in order to check whether zlib support isavailable.@subsection xml2dcm_limitations LimitationsDifferent versions of libxml might have different limits for the maximumlength of an XML element value. Therefore, it should be avoided to use verylong 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 updatedautomatically by this tool.@section xml2dcm_logging LOGGINGThe level of logging output of the various command line tools and underlyinglibraries can be specified by the user. By default, only errors and warningsare written to the standard error stream. Using option \e --verbose alsoinformational messages like processing details are reported. Option\e --debug can be used to get more details on the internal activity, e.g. fordebugging purposes. Other logging levels can be selected using option\e --log-level. In \e --quiet mode only fatal errors are reported. In suchvery severe error events, the application will usually terminate. For moredetails on the different logging levels, see documentation of module "oflog".In case the logging output should be written to file (optionally with logfilerotation), to syslog (Unix) or the event log (Windows) option \e --log-configcan be used. This configuration file also allows for directing only certainmessages to a particular output stream and for filtering certain messagesbased on the module or application where they are generated. An exampleconfiguration file is provided in <em>\<etcdir\>/logger.cfg</em>.@section xml2dcm_command_line COMMAND LINEAll command line tools use the following notation for parameters: squarebrackets enclose optional values (0-1), three trailing dots indicate thatmultiple 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 arearbitrary (i.e. they can appear anywhere). However, if options are mutuallyexclusive the rightmost appearance is used. This behavior conforms to thestandard evaluation rules of common Unix shells.In addition, one or more command files can be specified using an '@' sign as aprefix to the filename (e.g. <em>\@command.txt</em>). Such a command argumentis replaced by the content of the corresponding text file (multiplewhitespaces are treated as a single separator unless they appear between twoquotation marks) prior to any further evaluation. Please note that a commandfile cannot contain another command file. This simple but effective approachallows one to summarize common combinations of options/parameters and avoidslongish and confusing command lines (an example is provided in file<em>\<datadir\>/dumppat.txt</em>).@section xml2dcm_environment ENVIRONMENTThe \b xml2dcm utility will attempt to load DICOM data dictionaries specifiedin 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 builtinto the application (default for Windows).The default behavior should be preferred and the \e DCMDICTPATH environmentvariable 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.

FILES

<datadir>/dcm2xml.dtd - Document Type Definition (DTD) file

SEE ALSO

dcm2xml(1)

COPYRIGHT

Copyright (C) 2003-2025 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.