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 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 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.

(*) 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.

Compression

If libxml is compiled with zlib support, the input file (xmlfile-in) can also be compressed with ZIP, which usually results in much smaller files. See output of option --version in order to check whether zlib support is available.

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 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 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. @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 one 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 behavior 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