xenial (1) xml2dcm.1.gz

Provided by: dcmtk_3.6.1~20150924-5_amd64 bug

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="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)
       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.

   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

SEE ALSO

       dcm2xml(1)

       Copyright (C) 2003-2014 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.