Provided by: dcmtk_3.6.4-2.1_amd64 bug

NAME

       dcm2xml - Convert DICOM file and data set to XML

SYNOPSIS

       dcm2xml [options] dcmfile-in [xmlfile-out]

DESCRIPTION

       The dcm2xml utility converts the contents of a DICOM file (file format or raw data set) to
       XML (Extensible Markup Language). There are two output formats. The first one is  specific
       to  DCMTK  with  its DTD (Document Type Definition) described in the file dcm2xml.dtd. The
       second one refers to the 'Native DICOM Model' which is specified for the DICOM Application
       Hosting service found in DICOM part 19.

       If  dcm2xml  reads  a  raw data set (DICOM data without a file format meta-header) it will
       attempt to guess the transfer syntax by examining the first few bytes of the file.  It  is
       not  always  possible to correctly guess the transfer syntax and it is better to convert a
       data set to a file format whenever possible  (using  the  dcmconv  utility).  It  is  also
       possible  to  use  the  -f  and -t[ieb] options to force dcm2xml to read a data set with a
       particular transfer syntax.

PARAMETERS

       dcmfile-in   DICOM input filename to be converted

       xmlfile-out  XML output filename (default: 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-file
                 read file format or data set (default)

         +fo   --read-file-only
                 read file format only

         -f    --read-dataset
                 read data set without file meta information

       input transfer syntax:

         -t=   --read-xfer-auto
                 use TS recognition (default)

         -td   --read-xfer-detect
                 ignore TS specified in the file meta header

         -te   --read-xfer-little
                 read with explicit VR little endian TS

         -tb   --read-xfer-big
                 read with explicit VR big endian TS

         -ti   --read-xfer-implicit
                 read with implicit VR little endian TS

       long tag values:

         +M    --load-all
                 load very long tag values (e.g. pixel data)

         -M    --load-short
                 do not load very long values (default)

         +R    --max-read-length  [k]bytes: integer (4..4194302, default: 4)
                 set threshold for long values to k kbytes

   processing options
       specific character set:

         +Cr   --charset-require
                 require declaration of extended charset (default)

         +Ca   --charset-assume  [c]harset: string
                 assume charset c if no extended charset declared

         +Cc   --charset-check-all
                 check all data elements with string values
                 (default: only PN, LO, LT, SH, ST, UC and UT)

                 # this option is only used for the mapping to an appropriate
                 # XML character encoding, but not for the conversion to UTF-8

         +U8   --convert-to-utf8
                 convert all element values that are affected
                 by Specific Character Set (0008,0005) to UTF-8

                 # requires support from an underlying character encoding library
                 # (see output of --version on which one is available)

   output options
       general XML format:

         -dtk  --dcmtk-format
                 output in DCMTK-specific format (default)

         -nat  --native-format
                 output in Native DICOM Model format (part 19)

         +Xn   --use-xml-namespace
                 add XML namespace declaration to root element

       DCMTK-specific format (not with --native-format):

         +Xd   --add-dtd-reference
                 add reference to document type definition (DTD)

         +Xe   --embed-dtd-content
                 embed document type definition into XML document

         +Xf   --use-dtd-file  [f]ilename: string
                 use specified DTD file (only with +Xe)
                 (default: /usr/local/share/dcmtk/dcm2xml.dtd)

         +Wn   --write-element-name
                 write name of the DICOM data elements (default)

         -Wn   --no-element-name
                 do not write name of the DICOM data elements

         +Wb   --write-binary-data
                 write binary data of OB and OW elements
                 (default: off, be careful with --load-all)

       encoding of binary data:

         +Eh   --encode-hex
                 encode binary data as hex numbers
                 (default for DCMTK-specific format)

         +Eu   --encode-uuid
                 encode binary data as a UUID reference
                 (default for Native DICOM Model)

         +Eb   --encode-base64
                 encode binary data as Base64 (RFC 2045, MIME)

DCMTK Format

       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.

   XML Encoding
       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 information 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 or OF are not regarded as 'binary information'.

       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.

Native DICOM Model Format

       The  description of the Native DICOM Model format can be found in the DICOM standard, part
       19 ('Application Hosting').

   Bulk Data
       Binary data, i.e. DICOM element values with Value Representations (VR) of  OB  or  OW,  as
       well as OD, OF 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 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 --encode-base64 enables this encoding for
       the following VRs: OB, OD, OF, OW, and UN.

   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,  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).

NOTES

   Character Encoding
       The XML  encoding  is  determined  automatically  from  the  DICOM  attribute  (0008,0005)
       'Specific Character Set' using the following mapping:

       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"

       If  this  DICOM attribute is missing in the input file, although needed, option --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, cyrillic, arabic, greek,
       hebrew.

       Multiple character sets using code extension techniques  are  not  supported.  If  needed,
       option  --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.

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  dcm2xml  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

       xml2dcm(1), dcmconv(1)

COPYRIGHT

       Copyright (C) 2002-2016 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.