xenial (1) dcm2xml.1.gz

Provided by: dcmtk_3.6.1~20150924-5_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 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 the libiconv toolkit

   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).

       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 (C) 2002-2014 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.