dsr2xml(1)                        OFFIS DCMTK                       dsr2xml(1)

NAME
       dsr2xml - Convert DICOM SR file and data set to XML


SYNOPSIS
       dsr2xml [options] dsrfile-in [xmlfile-out]

DESCRIPTION
       The  dsr2xml  utility  converts  the  contents  of  a  DICOM Structured
       Reporting  (SR)  document  (file  format  or  raw  data  set)  to   XML
       (Extensible  Markup  Language). The XML Schema dsr2xml.xsd does not yet
       follow any standard format. However, the dsr2xml application  might  be
       enhanced  in  this  aspect  in the future (e.g. by supporting HL7/CDA -
       Clinical Document Architecture).

       If dsr2xml 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 dsr2xml to  read  a
       dataset with a particular transfer syntax.

PARAMETERS
       dsrfile-in   DICOM SR input filename to be converted ("-" for stdin)

       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

   processing options
       error handling:

         -Er  --unknown-relationship
                accept unknown/missing relationship type

         -Ev  --invalid-item-value
                accept invalid content item value
                (e.g. violation of VR or VM definition)

         -Ec  --ignore-constraints
                ignore relationship content constraints

         -Ee  --ignore-item-errors
                do not abort on content item errors, just warn
                (e.g. missing value type specific attributes)

         -Ei  --skip-invalid-items
                skip invalid content items (including sub-tree)

         -Dv  --disable-vr-checker
                disable check for VR-conformant string values

       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 extended check whether
                # the Specific Character Set (0008,0005) attribute should be
                # present, but not for the conversion of unaffected element
                # values to UTF-8 (e.g. element values with a VR of CS)

         +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
       encoding:

         +Ea  --attr-all
                encode everything as XML attribute
                (shortcut for +Ec, +Er, +Ev and +Et)

         +Ec  --attr-code
                encode code value, coding scheme designator
                and coding scheme version as XML attribute

         +Er  --attr-relationship
                encode relationship type as XML attribute

         +Ev  --attr-value-type
                encode value type as XML attribute

         +Et  --attr-template-id
                encode template id as XML attribute

         +Ee  --template-envelope
                template element encloses content items
                (requires +Wt, implies +Et)

       XML structure:

         +Xs  --add-schema-reference
                add reference to XML Schema "dsr2xml.xsd"
                (not with +Ea, +Ec, +Er, +Ev, +Et, +Ee, +We)

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

       writing:

         +We  --write-empty-tags
                write all tags even if their value is empty

         +Wi  --write-item-id
                always write item identifier

         +Wt  --write-template-id
                write template identification information

NOTES
   DICOM Conformance
       The dsr2xml utility supports the following SOP Classes:

       SpectaclePrescriptionReportStorage           1.2.840.10008.5.1.4.1.1.78.6
       MacularGridThicknessAndVolumeReportStorage   1.2.840.10008.5.1.4.1.1.79.1
       BasicTextSRStorage                           1.2.840.10008.5.1.4.1.1.88.11
       EnhancedSRStorage                            1.2.840.10008.5.1.4.1.1.88.22
       ComprehensiveSRStorage                       1.2.840.10008.5.1.4.1.1.88.33
       Comprehensive3DSRStorage                     1.2.840.10008.5.1.4.1.1.88.34
       ProcedureLogStorage                          1.2.840.10008.5.1.4.1.1.88.40
       MammographyCADSRStorage                      1.2.840.10008.5.1.4.1.1.88.50
       KeyObjectSelectionDocumentStorage            1.2.840.10008.5.1.4.1.1.88.59
       ChestCADSRStorage                            1.2.840.10008.5.1.4.1.1.88.65
       XRayRadiationDoseSRStorage                   1.2.840.10008.5.1.4.1.1.88.67
       RadiopharmaceuticalRadiationDoseSRStorage    1.2.840.10008.5.1.4.1.1.88.68
       ColonCADSRStorage                            1.2.840.10008.5.1.4.1.1.88.69
       ImplantationPlanSRStorage                    1.2.840.10008.5.1.4.1.1.88.70
       AcquisitionContextSRStorage                  1.2.840.10008.5.1.4.1.1.88.71
       SimplifiedAdultEchoSRStorage                 1.2.840.10008.5.1.4.1.1.88.72
       PatientRadiationDoseSRStorage                1.2.840.10008.5.1.4.1.1.88.73
       PlannedImagingAgentAdministrationSRStorage   1.2.840.10008.5.1.4.1.1.88.74
       PerformedImagingAgentAdministrationSRStorage 1.2.840.10008.5.1.4.1.1.88.75
       WaveformAnnotationSRStorage                  1.2.840.10008.5.1.4.1.1.88.77

       Please  note that currently only mandatory and some optional attributes
       are supported.

   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"
       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"
       Thai          "ISO_IR 166"                     =>  "TIS-620"
       Japanese      "ISO 2022 IR 13ISO 2022 IR 87"  =>  "ISO-2022-JP"
       Korean        "ISO 2022 IR 6ISO 2022 IR 149"  =>  "ISO-2022-KR"
       Chinese       "ISO 2022 IR 6ISO 2022 IR 58"   =>  "ISO-2022-CN"
       Chinese       "GB18030"                        =>  "GB18030"
       Chinese       "GBK"                            =>  "GBK"

       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, latin-9, cyrillic, arabic, greek, hebrew.

       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.

       If no mapping is defined and option --convert-to-utf8 is not used, non-
       ASCII characters and those below #32 are stored as '&#nnn;' where 'nnn'
       refers  to  the  numeric  character  code.  This  might lead to invalid
       character entity references (such as '&#27;' for ESC)  and  will  cause
       most XML parsers to reject the document.

   Error Handling
       Please  be  careful with the processing options --unknown-relationship,
       --invalid-item-value,  --ignore-constraints,  --ignore-item-errors  and
       --skip-invalid-items  since  they  disable certain validation checks on
       the DICOM SR input file and, therefore, might  result  in  non-standard
       conformant  output.  However,  there  might be reasons for using one or
       more of these options, e.g. in order to read and process an incorrectly
       encoded SR document.

   Limitations
       The XML Schema dsr2xml.xsd does  not  support  all  variations  of  the
       dsr2xml  output format. However, the default output format (plus option
       --use-xml-namespace) should work.

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 dsr2xml 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.

       Depending  on  the  command line options specified, the dsr2xml utility
       will attempt to load character set mapping tables.  This  happens  when
       DCMTK  was compiled with the oficonv library (which is the default) and
       the mapping tables are not built into the library (default  when  DCMTK
       uses shared libraries).

       The  mapping  table  files  are  expected  in  DCMTK's  <datadir>.  The
       DCMICONVPATH environment variable can be used to  specify  a  different
       location.  If  a  different location is specified, those mapping tables
       also replace any built-in tables.

FILES
       <datadir>/dsr2xml.xsd - XML Schema file

SEE ALSO
       xml2dsr(1), dcmconv(1)

COPYRIGHT
       Copyright (C) 2000-2024 by OFFIS e.V., Escherweg  2,  26121  Oldenburg,
       Germany.

Version 3.6.9                   Wed Dec 11 2024                     dsr2xml(1)
