xml2dsr(1)                        OFFIS DCMTK                       xml2dsr(1)

NAME
       xml2dsr - Convert XML document to DICOM SR file


SYNOPSIS
       xml2dsr [options] xmlfile-in dsrfile-out

DESCRIPTION
       The  xml2dsr utility converts the contents of an XML (Extensible Markup
       Language) document to DICOM  Structured  Reporting  (SR)  format  (file
       format or raw data set). The XML Schema dsr2xml.xsd does not yet follow
       any standard format. However, the xml2dsr application might be enhanced
       in  this  aspect  in the future (e. g. by supporting HL7/CDA - Clinical
       Document Architecture).

       An appropriate XML file can be created using the dsr2xml  tool  (option
       +Xn recommended to add XML namespace declaration to the root element).

PARAMETERS
       xmlfile-in   XML input filename to be converted ("-" for stdin)

       dsrfile-out  DICOM SR 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
       encoding:

         +Ee  --template-envelope
                template element encloses content items

   processing options
       validation:

         +Vs  --validate-schema
                validate XML document against Schema
                (not with --template-envelope)

         # requires libxml to be compiled with XML Schema support

         +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

       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
   DICOM Conformance
       The xml2dsr 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 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)
       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)

   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
       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.

       Different  versions  of  libxml  seem  to have different limits for the
       maximum length of an XML element value. Therefore, it should be avoided
       to use very long element values. A typical  limit  for  libxml  version
       2.7.3 (and above) is 10 MB for a single element value.

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  xml2dsr  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>/dsr2xml.xsd - XML Schema file

SEE ALSO
       dsr2xml(1)

COPYRIGHT
       Copyright (C) 2003-2024 by OFFIS e.V., Escherweg  2,  26121  Oldenburg,
       Germany.

Version 3.6.9                   Wed Dec 11 2024                     xml2dsr(1)
