Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages


home | help
dsr2xml(1)			  OFFIS	DCMTK			    dsr2xml(1)

       dsr2xml - Convert DICOM SR file and data	set to XML

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

       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.

       dsrfile-in   DICOM SR input filename to be converted

       xmlfile-out  XML	output filename	(default: stdout)

   general options
	 -h   --help
		print this help	text and exit

		print version information and exit

		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 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

	 +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


	 +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

   DICOM Conformance
       The dsr2xml utility supports the	following SOP Classes:

       SpectaclePrescriptionReportStorage	    1.2.840.10008.
       MacularGridThicknessAndVolumeReportStorage   1.2.840.10008.
       BasicTextSRStorage			    1.2.840.10008.
       EnhancedSRStorage			    1.2.840.10008.
       ComprehensiveSRStorage			    1.2.840.10008.
       Comprehensive3DSRStorage			    1.2.840.10008.
       ProcedureLogStorage			    1.2.840.10008.
       MammographyCADSRStorage			    1.2.840.10008.
       KeyObjectSelectionDocumentStorage	    1.2.840.10008.
       ChestCADSRStorage			    1.2.840.10008.
       XRayRadiationDoseSRStorage		    1.2.840.10008.
       RadiopharmaceuticalRadiationDoseSRStorage    1.2.840.10008.
       ColonCADSRStorage			    1.2.840.10008.
       ImplantationPlanSRDocumentStorage	    1.2.840.10008.
       AcquisitionContextSRStorage		    1.2.840.10008.
       SimplifiedAdultEchoSRStorage		    1.2.840.10008.
       PatientRadiationDoseSRStorage		    1.2.840.10008.
       PlannedImagingAgentAdministrationSRStorage   1.2.840.10008.
       PerformedImagingAgentAdministrationSRStorage 1.2.840.10008.

       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"
       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,	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 '' 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.

       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.

       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

       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

       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).

       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.

       _datadir_/dsr2xml.xsd - XML Schema file

       xml2dsr(1), dcmconv(1)

       Copyright  (C)  2000-2019  by OFFIS e.V., Escherweg 2, 26121 Oldenburg,

Version	3.6.5			Mon Oct	28 2019			    dsr2xml(1)


Want to link to this manual page? Use this URL:

home | help