dsr2xml(1) OFFIS DCMTK dsr2xml(1)NAMEdsr2xml - Convert DICOM SR file and data set to XML
SYNOPSISdsr2xml [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
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
processing options
character set:
+Cr --charset-require
require declaration of extended charset (default)
+Ca --charset-assume [c]harset: string constant
(latin-1 to -5, greek, cyrillic, arabic, hebrew)
assume charset c if no extended charset found
+Cc --charset-check-all
check all data elements with string values
(default: only PN, LO, LT, SH, ST and UT)
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
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
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
ColonCADSRStorage 1.2.840.10008.5.1.4.1.1.88.69
ImplantationPlanSRDocumentStorage 1.2.840.10008.5.1.4.1.1.88.70
Please note that currently only mandatory and some optional attributes
are supported.
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
behaviour 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 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 behaviour 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 ALSOxml2dsr(1), dcmconv(1)COPYRIGHT
Copyright (C) 2000-2010 by OFFIS e.V., Escherweg 2, 26121 Oldenburg,
Germany.
Version 3.6.0 6 Jan 2011 dsr2xml(1)
