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/*!
\if MANPAGES
\page dsr2xml Convert DICOM SR file and data set to XML
\else
\page dsr2xml dsr2xml: Convert DICOM SR file and data set to XML
\endif
\section dsr2xml_synopsis SYNOPSIS
\verbatim
dsr2xml [options] dsrfile-in [xmlfile-out]
\endverbatim
\section dsr2xml_description DESCRIPTION
The \b 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 <em>dsr2xml.xsd</em> does not yet follow any
standard format. However, the \b dsr2xml application might be enhanced in
this aspect in the future (e.g. by supporting HL7/CDA - Clinical Document
Architecture).
If \b 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 \b dcmconv utility). It is also possible to use
the \e -f and <em>-t[ieb]</em> options to force \b dsr2xml to read a dataset
with a particular transfer syntax.
\section dsr2xml_parameters PARAMETERS
\verbatim
dsrfile-in DICOM SR input filename to be converted ("-" for stdin)
xmlfile-out XML output filename (default: stdout)
\endverbatim
\section dsr2xml_options OPTIONS
\subsection dsr2xml_general_options general options
\verbatim
-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
\endverbatim
\subsection dsr2xml_input_options input options
\verbatim
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
\endverbatim
\subsection dsr2xml_processing_options processing options
\verbatim
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)
\endverbatim
\subsection dsr2xml_output_options output options
\verbatim
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
\endverbatim
\section dsr2xml_notes NOTES
\subsection dsr2xml_dicom_conformance DICOM Conformance
The \b dsr2xml utility supports the following SOP Classes:
\verbatim
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
\endverbatim
Please note that currently only mandatory and some optional attributes are
supported.
\subsection dsr2xml_character_encoding Character Encoding
The XML encoding is determined automatically from the DICOM attribute
(0008,0005) "Specific Character Set" using the following mapping:
\verbatim
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 13\ISO 2022 IR 87" => "ISO-2022-JP"
Korean "ISO 2022 IR 6\ISO 2022 IR 149" => "ISO-2022-KR"
Chinese "ISO 2022 IR 6\ISO 2022 IR 58" => "ISO-2022-CN"
Chinese "GB18030" => "GB18030"
Chinese "GBK" => "GBK"
\endverbatim
If this DICOM attribute is missing in the input file, although needed, option
\e --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 \e --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 \e --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.
\subsection dsr2xml_error_handling Error Handling
Please be careful with the processing options \e --unknown-relationship,
\e --invalid-item-value, \e --ignore-constraints, \e --ignore-item-errors and
\e --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.
\subsection dsr2xml_limitations Limitations
The XML Schema <em>dsr2xml.xsd</em> does not support all variations of the
\b dsr2xml output format. However, the default output format (plus option
\e --use-xml-namespace) should work.
\section dsr2xml_logging 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 \e --verbose also
informational messages like processing details are reported. Option
\e --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
\e --log-level. In \e --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 \e --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 <em>\<etcdir\>/logger.cfg</em>.
\section dsr2xml_command_line 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. <em>\@command.txt</em>). 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
<em>\<datadir\>/dumppat.txt</em>).
\section dsr2xml_environment ENVIRONMENT
The \b dsr2xml utility will attempt to load DICOM data dictionaries specified
in the \e DCMDICTPATH environment variable. By default, i.e. if the
\e DCMDICTPATH environment variable is not set, the file
<em>\<datadir\>/dicom.dic</em> will be loaded unless the dictionary is built
into the application (default for Windows).
The default behavior should be preferred and the \e DCMDICTPATH environment
variable only used when alternative data dictionaries are required. The
\e DCMDICTPATH environment variable has the same format as the Unix shell
\e 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 \e DCMDICTPATH environment variable.
It is an error if no data dictionary can be loaded.
Depending on the command line options specified, the \b 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 <em>\<datadir\></em>.
The \e 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.
\section dsr2xml_files FILES
<em>\<datadir\>/dsr2xml.xsd</em> - XML Schema file
\section dsr2xml_see_also SEE ALSO
<b>xml2dsr</b>(1), <b>dcmconv</b>(1)
\section dsr2xml_copyright COPYRIGHT
Copyright (C) 2000-2024 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.
*/
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