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/*!
\if MANPAGES
\page xml2dsr Convert XML document to DICOM SR file
\else
\page xml2dsr xml2dsr: Convert XML document to DICOM SR file
\endif
\section xml2dsr_synopsis SYNOPSIS
\verbatim
xml2dsr [options] xmlfile-in dsrfile-out
\endverbatim
\section xml2dsr_description DESCRIPTION
The \b 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 <em>dsr2xml.xsd</em> does not yet follow
any standard format. However, the \b 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 \b dsr2xml tool (option
\e +Xn recommended to add XML namespace declaration to the root element).
\section xml2dsr_parameters PARAMETERS
\verbatim
xmlfile-in XML input filename to be converted ("-" for stdin)
dsrfile-out DICOM SR output filename ("-" for stdout)
\endverbatim
\section xml2dsr_options OPTIONS
\subsection xml2dsr_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 xml2dsr_input_options input options
\verbatim
encoding:
+Ee --template-envelope
template element encloses content items
\endverbatim
\subsection xml2dsr_processing_options processing options
\verbatim
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
\endverbatim
\subsection xml2dsr_output_options output options
\verbatim
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
\endverbatim
\section xml2dsr_notes NOTES
\subsection xml2dsr_dicom_conformance DICOM Conformance
The \b xml2dsr 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 xml2dsr_character_encoding 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 \b libxml to include \b iconv
support, see \e --version output):
\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
\subsection xml2dsr_compression Compression
If libxml is compiled with zlib support, the input file (\e xmlfile-in) can
also be compressed with ZIP, which usually results in much smaller files. See
output of option \e --version in order to check whether zlib support is
available.
\subsection xml2dsr_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.
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.
\section xml2dsr_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 xml2dsr_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 xml2dsr_environment ENVIRONMENT
The \b xml2dsr 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.
\section xml2dsr_files FILES
<em>\<datadir\>/dsr2xml.xsd</em> - XML Schema file
\section xml2dsr_see_also SEE ALSO
<b>dsr2xml</b>(1)
\section xml2dsr_copyright COPYRIGHT
Copyright (C) 2003-2024 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.
*/
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