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xml2dsr - Online in the Cloud

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This is the command xml2dsr that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


xml2dsr - Convert DICOM SR file and data set to XML

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 (stdin: "-")

dsrfile-out DICOM SR output filename

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
ImplantationPlanSRDocumentStorage 1.2.840.10008.5.1.4.1.1.88.70

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)
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)

Multiple character sets are not supported (only the first value of the 'Specific Character
Set' is used for the character encoding in case of value multiplicity).

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.

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