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dsr2xml - Online in the Cloud

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This is the command dsr2xml 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


dsr2xml - Convert DICOM SR file and data set to XML

SYNOPSIS


dsr2xml [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

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 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 the libiconv toolkit

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
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 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"

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).

Multiple character sets are not supported (only the first attribute value is mapped in
case of value multiplicity). If needed, 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.

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.

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.

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 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.

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