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dsr2html - Render DICOM SR file and data set to HTML/XHTML


dsr2html [options] dsrfile-in [htmlfile-out]


The dsr2html utility renders the contents of a DICOM Structured Reporting (SR) document
(file format or raw data set) to HTML (Hyper Text Markup Language) version 3.2 or 4.01 as
well as to XHTML (Extensible Hyper Text Markup Language) version 1.1.

If dsr2html 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 dsr2html to read a dataset with a
particular transfer syntax.


dsrfile-in DICOM SR input filename to be rendered

htmlfile-out HTML/XHTML output filename (default: stdout)


general options
-h --help
print this help text and exit

print version information and exit

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
additional information:

-Ip --processing-details
show currently processed content item

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 (incl. 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

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
# HTML/XHTML 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
HTML/XHTML compatibility:

+H3 --html-3.2
use only HTML version 3.2 compatible features

+H4 --html-4.0
allow all HTML version 4.01 features (default)

+X1 --xhtml-1.1
comply with XHTML version 1.1 specification

+Hd --add-document-type
add reference to SGML document type definition

cascading style sheet (CSS), not with HTML 3.2:

+Sr --css-reference URL: string
add reference to specified CSS to document

+Sf --css-file [f]ilename: string
embed content of specified CSS into document

general rendering:

+Ri --expand-inline
expand short content items inline (default)

-Ri --never-expand-inline
never expand content items inline

+Ra --always-expand-inline
always expand content items inline

+Rd --render-full-data
render full data of content items

+Rt --section-title-inline
render section titles inline, not separately

document rendering:

+Dt --document-type-title
use document type as document title (default)

+Dp --patient-info-title
use patient information as document title

-Dh --no-document-header
do not render general document information

code rendering:

+Ci --render-inline-codes
render codes in continuous text blocks

+Cn --concept-name-codes
render code of concept names

+Cu --numeric-unit-codes
render code of numeric measurement units

+Cv --code-value-unit
use code value as measurement unit (default)

+Cm --code-meaning-unit
use code meaning as measurement unit

+Cc --render-all-codes
render all codes (implies +Ci, +Cn and +Cu)

+Ct --code-details-tooltip
render code details as a tooltip (implies +Cc)


DICOM Conformance
The dsr2html utility supports the following SOP Classes:

SpectaclePrescriptionReportStorage 1.2.840.10008.
MacularGridThicknessAndVolumeReportStorage 1.2.840.10008.
BasicTextSRStorage 1.2.840.10008.
EnhancedSRStorage 1.2.840.10008.
ComprehensiveSRStorage 1.2.840.10008.
Comprehensive3DSRStorage 1.2.840.10008.
ProcedureLogStorage 1.2.840.10008.
MammographyCADSRStorage 1.2.840.10008.
KeyObjectSelectionDocumentStorage 1.2.840.10008.
ChestCADSRStorage 1.2.840.10008.
XRayRadiationDoseSRStorage 1.2.840.10008.
RadiopharmaceuticalRadiationDoseSRStorage 1.2.840.10008.
ColonCADSRStorage 1.2.840.10008.
ImplantationPlanSRDocumentStorage 1.2.840.10008.

Character Encoding
The HTML/XHTML encoding is determined automatically from the DICOM attribute (0008,0005)
'Specific Character Set' using the following mapping:

ASCII (ISO_IR 6) => (none)
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 rendering to HTML/XHTML format.


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.


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).


The dsr2html 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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