dsr2html (1)
NAME
dsr2html - Render DICOM SR file and data set to HTML/XHTMLSYNOPSIS
dsr2html [options] dsrfile-in [htmlfile-out]
DESCRIPTION
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.
PARAMETERS
dsrfile-in DICOM SR input filename to be rendered htmlfile-out HTML/XHTML 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
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
--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 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 an underlying character encoding library
# (see output of --version on which one is available)
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)
NOTES
DICOM Conformance
The dsr2html 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 AcquisitionContextSRStorage 1.2.840.10008.5.1.4.1.1.88.71 SimplifiedAdultEchoSRStorage 1.2.840.10008.5.1.4.1.1.88.72
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" Thai "ISO_IR 166" => "TIS-620" Japanese "ISO 2022 IR 13ISO 2022 IR 87" => "ISO-2022-JP" Korean "ISO 2022 IR 6ISO 2022 IR 149" => "ISO-2022-KR" Chinese "ISO 2022 IR 6ISO 2022 IR 58" => "ISO-2022-CN" Chinese "GB18030" => "GB18030" Chinese "GBK" => "GBK"
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). 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, cyrillic, arabic, greek, hebrew.
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.
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 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.
FILES
<datadir>/report.css - Sample Cascading Stylesheet file for HTML <datadir>/reportx.css - Sample Cascading Stylesheet file for XHTML
SEE ALSO
COPYRIGHT
Copyright (C) 2000-2016 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.