dsr2html (1) - Linux Manuals

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


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

parsing options

additional information:

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

error handling:

  -Er  --unknown-relationship
         accept unknown/missing relationship type

  -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)

character set:

  +Cr  --charset-require
         require declaration of extended charset (default)

  +Ca  --charset-assume  [c]harset: string constant
         (latin-1 to -5, greek, cyrillic, arabic, hebrew)
         assume c if undeclared extended charset found

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.
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.
ColonCADSRStorage                           1.2.840.10008.
ImplantationPlanSRDocumentStorage           1.2.840.10008.


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 behaviour 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 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 behaviour 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.


<datadir>/report.css - Sample Cascading Stylesheet file for HTML <datadir>/reportx.css - Sample Cascading Stylesheet file for XHTML


Copyright (C) 2000-2010 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.