dsr2xml(1)

📦
version 3.7.1 · 10 versions
, in arch rolling

okay so bestie, this is the dsr2xml(1) page from OFFIS DCMTK — part one of the glow-up. Buckle up, because this tool is literally converting DICOM SR to XML and it has a lot to say. 🦋

🌸 NAME 🌸

dsr2xml — convert DICOM SR file and data set to XML. periodt. 💅

✨ 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 ("-" for stdin)
  • 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 — use level l for the logger. Values: (fatal, error, warn, info, debug, trace)
  • -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, UC and UT)
# this option is only used for the extended check whether # the Specific Character Set (0008,0005) attribute should be # present, but not for the conversion of unaffected element # values to UTF-8 (e.g. element values with a VR of CS)
  • +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 🎁

🏷️ 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
  • ImplantationPlanSRStorage — 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
  • PatientRadiationDoseSRStorage — 1.2.840.10008.5.1.4.1.1.88.73
  • PlannedImagingAgentAdministrationSRStorage — 1.2.840.10008.5.1.4.1.1.88.74
  • PerformedImagingAgentAdministrationSRStorage — 1.2.840.10008.5.1.4.1.1.88.75
  • WaveformAnnotationSRStorage — 1.2.840.10008.5.1.4.1.1.88.77
  • RenditionSelectionDocumentRealTimeCommunication — 1.2.840.10008.10.4 (*)
(*) This is not a Storage SOP Class, but used for Real-Time Communication.

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"
  • ISO Latin 9 "ISO_IR 203" → "ISO-8859-15"
  • 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 13\ISO 2022 IR 87" → "ISO-2022-JP"
  • Korean "ISO 2022 IR 6\ISO 2022 IR 149" → "ISO-2022-KR"
  • Chinese "ISO 2022 IR 6\ISO 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, latin-9, 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 conversion to XML format.

If no mapping is defined and option --convert-to-utf8 is not used, non-ASCII characters and those below #32 are stored as "&#nnn;" where "nnn" refers to the numeric character code. This might lead to invalid character entity references (such as "" for ESC) and will cause most XML parsers to reject the document.

🚨 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 (aka how much tea dsr2xml spills)

Okay bestie, so you can literally choose how chatty the command line tools and the underlying libraries are. The level of logging output is totally up to you.

By default? Only errors and warnings get written to the standard error stream. The bare minimum, no yapping.

  • --verbose — turns it up a notch, so you also get informational messages like processing details. She's opening up 💬
  • --debug — for when you really need the tea, this gives you way more details on the internal activity, e.g. for debugging purposes 🔍
  • --log-level — pick any of the other logging levels with this one
  • --quiet — in this mode only fatal errors are reported. And ngl, in such very severe error events, the application will usually terminate 😭 like it's done, it's over

For more details on the different logging levels, go check the documentation of module "oflog", iykyk.

Now, if you want that logging output going somewhere else — like to a file (optionally with logfile rotation ✨), to syslog (Unix) or to the event log (Windows) — use --log-config. This configuration file also lets you direct only certain messages to a particular output stream, and filter certain messages based on the module or application where they're generated. Iconic, honestly. An example configuration file is provided in <etcdir>/logger.cfg 🎀

✨ COMMAND LINE (the rules of the group chat)

All command line tools use the following notation for parameters, bestie, memorize it:

  • 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. Periodt. 💅

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.

⚠️ Heads up: a command file cannot contain another command file. No inception, no nesting, we don't do that here 🙈

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). So convenient, obsessed 🫶

🌸 ENVIRONMENT (the vibes your shell brings)

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 (which is the default for Windows). 🪟

The default behavior should be preferred, and the DCMDICTPATH environment variable only used when alternative data dictionaries are required. Fr fr, don't touch it unless you need to.

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. Like, actual error. Not a vibe.

Depending on the command line options specified, the dsr2xml utility will also attempt to load character set mapping tables. This happens when DCMTK was compiled with the oficonv library (which is the default) and the mapping tables are not built into the library (the default when DCMTK uses shared libraries). 🌈

The mapping table files are expected in DCMTK's <datadir>. The DCMICONVPATH environment variable can be used to specify a different location. If a different location is specified, those mapping tables also replace any built-in tables. 🦋

🎀 FILES (the one file, she's singular and she's iconic)

  • <datadir>/dsr2xml.xsd — XML Schema file

👑 SEE ALSO (go read these too, bestie)

xml2dsr(1), dcmconv(1)

Copyright (C) 2000-2026 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.

That's the whole page, bestie, you made it 💖 This was Version 3.7.1, dated Sat Oct 17 2026 09:34:01 — go forth and dsr2xml responsibly, mwah 🧚‍♀️✨

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