xml2dsr

Section: OFFIS DCMTK (1)
Updated: Thu Nov 29 2018
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NAME

xml2dsr - Convert DICOM SR file and data set to XML

SYNOPSIS

xml2dsr [options] xmlfile-in dsrfile-out

DESCRIPTION

The xml2dsr utility converts the contents of an XML (Extensible Markup Language) document to DICOM Structured Reporting (SR) format (file format or raw data set). The XML Schema dsr2xml.xsd does not yet follow any standard format. However, the xml2dsr application might be enhanced in this aspect in the future (e. g. by supporting HL7/CDA - Clinical Document Architecture).

An appropriate XML file can be created using the dsr2xml tool (option +Xn recommended to add XML namespace declaration to the root element).

PARAMETERS

xmlfile-in   XML input filename to be converted (stdin: "-")

dsrfile-out  DICOM SR output filename

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

encoding:

  +Ee  --template-envelope
         template element encloses content items

processing options

validation:

  +Vs  --validate-schema
         validate XML document against Schema
         (not with --template-envelope)

  # requires libxml to be compiled with XML Schema support

  +Vn  --check-namespace
         check XML namespace in document root

unique identifiers:

  +Ug  --generate-new-uids
         generate new Study/Series/SOP Instance UID

  -Uo  --dont-overwrite-uids
         do not overwrite existing UIDs (default)

  +Uo  --overwrite-uids
         overwrite existing UIDs

output options

output file format:

  +F   --write-file
         write file format (default)

  -F   --write-dataset
         write data set without file meta information

output transfer syntax:

  +t=  --write-xfer-same
         write with same TS as input (default)

  +te  --write-xfer-little
         write with explicit VR little endian TS

  +tb  --write-xfer-big
         write with explicit VR big endian TS

  +ti  --write-xfer-implicit
         write with implicit VR little endian TS

  +td  --write-xfer-deflated
         write with deflated explicit VR little endian TS

post-1993 value representations:

  +u   --enable-new-vr
         enable support for new VRs (UN/UT) (default)

  -u   --disable-new-vr
         disable support for new VRs, convert to OB

group length encoding:

  +g=  --group-length-recalc
         recalculate group lengths if present (default)

  +g   --group-length-create
         always write with group length elements

  -g   --group-length-remove
         always write without group length elements

length encoding in sequences and items:

  +e   --length-explicit
         write with explicit lengths (default)

  -e   --length-undefined
         write with undefined lengths

data set trailing padding (not with --write-dataset):

  -p=  --padding-retain
         do not change padding (default if not --write-dataset)

  -p   --padding-off
         no padding (implicit if --write-dataset)

  +p   --padding-create  [f]ile-pad [i]tem-pad: integer
         align file on multiple of f bytes
         and items on multiple of i bytes

deflate compression level (only with --write-xfer-deflated):

  +cl  --compression-level  [l]evel: integer (default: 6)
         0=uncompressed, 1=fastest, 9=best compression

NOTES

DICOM Conformance

The xml2dsr 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
PatientRadiationDoseSRStorage               1.2.840.10008.5.1.4.1.1.88.73

Please note that currently only mandatory and some optional attributes are supported.

Character Encoding

The DICOM character encoding is determined automatically from the element with tag '0008,0005' (Specific Character Set) - if present. The following character sets are currently supported (requires libxml to include iconv support, see --version output):

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)
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)

Compression

If libxml is compiled with zlib support, the input file (xmlfile-in) can also be compressed with ZIP, which usually results in much smaller files. See output of option --version in order to check whether zlib support is available.

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.

Different versions of libxml seem to have different limits for the maximum length of an XML element value. Therefore, it should be avoided to use very long element values. A typical limit for libxml version 2.7.3 (and above) is 10 MB for a single element value.

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 xml2dsr 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>/dsr2xml.xsd - XML Schema file