1xml2dsr(1) OFFIS DCMTK xml2dsr(1)
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6 xml2dsr - Convert DICOM SR file and data set to XML
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9 xml2dsr [options] xmlfile-in dsrfile-out
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12 The xml2dsr utility converts the contents of an XML (Extensible Markup
13 Language) document to DICOM Structured Reporting (SR) format (file
14 format or raw data set). The XML Schema dsr2xml.xsd does not yet follow
15 any standard format. However, the xml2dsr application might be enhanced
16 in this aspect in the future (e. g. by supporting HL7/CDA - Clinical
17 Document Architecture).
18 An appropriate XML file can be created using the dsr2xml tool (option
20 +Xn recommended to add XML namespace declaration to the root element).
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23 xmlfile-in XML input filename to be converted (stdin: "-")
24 dsrfile-out DICOM SR output filename
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28 general options
29 -h --help
30 print this help text and exit
31 --version
33 print version information and exit
34 --arguments
36 print expanded command line arguments
37 -q --quiet
39 quiet mode, print no warnings and errors
40 -v --verbose
42 verbose mode, print processing details
43 -d --debug
45 debug mode, print debug information
46 -ll --log-level [l]evel: string constant
48 (fatal, error, warn, info, debug, trace)
49 use level l for the logger
50 -lc --log-config [f]ilename: string
52 use config file f for the logger
53 input options
55 encoding:
56 +Ee --template-envelope
58 template element encloses content items
59 processing options
61 validation:
62 +Vs --validate-schema
64 validate XML document against Schema
65 (not with --template-envelope)
66 +Vn --check-namespace
68 check XML namespace in document root
69 unique identifiers:
71 +Ug --generate-new-uids
73 generate new Study/Series/SOP Instance UID
74 -Uo --dont-overwrite-uids
76 do not overwrite existing UIDs (default)
77 +Uo --overwrite-uids
79 overwrite existing UIDs
80 output options
82 output file format:
83 +F --write-file
85 write file format (default)
86 -F --write-dataset
88 write data set without file meta information
89 output transfer syntax:
91 +t= --write-xfer-same
93 write with same TS as input (default)
94 +te --write-xfer-little
96 write with explicit VR little endian TS
97 +tb --write-xfer-big
99 write with explicit VR big endian TS
100 +ti --write-xfer-implicit
102 write with implicit VR little endian TS
103 +td --write-xfer-deflated
105 write with deflated explicit VR little endian TS
106 post-1993 value representations:
108 +u --enable-new-vr
110 enable support for new VRs (UN/UT) (default)
111 -u --disable-new-vr
113 disable support for new VRs, convert to OB
114 group length encoding:
116 +g= --group-length-recalc
118 recalculate group lengths if present (default)
119 +g --group-length-create
121 always write with group length elements
122 -g --group-length-remove
124 always write without group length elements
125 length encoding in sequences and items:
127 +e --length-explicit
129 write with explicit lengths (default)
130 -e --length-undefined
132 write with undefined lengths
133 data set trailing padding (not with --write-dataset):
135 -p= --padding-retain
137 do not change padding (default if not --write-dataset)
138 -p --padding-off
140 no padding (implicit if --write-dataset)
141 +p --padding-create [f]ile-pad [i]tem-pad: integer
143 align file on multiple of f bytes
144 and items on multiple of i bytes
145 deflate compression level (only with --write-xfer-deflated):
147 +cl --compression-level [l]evel: integer (default: 6)
149 0=uncompressed, 1=fastest, 9=best compression
150
152 DICOM Conformance
153 The xml2dsr utility supports the following SOP Classes:
154 SpectaclePrescriptionReportStorage 1.2.840.10008.5.1.4.1.1.78.6
156 MacularGridThicknessAndVolumeReportStorage 1.2.840.10008.5.1.4.1.1.79.1
157 BasicTextSRStorage 1.2.840.10008.5.1.4.1.1.88.11
158 EnhancedSRStorage 1.2.840.10008.5.1.4.1.1.88.22
159 ComprehensiveSRStorage 1.2.840.10008.5.1.4.1.1.88.33
160 ProcedureLogStorage 1.2.840.10008.5.1.4.1.1.88.40
161 MammographyCADSRStorage 1.2.840.10008.5.1.4.1.1.88.50
162 KeyObjectSelectionDocumentStorage 1.2.840.10008.5.1.4.1.1.88.59
163 ChestCADSRStorage 1.2.840.10008.5.1.4.1.1.88.65
164 XRayRadiationDoseSRStorage 1.2.840.10008.5.1.4.1.1.88.67
165 ColonCADSRStorage 1.2.840.10008.5.1.4.1.1.88.69
166 ImplantationPlanSRDocumentStorage 1.2.840.10008.5.1.4.1.1.88.70
167 Please note that currently only mandatory and some optional attributes
169 are supported.
170
172 The level of logging output of the various command line tools and
173 underlying libraries can be specified by the user. By default, only
174 errors and warnings are written to the standard error stream. Using
175 option --verbose also informational messages like processing details
176 are reported. Option --debug can be used to get more details on the
177 internal activity, e.g. for debugging purposes. Other logging levels
178 can be selected using option --log-level. In --quiet mode only fatal
179 errors are reported. In such very severe error events, the application
180 will usually terminate. For more details on the different logging
181 levels, see documentation of module 'oflog'.
182 In case the logging output should be written to file (optionally with
184 logfile rotation), to syslog (Unix) or the event log (Windows) option
185 --log-config can be used. This configuration file also allows for
186 directing only certain messages to a particular output stream and for
187 filtering certain messages based on the module or application where
188 they are generated. An example configuration file is provided in
189 <etcdir>/logger.cfg).
190
192 All command line tools use the following notation for parameters:
193 square brackets enclose optional values (0-1), three trailing dots
194 indicate that multiple values are allowed (1-n), a combination of both
195 means 0 to n values.
196 Command line options are distinguished from parameters by a leading '+'
198 or '-' sign, respectively. Usually, order and position of command line
199 options are arbitrary (i.e. they can appear anywhere). However, if
200 options are mutually exclusive the rightmost appearance is used. This
201 behaviour conforms to the standard evaluation rules of common Unix
202 shells.
203 In addition, one or more command files can be specified using an '@'
205 sign as a prefix to the filename (e.g. @command.txt). Such a command
206 argument is replaced by the content of the corresponding text file
207 (multiple whitespaces are treated as a single separator unless they
208 appear between two quotation marks) prior to any further evaluation.
209 Please note that a command file cannot contain another command file.
210 This simple but effective approach allows to summarize common
211 combinations of options/parameters and avoids longish and confusing
212 command lines (an example is provided in file <datadir>/dumppat.txt).
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215 The xml2dsr utility will attempt to load DICOM data dictionaries
216 specified in the DCMDICTPATH environment variable. By default, i.e. if
217 the DCMDICTPATH environment variable is not set, the file
218 <datadir>/dicom.dic will be loaded unless the dictionary is built into
219 the application (default for Windows).
220 The default behaviour should be preferred and the DCMDICTPATH
222 environment variable only used when alternative data dictionaries are
223 required. The DCMDICTPATH environment variable has the same format as
224 the Unix shell PATH variable in that a colon (':') separates entries.
225 On Windows systems, a semicolon (';') is used as a separator. The data
226 dictionary code will attempt to load each file specified in the
227 DCMDICTPATH environment variable. It is an error if no data dictionary
228 can be loaded.
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231 <datadir>/dsr2xml.xsd - XML Schema file
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234 dsr2xml(1)
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237 Copyright (C) 2003-2010 by OFFIS e.V., Escherweg 2, 26121 Oldenburg,
238 Germany.
239Version 3.6.0 6 Jan 2011 xml2dsr(1)