OFFIS DCMTK  Version 3.6.0
xml2dsr.man
1 /*!
2 
3 \if MANPAGES
4 \page xml2dsr Convert DICOM SR file and data set to XML
5 \else
6 \page xml2dsr xml2dsr: Convert DICOM SR file and data set to XML
7 \endif
8 
9 \section synopsis SYNOPSIS
10 
11 \verbatim
12 xml2dsr [options] xmlfile-in dsrfile-out
13 \endverbatim
14 
15 \section description DESCRIPTION
16 
17 The \b xml2dsr utility converts the contents of an XML (Extensible Markup
18 Language) document to DICOM Structured Reporting (SR) format (file format
19 or raw data set). The XML Schema <em>dsr2xml.xsd</em> does not yet follow
20 any standard format. However, the \b xml2dsr application might be enhanced
21 in this aspect in the future (e. g. by supporting HL7/CDA - Clinical
22 Document Architecture).
23 
24 An appropriate XML file can be created using the \b dsr2xml tool (option
25 \e +Xn recommended to add XML namespace declaration to the root element).
26 
27 \section parameters PARAMETERS
28 
29 \verbatim
30 xmlfile-in XML input filename to be converted (stdin: "-")
31 
32 dsrfile-out DICOM SR output filename
33 \endverbatim
34 
35 \section options OPTIONS
36 
37 \subsection general_options general options
38 \verbatim
39  -h --help
40  print this help text and exit
41 
42  --version
43  print version information and exit
44 
45  --arguments
46  print expanded command line arguments
47 
48  -q --quiet
49  quiet mode, print no warnings and errors
50 
51  -v --verbose
52  verbose mode, print processing details
53 
54  -d --debug
55  debug mode, print debug information
56 
57  -ll --log-level [l]evel: string constant
58  (fatal, error, warn, info, debug, trace)
59  use level l for the logger
60 
61  -lc --log-config [f]ilename: string
62  use config file f for the logger
63 \endverbatim
64 
65 \subsection input_options input options
66 \verbatim
67 encoding:
68 
69  +Ee --template-envelope
70  template element encloses content items
71 \endverbatim
72 
73 \subsection processing_options processing options
74 \verbatim
75 validation:
76 
77  +Vs --validate-schema
78  validate XML document against Schema
79  (not with --template-envelope)
80 
81  +Vn --check-namespace
82  check XML namespace in document root
83 
84 unique identifiers:
85 
86  +Ug --generate-new-uids
87  generate new Study/Series/SOP Instance UID
88 
89  -Uo --dont-overwrite-uids
90  do not overwrite existing UIDs (default)
91 
92  +Uo --overwrite-uids
93  overwrite existing UIDs
94 \endverbatim
95 
96 \subsection output_options output options
97 \verbatim
98 output file format:
99 
100  +F --write-file
101  write file format (default)
102 
103  -F --write-dataset
104  write data set without file meta information
105 
106 output transfer syntax:
107 
108  +t= --write-xfer-same
109  write with same TS as input (default)
110 
111  +te --write-xfer-little
112  write with explicit VR little endian TS
113 
114  +tb --write-xfer-big
115  write with explicit VR big endian TS
116 
117  +ti --write-xfer-implicit
118  write with implicit VR little endian TS
119 
120  +td --write-xfer-deflated
121  write with deflated explicit VR little endian TS
122 
123 post-1993 value representations:
124 
125  +u --enable-new-vr
126  enable support for new VRs (UN/UT) (default)
127 
128  -u --disable-new-vr
129  disable support for new VRs, convert to OB
130 
131 group length encoding:
132 
133  +g= --group-length-recalc
134  recalculate group lengths if present (default)
135 
136  +g --group-length-create
137  always write with group length elements
138 
139  -g --group-length-remove
140  always write without group length elements
141 
142 length encoding in sequences and items:
143 
144  +e --length-explicit
145  write with explicit lengths (default)
146 
147  -e --length-undefined
148  write with undefined lengths
149 
150 data set trailing padding (not with --write-dataset):
151 
152  -p= --padding-retain
153  do not change padding (default if not --write-dataset)
154 
155  -p --padding-off
156  no padding (implicit if --write-dataset)
157 
158  +p --padding-create [f]ile-pad [i]tem-pad: integer
159  align file on multiple of f bytes
160  and items on multiple of i bytes
161 
162 deflate compression level (only with --write-xfer-deflated):
163 
164  +cl --compression-level [l]evel: integer (default: 6)
165  0=uncompressed, 1=fastest, 9=best compression
166 \endverbatim
167 
168 \section notes NOTES
169 
170 \subsection dicom_conformance DICOM Conformance
171 
172 The \b xml2dsr utility supports the following SOP Classes:
173 
174 \verbatim
175 SpectaclePrescriptionReportStorage 1.2.840.10008.5.1.4.1.1.78.6
176 MacularGridThicknessAndVolumeReportStorage 1.2.840.10008.5.1.4.1.1.79.1
177 BasicTextSRStorage 1.2.840.10008.5.1.4.1.1.88.11
178 EnhancedSRStorage 1.2.840.10008.5.1.4.1.1.88.22
179 ComprehensiveSRStorage 1.2.840.10008.5.1.4.1.1.88.33
180 ProcedureLogStorage 1.2.840.10008.5.1.4.1.1.88.40
181 MammographyCADSRStorage 1.2.840.10008.5.1.4.1.1.88.50
182 KeyObjectSelectionDocumentStorage 1.2.840.10008.5.1.4.1.1.88.59
183 ChestCADSRStorage 1.2.840.10008.5.1.4.1.1.88.65
184 XRayRadiationDoseSRStorage 1.2.840.10008.5.1.4.1.1.88.67
185 ColonCADSRStorage 1.2.840.10008.5.1.4.1.1.88.69
186 ImplantationPlanSRDocumentStorage 1.2.840.10008.5.1.4.1.1.88.70
187 \endverbatim
188 
189 Please note that currently only mandatory and some optional attributes are
190 supported.
191 
192 \section logging LOGGING
193 
194 The level of logging output of the various command line tools and underlying
195 libraries can be specified by the user. By default, only errors and warnings
196 are written to the standard error stream. Using option \e --verbose also
197 informational messages like processing details are reported. Option
198 \e --debug can be used to get more details on the internal activity, e.g. for
199 debugging purposes. Other logging levels can be selected using option
200 \e --log-level. In \e --quiet mode only fatal errors are reported. In such
201 very severe error events, the application will usually terminate. For more
202 details on the different logging levels, see documentation of module "oflog".
203 
204 In case the logging output should be written to file (optionally with logfile
205 rotation), to syslog (Unix) or the event log (Windows) option \e --log-config
206 can be used. This configuration file also allows for directing only certain
207 messages to a particular output stream and for filtering certain messages
208 based on the module or application where they are generated. An example
209 configuration file is provided in <em><etcdir>/logger.cfg</em>).
210 
211 \section command_line COMMAND LINE
212 
213 All command line tools use the following notation for parameters: square
214 brackets enclose optional values (0-1), three trailing dots indicate that
215 multiple values are allowed (1-n), a combination of both means 0 to n values.
216 
217 Command line options are distinguished from parameters by a leading '+' or '-'
218 sign, respectively. Usually, order and position of command line options are
219 arbitrary (i.e. they can appear anywhere). However, if options are mutually
220 exclusive the rightmost appearance is used. This behaviour conforms to the
221 standard evaluation rules of common Unix shells.
222 
223 In addition, one or more command files can be specified using an '@' sign as a
224 prefix to the filename (e.g. <em>\@command.txt</em>). Such a command argument
225 is replaced by the content of the corresponding text file (multiple
226 whitespaces are treated as a single separator unless they appear between two
227 quotation marks) prior to any further evaluation. Please note that a command
228 file cannot contain another command file. This simple but effective approach
229 allows to summarize common combinations of options/parameters and avoids
230 longish and confusing command lines (an example is provided in file
231 <em><datadir>/dumppat.txt</em>).
232 
233 \section environment ENVIRONMENT
234 
235 The \b xml2dsr utility will attempt to load DICOM data dictionaries specified
236 in the \e DCMDICTPATH environment variable. By default, i.e. if the
237 \e DCMDICTPATH environment variable is not set, the file
238 <em><datadir>/dicom.dic</em> will be loaded unless the dictionary is built
239 into the application (default for Windows).
240 
241 The default behaviour should be preferred and the \e DCMDICTPATH environment
242 variable only used when alternative data dictionaries are required. The
243 \e DCMDICTPATH environment variable has the same format as the Unix shell
244 \e PATH variable in that a colon (":") separates entries. On Windows systems,
245 a semicolon (";") is used as a separator. The data dictionary code will
246 attempt to load each file specified in the \e DCMDICTPATH environment variable.
247 It is an error if no data dictionary can be loaded.
248 
249 \section files FILES
250 
251 <em><datadir>/dsr2xml.xsd</em> - XML Schema file
252 
253 \section see_also SEE ALSO
254 
255 <b>dsr2xml</b>(1)
256 
257 \section copyright COPYRIGHT
258 
259 Copyright (C) 2003-2010 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.
260 
261 */


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