OFFIS DCMTK  Version 3.6.0
dsr2xml.man
1 /*!
2 
3 \if MANPAGES
4 \page dsr2xml Convert DICOM SR file and data set to XML
5 \else
6 \page dsr2xml dsr2xml: Convert DICOM SR file and data set to XML
7 \endif
8 
9 \section synopsis SYNOPSIS
10 
11 \verbatim
12 dsr2xml [options] dsrfile-in [xmlfile-out]
13 \endverbatim
14 
15 \section description DESCRIPTION
16 
17 The \b dsr2xml utility converts the contents of a DICOM Structured Reporting
18 (SR) document (file format or raw data set) to XML (Extensible Markup
19 Language). The XML Schema <em>dsr2xml.xsd</em> does not yet follow any
20 standard format. However, the \b dsr2xml application might be enhanced in
21 this aspect in the future (e.g. by supporting HL7/CDA - Clinical Document
22 Architecture).
23 
24 If \b dsr2xml reads a raw data set (DICOM data without a file format
25 meta-header) it will attempt to guess the transfer syntax by examining the
26 first few bytes of the file. It is not always possible to correctly guess the
27 transfer syntax and it is better to convert a data set to a file format
28 whenever possible (using the \b dcmconv utility). It is also possible to use
29 the \e -f and <em>-t[ieb]</em> options to force \b dsr2xml to read a dataset
30 with a particular transfer syntax.
31 
32 \section parameters PARAMETERS
33 
34 \verbatim
35 dsrfile-in DICOM SR input filename to be converted
36 
37 xmlfile-out XML output filename (default: stdout)
38 \endverbatim
39 
40 \section options OPTIONS
41 
42 \subsection general_options general options
43 \verbatim
44  -h --help
45  print this help text and exit
46 
47  --version
48  print version information and exit
49 
50  --arguments
51  print expanded command line arguments
52 
53  -q --quiet
54  quiet mode, print no warnings and errors
55 
56  -v --verbose
57  verbose mode, print processing details
58 
59  -d --debug
60  debug mode, print debug information
61 
62  -ll --log-level [l]evel: string constant
63  (fatal, error, warn, info, debug, trace)
64  use level l for the logger
65 
66  -lc --log-config [f]ilename: string
67  use config file f for the logger
68 \endverbatim
69 
70 \subsection processing_options processing options
71 \verbatim
72 character set:
73 
74  +Cr --charset-require
75  require declaration of extended charset (default)
76 
77  +Ca --charset-assume [c]harset: string constant
78  (latin-1 to -5, greek, cyrillic, arabic, hebrew)
79  assume charset c if no extended charset found
80 
81  +Cc --charset-check-all
82  check all data elements with string values
83  (default: only PN, LO, LT, SH, ST and UT)
84 \endverbatim
85 
86 \subsection input_options input options
87 \verbatim
88 input file format:
89 
90  +f --read-file
91  read file format or data set (default)
92 
93  +fo --read-file-only
94  read file format only
95 
96  -f --read-dataset
97  read data set without file meta information
98 
99 input transfer syntax:
100 
101  -t= --read-xfer-auto
102  use TS recognition (default)
103 
104  -td --read-xfer-detect
105  ignore TS specified in the file meta header
106 
107  -te --read-xfer-little
108  read with explicit VR little endian TS
109 
110  -tb --read-xfer-big
111  read with explicit VR big endian TS
112 
113  -ti --read-xfer-implicit
114  read with implicit VR little endian TS
115 \endverbatim
116 
117 \subsection output_options output options
118 \verbatim
119 encoding:
120 
121  +Ea --attr-all
122  encode everything as XML attribute
123  (shortcut for +Ec, +Er, +Ev and +Et)
124 
125  +Ec --attr-code
126  encode code value, coding scheme designator
127  and coding scheme version as XML attribute
128 
129  +Er --attr-relationship
130  encode relationship type as XML attribute
131 
132  +Ev --attr-value-type
133  encode value type as XML attribute
134 
135  +Et --attr-template-id
136  encode template id as XML attribute
137 
138  +Ee --template-envelope
139  template element encloses content items
140  (requires +Wt, implies +Et)
141 
142 XML structure:
143 
144  +Xs --add-schema-reference
145  add reference to XML Schema "dsr2xml.xsd"
146  (not with +Ea, +Ec, +Er, +Ev, +Et, +Ee, +We)
147 
148  +Xn --use-xml-namespace
149  add XML namespace declaration to root element
150 
151 writing:
152 
153  +We --write-empty-tags
154  write all tags even if their value is empty
155 
156  +Wi --write-item-id
157  always write item identifier
158 
159  +Wt --write-template-id
160  write template identification information
161 \endverbatim
162 
163 \section notes NOTES
164 
165 \subsection dicom_conformance DICOM Conformance
166 
167 The \b dsr2xml utility supports the following SOP Classes:
168 
169 \verbatim
170 SpectaclePrescriptionReportStorage 1.2.840.10008.5.1.4.1.1.78.6
171 MacularGridThicknessAndVolumeReportStorage 1.2.840.10008.5.1.4.1.1.79.1
172 BasicTextSRStorage 1.2.840.10008.5.1.4.1.1.88.11
173 EnhancedSRStorage 1.2.840.10008.5.1.4.1.1.88.22
174 ComprehensiveSRStorage 1.2.840.10008.5.1.4.1.1.88.33
175 ProcedureLogStorage 1.2.840.10008.5.1.4.1.1.88.40
176 MammographyCADSRStorage 1.2.840.10008.5.1.4.1.1.88.50
177 KeyObjectSelectionDocumentStorage 1.2.840.10008.5.1.4.1.1.88.59
178 ChestCADSRStorage 1.2.840.10008.5.1.4.1.1.88.65
179 XRayRadiationDoseSRStorage 1.2.840.10008.5.1.4.1.1.88.67
180 ColonCADSRStorage 1.2.840.10008.5.1.4.1.1.88.69
181 ImplantationPlanSRDocumentStorage 1.2.840.10008.5.1.4.1.1.88.70
182 \endverbatim
183 
184 Please note that currently only mandatory and some optional attributes are
185 supported.
186 
187 \section logging LOGGING
188 
189 The level of logging output of the various command line tools and underlying
190 libraries can be specified by the user. By default, only errors and warnings
191 are written to the standard error stream. Using option \e --verbose also
192 informational messages like processing details are reported. Option
193 \e --debug can be used to get more details on the internal activity, e.g. for
194 debugging purposes. Other logging levels can be selected using option
195 \e --log-level. In \e --quiet mode only fatal errors are reported. In such
196 very severe error events, the application will usually terminate. For more
197 details on the different logging levels, see documentation of module "oflog".
198 
199 In case the logging output should be written to file (optionally with logfile
200 rotation), to syslog (Unix) or the event log (Windows) option \e --log-config
201 can be used. This configuration file also allows for directing only certain
202 messages to a particular output stream and for filtering certain messages
203 based on the module or application where they are generated. An example
204 configuration file is provided in <em><etcdir>/logger.cfg</em>).
205 
206 \section command_line COMMAND LINE
207 
208 All command line tools use the following notation for parameters: square
209 brackets enclose optional values (0-1), three trailing dots indicate that
210 multiple values are allowed (1-n), a combination of both means 0 to n values.
211 
212 Command line options are distinguished from parameters by a leading '+' or '-'
213 sign, respectively. Usually, order and position of command line options are
214 arbitrary (i.e. they can appear anywhere). However, if options are mutually
215 exclusive the rightmost appearance is used. This behaviour conforms to the
216 standard evaluation rules of common Unix shells.
217 
218 In addition, one or more command files can be specified using an '@' sign as a
219 prefix to the filename (e.g. <em>\@command.txt</em>). Such a command argument
220 is replaced by the content of the corresponding text file (multiple
221 whitespaces are treated as a single separator unless they appear between two
222 quotation marks) prior to any further evaluation. Please note that a command
223 file cannot contain another command file. This simple but effective approach
224 allows to summarize common combinations of options/parameters and avoids
225 longish and confusing command lines (an example is provided in file
226 <em><datadir>/dumppat.txt</em>).
227 
228 \section environment ENVIRONMENT
229 
230 The \b dsr2xml utility will attempt to load DICOM data dictionaries specified
231 in the \e DCMDICTPATH environment variable. By default, i.e. if the
232 \e DCMDICTPATH environment variable is not set, the file
233 <em><datadir>/dicom.dic</em> will be loaded unless the dictionary is built
234 into the application (default for Windows).
235 
236 The default behaviour should be preferred and the \e DCMDICTPATH environment
237 variable only used when alternative data dictionaries are required. The
238 \e DCMDICTPATH environment variable has the same format as the Unix shell
239 \e PATH variable in that a colon (":") separates entries. On Windows systems,
240 a semicolon (";") is used as a separator. The data dictionary code will
241 attempt to load each file specified in the \e DCMDICTPATH environment variable.
242 It is an error if no data dictionary can be loaded.
243 
244 \section files FILES
245 
246 <em><datadir>/dsr2xml.xsd</em> - XML Schema file
247 
248 \section see_also SEE ALSO
249 
250 <b>xml2dsr</b>(1), <b>dcmconv</b>(1)
251 
252 \section copyright COPYRIGHT
253 
254 Copyright (C) 2000-2010 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.
255 
256 */


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