1dsr2xml(1) OFFIS DCMTK dsr2xml(1)
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6 dsr2xml - Convert DICOM SR file and data set to XML
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9 dsr2xml [options] dsrfile-in [xmlfile-out]
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12 The dsr2xml utility converts the contents of a DICOM Structured
13 Reporting (SR) document (file format or raw data set) to XML
14 (Extensible Markup Language). The XML Schema dsr2xml.xsd does not yet
15 follow any standard format. However, the dsr2xml application might be
16 enhanced in this aspect in the future (e.g. by supporting HL7/CDA -
17 Clinical Document Architecture).
18 If dsr2xml reads a raw data set (DICOM data without a file format meta-
20 header) it will attempt to guess the transfer syntax by examining the
21 first few bytes of the file. It is not always possible to correctly
22 guess the transfer syntax and it is better to convert a data set to a
23 file format whenever possible (using the dcmconv utility). It is also
24 possible to use the -f and -t[ieb] options to force dsr2xml to read a
25 dataset with a particular transfer syntax.
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28 dsrfile-in DICOM SR input filename to be converted
29 xmlfile-out XML output filename (default: stdout)
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33 general options
34 -h --help
35 print this help text and exit
36 --version
38 print version information and exit
39 --arguments
41 print expanded command line arguments
42 -q --quiet
44 quiet mode, print no warnings and errors
45 -v --verbose
47 verbose mode, print processing details
48 -d --debug
50 debug mode, print debug information
51 -ll --log-level [l]evel: string constant
53 (fatal, error, warn, info, debug, trace)
54 use level l for the logger
55 -lc --log-config [f]ilename: string
57 use config file f for the logger
58 processing options
60 character set:
61 +Cr --charset-require
63 require declaration of extended charset (default)
64 +Ca --charset-assume [c]harset: string constant
66 (latin-1 to -5, greek, cyrillic, arabic, hebrew)
67 assume charset c if no extended charset found
68 +Cc --charset-check-all
70 check all data elements with string values
71 (default: only PN, LO, LT, SH, ST and UT)
72 input options
74 input file format:
75 +f --read-file
77 read file format or data set (default)
78 +fo --read-file-only
80 read file format only
81 -f --read-dataset
83 read data set without file meta information
84 input transfer syntax:
86 -t= --read-xfer-auto
88 use TS recognition (default)
89 -td --read-xfer-detect
91 ignore TS specified in the file meta header
92 -te --read-xfer-little
94 read with explicit VR little endian TS
95 -tb --read-xfer-big
97 read with explicit VR big endian TS
98 -ti --read-xfer-implicit
100 read with implicit VR little endian TS
101 output options
103 encoding:
104 +Ea --attr-all
106 encode everything as XML attribute
107 (shortcut for +Ec, +Er, +Ev and +Et)
108 +Ec --attr-code
110 encode code value, coding scheme designator
111 and coding scheme version as XML attribute
112 +Er --attr-relationship
114 encode relationship type as XML attribute
115 +Ev --attr-value-type
117 encode value type as XML attribute
118 +Et --attr-template-id
120 encode template id as XML attribute
121 +Ee --template-envelope
123 template element encloses content items
124 (requires +Wt, implies +Et)
125 XML structure:
127 +Xs --add-schema-reference
129 add reference to XML Schema "dsr2xml.xsd"
130 (not with +Ea, +Ec, +Er, +Ev, +Et, +Ee, +We)
131 +Xn --use-xml-namespace
133 add XML namespace declaration to root element
134 writing:
136 +We --write-empty-tags
138 write all tags even if their value is empty
139 +Wi --write-item-id
141 always write item identifier
142 +Wt --write-template-id
144 write template identification information
145
147 DICOM Conformance
148 The dsr2xml utility supports the following SOP Classes:
149 SpectaclePrescriptionReportStorage 1.2.840.10008.5.1.4.1.1.78.6
151 MacularGridThicknessAndVolumeReportStorage 1.2.840.10008.5.1.4.1.1.79.1
152 BasicTextSRStorage 1.2.840.10008.5.1.4.1.1.88.11
153 EnhancedSRStorage 1.2.840.10008.5.1.4.1.1.88.22
154 ComprehensiveSRStorage 1.2.840.10008.5.1.4.1.1.88.33
155 ProcedureLogStorage 1.2.840.10008.5.1.4.1.1.88.40
156 MammographyCADSRStorage 1.2.840.10008.5.1.4.1.1.88.50
157 KeyObjectSelectionDocumentStorage 1.2.840.10008.5.1.4.1.1.88.59
158 ChestCADSRStorage 1.2.840.10008.5.1.4.1.1.88.65
159 XRayRadiationDoseSRStorage 1.2.840.10008.5.1.4.1.1.88.67
160 ColonCADSRStorage 1.2.840.10008.5.1.4.1.1.88.69
161 ImplantationPlanSRDocumentStorage 1.2.840.10008.5.1.4.1.1.88.70
162 Please note that currently only mandatory and some optional attributes
164 are supported.
165
167 The level of logging output of the various command line tools and
168 underlying libraries can be specified by the user. By default, only
169 errors and warnings are written to the standard error stream. Using
170 option --verbose also informational messages like processing details
171 are reported. Option --debug can be used to get more details on the
172 internal activity, e.g. for debugging purposes. Other logging levels
173 can be selected using option --log-level. In --quiet mode only fatal
174 errors are reported. In such very severe error events, the application
175 will usually terminate. For more details on the different logging
176 levels, see documentation of module 'oflog'.
177 In case the logging output should be written to file (optionally with
179 logfile rotation), to syslog (Unix) or the event log (Windows) option
180 --log-config can be used. This configuration file also allows for
181 directing only certain messages to a particular output stream and for
182 filtering certain messages based on the module or application where
183 they are generated. An example configuration file is provided in
184 <etcdir>/logger.cfg).
185
187 All command line tools use the following notation for parameters:
188 square brackets enclose optional values (0-1), three trailing dots
189 indicate that multiple values are allowed (1-n), a combination of both
190 means 0 to n values.
191 Command line options are distinguished from parameters by a leading '+'
193 or '-' sign, respectively. Usually, order and position of command line
194 options are arbitrary (i.e. they can appear anywhere). However, if
195 options are mutually exclusive the rightmost appearance is used. This
196 behaviour conforms to the standard evaluation rules of common Unix
197 shells.
198 In addition, one or more command files can be specified using an '@'
200 sign as a prefix to the filename (e.g. @command.txt). Such a command
201 argument is replaced by the content of the corresponding text file
202 (multiple whitespaces are treated as a single separator unless they
203 appear between two quotation marks) prior to any further evaluation.
204 Please note that a command file cannot contain another command file.
205 This simple but effective approach allows to summarize common
206 combinations of options/parameters and avoids longish and confusing
207 command lines (an example is provided in file <datadir>/dumppat.txt).
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210 The dsr2xml utility will attempt to load DICOM data dictionaries
211 specified in the DCMDICTPATH environment variable. By default, i.e. if
212 the DCMDICTPATH environment variable is not set, the file
213 <datadir>/dicom.dic will be loaded unless the dictionary is built into
214 the application (default for Windows).
215 The default behaviour should be preferred and the DCMDICTPATH
217 environment variable only used when alternative data dictionaries are
218 required. The DCMDICTPATH environment variable has the same format as
219 the Unix shell PATH variable in that a colon (':') separates entries.
220 On Windows systems, a semicolon (';') is used as a separator. The data
221 dictionary code will attempt to load each file specified in the
222 DCMDICTPATH environment variable. It is an error if no data dictionary
223 can be loaded.
224
226 <datadir>/dsr2xml.xsd - XML Schema file
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229 xml2dsr(1), dcmconv(1)
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232 Copyright (C) 2000-2010 by OFFIS e.V., Escherweg 2, 26121 Oldenburg,
233 Germany.
234Version 3.6.0 6 Jan 2011 dsr2xml(1)