1xml2dsr(1) OFFIS DCMTK xml2dsr(1)
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6 xml2dsr - Convert XML document to DICOM SR file
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10 xml2dsr [options] xmlfile-in dsrfile-out
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13 The xml2dsr utility converts the contents of an XML (Extensible Markup
14 Language) document to DICOM Structured Reporting (SR) format (file
15 format or raw data set). The XML Schema dsr2xml.xsd does not yet follow
16 any standard format. However, the xml2dsr application might be enhanced
17 in this aspect in the future (e. g. by supporting HL7/CDA - Clinical
18 Document Architecture).
19 An appropriate XML file can be created using the dsr2xml tool (option
21 +Xn recommended to add XML namespace declaration to the root element).
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24 xmlfile-in XML input filename to be converted (stdin: "-")
25 dsrfile-out DICOM SR output filename
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29 general options
30 -h --help
31 print this help text and exit
32 --version
34 print version information and exit
35 --arguments
37 print expanded command line arguments
38 -q --quiet
40 quiet mode, print no warnings and errors
41 -v --verbose
43 verbose mode, print processing details
44 -d --debug
46 debug mode, print debug information
47 -ll --log-level [l]evel: string constant
49 (fatal, error, warn, info, debug, trace)
50 use level l for the logger
51 -lc --log-config [f]ilename: string
53 use config file f for the logger
54 input options
56 encoding:
57 +Ee --template-envelope
59 template element encloses content items
60 processing options
62 validation:
63 +Vs --validate-schema
65 validate XML document against Schema
66 (not with --template-envelope)
67 # requires libxml to be compiled with XML Schema support
69 +Vn --check-namespace
71 check XML namespace in document root
72 unique identifiers:
74 +Ug --generate-new-uids
76 generate new Study/Series/SOP Instance UID
77 -Uo --dont-overwrite-uids
79 do not overwrite existing UIDs (default)
80 +Uo --overwrite-uids
82 overwrite existing UIDs
83 output options
85 output file format:
86 +F --write-file
88 write file format (default)
89 -F --write-dataset
91 write data set without file meta information
92 output transfer syntax:
94 +t= --write-xfer-same
96 write with same TS as input (default)
97 +te --write-xfer-little
99 write with explicit VR little endian TS
100 +tb --write-xfer-big
102 write with explicit VR big endian TS
103 +ti --write-xfer-implicit
105 write with implicit VR little endian TS
106 +td --write-xfer-deflated
108 write with deflated explicit VR little endian TS
109 post-1993 value representations:
111 +u --enable-new-vr
113 enable support for new VRs (UN/UT) (default)
114 -u --disable-new-vr
116 disable support for new VRs, convert to OB
117 group length encoding:
119 +g= --group-length-recalc
121 recalculate group lengths if present (default)
122 +g --group-length-create
124 always write with group length elements
125 -g --group-length-remove
127 always write without group length elements
128 length encoding in sequences and items:
130 +e --length-explicit
132 write with explicit lengths (default)
133 -e --length-undefined
135 write with undefined lengths
136 data set trailing padding (not with --write-dataset):
138 -p= --padding-retain
140 do not change padding (default if not --write-dataset)
141 -p --padding-off
143 no padding (implicit if --write-dataset)
144 +p --padding-create [f]ile-pad [i]tem-pad: integer
146 align file on multiple of f bytes
147 and items on multiple of i bytes
148 deflate compression level (only with --write-xfer-deflated):
150 +cl --compression-level [l]evel: integer (default: 6)
152 0=uncompressed, 1=fastest, 9=best compression
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155 DICOM Conformance
156 The xml2dsr utility supports the following SOP Classes:
157 SpectaclePrescriptionReportStorage 1.2.840.10008.5.1.4.1.1.78.6
159 MacularGridThicknessAndVolumeReportStorage 1.2.840.10008.5.1.4.1.1.79.1
160 BasicTextSRStorage 1.2.840.10008.5.1.4.1.1.88.11
161 EnhancedSRStorage 1.2.840.10008.5.1.4.1.1.88.22
162 ComprehensiveSRStorage 1.2.840.10008.5.1.4.1.1.88.33
163 Comprehensive3DSRStorage 1.2.840.10008.5.1.4.1.1.88.34
164 ProcedureLogStorage 1.2.840.10008.5.1.4.1.1.88.40
165 MammographyCADSRStorage 1.2.840.10008.5.1.4.1.1.88.50
166 KeyObjectSelectionDocumentStorage 1.2.840.10008.5.1.4.1.1.88.59
167 ChestCADSRStorage 1.2.840.10008.5.1.4.1.1.88.65
168 XRayRadiationDoseSRStorage 1.2.840.10008.5.1.4.1.1.88.67
169 RadiopharmaceuticalRadiationDoseSRStorage 1.2.840.10008.5.1.4.1.1.88.68
170 ColonCADSRStorage 1.2.840.10008.5.1.4.1.1.88.69
171 ImplantationPlanSRDocumentStorage 1.2.840.10008.5.1.4.1.1.88.70
172 AcquisitionContextSRStorage 1.2.840.10008.5.1.4.1.1.88.71
173 SimplifiedAdultEchoSRStorage 1.2.840.10008.5.1.4.1.1.88.72
174 PatientRadiationDoseSRStorage 1.2.840.10008.5.1.4.1.1.88.73
175 PlannedImagingAgentAdministrationSRStorage 1.2.840.10008.5.1.4.1.1.88.74
176 PerformedImagingAgentAdministrationSRStorage 1.2.840.10008.5.1.4.1.1.88.75
177 Please note that currently only mandatory and some optional attributes
179 are supported.
180 Character Encoding
182 The DICOM character encoding is determined automatically from the
183 element with tag '0008,0005' (Specific Character Set) - if present. The
184 following character sets are currently supported (requires libxml to
185 include iconv support, see --version output):
186 ASCII (ISO_IR 6) (UTF-8)
188 UTF-8 "ISO_IR 192" (UTF-8)
189 ISO Latin 1 "ISO_IR 100" (ISO-8859-1)
190 ISO Latin 2 "ISO_IR 101" (ISO-8859-2)
191 ISO Latin 3 "ISO_IR 109" (ISO-8859-3)
192 ISO Latin 4 "ISO_IR 110" (ISO-8859-4)
193 ISO Latin 5 "ISO_IR 148" (ISO-8859-9)
194 Cyrillic "ISO_IR 144" (ISO-8859-5)
195 Arabic "ISO_IR 127" (ISO-8859-6)
196 Greek "ISO_IR 126" (ISO-8859-7)
197 Hebrew "ISO_IR 138" (ISO-8859-8)
198 Thai "ISO_IR 166" (TIS-620)
199 Japanese "ISO 2022 IR 13ISO 2022 IR 87" (ISO-2022-JP)
200 Korean "ISO 2022 IR 6ISO 2022 IR 149" (ISO-2022-KR)
201 Chinese "ISO 2022 IR 6ISO 2022 IR 58" (ISO-2022-CN)
202 Chinese "GB18030" (GB18030)
203 Chinese "GBK" (GBK)
204 Compression
206 If libxml is compiled with zlib support, the input file (xmlfile-in)
207 can also be compressed with ZIP, which usually results in much smaller
208 files. See output of option --version in order to check whether zlib
209 support is available.
210 Limitations
212 The XML Schema dsr2xml.xsd does not support all variations of the
213 dsr2xml output format. However, the default output format (plus option
214 --use-xml-namespace) should work.
215 Different versions of libxml seem to have different limits for the
217 maximum length of an XML element value. Therefore, it should be avoided
218 to use very long element values. A typical limit for libxml version
219 2.7.3 (and above) is 10 MB for a single element value.
220
222 The level of logging output of the various command line tools and
223 underlying libraries can be specified by the user. By default, only
224 errors and warnings are written to the standard error stream. Using
225 option --verbose also informational messages like processing details
226 are reported. Option --debug can be used to get more details on the
227 internal activity, e.g. for debugging purposes. Other logging levels
228 can be selected using option --log-level. In --quiet mode only fatal
229 errors are reported. In such very severe error events, the application
230 will usually terminate. For more details on the different logging
231 levels, see documentation of module 'oflog'.
232 In case the logging output should be written to file (optionally with
234 logfile rotation), to syslog (Unix) or the event log (Windows) option
235 --log-config can be used. This configuration file also allows for
236 directing only certain messages to a particular output stream and for
237 filtering certain messages based on the module or application where
238 they are generated. An example configuration file is provided in
239 <etcdir>/logger.cfg.
240
242 All command line tools use the following notation for parameters:
243 square brackets enclose optional values (0-1), three trailing dots
244 indicate that multiple values are allowed (1-n), a combination of both
245 means 0 to n values.
246 Command line options are distinguished from parameters by a leading '+'
248 or '-' sign, respectively. Usually, order and position of command line
249 options are arbitrary (i.e. they can appear anywhere). However, if
250 options are mutually exclusive the rightmost appearance is used. This
251 behavior conforms to the standard evaluation rules of common Unix
252 shells.
253 In addition, one or more command files can be specified using an '@'
255 sign as a prefix to the filename (e.g. @command.txt). Such a command
256 argument is replaced by the content of the corresponding text file
257 (multiple whitespaces are treated as a single separator unless they
258 appear between two quotation marks) prior to any further evaluation.
259 Please note that a command file cannot contain another command file.
260 This simple but effective approach allows one to summarize common
261 combinations of options/parameters and avoids longish and confusing
262 command lines (an example is provided in file <datadir>/dumppat.txt).
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265 The xml2dsr utility will attempt to load DICOM data dictionaries
266 specified in the DCMDICTPATH environment variable. By default, i.e. if
267 the DCMDICTPATH environment variable is not set, the file
268 <datadir>/dicom.dic will be loaded unless the dictionary is built into
269 the application (default for Windows).
270 The default behavior should be preferred and the DCMDICTPATH
272 environment variable only used when alternative data dictionaries are
273 required. The DCMDICTPATH environment variable has the same format as
274 the Unix shell PATH variable in that a colon (':') separates entries.
275 On Windows systems, a semicolon (';') is used as a separator. The data
276 dictionary code will attempt to load each file specified in the
277 DCMDICTPATH environment variable. It is an error if no data dictionary
278 can be loaded.
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281 <datadir>/dsr2xml.xsd - XML Schema file
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284 dsr2xml(1)
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287 Copyright (C) 2003-2019 by OFFIS e.V., Escherweg 2, 26121 Oldenburg,
288 Germany.
289Version 3.6.6 Thu Jan 14 2021 xml2dsr(1)