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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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 Please note that currently only mandatory and some optional attributes
177 are supported.
178 Character Encoding
180 The DICOM character encoding is determined automatically from the
181 element with tag '0008,0005' (Specific Character Set) - if present. The
182 following character sets are currently supported (requires libxml to
183 include iconv support, see --version output):
184 ASCII (ISO_IR 6) (UTF-8)
186 UTF-8 "ISO_IR 192" (UTF-8)
187 ISO Latin 1 "ISO_IR 100" (ISO-8859-1)
188 ISO Latin 2 "ISO_IR 101" (ISO-8859-2)
189 ISO Latin 3 "ISO_IR 109" (ISO-8859-3)
190 ISO Latin 4 "ISO_IR 110" (ISO-8859-4)
191 ISO Latin 5 "ISO_IR 148" (ISO-8859-9)
192 Cyrillic "ISO_IR 144" (ISO-8859-5)
193 Arabic "ISO_IR 127" (ISO-8859-6)
194 Greek "ISO_IR 126" (ISO-8859-7)
195 Hebrew "ISO_IR 138" (ISO-8859-8)
196 Thai "ISO_IR 166" (TIS-620)
197 Japanese "ISO 2022 IR 13ISO 2022 IR 87" (ISO-2022-JP)
198 Korean "ISO 2022 IR 6ISO 2022 IR 149" (ISO-2022-KR)
199 Chinese "ISO 2022 IR 6ISO 2022 IR 58" (ISO-2022-CN)
200 Chinese "GB18030" (GB18030)
201 Chinese "GBK" (GBK)
202 Compression
204 If libxml is compiled with zlib support, the input file (xmlfile-in)
205 can also be compressed with ZIP, which usually results in much smaller
206 files. See output of option --version in order to check whether zlib
207 support is available.
208 Limitations
210 The XML Schema dsr2xml.xsd does not support all variations of the
211 dsr2xml output format. However, the default output format (plus option
212 --use-xml-namespace) should work.
213 Different versions of libxml seem to have different limits for the
215 maximum length of an XML element value. Therefore, it should be avoided
216 to use very long element values. A typical limit for libxml version
217 2.7.3 (and above) is 10 MB for a single element value.
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220 The level of logging output of the various command line tools and
221 underlying libraries can be specified by the user. By default, only
222 errors and warnings are written to the standard error stream. Using
223 option --verbose also informational messages like processing details
224 are reported. Option --debug can be used to get more details on the
225 internal activity, e.g. for debugging purposes. Other logging levels
226 can be selected using option --log-level. In --quiet mode only fatal
227 errors are reported. In such very severe error events, the application
228 will usually terminate. For more details on the different logging
229 levels, see documentation of module 'oflog'.
230 In case the logging output should be written to file (optionally with
232 logfile rotation), to syslog (Unix) or the event log (Windows) option
233 --log-config can be used. This configuration file also allows for
234 directing only certain messages to a particular output stream and for
235 filtering certain messages based on the module or application where
236 they are generated. An example configuration file is provided in
237 <etcdir>/logger.cfg.
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240 All command line tools use the following notation for parameters:
241 square brackets enclose optional values (0-1), three trailing dots
242 indicate that multiple values are allowed (1-n), a combination of both
243 means 0 to n values.
244 Command line options are distinguished from parameters by a leading '+'
246 or '-' sign, respectively. Usually, order and position of command line
247 options are arbitrary (i.e. they can appear anywhere). However, if
248 options are mutually exclusive the rightmost appearance is used. This
249 behavior conforms to the standard evaluation rules of common Unix
250 shells.
251 In addition, one or more command files can be specified using an '@'
253 sign as a prefix to the filename (e.g. @command.txt). Such a command
254 argument is replaced by the content of the corresponding text file
255 (multiple whitespaces are treated as a single separator unless they
256 appear between two quotation marks) prior to any further evaluation.
257 Please note that a command file cannot contain another command file.
258 This simple but effective approach allows one to summarize common
259 combinations of options/parameters and avoids longish and confusing
260 command lines (an example is provided in file <datadir>/dumppat.txt).
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263 The xml2dsr utility will attempt to load DICOM data dictionaries
264 specified in the DCMDICTPATH environment variable. By default, i.e. if
265 the DCMDICTPATH environment variable is not set, the file
266 <datadir>/dicom.dic will be loaded unless the dictionary is built into
267 the application (default for Windows).
268 The default behavior should be preferred and the DCMDICTPATH
270 environment variable only used when alternative data dictionaries are
271 required. The DCMDICTPATH environment variable has the same format as
272 the Unix shell PATH variable in that a colon (':') separates entries.
273 On Windows systems, a semicolon (';') is used as a separator. The data
274 dictionary code will attempt to load each file specified in the
275 DCMDICTPATH environment variable. It is an error if no data dictionary
276 can be loaded.
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279 <datadir>/dsr2xml.xsd - XML Schema file
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282 dsr2xml(1)
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285 Copyright (C) 2003-2018 by OFFIS e.V., Escherweg 2, 26121 Oldenburg,
286 Germany.
287Version 3.6.4 Thu Nov 29 2018 xml2dsr(1)