1xml2dcm(1) OFFIS DCMTK xml2dcm(1)
2
6 xml2dcm - Convert XML document to DICOM file or data set
7
10 xml2dcm [options] xmlfile-in dcmfile-out
11
13 The xml2dcm utility converts the contents of an XML (Extensible Markup
14 Language) document to DICOM file or data set. The XML document is
15 expected to validate against the DTD (Document Type Definition) which
16 is described in file dcm2xml.dtd. An appropriate XML file can be
17 created using the dcm2xml tool (option +Wb recommended to include
18 binary data).
19
21 xmlfile-in XML input filename to be converted (stdin: "-")
22 dcmfile-out DICOM output filename
24
26 general options
27 -h --help
28 print this help text and exit
29 --version
31 print version information and exit
32 --arguments
34 print expanded command line arguments
35 -q --quiet
37 quiet mode, print no warnings and errors
38 -v --verbose
40 verbose mode, print processing details
41 -d --debug
43 debug mode, print debug information
44 -ll --log-level [l]evel: string constant
46 (fatal, error, warn, info, debug, trace)
47 use level l for the logger
48 -lc --log-config [f]ilename: string
50 use config file f for the logger
51 input options
53 input file format:
54 +f --read-meta-info
56 read meta information if present (default)
57 -f --ignore-meta-info
59 ignore file meta information
60 processing options
62 validation:
63 +Vd --validate-document
65 validate XML document against DTD
66 +Vn --check-namespace
68 check XML namespace in document root
69 unique identifiers:
71 +Ug --generate-new-uids
73 generate new Study/Series/SOP Instance UID
74 -Uo --dont-overwrite-uids
76 do not overwrite existing UIDs (default)
77 +Uo --overwrite-uids
79 overwrite existing UIDs
80 output options
82 output file format:
83 +F --write-file
85 write file format (default)
86 -F --write-dataset
88 write data set without file meta information
89 +Fu --update-meta-info
91 update particular 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 and items on
147 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
153
155 The basic structure of the XML input expected looks like the following:
156 <?xml version="1.0" encoding="ISO-8859-1"?>
158 <!DOCTYPE file-format SYSTEM "dcm2xml.dtd">
159 <file-format xmlns="http://dicom.offis.de/dcmtk">
160 <meta-header xfer="1.2.840.10008.1.2.1" name="Little Endian Explicit">
161 <element tag="0002,0000" vr="UL" vm="1" len="4"
162 name="MetaElementGroupLength">
163 166
164 </element>
165 ...
166 <element tag="0002,0013" vr="SH" vm="1" len="16"
167 name="ImplementationVersionName">
168 OFFIS_DCMTK_353
169 </element>
170 </meta-header>
171 <data-set xfer="1.2.840.10008.1.2" name="Little Endian Implicit">
172 <element tag="0008,0005" vr="CS" vm="1" len="10"
173 name="SpecificCharacterSet">
174 ISO_IR 100
175 </element>
176 ...
177 <sequence tag="0028,3010" vr="SQ" card="2" name="VOILUTSequence">
178 <item card="3">
179 <element tag="0028,3002" vr="xs" vm="3" len="6"
180 name="LUTDescriptor">
181 256\0\8
182 </element>
183 ...
184 </item>
185 ...
186 </sequence>
187 ...
188 <element tag="7fe0,0010" vr="OW" vm="1" len="262144"
189 name="PixelData" loaded="no" binary="hidden">
190 </element>
191 </data-set>
192 </file-format>
193 The 'file-format' and 'meta-header' tags may be absent for DICOM data
195 sets.
196 Character Encoding
198 The DICOM character encoding is determined automatically from the
199 element with tag '0008,0005' (Specific Character Set) - if present. The
200 following character sets are currently supported (requires libxml to
201 include iconv support, see --version output):
202 ASCII (ISO_IR 6) (UTF-8)
204 UTF-8 "ISO_IR 192" (UTF-8)
205 ISO Latin 1 "ISO_IR 100" (ISO-8859-1)
206 ISO Latin 2 "ISO_IR 101" (ISO-8859-2)
207 ISO Latin 3 "ISO_IR 109" (ISO-8859-3)
208 ISO Latin 4 "ISO_IR 110" (ISO-8859-4)
209 ISO Latin 5 "ISO_IR 148" (ISO-8859-9)
210 Cyrillic "ISO_IR 144" (ISO-8859-5)
211 Arabic "ISO_IR 127" (ISO-8859-6)
212 Greek "ISO_IR 126" (ISO-8859-7)
213 Hebrew "ISO_IR 138" (ISO-8859-8)
214 Multiple character sets are not supported (only the first value of the
216 'Specific Character Set' is used for the character encoding in case of
217 value multiplicity).
218 See dcm2xml documentation for more details on the XML structure.
220 Binary Data
222 Binary data can be encoded either as a sequence of hex numbers
223 separated by a backslash '\' or in Base64 format (binary='base64'). In
224 addition, binary data can also be read from file (binary='file'). In
225 this case, the filename has to be specified as the element value, e.g.
226 <element tag="7fe0,0010" vr="OW" ... binary="file">subdir/pixeldata.raw</element>
228 Please note that the contents of the file will be read as is. OW data
230 is expected to be little endian ordered and will be swapped if
231 necessary. No checks will be made to ensure that the amount of data is
232 reasonable in terms of other attributes such as Rows or Columns.
233 Compression
235 If libxml is compiled with zlib support, the input file (xmlfile-in)
236 can also be compressed with ZIP, which usually results in much smaller
237 files. See output of option --version in order to check whether zlib
238 support is available.
239 Limitations
241 Different versions of libxml might have different limits for the
242 maximum length of an XML element value. Therefore, it should be avoided
243 to use very long element values (e.g. for pixel data).
244 Please note that xml2dcm currently does not fully support DICOMDIR
246 files. Specifically, the value of the various offset data elements is
247 not updated automatically by this tool.
248
250 The level of logging output of the various command line tools and
251 underlying libraries can be specified by the user. By default, only
252 errors and warnings are written to the standard error stream. Using
253 option --verbose also informational messages like processing details
254 are reported. Option --debug can be used to get more details on the
255 internal activity, e.g. for debugging purposes. Other logging levels
256 can be selected using option --log-level. In --quiet mode only fatal
257 errors are reported. In such very severe error events, the application
258 will usually terminate. For more details on the different logging
259 levels, see documentation of module 'oflog'.
260 In case the logging output should be written to file (optionally with
262 logfile rotation), to syslog (Unix) or the event log (Windows) option
263 --log-config can be used. This configuration file also allows for
264 directing only certain messages to a particular output stream and for
265 filtering certain messages based on the module or application where
266 they are generated. An example configuration file is provided in
267 <etcdir>/logger.cfg.
268
270 All command line tools use the following notation for parameters:
271 square brackets enclose optional values (0-1), three trailing dots
272 indicate that multiple values are allowed (1-n), a combination of both
273 means 0 to n values.
274 Command line options are distinguished from parameters by a leading '+'
276 or '-' sign, respectively. Usually, order and position of command line
277 options are arbitrary (i.e. they can appear anywhere). However, if
278 options are mutually exclusive the rightmost appearance is used. This
279 behavior conforms to the standard evaluation rules of common Unix
280 shells.
281 In addition, one or more command files can be specified using an '@'
283 sign as a prefix to the filename (e.g. @command.txt). Such a command
284 argument is replaced by the content of the corresponding text file
285 (multiple whitespaces are treated as a single separator unless they
286 appear between two quotation marks) prior to any further evaluation.
287 Please note that a command file cannot contain another command file.
288 This simple but effective approach allows one to summarize common
289 combinations of options/parameters and avoids longish and confusing
290 command lines (an example is provided in file <datadir>/dumppat.txt).
291
293 The xml2dcm utility will attempt to load DICOM data dictionaries
294 specified in the DCMDICTPATH environment variable. By default, i.e. if
295 the DCMDICTPATH environment variable is not set, the file
296 <datadir>/dicom.dic will be loaded unless the dictionary is built into
297 the application (default for Windows).
298 The default behavior should be preferred and the DCMDICTPATH
300 environment variable only used when alternative data dictionaries are
301 required. The DCMDICTPATH environment variable has the same format as
302 the Unix shell PATH variable in that a colon (':') separates entries.
303 On Windows systems, a semicolon (';') is used as a separator. The data
304 dictionary code will attempt to load each file specified in the
305 DCMDICTPATH environment variable. It is an error if no data dictionary
306 can be loaded.
307
309 <datadir>/dcm2xml.dtd - Document Type Definition (DTD) file
310
312 dcm2xml(1)
313
315 Copyright (C) 2003-2014 by OFFIS e.V., Escherweg 2, 26121 Oldenburg,
316 Germany.
317Version 3.6.4 Thu Nov 29 2018 xml2dcm(1)