1dsr2xml(1)                        OFFIS DCMTK                       dsr2xml(1)
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NAME

6       dsr2xml - Convert DICOM SR file and data set to XML
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SYNOPSIS

10       dsr2xml [options] dsrfile-in [xmlfile-out]
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DESCRIPTION

13       The  dsr2xml  utility  converts  the  contents  of  a  DICOM Structured
14       Reporting  (SR)  document  (file  format  or  raw  data  set)  to   XML
15       (Extensible  Markup  Language). The XML Schema dsr2xml.xsd does not yet
16       follow any standard format. However, the dsr2xml application  might  be
17       enhanced  in  this  aspect  in the future (e.g. by supporting HL7/CDA -
18       Clinical Document Architecture).
19
20       If dsr2xml reads a raw data set (DICOM data without a file format meta-
21       header)  it  will attempt to guess the transfer syntax by examining the
22       first few bytes of the file. It is not  always  possible  to  correctly
23       guess  the  transfer syntax and it is better to convert a data set to a
24       file format whenever possible (using the dcmconv utility). It  is  also
25       possible  to  use the -f and -t[ieb] options to force dsr2xml to read a
26       dataset with a particular transfer syntax.
27

PARAMETERS

29       dsrfile-in   DICOM SR input filename to be converted
30
31       xmlfile-out  XML output filename (default: stdout)
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OPTIONS

34   general options
35         -h   --help
36                print this help text and exit
37
38              --version
39                print version information and exit
40
41              --arguments
42                print expanded command line arguments
43
44         -q   --quiet
45                quiet mode, print no warnings and errors
46
47         -v   --verbose
48                verbose mode, print processing details
49
50         -d   --debug
51                debug mode, print debug information
52
53         -ll  --log-level  [l]evel: string constant
54                (fatal, error, warn, info, debug, trace)
55                use level l for the logger
56
57         -lc  --log-config  [f]ilename: string
58                use config file f for the logger
59
60   input options
61       input file format:
62
63         +f   --read-file
64                read file format or data set (default)
65
66         +fo  --read-file-only
67                read file format only
68
69         -f   --read-dataset
70                read data set without file meta information
71
72       input transfer syntax:
73
74         -t=  --read-xfer-auto
75                use TS recognition (default)
76
77         -td  --read-xfer-detect
78                ignore TS specified in the file meta header
79
80         -te  --read-xfer-little
81                read with explicit VR little endian TS
82
83         -tb  --read-xfer-big
84                read with explicit VR big endian TS
85
86         -ti  --read-xfer-implicit
87                read with implicit VR little endian TS
88
89   processing options
90       error handling:
91
92         -Er  --unknown-relationship
93                accept unknown/missing relationship type
94
95         -Ev  --invalid-item-value
96                accept invalid content item value
97                (e.g. violation of VR or VM definition)
98
99         -Ec  --ignore-constraints
100                ignore relationship content constraints
101
102         -Ee  --ignore-item-errors
103                do not abort on content item errors, just warn
104                (e.g. missing value type specific attributes)
105
106         -Ei  --skip-invalid-items
107                skip invalid content items (including sub-tree)
108
109         -Dv  --disable-vr-checker
110                disable check for VR-conformant string values
111
112       specific character set:
113
114         +Cr  --charset-require
115                require declaration of extended charset (default)
116
117         +Ca  --charset-assume  [c]harset: string
118                assume charset c if no extended charset declared
119
120         +Cc  --charset-check-all
121                check all data elements with string values
122                (default: only PN, LO, LT, SH, ST, UC and UT)
123
124                # this option is only used for the mapping to an appropriate
125                # XML character encoding, but not for the conversion to UTF-8
126
127         +U8  --convert-to-utf8
128                convert all element values that are affected
129                by Specific Character Set (0008,0005) to UTF-8
130
131                # requires support from an underlying character encoding library
132                # (see output of --version on which one is available)
133
134   output options
135       encoding:
136
137         +Ea  --attr-all
138                encode everything as XML attribute
139                (shortcut for +Ec, +Er, +Ev and +Et)
140
141         +Ec  --attr-code
142                encode code value, coding scheme designator
143                and coding scheme version as XML attribute
144
145         +Er  --attr-relationship
146                encode relationship type as XML attribute
147
148         +Ev  --attr-value-type
149                encode value type as XML attribute
150
151         +Et  --attr-template-id
152                encode template id as XML attribute
153
154         +Ee  --template-envelope
155                template element encloses content items
156                (requires +Wt, implies +Et)
157
158       XML structure:
159
160         +Xs  --add-schema-reference
161                add reference to XML Schema "dsr2xml.xsd"
162                (not with +Ea, +Ec, +Er, +Ev, +Et, +Ee, +We)
163
164         +Xn  --use-xml-namespace
165                add XML namespace declaration to root element
166
167       writing:
168
169         +We  --write-empty-tags
170                write all tags even if their value is empty
171
172         +Wi  --write-item-id
173                always write item identifier
174
175         +Wt  --write-template-id
176                write template identification information
177

NOTES

179   DICOM Conformance
180       The dsr2xml utility supports the following SOP Classes:
181
182       SpectaclePrescriptionReportStorage           1.2.840.10008.5.1.4.1.1.78.6
183       MacularGridThicknessAndVolumeReportStorage   1.2.840.10008.5.1.4.1.1.79.1
184       BasicTextSRStorage                           1.2.840.10008.5.1.4.1.1.88.11
185       EnhancedSRStorage                            1.2.840.10008.5.1.4.1.1.88.22
186       ComprehensiveSRStorage                       1.2.840.10008.5.1.4.1.1.88.33
187       Comprehensive3DSRStorage                     1.2.840.10008.5.1.4.1.1.88.34
188       ProcedureLogStorage                          1.2.840.10008.5.1.4.1.1.88.40
189       MammographyCADSRStorage                      1.2.840.10008.5.1.4.1.1.88.50
190       KeyObjectSelectionDocumentStorage            1.2.840.10008.5.1.4.1.1.88.59
191       ChestCADSRStorage                            1.2.840.10008.5.1.4.1.1.88.65
192       XRayRadiationDoseSRStorage                   1.2.840.10008.5.1.4.1.1.88.67
193       RadiopharmaceuticalRadiationDoseSRStorage    1.2.840.10008.5.1.4.1.1.88.68
194       ColonCADSRStorage                            1.2.840.10008.5.1.4.1.1.88.69
195       ImplantationPlanSRDocumentStorage            1.2.840.10008.5.1.4.1.1.88.70
196       AcquisitionContextSRStorage                  1.2.840.10008.5.1.4.1.1.88.71
197       SimplifiedAdultEchoSRStorage                 1.2.840.10008.5.1.4.1.1.88.72
198       PatientRadiationDoseSRStorage                1.2.840.10008.5.1.4.1.1.88.73
199       PlannedImagingAgentAdministrationSRStorage   1.2.840.10008.5.1.4.1.1.88.74
200       PerformedImagingAgentAdministrationSRStorage 1.2.840.10008.5.1.4.1.1.88.75
201
202       Please note that currently only mandatory and some optional  attributes
203       are supported.
204
205   Character Encoding
206       The  XML  encoding is determined automatically from the DICOM attribute
207       (0008,0005) 'Specific Character Set' using the following mapping:
208
209       ASCII         (ISO_IR 6)                       =>  "UTF-8"
210       UTF-8         "ISO_IR 192"                     =>  "UTF-8"
211       ISO Latin 1   "ISO_IR 100"                     =>  "ISO-8859-1"
212       ISO Latin 2   "ISO_IR 101"                     =>  "ISO-8859-2"
213       ISO Latin 3   "ISO_IR 109"                     =>  "ISO-8859-3"
214       ISO Latin 4   "ISO_IR 110"                     =>  "ISO-8859-4"
215       ISO Latin 5   "ISO_IR 148"                     =>  "ISO-8859-9"
216       Cyrillic      "ISO_IR 144"                     =>  "ISO-8859-5"
217       Arabic        "ISO_IR 127"                     =>  "ISO-8859-6"
218       Greek         "ISO_IR 126"                     =>  "ISO-8859-7"
219       Hebrew        "ISO_IR 138"                     =>  "ISO-8859-8"
220       Thai          "ISO_IR 166"                     =>  "TIS-620"
221       Japanese      "ISO 2022 IR 13ISO 2022 IR 87"  =>  "ISO-2022-JP"
222       Korean        "ISO 2022 IR 6ISO 2022 IR 149"  =>  "ISO-2022-KR"
223       Chinese       "ISO 2022 IR 6ISO 2022 IR 58"   =>  "ISO-2022-CN"
224       Chinese       "GB18030"                        =>  "GB18030"
225       Chinese       "GBK"                            =>  "GBK"
226
227       If this DICOM attribute is missing in the input file, although  needed,
228       option --charset-assume can be used to specify an appropriate character
229       set manually (using one of the DICOM defined  terms).  For  reasons  of
230       backward  compatibility  with  previous  versions  of  this  tool,  the
231       following terms are also supported  and  mapped  automatically  to  the
232       associated  DICOM  defined  terms:  latin-1, latin-2, latin-3, latin-4,
233       latin-5, cyrillic, arabic, greek, hebrew.
234
235       Option --convert-to-utf8 can be used to convert the DICOM file or  data
236       set to UTF-8 encoding prior to the conversion to XML format.
237
238       If no mapping is defined and option --convert-to-utf8 is not used, non-
239       ASCII characters and those below #32 are stored as '&#nnn;' where 'nnn'
240       refers  to  the  numeric  character  code.  This  might lead to invalid
241       character entity references (such as '' for ESC)  and  will  cause
242       most XML parsers to reject the document.
243
244   Error Handling
245       Please  be  careful with the processing options --unknown-relationship,
246       --invalid-item-value,  --ignore-constraints,  --ignore-item-errors  and
247       --skip-invalid-items  since  they  disable certain validation checks on
248       the DICOM SR input file and, therefore, might  result  in  non-standard
249       conformant  output.  However,  there  might be reasons for using one or
250       more of these options, e.g. in order to read and process an incorrectly
251       encoded SR document.
252
253   Limitations
254       The  XML  Schema  dsr2xml.xsd  does  not  support all variations of the
255       dsr2xml output format. However, the default output format (plus  option
256       --use-xml-namespace) should work.
257

LOGGING

259       The  level  of  logging  output  of  the various command line tools and
260       underlying libraries can be specified by the  user.  By  default,  only
261       errors  and  warnings  are  written to the standard error stream. Using
262       option --verbose also informational messages  like  processing  details
263       are  reported.  Option  --debug  can be used to get more details on the
264       internal activity, e.g. for debugging purposes.  Other  logging  levels
265       can  be  selected  using option --log-level. In --quiet mode only fatal
266       errors are reported. In such very severe error events, the  application
267       will  usually  terminate.  For  more  details  on the different logging
268       levels, see documentation of module 'oflog'.
269
270       In case the logging output should be written to file  (optionally  with
271       logfile  rotation),  to syslog (Unix) or the event log (Windows) option
272       --log-config can be used.  This  configuration  file  also  allows  for
273       directing  only  certain messages to a particular output stream and for
274       filtering certain messages based on the  module  or  application  where
275       they  are  generated.  An  example  configuration  file  is provided in
276       <etcdir>/logger.cfg.
277

COMMAND LINE

279       All command line tools  use  the  following  notation  for  parameters:
280       square  brackets  enclose  optional  values  (0-1), three trailing dots
281       indicate that multiple values are allowed (1-n), a combination of  both
282       means 0 to n values.
283
284       Command line options are distinguished from parameters by a leading '+'
285       or '-' sign, respectively. Usually, order and position of command  line
286       options  are  arbitrary  (i.e.  they  can appear anywhere). However, if
287       options are mutually exclusive the rightmost appearance is  used.  This
288       behavior  conforms  to  the  standard  evaluation  rules of common Unix
289       shells.
290
291       In addition, one or more command files can be specified  using  an  '@'
292       sign  as  a  prefix to the filename (e.g. @command.txt). Such a command
293       argument is replaced by the content  of  the  corresponding  text  file
294       (multiple  whitespaces  are  treated  as a single separator unless they
295       appear between two quotation marks) prior to  any  further  evaluation.
296       Please  note  that  a command file cannot contain another command file.
297       This simple but effective  approach  allows  one  to  summarize  common
298       combinations  of  options/parameters  and  avoids longish and confusing
299       command lines (an example is provided in file <datadir>/dumppat.txt).
300

ENVIRONMENT

302       The dsr2xml utility  will  attempt  to  load  DICOM  data  dictionaries
303       specified  in the DCMDICTPATH environment variable. By default, i.e. if
304       the  DCMDICTPATH  environment   variable   is   not   set,   the   file
305       <datadir>/dicom.dic  will be loaded unless the dictionary is built into
306       the application (default for Windows).
307
308       The  default  behavior  should  be  preferred   and   the   DCMDICTPATH
309       environment  variable  only used when alternative data dictionaries are
310       required. The DCMDICTPATH environment variable has the same  format  as
311       the  Unix  shell PATH variable in that a colon (':') separates entries.
312       On Windows systems, a semicolon (';') is used as a separator. The  data
313       dictionary  code  will  attempt  to  load  each  file  specified in the
314       DCMDICTPATH environment variable. It is an error if no data  dictionary
315       can be loaded.
316

FILES

318       <datadir>/dsr2xml.xsd - XML Schema file
319

SEE ALSO

321       xml2dsr(1), dcmconv(1)
322
324       Copyright  (C)  2000-2019  by OFFIS e.V., Escherweg 2, 26121 Oldenburg,
325       Germany.
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328
329Version 3.6.6                   Thu Jan 14 2021                     dsr2xml(1)
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