4 \page img2dcm Convert standard image formats into DICOM format
6 \page img2dcm img2dcm: Convert standard image formats into DICOM format
9 \section synopsis SYNOPSIS
12 img2dcm [options] imgfile-in dcmfile-out
15 \section description DESCRIPTION
17 The \b img2dcm tool serves as a conversion tool from a standard image format
18 like JPEG or BMP to DICOM. Different output SOP Classes can be selected. The
19 additional information (regarding patients, series, etc.) stored in the DICOM
20 output file can be extracted from other DICOM files which serve as a "template"
21 for the resulting DICOM object. \b img2dcm can also be configured to invent
22 missing DICOM type 1 and type 2 attributes to work even without any template
25 \section parameters PARAMETERS
27 imgfile-in image file to be imported
29 dcmfile-out DICOM output file
32 \section options OPTIONS
33 \subsection general_options general options
36 print this help text and exit
39 print version information and exit
42 print expanded command line arguments
45 quiet mode, print no warnings and errors
48 verbose mode, print processing details
51 debug mode, print debug information
53 -ll --log-level [l]evel: string constant
54 (fatal, error, warn, info, debug, trace)
55 use level l for the logger
57 -lc --log-config [f]ilename: string
58 use config file f for the logger
61 \subsection input_options input options
65 -i --input-format [i]nput file format: string
66 supported formats: JPEG (default), BMP
68 -df --dataset-from [f]ilename: string
69 use dataset from DICOM file f
71 -stf --study-from [f]ilename: string
72 read patient/study from DICOM file f
74 -sef --series-from [f]ilename: string
75 read patient/study/series from DICOM file f
78 increase instance number read from DICOM file
83 disable support for progressive JPEG
86 disable support for extended sequential JPEG
89 insist on JFIF header existence
92 keep APPn sections (except JFIF)
95 \subsection processing_options processing options
100 enable attribute validity checking (default)
103 disable attribute validity checking
106 insert missing type 2 attributes (default)
107 (only with --do-checks)
109 -i2 --no-type2-insert
110 do not insert missing type 2 attributes
111 (only with --do-checks)
114 invent missing type 1 attributes
115 (only with --do-checks)
117 -i1 --no-type1-invent
118 do not invent missing type 1 attributes
119 (only with --do-checks)
124 set latin-1 as standard character set (default)
127 keep 7-bit ASCII as standard character set
129 other processing options:
131 -k --key [k]ey: gggg,eeee="str", path or dictionary name="str"
132 add further attribute
135 \subsection output_options output options
140 write Secondary Capture SOP class
143 write new Secondary Capture SOP classes
146 write Visible Light Photographic SOP class (default)
151 write file format (default)
154 write data set without file meta information
156 group length encoding:
158 +g= --group-length-recalc
159 recalculate group lengths if present (default)
161 +g --group-length-create
162 always write with group length elements
164 -g --group-length-remove
165 always write without group length elements
167 length encoding in sequences and items:
170 write with explicit lengths (default)
172 -e --length-undefined
173 write with undefined lengths
175 data set trailing padding (not with --write-dataset):
178 no padding (implicit if --write-dataset)
180 +p --padding-create [f]ile-pad [i]tem-pad: integer
181 align file on multiple of f bytes
182 and items on multiple of i bytes
187 \subsection attribute_sources Attribute Sources
189 For converting a general image format into DICOM format, the \b img2dcm
190 application may be fed with some additional input for filling mandatory (and
191 optional) attributes in the new DICOM file like patient, study and series
192 information. This information can be collected using different approaches,
193 which can be combined and are applied to the result file in the following
196 \li Using the \e --dataset-from option \b img2dcm is forced to import
197 attributes from an existing DICOM file. The given DICOM file is fully
198 imported and serves as the basis for all further export operations.
199 As an exception, the SOP Instance UID is not copied by this option.
200 Also image related data like Rows, Columns etc. is exchanged during
201 conversion. Note that \b img2dcm does not check any other attribute
202 values for validity, e. g. it does not look into sequences to adapt any
203 attributes to the new object (referenced images etc.). Therefore, it is
204 recommended to use the templates in the data directory for (old) SC and
205 VLP objects. See also section "Input Templates".
207 \li The \e --study-from and \e --series-from options (mutually exclusive) can
208 be used to import patient, study and series information from an existing
209 DICOM file. If \e --series-from is specified, then the given DICOM file
210 is opened by \b img2dcm and all mandatory information down to the series
211 level is imported. Note that this includes patient, study and series
212 information. In case of \e --study-from, the series information is
213 excluded. The following attributes are taken over:
220 Specific Character Set
226 Referring Physician's Name
230 Series Level (only in case of option --series-from):
236 \li With the \e --insert-type2 and \e --invent-type1 options (both enabled per
237 default), missing attributes (type 2 attributes) and/or missing attribute
238 values (for type 1 attributes) are automatically added and invented by
239 \b img2dcm. Please note that these options are only evaluated if option
240 \e --do-checks is enabled (default). If the \e --no-checks options is
241 enabled, no automatic attribute insertion will take place.
243 \li The \e --key option can be used to add further attributes to the DICOM
244 output file. This option is applied at the very end, just before saving the
245 DICOM file. It is also possible to specify sequences, items and nested
246 attributes using the \e --key option. In these cases, a special "path"
247 notation has to be used. Details on this path notation can be found in the
248 documentation of \b dcmodify.
250 \subsection uids UIDs
252 New Study and Series Instance UIDs are generated <b>if necessary</b> after
253 applying the \e --study-from and \e --series options. If Study Instance UID or
254 Series Instance UID are not present after these steps, they are newly generated,
255 independently from each other.
256 A contrary behaviour is choosen for the SOP Instance UID that one could expect
257 to be taken over when using the \e --dataset-from option. This is \b not the
258 case, the SOP Instance UID is \b not copied to the new object. This should
259 be the desirable behaviour for most use cases. However, if a certain SOP
260 Instance UID should be inserted into the new object, the \e --key option should
263 \subsection inputtemplates Input Templates
265 For supporting the conversion into DICOM, \b img2dcm comes with some
266 pre-defined templates which can be used for the \e --dataset-from option (see
267 sample files \e SC.dump and \e VLP.dump). These templates should be filled with
268 the desired values and then must be dumped (converted) to a DICOM file before
269 actually being used with \b img2dcm. Use \b dump2dcm to convert the dump to
272 dump2dcm SC.dump SC.dcm
275 It is possible to use any DICOM file as a template. Please note that the
276 complete DICOM dataset is imported; hence, it should be assured that only
277 attributes are present which should be part of the constructed DICOM object.
278 The SOP Class UID and the Pixel Data attributes (including attributes like
279 Rows, Columns etc.) are not copied but replaced by \b img2dcm during conversion.
281 \subsection inputplugins Input Plugins
283 The \b img2dcm application currently supports the JPEG and the BMP image format
286 \subsubsection jpeginputplugin JPEG Input Plugin
288 For JPEG, the original JPEG from the source file is not decoded but extracted
289 and slightly transformed (e. g. JFIF header is cut off) to allow fast
290 conversion of even big JPEG files without the need of decoding and re-encoding.
291 The JPEG plugin chooses the necessary output transfer syntax automatically
292 depending on the actual encoding of the data inside the JPEG file. Therefore,
293 the following Transfer Syntaxes (and their corresponding JPEG encodings) are used
296 \li JPEG Coding Process 1
297 Baseline, Lossy, Non-Hierarchical, Sequential, DCT, Huffman, 8 Bit
298 SOP Class = 1.2.840.10008.1.2.4.50
300 \li JPEG Coding Process 2 (8-bit) and 4 (12-bit)
301 Extended, Lossy, Non-Hierarchical, Sequential, DCT, Huffman, 8/12 Bit
302 SOP Class = 1.2.840.10008.1.2.4.51
304 \li JPEG Coding Process 10 (8-bit) and 12 (12-bit)
305 Full Progression, lossy, Non-Hierarch., Progressive, DCT, Huffman, 8/12 Bit
306 SOP Class = 1.2.840.10008.1.2.4.55
308 Color and grayscale images are supported.
310 The support for the Extended JPEG Transfer Syntax can be disabled
311 (\e --disable-ext option) as well as the support for the (retired) Progressive
312 JPEG Transfer Syntax (\e --disable-progr option).
314 JPEG lossless encoding as well as any arithmethic or hierarchical JPEG encoding
315 modes are not supported by the plugin.
317 JFIF (JPEG File Interchange Format) information facilitates optional APPn
318 markers in a JPEG file. Many digital cameras do not integrate such JFIF
319 information into the JPEG output they create. For example, JFIF contains
320 information about the pixel aspect ratio of the compressed image. If you want
321 the \b img2dcm application to insist on a JFIF header in the JPEG stream, you
322 can use the option \e --insist-on-jfif which will abort if no JFIF information
323 can be found. By default, missing JFIF information is ignored.
325 For DICOM it is kind of a "gray zone", whether the integration of JFIF (or any
326 other APPn) data into the DICOM object's internal JPEG stream is allowed or
327 not. However, the most reliable approach is to cut those markers and their
328 information off the JPEG stream. This approach is also taken by the \b img2dcm
329 application. By default, all APPn markers are cut off from the original JPEG
330 stream. However, if you want to keep other APPn markers than JFIF (e. g.
331 EXIF information) inside the DICOM stream, the option \e --keep-appn
332 does the trick. It should also be slightly faster than cutting off APPn
333 information, because it is not necessary to scan the whole JPEG stream for
334 such data. JFIF information is \b always removed by \b img2dcm.
336 \subsubsection bmpinputplugin BMP Input Plugin
338 \b img2dcm supports BMP as input format. However, so far only the most commmon
339 BMP images are supported. In particular, BMP images which use bitfields or
340 run length encoding will be rejected. Such images are uncommon. All input images
341 will be converted into a DICOM image with RGB color model and a bit depth of 24.
342 There are no specific options for fine-tuning BMP format conversion.
344 \subsection outputplugins Output Plugins
346 The desired output SOP Class can be selected on the command line. Currently,
347 an export plugin for the Secondary Capture Image SOP class (default, option
348 \e -sc), the new Secondary Capture Image SOP classes (option \e -nsc) and
349 Visible Light Photographic Image SOP class (option \e -vl) are available.
350 Please note that the first one is deprecated according to the DICOM standard
351 but is selected as a default because it is widely supported. Future versions
352 of \b img2dcm might provide further output plugins for other SOP Classes.
354 For the new Secondary Capture SOP classes, it is not possible to specifiy which
355 specific SOP class should be used for output. That is because these new SOP
356 classes are differentiated from each other by colour depth (1/8/16) and the
357 fact whether the image is black/white or colour. That is why \b img2dcm decides
358 during conversion, which output SOP class is suitable for a given source image.
360 \section examples EXAMPLES
362 Here are some examples that show how the \b img2dcm application can be used.
367 img2dcm image.jpg out.dcm
368 <br>Read JPEG file "image.jpg", convert to the old Secondary Capture SOP class
369 and save the result to DICOM file "out.dcm". This is the easiest way of using
370 \b img2dcm. Any type 1 and type 2 attributes required for writing valid objects
371 of this SOP class are inserted automatically.
375 img2dcm -i BMP image.bmp out.dcm
376 <br>Same as above but tells img2dcm to read a BMP file instead of JPEG.
380 img2dcm image.jpg out.dcm -vlp -k "PatientName=Bond^James"
381 <br>Same as first example, but writes Visible Light Photographic Image object
382 to "out.dcm" and sets PatientName to "Bond^James" which otherwise would be
387 img2dcm image.jpg out.dcm --series-from template.dcm -k
388 "PatientName=Bond^James"
389 <br>Same as 1), but imports patient/study/series infomation from DICOM file
390 "template.dcm". Please note that attribute PatientName will contain
391 "Bond^James" at the end, any value from "template.dcm" will be overwritten.
392 That is, because the -k option is applied at the very end of the conversion
393 pipeline (see above).
397 img2dcm image.jpg out.dcm --no-checks
398 <br>Same as 1), but does not perform any attribute checking and no type 1 and
399 type 2 attribute insertion! So in this case, an invalid DICOM object would be
400 generated. This can be interesting if the output file is not meant to be
401 completed but will undergo further transformations, e. g. adding attributes
402 using \b dcmodify. Only use option \e --no-checks if you know what you are
407 img2dcm image.jpg out.dcm --no-type1-invent
408 <br>Same as 1), but does not insert missing type 1 attributes and/or their
409 values. Type 2 attributes will be inserted. Note that in this case it must be
410 assured that all type 1 attributes are provided by other means, i. e. by adding
411 them with the \e --key option. Otherwise, \b img2dcm will report an error and
412 will stop converting.
416 img2dcm image.jpg out.dcm --keep-appn --insist-on-jfif
417 <br>Same as 1), but takes over APPn information like EXIF into the DICOM
418 object's resulting JPEG stream. Further, \e --insist-on-jfif will force
419 \b img2dcm to abort if no JFIF information is existent in the source file.
424 \section logging LOGGING
426 The level of logging output of the various command line tools and underlying
427 libraries can be specified by the user. By default, only errors and warnings
428 are written to the standard error stream. Using option \e --verbose also
429 informational messages like processing details are reported. Option
430 \e --debug can be used to get more details on the internal activity, e.g. for
431 debugging purposes. Other logging levels can be selected using option
432 \e --log-level. In \e --quiet mode only fatal errors are reported. In such
433 very severe error events, the application will usually terminate. For more
434 details on the different logging levels, see documentation of module "oflog".
436 In case the logging output should be written to file (optionally with logfile
437 rotation), to syslog (Unix) or the event log (Windows) option \e --log-config
438 can be used. This configuration file also allows for directing only certain
439 messages to a particular output stream and for filtering certain messages
440 based on the module or application where they are generated. An example
441 configuration file is provided in <em><etcdir>/logger.cfg</em>).
443 \section command_line COMMAND LINE
445 All command line tools use the following notation for parameters: square
446 brackets enclose optional values (0-1), three trailing dots indicate that
447 multiple values are allowed (1-n), a combination of both means 0 to n values.
449 Command line options are distinguished from parameters by a leading '+' or '-'
450 sign, respectively. Usually, order and position of command line options are
451 arbitrary (i.e. they can appear anywhere). However, if options are mutually
452 exclusive the rightmost appearance is used. This behaviour conforms to the
453 standard evaluation rules of common Unix shells.
455 In addition, one or more command files can be specified using an '@' sign as a
456 prefix to the filename (e.g. <em>\@command.txt</em>). Such a command argument
457 is replaced by the content of the corresponding text file (multiple
458 whitespaces are treated as a single separator unless they appear between two
459 quotation marks) prior to any further evaluation. Please note that a command
460 file cannot contain another command file. This simple but effective approach
461 allows to summarize common combinations of options/parameters and avoids
462 longish and confusing command lines (an example is provided in file
463 <em><datadir>/dumppat.txt</em>).
465 \section environment ENVIRONMENT
467 The \b img2dcm utility will attempt to load DICOM data dictionaries specified
468 in the \e DCMDICTPATH environment variable. By default, i.e. if the
469 \e DCMDICTPATH environment variable is not set, the file
470 <em><datadir>/dicom.dic</em> will be loaded unless the dictionary is built
471 into the application (default for Windows).
473 The default behaviour should be preferred and the \e DCMDICTPATH environment
474 variable only used when alternative data dictionaries are required. The
475 \e DCMDICTPATH environment variable has the same format as the Unix shell
476 \e PATH variable in that a colon (":") separates entries. On Windows systems,
477 a semicolon (";") is used as a separator. The data dictionary code will
478 attempt to load each file specified in the \e DCMDICTPATH environment variable.
479 It is an error if no data dictionary can be loaded.
483 <em><datadir>/SC.dump</em> - Sample dump file for Secondary Capture images
484 \n<em><datadir>/VLP.dump</em> - Sample dump file for Visible Light Photographic
487 \section see_also SEE ALSO
489 <b>dcm2pnm</b>(1), <b>dcmj2pnm</b>(1), <b>dump2dcm</b>(1), <b>dcmconv</b>(1),
492 \section copyright COPYRIGHT
494 Copyright (C) 2007-2010 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.