img2dcm [options] imgfile-in dcmfile-out
The img2dcm tool serves as a conversion tool from a standard image format like JPEG or BMP to DICOM. Different output SOP Classes can be selected. The additional information (regarding patients, series, etc.) stored in the DICOM output file can be extracted from other DICOM files which serve as a 'template' for the resulting DICOM object. img2dcm can also be configured to invent missing DICOM type 1 and type 2 attributes to work even without any template dataset.
imgfile-in image file to be imported dcmfile-out DICOM output file
-h --help print this help text and exit --version print version information and exit --arguments print expanded command line arguments -q --quiet quiet mode, print no warnings and errors -v --verbose verbose mode, print processing details -d --debug debug mode, print debug information -ll --log-level [l]evel: string constant (fatal, error, warn, info, debug, trace) use level l for the logger -lc --log-config [f]ilename: string use config file f for the logger
general: -i --input-format [i]nput file format: string supported formats: JPEG (default), BMP -df --dataset-from [f]ilename: string use dataset from DICOM file f -stf --study-from [f]ilename: string read patient/study from DICOM file f -sef --series-from [f]ilename: string read patient/study/series from DICOM file f -ii --instance-inc increase instance number read from DICOM file JPEG format: -dp --disable-progr disable support for progressive JPEG -de --disable-ext disable support for extended sequential JPEG -jf --insist-on-jfif insist on JFIF header existence -ka --keep-appn keep APPn sections (except JFIF)
attribute checking: --do-checks enable attribute validity checking (default) --no-checks disable attribute validity checking +i2 --insert-type2 insert missing type 2 attributes (default) (only with --do-checks) -i2 --no-type2-insert do not insert missing type 2 attributes (only with --do-checks) +i1 --invent-type1 invent missing type 1 attributes (only with --do-checks) -i1 --no-type1-invent do not invent missing type 1 attributes (only with --do-checks) character set: +l1 --latin1 set latin-1 as standard character set (default) -l1 --no-latin1 keep 7-bit ASCII as standard character set other processing options: -k --key [k]ey: gggg,eeee="str", path or dictionary name="str" add further attribute
target SOP class: -sc --sec-capture write Secondary Capture SOP class -nsc --new-sc write new Secondary Capture SOP classes -vlp --vl-photo write Visible Light Photographic SOP class (default) output file format: +F --write-file write file format (default) -F --write-dataset write data set without file meta information group length encoding: +g= --group-length-recalc recalculate group lengths if present (default) +g --group-length-create always write with group length elements -g --group-length-remove always write without group length elements length encoding in sequences and items: +e --length-explicit write with explicit lengths (default) -e --length-undefined write with undefined lengths data set trailing padding (not with --write-dataset): -p --padding-off no padding (implicit if --write-dataset) +p --padding-create [f]ile-pad [i]tem-pad: integer align file on multiple of f bytes and items on multiple of i bytes
Patient Level: Patient's Name Patient ID Patient's Sex Patient's Birth Date Specific Character Set Study Level: Study Instance UID Study Date Study Time Referring Physician's Name Study ID Accession Number Series Level (only in case of option --series-from): Series Instance UID Series Number Manufacturer
dump2dcm SC.dump SC.dcm
It is possible to use any DICOM file as a template. Please note that the complete DICOM dataset is imported; hence, it should be assured that only attributes are present which should be part of the constructed DICOM object. The SOP Class UID and the Pixel Data attributes (including attributes like Rows, Columns etc.) are not copied but replaced by img2dcm during conversion.
Color and grayscale images are supported.
The support for the Extended JPEG Transfer Syntax can be disabled (--disable-ext option) as well as the support for the (retired) Progressive JPEG Transfer Syntax (--disable-progr option).
JPEG lossless encoding as well as any arithmetic or hierarchical JPEG encoding modes are not supported by the plugin.
JFIF (JPEG File Interchange Format) information facilitates optional APPn markers in a JPEG file. Many digital cameras do not integrate such JFIF information into the JPEG output they create. For example, JFIF contains information about the pixel aspect ratio of the compressed image. If you want the img2dcm application to insist on a JFIF header in the JPEG stream, you can use the option --insist-on-jfif which will abort if no JFIF information can be found. By default, missing JFIF information is ignored.
For DICOM it is kind of a 'gray zone', whether the integration of JFIF (or any other APPn) data into the DICOM object's internal JPEG stream is allowed or not. However, the most reliable approach is to cut those markers and their information off the JPEG stream. This approach is also taken by the img2dcm application. By default, all APPn markers are cut off from the original JPEG stream. However, if you want to keep other APPn markers than JFIF (e. g. EXIF information) inside the DICOM stream, the option --keep-appn does the trick. It should also be slightly faster than cutting off APPn information, because it is not necessary to scan the whole JPEG stream for such data. JFIF information is always removed by img2dcm.
For the new Secondary Capture SOP classes, it is not possible to specify which specific SOP class should be used for output. That is because these new SOP classes are differentiated from each other by color depth (1/8/16) and the fact whether the image is black/white or color. That is why img2dcm decides during conversion, which output SOP class is suitable for a given source image.
Here are some examples that show how the img2dcm application can be used.
The level of logging output of the various command line tools and underlying libraries can be specified by the user. By default, only errors and warnings are written to the standard error stream. Using option --verbose also informational messages like processing details are reported. Option --debug can be used to get more details on the internal activity, e.g. for debugging purposes. Other logging levels can be selected using option --log-level. In --quiet mode only fatal errors are reported. In such very severe error events, the application will usually terminate. For more details on the different logging levels, see documentation of module 'oflog'.
In case the logging output should be written to file (optionally with logfile rotation), to syslog (Unix) or the event log (Windows) option --log-config can be used. This configuration file also allows for directing only certain messages to a particular output stream and for filtering certain messages based on the module or application where they are generated. An example configuration file is provided in <etcdir>/logger.cfg.
All command line tools use the following notation for parameters: square brackets enclose optional values (0-1), three trailing dots indicate that multiple values are allowed (1-n), a combination of both means 0 to n values.
Command line options are distinguished from parameters by a leading '+' or '-' sign, respectively. Usually, order and position of command line options are arbitrary (i.e. they can appear anywhere). However, if options are mutually exclusive the rightmost appearance is used. This behavior conforms to the standard evaluation rules of common Unix shells.
In addition, one or more command files can be specified using an '@' sign as a prefix to the filename (e.g. @command.txt). Such a command argument is replaced by the content of the corresponding text file (multiple whitespaces are treated as a single separator unless they appear between two quotation marks) prior to any further evaluation. Please note that a command file cannot contain another command file. This simple but effective approach allows one to summarize common combinations of options/parameters and avoids longish and confusing command lines (an example is provided in file <datadir>/dumppat.txt).
The img2dcm utility will attempt to load DICOM data dictionaries specified in the DCMDICTPATH environment variable. By default, i.e. if the DCMDICTPATH environment variable is not set, the file <datadir>/dicom.dic will be loaded unless the dictionary is built into the application (default for Windows).
The default behavior should be preferred and the DCMDICTPATH environment variable only used when alternative data dictionaries are required. The DCMDICTPATH environment variable has the same format as the Unix shell PATH variable in that a colon (':') separates entries. On Windows systems, a semicolon (';') is used as a separator. The data dictionary code will attempt to load each file specified in the DCMDICTPATH environment variable. It is an error if no data dictionary can be loaded.
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