| img2dcm(1) | OFFIS DCMTK | img2dcm(1) |
img2dcm - Convert standard image formats into DICOM format
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
For converting a general image format into DICOM format, the img2dcm application may be fed with some additional input for filling mandatory (and optional) attributes in the new DICOM file like patient, study and series information. This information can be collected using different approaches, which can be combined and are applied to the result file in the following order:
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
New Study and Series Instance UIDs are generated if necessary after applying the --study-from and --series options. If Study Instance UID or Series Instance UID are not present after these steps, they are newly generated, independently from each other. A contrary behavior is chosen for the SOP Instance UID that one could expect to be taken over when using the --dataset-from option. This is not the case, the SOP Instance UID is not copied to the new object. This should be the desirable behavior for most use cases. However, if a certain SOP Instance UID should be inserted into the new object, the --key option should be used.
For supporting the conversion into DICOM, img2dcm comes with some pre-defined templates which can be used for the --dataset-from option (see sample files SC.dump and VLP.dump). These templates should be filled with the desired values and then must be dumped (converted) to a DICOM file before actually being used with img2dcm. Use dump2dcm to convert the dump to DICOM. Example:
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.
The img2dcm application currently supports the JPEG and the BMP image format as input.
For JPEG, the original JPEG from the source file is not decoded but extracted and slightly transformed (e. g. JFIF header is cut off) to allow fast conversion of even big JPEG files without the need of decoding and re-encoding. The JPEG plugin chooses the necessary output transfer syntax automatically depending on the actual encoding of the data inside the JPEG file. Therefore, the following Transfer Syntaxes (and their corresponding JPEG encodings) are used by the JPEG plugin:
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.
img2dcm supports BMP as input format. However, so far only the most common BMP images are supported. In particular, BMP images which use bit fields or run length encoding will be rejected. Such images are uncommon. All input images will be converted into a DICOM image with RGB color model and a bit depth of 24. There are no specific options for fine-tuning BMP format conversion.
The desired output SOP Class can be selected on the command line. Currently, an export plugin for the Secondary Capture Image SOP class (default, option -sc), the new Secondary Capture Image SOP classes (option -nsc) and Visible Light Photographic Image SOP class (option -vl) are available. Please note that the first one is deprecated according to the DICOM standard but is selected as a default because it is widely supported. Future versions of img2dcm might provide further output plugins for other SOP Classes.
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.
<datadir>/SC.dump - Sample dump file for Secondary
Capture images
<datadir>/VLP.dump - Sample dump file for Visible Light
Photographic images
dcm2pnm(1), dcmj2pnm(1), dump2dcm(1), dcmconv(1), dcmodify(1)
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| Thu Nov 29 2018 | Version 3.6.4 |