img2dcm(1)
NAME
img2dcm - Convert standard image formats into DICOM format
SYNOPSIS
img2dcm [options] imgfile-in dcmfile-out
DESCRIPTION
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.
PARAMETERS
imgfile-in image file to be imported dcmfile-out DICOM output file
OPTIONS
general options
-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
input options
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)
processing options
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
output options
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
NOTES
Attribute Sources
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:
* Using the --dataset-from option img2dcm is forced to import
attributes from an existing DICOM file. The given DICOM file is fully
imported and serves as the basis for all further export operations.
As an exception, the SOP Instance UID is not copied by this option.
Also image related data like Rows, Columns etc. is exchanged during
conversion. Note that img2dcm does not check any other attribute
values for validity, e. g. it does not look into sequences to adapt
any attributes to the new object (referenced images etc.). Therefore,
it is recommended to use the templates in the data directory for
(old) SC and VLP objects. See also section 'Input Templates'.
* The --study-from and --series-from options (mutually exclusive) can
be used to import patient, study and series information from an
existing DICOM file. If --series-from is specified, then the given
DICOM file is opened by img2dcm and all mandatory information down to
the series level is imported. Note that this includes patient, study
and series information. In case of --study-from, the series
information is excluded. The following attributes are taken over:
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
* With the --insert-type2 and --invent-type1 options (both enabled per
default), missing attributes (type 2 attributes) and/or missing
attribute values (for type 1 attributes) are automatically added and
invented by img2dcm. Please note that these options are only
evaluated if option --do-checks is enabled (default). If the --no-
checks options is enabled, no automatic attribute insertion will take
place.
* The --key option can be used to add further attributes to the DICOM
output file. This option is applied at the very end, just before
saving the DICOM file. It is also possible to specify sequences,
items and nested attributes using the --key option. In these cases, a
special 'path' notation has to be used. Details on this path notation
can be found in the documentation of dcmodify.
UIDs
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.
Input Templates
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.
Input Plugins
The img2dcm application currently supports the JPEG and the BMP image
format as input.
JPEG Input Plugin
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:
* JPEG Coding Process 1 Baseline, Lossy, Non-Hierarchical, Sequential,
DCT, Huffman, 8 Bit SOP Class = 1.2.840.10008.1.2.4.50
* JPEG Coding Process 2 (8-bit) and 4 (12-bit) Extended, Lossy, Non-
Hierarchical, Sequential, DCT, Huffman, 8/12 Bit SOP Class =
1.2.840.10008.1.2.4.51
* JPEG Coding Process 10 (8-bit) and 12 (12-bit) Full Progression,
lossy, Non-Hierarch., Progressive, DCT, Huffman, 8/12 Bit SOP Class =
1.2.840.10008.1.2.4.55
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.
BMP Input Plugin
img2dcm supports BMP as input format. However, so far only the most
commmon BMP images are supported. In particular, BMP images which use
bitfields 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.
Output Plugins
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.
EXAMPLES
Here are some examples that show how the img2dcm application can be
used.
1. img2dcm image.jpg out.dcm
Read JPEG file 'image.jpg', convert to the old Secondary Capture
SOP class and save the result to DICOM file 'out.dcm'. This is the
easiest way of using img2dcm. Any type 1 and type 2 attributes
required for writing valid objects of this SOP class are inserted
automatically.
2. img2dcm -i BMP image.bmp out.dcm
Same as above but tells img2dcm to read a BMP file instead of JPEG.
3. img2dcm image.jpg out.dcm -vlp -k 'PatientName=Bond^James'
Same as first example, but writes Visible Light Photographic Image
object to 'out.dcm' and sets PatientName to 'Bond^James' which
otherwise would be left empty.
4. img2dcm image.jpg out.dcm --series-from template.dcm -k
'PatientName=Bond^James'
Same as 1), but imports patient/study/series infomation from DICOM
file 'template.dcm'. Please note that attribute PatientName will
contain 'Bond^James' at the end, any value from 'template.dcm' will
be overwritten. That is, because the -k option is applied at the
very end of the conversion pipeline (see above).
5. img2dcm image.jpg out.dcm --no-checks
Same as 1), but does not perform any attribute checking and no type
1 and type 2 attribute insertion! So in this case, an invalid DICOM
object would be generated. This can be interesting if the output
file is not meant to be completed but will undergo further
transformations, e. g. adding attributes using dcmodify. Only use
option --no-checks if you know what you are doing!
6. img2dcm image.jpg out.dcm --no-type1-invent
Same as 1), but does not insert missing type 1 attributes and/or
their values. Type 2 attributes will be inserted. Note that in this
case it must be assured that all type 1 attributes are provided by
other means, i. e. by adding them with the --key option. Otherwise,
img2dcm will report an error and will stop converting.
7. img2dcm image.jpg out.dcm --keep-appn --insist-on-jfif
Same as 1), but takes over APPn information like EXIF into the
DICOM object's resulting JPEG stream. Further, --insist-on-jfif
will force img2dcm to abort if no JFIF information is existent in
the source file.
LOGGING
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.
COMMAND LINE
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).
ENVIRONMENT
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.
FILES
<datadir>/SC.dump - Sample dump file for Secondary Capture images <datadir>/VLP.dump - Sample dump file for Visible Light Photographic images
SEE ALSO
dcm2pnm(1), dcmj2pnm(1), dump2dcm(1), dcmconv(1), dcmodify(1)
COPYRIGHT
Copyright (C) 2007-2014 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.
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