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
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 behaviour is
choosen 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 behaviour 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:
- •
- 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 arithmethic 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
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 specifiy which
specific SOP class should be used for output. That is because these new SOP
classes are differentiated from each other by colour depth (1/8/16) and the
fact whether the image is black/white or colour. 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 behaviour 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 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 behaviour 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) 2007-2010 by OFFIS e.V., Escherweg 2, 26121 Oldenburg,
Germany.