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


  -dx   --dataset-from-xml  [f]ilename: string


          use dataset from XML 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)


  -rc   --remove-com


          remove COM segment
XML validation:


  +Vd   --validate-document


          validate XML document against DTD


  +Vn   --check-namespace


          check XML namespace in document root

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 (default)


          (only with --do-checks)


  -i1   --no-type1-invent


          do not invent missing type 1 attributes


          (only with --do-checks)
character set conversion of study/series file:


  -Ct   --transliterate


          try to approximate characters that cannot be


          represented through similar looking characters


  -Cd   --discard-illegal


          discard characters that cannot be represented


          in destination 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 (default)


  -nsc  --new-sc


          write new Secondary Capture SOP classes


  -vlp  --vl-photo


          write Visible Light Photographic SOP class


  -oph  --oph-photo


          write Ophthalmic Photography SOP classes
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

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'. As an alternative to option --dataset-from the mutually exclusive option --dataset-from-xml can be used. In this case, however, the file must contain XML data in the format as produced by dcm2xml.
• The --study-from and --series-from options 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. Using --study-from and --series-from at the same time does make sense. If both options are provided on the command line, the rightmost option wins. 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. 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. The --key option can be present more than once. The value part (after the '=') may be absent causing the attribute to be set with zero length. Please be advised that the --key option is applied at the very end, just before saving the DICOM file, so there is no value checking whatsoever.

UIDs¶

New Study and Series Instance UIDs are generated if necessary after applying the --study-from and --series-from 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 or --dataset-from-xml 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

For Ophthalmic Photography images, XML templates are provided (see sample file OP_template_utf_8.xml and OP_template_latin_1.xml).

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.

Character Sets¶

When an input template is loaded using --dataset-from or --dataset-from-xml, the specific character set of that template is used for the generated DICOM file. If the --study-from or --series-from options are used additionally, img2dcm will try to convert the character set of these attributes to that of the template, and will report an error if that is not possible.

If the --study-from or --series-from options are used without a template, the specific character set of this source is used for the generated DICOM file. Any keys specified on the command line with the --key option are treated as raw bytes and override any attributes that may already be present due to a template or study/series file. Therefore, care should be taken to not specify a specific character set on the command line if one might be loaded from another file. It is also the user's responsibility to ensure that attribute values specified on the command line use the correct encoding, as no conversion will take place before the values are stored in the DICOM file.

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
  Transfer Syntax UID = 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
  Transfer Syntax UID = 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
  Transfer Syntax UID = 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. As stated before, JFIF information is always removed by img2dcm. However, when using this option, the APP2 marker is retained, but img2dcm does not create an equivalent ICC Profile (0028,2000) attribute.

JPEG-LS Input Plugin¶

The JPEG-LS plugin has been integrated directly into the main JPEG plugin. There is no need for the user to explicitly state in advance if input is JPEG or JPEG-LS.

For JPEGL-LS, the original JPEG-LS from the source file is not decoded but extracted and slightly transformed (e. g. APP8 marker is cut off) to allow fast conversion of even big JPEG-LS files without the need of decoding and re-encoding.

The JPEG-LS plugin chooses the necessary output transfer syntax automatically depending on the actual encoding of the data inside the JPEG-LS file. Therefore, the following Transfer Syntaxes (and there corresponding JPEG-LS encodings) are used by the JPEG-LS plugin:

• JPEG-LS Lossless Image Compression
  Transfer Syntax UID = 1.2.840.10008.1.2.4.80
• JPEG-LS Lossy (Near-Lossless) Image Compression
  Transfer Syntax UID = 1.2.840.10008.1.2.4.81

Color and grayscale images are supported. CP-1843 enforce that the value of Planar Configuration (0028,0006) is irrelevant since the manner of encoding components is specified in the JPEG-LS bit stream as component, line or sample interleaved, hence it shall be set to 0. Since no color transformation specific for JPEG-LS is currently defined in DICOM, it is assumed that the JPEG-LS stream is encoded in RGB color space.

For DICOM it is clear that SPIFF header should not be present in the DICOM object's internal JPEG-LS stream. The plugin will simply rejects any input JPEG-LS file containing a SPIFF header at marker APP8.

By default, all APPn markers are cut off from the original JPEG-LS stream. However, if you want to keep APPn markers (e.g. APP8/HP color transform information, aka 'mrfx') inside the DICOM stream, the option --keep-appn does the trick. Pay attention that the plugin will check the actual color transform specified in the APP8/HP marker. Since DICOM does not allow any color transform to be specified in the APP8 marker, only a value of 0 (no color transform) is accepted.

BMP Input Plugin¶

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. Input images will either be converted into a DICOM image with RGB color model and a bit depth of 24, or into an image with MONOCHROME2 color model an 8 bits per pixel. 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, export plugins for the Secondary Capture Image SOP Class (default, option -sc), the Multiframe Secondary Capture Image SOP Classes (option -nsc), Visible Light Photographic Image SOP Class (option -vl), and the Ophthalmic Photography Image SOP Classes (option -oph) 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.