12.7. Data Types for DICOM and TIFF

12.7. Data Types for DICOM and TIFF
	Chapter 12. Excursion: Image Processing in ML

The DICOM standard does not support pixel data types other than signed and unsigned integer, and the maximum bit depth is 16. This is the reason why in MeVisLab, the data is saved as float and (u)int32 data in DCM/TIFF format. This data type is correctly encoded in the TIFF format, and the DICOM file is written as if it was an (u)int16 image.

The data is saved as follows:

The TIFF file stored as part of a DCM/TIFF pair is a fairly standard TIFF file. For storing 3D images, the SGI 3D TIFF extension is used. 4D images are stored as 3D, the time dimension being unfold into the z-dimension.
The DCM file in a DCM/TIFF pair is a fairly standard DICOM file, except that it does not contain the pixel data tag. The contents of such a file can be read with the dcmdump tool by DICOM@offis, for example. Some information gathered during the original DICOM import, such as the individual time points in a 4D data set and the values of frame specific tags, are stored in private DICOM tags. There is no official documentation of these private tags.

In MeVisLab, the libraries libtiff and dcmtk (by DICOM@offis) are used to read these files. The following applies:

When opening such a DCM/TIFF pair, the data type stored in the TIFF file has precedence over the one in the DCM file. This mechanism is described in the help pages of the ImageSave and ImageLoad modules.
If a DICOM file contains illegal values, the data is not regarded as valid DICOM and is completely ignored. The TIFF file is handled as if the DICOM file did not exist.

The MeVisLab binding (for example as used in ImageSave and ImageLoad) does not support the double image data type for TIFF.

As consequence, images with data of the type double cannot be saved as TIFF by ImageSave. As a workaround, you can either convert the data type to float or use MLImageFormatSave and MLImageFormatLoad.

However, the images can be saved as RAW images with double data type.

	Tip
	For loading several TIFF files, use the module `ImageLoadMulti`. This should not be confused with loading a multi-page TIFF file (in which several images are saved); that format is not supported by MeVisLab.

Tip

The page size delivered by the ImageLoad module is actually not determined by the pageSizeHint field, but by the file format module reading the image data. Only if the file format allows reading the image data in different (or even arbitrary) pages, the pageSizeHint is used. (That is why it is called page size hint and not page size.) For the TIFF format, the page size is fixed by the size of the tiles in the TIFF file holding the image data. To change the page size for successive modules, ImagePropertyConvert needs to be used. For RAW images, the page size hint can be set.


12.6. Coordinate Systems in the MeVisLab GUI		12.8. Image Processing Concepts: Pages, Slices, VirtualVolumes, and More