IRIS is a piece of Windows software that will readily convert CR2 files into FITS files. It can be done via pull-down menus or via 'scripts'
A typical script is:
Image files named IMG_XXXX.CR2 are here being loaded and saved as 16-bit FITS named IMG_XXXX.fit
It is necessary to first, via pull-down menus, set up IRIS to expect a Canon EOS camera (hence it understands to look for CR2 files in the script). You must also set the paths (in Settings...) to where the data are and where the scripts are. When you want to process .X3F images you must pick the SIGMA SD10 camera from the 'camera' menu in IRIS.
The script is a text file with extention '.pgm' and is run from the 'console' in IRIS - this is the 11th icon along the toolbar. Simply write
RUN nameofscript (omit the .pgm, apparently)
and it will run, saving files for you.
X3F files are not yet understood - IRIS will open a file and save a FITS but there is only one 'colour-plane' in the FITS file - in the CR2 files converted above we get 3.
IRIS can be run from 'wine' in Ubuntu.