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Run multiple tests in parallel using Imatest IT Parallel
decrease the number of selected SFR regions to a minimum
disable other calculation settings that are not necessary
Use the DLL version of Imatest IT instead of the EXE
Use direct passing of image data in an array instead of a file on disk
Throw hardware at the problem. Imatest loves to have lots of CPU cores to calculate its Fourier transforms, our 6-core LGA-2011 i7 processors are screaming fast. The more cores the merrier, clock speed is also your friend.