I'm doing spectral imaging analysis and have a large number of spectra I would like to filter using FFT.  Each spectra is ~2000 points long, and there are 250,000 of them.  The best references I can find suggest that each transform will take about 100 msec, which leads to an unacceptably long time (7 hrs) to analyze the whole image. Does anyone know of Fourier transform algorithms that are significantly faster, or of any benchmark studies I could use to estimate how long this analysis should take on a modern PC?