I have some terahertz spectroscopy time series data, a reference set with 2048 data points taken every 0.0521 picoseconds, and the sample data set with 544 data points taken every 0.0781 picoseconds. I'm using Matlab to take a FFT of both sets, with zero padding on the sample set up to 2048 points, and I'm supposed to do a deconvolution on those transformed sets on a specific range of frequencies, but because the sampling rate is different for the two, these correspond to different starting points in the data sets, and the lengths won't match up either. When plotting the two DFTs, they only line up properly when accounting for the different sampling rates when spacing the frequency axis.
Is there something I'm doing wrong, or how should I do the deconvolution?
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