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What seems really strange here is that the blue "command" line is also affected by the spikes.. You would think that would be noise free (if that is indeed what I am looking at) since it would not be noise dependent? Wouldn't that be the software telling the drive what to do?
That is true. The command is just mathematically computed and placed into KFLOP's memory and then uploaded to the PC and plotted. As well as the Output glitching to a trillion even though the limit is 5000 (which should be 2047 for Kanalog btw). I'm thinking the motion, trajectory, and encoder measurement is all working fine but then afterward the data is some how corrupted. Maybe noise somehow corrupting KFLOP's internal memory or the PC's memory? Although I've never heard of anyone having such an issue. Or possibly a rogue program corrupting memory?