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Continuous aquisition of N Samples

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How long are you going to be reading samples for? If it is only for a short amount of time (a few seconds) you might as well record data as fast as you can with your hardware, write to file, then process the data after. Since your transition time is so short it might be hard to capture all the data in real time. Good luck!

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Unfortunately, I'll be recording over a period of several hours.  The trigger won't be continuous over a few hours, but it may come in bursts at more than 30 Hz.
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