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Entry  Thu Sep 17 19:58:06 2015, gautam, Summary, Computer Scripts / Programs, Frequency counting algorithm 
    Reply  Mon Sep 21 18:31:06 2015, gautam, Summary, Computer Scripts / Programs, Frequency counting algorithm 6x
       Reply  Mon Sep 21 23:18:55 2015, ericq, Summary, Computer Scripts / Programs, Frequency counting algorithm 
          Reply  Tue Sep 22 02:11:17 2015, rana, Summary, Computer Scripts / Programs, Frequency counting algorithm 
Message ID: 11629     Entry time: Mon Sep 21 23:18:55 2015     In reply to: 11628     Reply to this: 11631
Author: ericq 
Type: Summary 
Category: Computer Scripts / Programs 
Subject: Frequency counting algorithm 

I definitely think lowpassing the output is the way to go. Since this frequency readback will be used for slow control of the beatnote frequency via auxillary laser temperature, even lowpassing at tens of Hz is fine. The jitter doesn't mean its useless, though.

If we lowpass at 16Hz, we're effectively averaging over 1024 samples, bringing, for example, a +-2kHz jitter of a 6kHz signal as you post down to 2kHz/sqrt(1024) ~ 60Hz, which is 1% of the carrier. This seems ok to me. 

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