Deanna,
First, I would point you toward the example 'Measure Buffered Period (NI-TIO)' as (very likely) a better starting point for your app. This method only requires one counter per measurement channel and is well suited to low and medium frequency inputs. Just realize that your sampling rate is going to be equal to the pulse rate coming in. If your signal comes in at 50 kHz, you'll be collecting 50000 period meaurements per second and need to size your buffers accordingly.
You can easily set up separate buffered period measurements on counters 0 and 1 simultaneously -- just be sure to define a unique group # to each when calling "Counter Group Config.vi". Since frequency is simply 1/period, you can easily generate your frequency arrays.
If you only need a single average value, you could use the mean or median of each array.
Now a quick explanation of the example you were trying. First off, the idea of "adjacent counter" has a very specific meaning. The following are the only pairs that can be considered "adjacent" on the 6602: (0,1), (2,3), (4,5), (6,7). 1 and 2 are not considered adjacent to one another.
The purpose of the 2nd half of your example was to "gate" the counting operation in the first half. The first counter would only count while the second counter's output was high. The second counter generates a single pulse which precisely defines the first counter's counting time. Then frequency is given by (# counts) / (pulse time).
-Kevin P.
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