Number of cycles using power spectrum for getting frequency

Hi,
I have a square wave that I am getting a frequency estimate from using power and frequency estimate.vi
I was wondering if it mattered how many cycles were inputted for the frequency estimate. Also, the signal may end in between cycles.
Thanks,
Jennifer

Sorry for the vague first post. The software was already written for the device and I am just trying to understand a few things in order to make some changes.
I am measuring the speed of a turning rotor using the square wave signal generated from a pattern on the turning rotor. I need to know the frequency of the square wave in order to determine the speed of the rotor. The pulse pattern is used in power spectrum and estimate frequency icons (appears to be similar to an example program for spectrum analyzer). The speed of the rotor is variable until it reaches steady state which can take minutes or hours. Speeds are not too high (Freq 1-100Hz). Right now the measurement is set up to sample a given number of points at a given scan rate. This means that the data most likely does not end exactly as a pulse cycle ends but somewhere in the middle of a cycle.
We are interested in seeing the transient change in speed from start-up to steady-state. How short of a sampling period (i.e. # of cycles can be put into the power spectrum and estimate frequency.vi's) would give reliable measurments. Right now I just scan for a reasonable time in order to make sure I get enough pulses in order to better estimate the frequency of the pulse signal.
In the future I will work with completing pulse width measurements which most likely would be the fastest I can complete a transient measurement although my data will have a bit more fluctuations. That's due to each pulse not being exactly the same width.
Hope that gives you a better idea what's going on here.

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