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Consider the following picture of a chopper head. It
shows three different beams (A, B and C) being chopped by a 2 slot chopping
disc. An opto-switch at the base of the chopping head produces the reference
signal.

As the disc rotates, the 3 beams will be modulated (or chopped) as
shown below. Due to the size of the beam and the time it takes for the disc to
cross it, the output signal strength does not instantly change from zero to
full output.
The reference signal is produced from the opto-switch and has a
square wave output.

As can be clearly seen, the position of the optical beam being
chopped in relation to the chopping disc directly affects the phase
relationship with the reference signal. By inspection, it is easy to see that
for the two slot disc, a beam at position A will be in phase with the
reference. Likewise, that in position B will be 90° out of phase and that
at position C will be 180° out of phase.
More generally, the phase difference between the reference signal
and the beam being chopped can be calculated using the following equation:

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