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I'm sorry to take so long to grasp how you are comparing the pulse shapes. I may still not understand it completely. I recall you said you were going to match the peaks of the 2 sides and then minimize the variance of the time-difference of the pulses. Wouldn't it be better to first match the area of the pulses rather than their peaks? I think of (lossless) dispersion in a MMF as conserving optical power (area). Or, is this what you are already doing?
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