Going back to PAM4, single gate test (uneven distribution). Note that the gaps are no longer present. Any idea what causes there to be a harsh lines when looking at the speckles? Note at the start of the first transition, they are fairly sparse. Then as we work our way to the next transition, they don't has the same density. As the scope continues to sweep this pattern repeats.
This is a subtle point.
The root cause is the fact that we change the query voltage for all channels in parallel when acquiring CDF data. If the query voltage for Channels 1, 3, 4 (hidden) were fixed during CH2 acquisition, the speckles would not appear. A hacky way to do this is to set CH1,3,4 to 5 mV/div and CH3,4 offset to -10V to force the comparator outputs to a constant at each post-trigger delay, by always clipping the waveform.
There's a small (~100 uV) digital-to-analog crosstalk from the comparator output of CH1,3,4 to the analog input of CH2. Since the PDF is computed using CDF differences, this doesn't matter if the comparator outputs of CH1,3,4 are constant. But if they're not, then the input of CH2 is bumped up or down by ~100 uV depending on what the other channels are doing. This is enough to perturb the CDF up or down by a fraction of a percent, in a way that does not cancel upon subtraction.
Of course, when multiple channels are visible, the only way to avoid this is to issue one R command per visible channel, each keeping all but one query voltage constant. This would slow down acquisition if multiple channels are visible. We could add this mode in software, and it would allow acquisition of very clean eye diagrams. But you're now probing the limits of the hardware.
To be clear, if you change the CH1 clock duty cycle, the speckled regions will change accordingly. If CH1,3,4, are always clipped (either high or low), the speckles should largely go away.