Well, now I measured with a 3.5" drive. Hall sensor or not, the jitter is not much better than the 5.25" drive I measured before. Index edge jitter is still in the order of microseconds. This is not a track shift, I captured multiple consecutive revolutions, and the index pulse relation to the flux transitions changes (slightly) across revolutions.
I used a different logic analyzer that can capture in segmented mode. The beginning of each revolution, just around the active (falling) edge of the index is captured:
Segmented-Annotated.png
The image shows two segments, numbered 6 and 7. They correspond to two consecutive revolutions. Each segment starts just before the index edge. The top waveform signal is the flux transitions on the Read signal. The bottom one is the Index signal. The green dotted bars (one on each revolution) mark a couple of shorter transitions that I recorded to measure the position. If there wouldn't be any Index jitter at all, the distance from the index edge to the bar should be always the same.
Count the transitions between the falling edge of the index and the green dotted bar. The first revolution has three transitions. The second one has four. The fourth transitions before the green bar is marked with a blue oval. In the first revolution is before the index edge, but in the second one is after the edge. This simply means that this particular transitions is omitted if the first revolution is captured edge to edge.
Conclusion:
As I was saying, capturing a single revolution might not get the complete track, one (or more) transitions might be missing. If the track has, so called, data under the index, then simply some data might be missing.
Obviously this doesn't happen always. Not every track has data under the index. In some platforms is very common (typically 8-bit ones), in others not so much. And even then, the jitter is not always that bad that a transition is missed in a revolution as shown in the posted image.
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