Some rare comments:
1) In the upper image: I cannot comment on what is best between filtering and filter, although the offset in the filterfilt frequency is disturbing. You can get a similar result by applying a low-pass filter to the filter signal.
2) There is no โtrueโ instantaneous frequency unless the signal has been detected with a specific tone. However, in my experience of unfolding the Hilbert transform phase, it works well. It is becoming less and less reliable, as the ratio of noise to signal intensity is increasing.
3) Regarding the bottom image, you say that sometimes you need a large band-pass filter. Is it because the signal is very long and the instantaneous frequency varies between 500 and 800 Hz? If so, you can continue processing the window with a length at which the filtered signal has an excellent peak in the Fourier spectrum, extract this peak, set your bandage filter to this peak, apply Hilbert to the window signal, extract the phase, filter the phase.
This is worth doing if you are sure that the signal has other harmonics than the noise and the one that interests you, and it takes time. Before doing this, I would like to make sure that the data I receive is incorrect.
If it is only 1 harmonics + noise, I would again say + hilbert + emergency instant phase + lower limit on the instant phase
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