The pyscope normalizeLens function may never have been tested before, so you should first test it in a small python script or from the python command line. Especially on the Krios, it is possible that the Tecnai Scripting functions have changed since the code was written. Here is a quick test:
from pyscope import tecnai
t = tecnai.Tecnai()
t.normalizeLens('objective')Hopefully that works, otherwise some changes can be made to tecnai.py.
Try to note how long it takes the scope to do the normalization, and how that relates to how quickly the normalizeLens function returns. It is possible that the function will return even though the scope has not finished the operation. If that happens, it will be a good idea to put a time.sleep(s) in the normalizeLens function.
Next, you can decide where in leginon you want to put it, probably immediately before the call to measureDefocusStig in focuser.py, at line 260 maybe. It could also be done right after the preset change to fa. In any case, this is how to call it:
self.instrument.tem.normalizeLens('objective')
If you get it working the way you like, we should add this as a checkbox option in the focus sequence. It could also be added as checkbox option to any preset, such that the normalization happens after the preset change.