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Hi Nevzat,
here is my best guess:
1) The particles at ECin=ECtot are possibly photons that convert in the inner calorimeter, or neutrons. It could also be any kind of particles that for some reason fail to make a signal in the outer calorimeter (including by stopping in the inner one). In any case, I don't think they can be assigned to one specific particle type and that should therefore be cut out if you want a pure sample of any particle kind.
2) As we know, all of the 3 values ECtot, ECin and ECout can occasionally be zero because of a hardware glitch. That's why we use the code which takes ECtot = ECin+ECout if it is lower than either, and ECin = ECtot-ECout if the ECin is zero and neither ECtot nor ECout are. There may be still cases where 2 or all 3 signals are zero which we cannot resolve. But if applying our 2 fixes above you still get zero for either ECtot or ECin, there's nothing you can do but to cut the event. Note that even a "huge" peak at zero doesn't mean much because it's just a single bin.
- Sebastian