IK Multimedia TONEX

Well, depending on the captured amp, the file might be altered quite dramatically, so the first transient isn't as clear anymore - and that'd be the only thing it could use as an anchor for autotrimming. Capturing a noisy amp might add to the issue.

Fwiw, I have been running into this issue before, when shooting some IRs using Logic's Impulse Response Utility quite some years back. The resulting IRs had some silence in the beginning ocassionally (I was capturing some kinda wild stuff which involved running the signal through some DAW processing). Didn't happen again when I did a similar thing not that long ago, but I'm still curious.

Possibly best to just give it a try.

The beginning of the first transient should be pretty discernible and easy enough for software to automatically align to. It doesn't matter how distorted the signal gets, just when it starts to exceed the noise floor.
 
This whole magic trick is basically a per sample diffing engine comparing clean and processed files, isn’t it? We can assume the alignment is inherent or the accuracy of the models could be WAY off.
 
it’s probably more important to have a constant/steady latency than a low one during capturing. I guess an Computer/interface setup set to the lowest possible latency might be more prone to hickups, than when it’s deliberately set a little higher value- pure speculation though.
 
Latency for this doesnt come into the equation at all, its just auto aligning the files

That makes no sense. In case the return file is longer than the training file, it needs to be trimmed somehow. Auto aligning would only work in case the files were of the same length, which they aren't. So the returning file must be trimmed at some point.
 
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