> Also running autooptimiser in between does not affect the results because 
> cpclean does its own optimisation for each step before calculating mean and 
> sigma.

it actually does and I just verified it. There may be one or two reasons:

1: as you may have noticed, my script uses the -n argument with autooptimiser, 
which does:
Optimize parameters specified in script file

Maybe cpclean does one type of optimization regardless of what's specified in 
the pto.

2: As you said in [the other 
topic](https://groups.google.com/g/hugin-ptx/c/A_Rh5KRVkcE) :

> after running cpclean the image positions remain always unchanged

​
So if you run autooptimizer, you do move the images and maybe it affects which 
cps will be deleted. I'm less sure of this one because cpclean optimizes before 
removing cps, so if the optimization type is the same as autooptimizer, it 
should get the same cp distances regardless.

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