Yeti answered a very similar request some months ago, with code directly 
usable. See:

http://www.mail-archive.com/[email protected]/msg00417.html

Jérôme Borme

Le Wednesday 25 May 2011 17:01:27, Andrés Muñiz Piniella a écrit :
> I think I can answer this one as it's in my to do list as well. I
> would use python to do this for you. There is an example here [0].
> 
> But if anyone has a homemade code it would be great if you can share it.
> 
> [0] http://gwyddion.net/documentation/pygwy.php
> 
> On 5/25/11, Denny Köhler <[email protected]> wrote:
> > Hello all,
> > 
> > I'm in search of a possibility to do some batch processing to my data.
> > The problem is that I have somewhat 50 data files with each containing
> > lets say 8 channels and I want to do some line wise averaging and then
> > save each of those resulting graphs as a .txt file. So that means I have
> > to do this about 400 times, which I want to do automatically. So is
> > there a possibility to tell gwyddion to load every file in a directory
> > and tell it to do the same thing to all the channels in all the files?
> > 
> > Thanks in advance and kind regards,
> > Denny

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