[Ifeffit] Fitting on Athena

bruceravel1 at gmail.com bruceravel1 at gmail.com
Sat Sep 3 07:43:27 CDT 2011

Niken Wijaya writes:
 > Hi Everyone,
 > I am facing a lot of problems when I am trying to fit my sample's
 > spectra with my standards one. Initially, I used Athena to do the
 > background subtraction, but the fitting results are just too "funny".
 > The fitting does not really fit the actual spectra. Since I am analyzing
 > Sulphur and many papers has reported how it is prone to self-absorption
 > effect, I thought, probably if I am using a better background
 > subtraction such as MBACK, I would get a better results. So I decided to
 > use it for the normalization and unlike in Athena, the normalized
 > intensity of the spectra does not equal to 1. By saying this, the
 > intensity of my standard models is way higher than the actual samples.
 > Hence, when I use Athena to fit my real spectra, I would not get a good
 > results. I have also tried using the 3rd derivative of my absorption
 > spectra, but the fitting results are even worse. The intensity of the
 > "fit" spectra is way higher than the actual spectra of my samples that I
 > am trying to fit it with. In fact, when I stack the spectra from the
 > standards and the sample together, the 3rd derivative peak of the
 > samples is almost completely flat due to the very high intensity of the
 > standards themselves.
 > What did I do wrong? and what can I do to fix it? I have also attached
 > my samples and standards spectra.
 > Thank you very much for the assistance.

Hi Niken,

It's a little hard to know what's going on.  The reason that we like
having Athena project files attached to these postings is because it
is then much easier to evaluate the provenance of the problem.  That
is, the Athena project file retains some of the history of the data.
We can evaluate how you have processed the data to arrive at the point
of having a problem with the analysis.

Given the text files you have attached, it is very difficult to know
how to advise you because it is very difficult to understand the
problem you are having.  I know that you tried to explain the problem,
but a picture is, as they say, worth a thousand (unlear, slightly
rambly) words.

That said, I do have a few comments.

1. There are good reasons to use an algorithm like MBACK rather than
   the simpler pre- and post-edge normalizaton that Athena offers.
   Fixing the problem of self-absorption is not one of those reasons.
   Self-absorption makes the fine structure oscillations smaller.  No
   normalization algorithm will magically undo that problem.

   Although Athena (or other software) might have a tool for
   correcting self-absorption, the only really good way of dealing
   with that problem is to not have it inthe first place.  For some
   samples, self absorption is unavoidable.  But if it is possible to
   modify your sample to minimize that effect, then you should most
   certainly do so.

2. The third derivative might be a useful tool, as you say.  It is,
   however, esential that you make your Nth derivative spectrum
   (regardless of the value of N) on normalized data or else the data
   you examine will not be on the same scale.  Another issue with high
   order derivatives is that they tend to amplify the size of the
   noise with respect to the signal.  One of your spectra has that
   problem.  Analysis of derivative spectra is one of the few
   situations in which I think that smoothing is helpful and

If you choose to pursue this issue further here on the mailing list, I
encourage you not only to add a project file, but to avoid the sort of
fuzzy language you used in this posting.  Saying things like "funny
fitting results" and "way higher intensities" is just to unclear and
subjective.  It often helps to attach a screenshot to better
demonstrate what you are trying to say.


 Bruce Ravel ------------ bruceravel1 at gmail.com
 Homepage --------------- http://xafs.org/BruceRavel
 EXAFS software --------- http://github.com/bruceravel/demeter/

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