[Ifeffit] Fitting on Athena

Niken Wijaya niken.wijaya at monash.edu
Sun Sep 4 19:52:30 CDT 2011

On 3/09/2011 10:43 PM, bruceravel1 at gmail.com wrote:
> 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
>     defensible.
> 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.
> B
Hi Bruce,

Thank you for the comments. Attached is the project files and the 
figure. Here are the problems and comments I am having right now.

1. As you can see on the figure (i.e. filename: ifeffitlist-sample1 
fitting), the intensity of the fitting spectra is higher than the actual 
sample. This is I believe due to the higher intensity of the individual 
standard compounds when compared to the spectra of my samples (i.e. 
filename: ifeffitlist-intensity). This is the case for every fitting I 
did for my sample so I am just not sure with the fitting results.

2. If we see figure "ifeffitlist-sample39", we can see that the spectra 
has different slopes on the pre and post-edge region. When I used MBACK 
for background removal, the normalized spectra is weird, illustrated in 
"sample39-fig-norm.pdf". What is the best way to fix this issue? I have 
5 samples with this feature that I cannot process due to the weird 
normalized spectra.

3. Regarding the self-absorption correction, I was not aware that Athena 
has this function. I will have a look at the manual again. Thank you for 
letting me know.

4. With the 3rd derivative spectrum, I did indeed derive it from the 
normalized values. As you can see from the file I attached earlier, from 
the experts points of view, do you think I should go on with the Nth 
derivative spectra or due to the very low signal-to-noise ratio of the 
spectra, I should just focus on the absorption spectra?

Again, thank you for the invaluable inputs.


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