[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.
Regards,
Niken
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ifeffitlist-sample39.docx
Type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
Size: 72247 bytes
Desc: not available
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20110905/19d3c239/attachment.docx>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ifeffitlist-intensity.docx
Type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
Size: 80317 bytes
Desc: not available
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20110905/19d3c239/attachment-0001.docx>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ifeffitlist-sample1 fitting.docx
Type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
Size: 83102 bytes
Desc: not available
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20110905/19d3c239/attachment-0002.docx>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: sample39-fig-norm.pdf
Type: image/pdf
Size: 4890 bytes
Desc: not available
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20110905/19d3c239/attachment.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ifeffitlist-project.prj
Type: application/octet-stream
Size: 22966 bytes
Desc: not available
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20110905/19d3c239/attachment.obj>
More information about the Ifeffit
mailing list