[Ifeffit] What you see is "not" what you get: help

Leandro L. Araujo leandrolangie at gmail.com
Thu Jul 9 20:33:53 CDT 2009

Dear All,

I think I understand the point here. Ismael, please correct me if I'm wrong.

1) The experimental data is imported into Athena and fitted through the 
"peak fitting with lineshapes" feature. The fitting looks very good in 
Athena - the red curve matches the experimental spectrum well, as seen 
in the file "plot athena.ps" attached on Ismael's previous email.
So far, so good.

2) But then Ismael needs to plot the data and the fit in another 
program, because he wants high-quality graphs for journal publications. 
That's where the problem starts. He clicks on the "write a log file" 
button in the peak fit page in Athena and generates a .log file where 
the fitting results - both the functions/parameters and the columns for 
mu(E), experimental data, fit and each  component - are included. That 
would be file "fitting results.log" attached to Ismael's previous email, 
which can be read in any text editor.

3) But when Ismael plots the data from the "fitting results.log" file 
into Origin (or whatever), there is a significantly higher mismatch 
between the experimental spectrum and the fit, as shown in the file 
"graph origin.jpg". I guess that's what prompted Ismael to write "What 
you see is "not" what you get", since the graph in Origin looks 
different from the graph in Athena.

4) If we pay close attention to both graphs, we can see that the 
experimental spectrum peaks at different mu(E) values: in "plot 
athena.ps" it peaks at ~ 2.3 while in "graph origin.jpg" it peaks at ~ 
2.5. The fit, on the other hand, peaks at ~ 2.3 in both graphs.

5) Thus, my guess is that when Athena exports the data through the 
"write a log file" button in the peak fit page it spits out the raw 
mu(E) instead of the normalized mu(E). That's why there seems to be a 
mismatch in Origin: while in the Athena graph the experimental data is 
plotted as normalized mu(E), in the exported file and the origin graph 
we have the raw mu(E). The fit doesn't seem to change, but it was 
optimized for the normalized mu(E) and doesn't match the raw mu(E) that 

6) One easy workaround would be exporting just the experimental data as 
normalized mu(E) through the "file" dialog in Athena and then overlaying 
it on the same graph with the fit exported through the "fitting 
results.log" file.


Ismael Graff wrote:
> Hi folks,
> I´ve been working on Xanes peaks fitting with Athena (last version) and I
> found a strange behaviour. I get a "good" fit looking to the Graphics
> Window of Athena and to the minimized parameters (R-factor, etc). However,
> when I use the data of the fit generated by Athena "write a log file"
> feature and plot them in Origin, the fit looks bad! In order to get a
> "good looking" fit in Origin I have to change the parameters ad-hoc in
> Athena fitting dialog box. When I do this, the fit looks bad in Athena
> Graphics window and better in Origin.
> The values that are inserted ad-hoc in Athena are not the optimized ones
> from the fitting procedure output. I have attached the log file from
> Athena fit and two figures: a PS figure from Athena and a JPG figure from
> Origin.
> It resembles that the generated data from Athena are not exactly these
> ones that I see in the Graphics window!
> I´m looking for help from someone out there.
> Kind regards, Ismael.
> ------------------------------------------------------------------------
> ------------------------------------------------------------------------
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> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
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