Hey everybody, while I try to figure what effect normalization has on Linear combination fitting in my lead L3 edge XANES system, I came accross this problem: Athena does not normalize correctly: Normalization in Athena (post-edge): using 1.order normalization, no flattening (which in this case is irrelevant anyway), points +199 eV and +200 eV above E0. Normalization in Origin (post-edge): using point 13235 eV (+200 eV above E0); dividing the spectrum column by that value. See the two examples in the attachment. In both examples the normalized spectrum imported from Athena does not have the norm value of 1 at 13235 eV. Why is that? The offset is also not the same for every spectrum. That undoes the normalization routine. Greetings, Lisa
Hi Lisa, Be sure that Athena has been rigorously tested and she does know how to normalize data. It is much more likely that the default values are not the "best" ones for your data. My book chapter goes over how Athena normalizes data in detail. If you send me your email address I'll send you a copy. In particular see figure 14-16. Cheers, Shelly dr.sdkelly@gmail.com
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit- bounces@millenia.cars.aps.anl.gov] On Behalf Of Gudrun Bovenkamp Sent: Monday, October 26, 2009 8:42 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Normalization in Athena
Hey everybody,
while I try to figure what effect normalization has on Linear combination fitting in my lead L3 edge XANES system, I came accross this problem: Athena does not normalize correctly:
Normalization in Athena (post-edge): using 1.order normalization, no flattening (which in this case is irrelevant anyway), points +199 eV and +200 eV above E0.
Normalization in Origin (post-edge): using point 13235 eV (+200 eV above E0); dividing the spectrum column by that value.
See the two examples in the attachment.
In both examples the normalized spectrum imported from Athena does not have the norm value of 1 at 13235 eV. Why is that? The offset is also not the same for every spectrum. That undoes the normalization routine.
Greetings, Lisa
Shelly, I agree that Athena applies its (her) algorithm correctly. Whether that algorithm is correct may be a matter of opinion. The apparent discrepency Lisa sees is due to Athena's algorithm: i.e., fit preedge line, fit postedge function to normalization range, extrapolate both functions to edge energy to find edge step. Another option would be to fit predge line and subtract it. After that, fit the post edge normalization range. With Athena, if there is a non-zero slope to the preedge line and you choose norm order 1, you get Lisa's result. With normalization order 2 or 3, the results should either be the same, or at least, much closer. Jeremy
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Kelly, Shelly Sent: Monday, October 26, 2009 9:08 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Normalization in Athena
Hi Lisa,
Be sure that Athena has been rigorously tested and she does know how to normalize data. It is much more likely that the default values are not the "best" ones for your data.
My book chapter goes over how Athena normalizes data in detail. If you send me your email address I'll send you a copy. In particular see figure 14-16.
Cheers, Shelly dr.sdkelly@gmail.com
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit- bounces@millenia.cars.aps.anl.gov] On Behalf Of Gudrun Bovenkamp Sent: Monday, October 26, 2009 8:42 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Normalization in Athena
Hey everybody,
while I try to figure what effect normalization has on Linear combination fitting in my lead L3 edge XANES system, I came accross this problem: Athena does not normalize correctly:
Normalization in Athena (post-edge): using 1.order normalization, no flattening (which in this case is irrelevant anyway), points +199 eV and +200 eV above E0.
Normalization in Origin (post-edge): using point 13235 eV (+200 eV above E0); dividing the spectrum column by that value.
See the two examples in the attachment.
In both examples the normalized spectrum imported from Athena does not have the norm value of 1 at 13235 eV. Why is that? The offset is also not the same for every spectrum. That undoes the normalization routine.
Greetings, Lisa
Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
It is a little hard to evaluate your results, Lisa, without an example. It may help to attach a small project file which demonstrates your question. Without an actual example, I would have to guess that the bottom line is an odd choice of parameters. This page from the document might be helpful: http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/bkg/norm.html B On Monday 26 October 2009 10:27:28 am Kropf, Arthur Jeremy wrote:
Shelly,
I agree that Athena applies its (her) algorithm correctly. Whether that algorithm is correct may be a matter of opinion. The apparent discrepency Lisa sees is due to Athena's algorithm:
i.e., fit preedge line, fit postedge function to normalization range, extrapolate both functions to edge energy to find edge step.
Another option would be to fit predge line and subtract it. After that, fit the post edge normalization range.
With Athena, if there is a non-zero slope to the preedge line and you choose norm order 1, you get Lisa's result. With normalization order 2 or 3, the results should either be the same, or at least, much closer.
Jeremy
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Kelly, Shelly Sent: Monday, October 26, 2009 9:08 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Normalization in Athena
Hi Lisa,
Be sure that Athena has been rigorously tested and she does know how to normalize data. It is much more likely that the default values are not the "best" ones for your data.
My book chapter goes over how Athena normalizes data in detail. If you send me your email address I'll send you a copy. In particular see figure 14-16.
Cheers, Shelly dr.sdkelly@gmail.com
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit- bounces@millenia.cars.aps.anl.gov] On Behalf Of Gudrun Bovenkamp Sent: Monday, October 26, 2009 8:42 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Normalization in Athena
Hey everybody,
while I try to figure what effect normalization has on Linear combination fitting in my lead L3 edge XANES system, I came accross this problem: Athena does not normalize correctly:
Normalization in Athena (post-edge): using 1.order
normalization, no
flattening (which in this case is irrelevant anyway),
points +199 eV
and +200 eV above E0.
Normalization in Origin (post-edge): using point 13235 eV (+200 eV above E0); dividing the spectrum column by that value.
See the two examples in the attachment.
In both examples the normalized spectrum imported from
Athena does not
have the norm value of 1 at 13235 eV. Why is that? The
offset is also
not the same for every spectrum. That undoes the normalization routine.
Greetings, Lisa
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Lisa, I think the issue you're seeing is most likely due to telling athena to fit the data between E0+199 and E0+200 with a constant. I'd recommend expanding that range some to give Athena a chance -- if there isn't any data between E=E0+199 and E0+200, Athena won't be able to figure out what the edge step should be. If you really want the edge step to be the value of pre-edge subtracted mu(E) at E=E0+200eV, you'll have to do that by hand. --Matt
participants (5)
-
Bruce Ravel -
Gudrun Bovenkamp -
Kelly, Shelly -
Kropf, Arthur Jeremy -
Matt Newville