Problems with linear combination fitting S-XANES data in Athena
Hello, First of all, thank you all so very much for offering this platform to address XAS data processing!! It is wonderful to know it is available. I am having a problem using Athena "Linear Combination Fitting" with x-ray fluorescence data from SSRL. Last year, we collected sulfur K-edge XANES data at SSRL, beamline 4-3 and processed them using SixPack (averaging 5 sweeps and normalization) and then used Athena to conduct linear combination fitting of the XANES region. It worked great! This year's data are presenting a problem when I get to the LCF step, however. When I import the sample data .mu file into Athena and plot it by pressing the orange "E" button, the normalized spectrum looks like it should (albeit noisy and sometimes not the best data, but that is not Athena's fault). When I attempt to apply the Linear Combination Fitting algorithm, fitting a number of spectra from reference samples also collected last year and this year, Athena inverts the sample.mu spectrum (between -1 and 0 rather than 0 and 1). It does not invert old or new reference sample spectra. When I try this with old data, using old and new reference sample spectra, I do not have this problem. With the inverted sample spectrum, it often does not find a fit, but sometimes it does. Attached is an example Athena project file, the .mu file, and a plot of the output of a test fit, for your reference. I am hoping someone can please help me figure out why this is happening. I cannot see anything wrong, based on my limited experience, but hopefully it is something I have done wrong that can be easily corrected. Thank you in advance, Julie Julie Muretta, Ph.D. Materials Testing Laboratory Manager Center for Advanced Materials Processing (CAMP) (406) 496-4808 | jmuretta@mtech.edu [Montana Technological University]<https://urldefense.us/v3/__https://www.mtech.edu/__;!!G_uCfscf7eWS!cA8TPa7rl... >
Dear Julie, Thank you for sharing this issue. I have reviewed the test.mu file, which contains the normalized spectrum, and would like to share a couple of observations: In the pre-edge region (2400-2440 eV): The spectrum exhibits NEGATIVE intensity values and a noticeable increase in intensity across this energy range. In the EXAFS region (from ~2557 eV onward): The spectrum shows a monotonic decrease in intensity, which contrasts with the increasing trend seen in the pre-edge region. This pattern suggests that the normalization may not have sufficiently flattened the post-edge portion of the data. I recommend the following steps to improve the processing: Truncate the data between 2400-2440 eV before normalization or fitting, as the negative values and rising trend in this pre-edge region might be disrupting the scaling and background correction. Additionally, redo the normalization in Athena, and set the "Normalization order" to 3. This higher-order polynomial fit is better suited for flattening the post-edge region, especially in cases where a residual slope is present. I hope these adjustments help resolve the issue you're encountering with Linear Combination Fitting. Wishing you success with the rest of your analysis! Warm regards, Bokky, D.C. Nguyen ALBA Synchrotron On 2025-07-24 22:28, Muretta, Julie via Ifeffit wrote:
Hello, First of all, thank you all so very much for offering this platform to address XAS data processing!! It is wonderful to know it is available. I am having a problem using Athena "Linear Combination Fitting" with x-ray fluorescence ZjQcmQRYFpfptBannerStart
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Hello,
First of all, thank you all so very much for offering this platform to address XAS data processing!! It is wonderful to know it is available.
I am having a problem using Athena "Linear Combination Fitting" with x-ray fluorescence data from SSRL. Last year, we collected sulfur K-edge XANES data at SSRL, beamline 4-3 and processed them using SixPack (averaging 5 sweeps and normalization) and then used Athena to conduct linear combination fitting of the XANES region. It worked great!
This year's data are presenting a problem when I get to the LCF step, however. When I import the sample data .mu file into Athena and plot it by pressing the orange "E" button, the normalized spectrum looks like it should (albeit noisy and sometimes not the best data, but that is not Athena's fault). When I attempt to apply the Linear Combination Fitting algorithm, fitting a number of spectra from reference samples also collected last year and this year, Athena inverts the sample.mu spectrum (between -1 and 0 rather than 0 and 1). It does not invert old or new reference sample spectra. When I try this with old data, using old and new reference sample spectra, I do not have this problem. With the inverted sample spectrum, it often does not find a fit, but sometimes it does.
Attached is an example Athena project file, the .mu file, and a plot of the output of a test fit, for your reference.
I am hoping someone can please help me figure out why this is happening. I cannot see anything wrong, based on my limited experience, but hopefully it is something I have done wrong that can be easily corrected.
Thank you in advance, Julie
Julie Muretta, Ph.D.
_Materials Testing Laboratory Manager_
_Center for Advanced Materials Processing (CAMP)_
(406) 496-4808 | jmuretta@mtech.edu
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Hi Bruce,
Thank you for the time spent trying to figure out what I am doing wrong. I am new to XAFS data processing, and it is not surprising that what was happening was due to user error!
I will go through the Athena manual as you suggested and try to set up the normalization parameters differently for our data.
Thank you, again,
Julie
Julie Muretta, Ph.D.
Materials Testing Laboratory Manager
Center for Advanced Materials Processing (CAMP)
(406) 496-4808 | jmuretta@mtech.edu
[Montana Technological University]<https://urldefense.us/v3/__https://www.mtech.edu/__;!!G_uCfscf7eWS!dJ3Z2OeOn... >
________________________________
From: Ravel, Bruce via Ifeffit
Investigating further, it seems that the problem might instead be that you are putting too much faith in the default values for the various parameters used to process the data. I mean this in the sense of the third paragraph of this page:
https://urldefense.us/v3/__https://bruceravel.github.io/demeter/documents/At...
In short, you need to be more mindful of the values of the various processing parameters. I am skeptical of the value of E0. The values of the normalization parameters are certainly incorrect for this measurement, as is clear from the green and purple lines. And when I click the orange normalization button, sure enough ... it plots the data inverted.
Playing around just a bit with the parameters explained here:
https://urldefense.us/v3/__https://bruceravel.github.io/demeter/documents/At...
and setting them to sensible values for your data completely fixes the problem.
Professorial advice: don't just trust things, make sure you understand what is happening with your data.
B
On 7/24/25 16:28, Muretta, Julie via Ifeffit wrote:
Hello, First of all, thank you all so very much for offering this platform to address XAS data processing!! It is wonderful to know it is available. I am having a problem using Athena "Linear Combination Fitting" with x-ray fluorescence ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd Hello,
First of all, thank you all so very much for offering this platform to address XAS data processing!! It is wonderful to know it is available.
I am having a problem using Athena "Linear Combination Fitting" with x- ray fluorescence data from SSRL. Last year, we collected sulfur K-edge XANES data at SSRL, beamline 4-3 and processed them using SixPack (averaging 5 sweeps and normalization) and then used Athena to conduct linear combination fitting of the XANES region. It worked great!
This year's data are presenting a problem when I get to the LCF step, however. When I import the sample data .mu file into Athena and plot it by pressing the orange "E" button, the normalized spectrum looks like it should (albeit noisy and sometimes not the best data, but that is not Athena's fault). When I attempt to apply the Linear Combination Fitting algorithm, fitting a number of spectra from reference samples also collected _last year and this year_, Athena inverts the sample.mu spectrum (between -1 and 0 rather than 0 and 1). It does not invert old or new reference sample spectra. When I try this with old data, using old and new reference sample spectra, I do not have this problem. With the inverted sample spectrum, it often does not find a fit, but sometimes it does.
Attached is an example Athena project file, the .mu file, and a plot of the output of a test fit, for your reference.
I am hoping someone can please help me figure out why this is happening. I cannot see anything wrong, based on my limited experience, but hopefully it is something I have done wrong that can be easily corrected.
Thank you in advance, Julie
*Julie Muretta, Ph.D.*
/Materials Testing Laboratory Manager/
/Center for Advanced Materials Processing (CAMP)/
_(406) 496-4808_ | jmuretta@mtech.edu
_Montana Technological University <https://urldefense.com/v3/__https:// urldefense.us/v3/__https://urldefense.us/v3/__https://*www.mtech.edu/__;!!G_uCfscf7eWS!__;Kg!!G... cA8TPa7rlyGu5Vmwp--j7WUFcufVPj1XStOTpvP1kNOf8HO7A1eqt_eFg- C5Pa8ui9EE_-0t6oRf1MKw_luMhQCZfKEoU_0S$__;Lw!!P4SdNyxKAPE! EsJaL2BxJwKvOZafj458aUdip_eUgtx- lizGzLA_TcIfEF8XzVrbH_6BmEsPZ2iUMyPZTovwBZO2jrF7WP-1CaTNdG6yRw$>_
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-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 6BM (BMM) Building 743, Room 114 Upton NY, 11973 Homepage: https://urldefense.us/v3/__http://bruceravel.github.io/home/__;!!G_uCfscf7eW... Beamline: https://urldefense.us/v3/__https://www.bnl.gov/ps/beamlines/beamline.php?r=6... Software: https://urldefense.us/v3/__https://github.com/bruceravel__;!!G_uCfscf7eWS!cT... Demeter: https://urldefense.us/v3/__http://bruceravel.github.io/demeter/__;!!G_uCfscf...
Good afternoon, Matt,
Thanks so much for the information. I was able to apply the settings you mentioned as a starting point in Athena, and now I am getting much better results. Still some tweaking to get the best background, but things are much better.
Re: reference spectra, I will discuss with my collaborator, but I don't think he will mind if anyone finds our data useful and would like to use it in a database. 🙂 From my perspective, it would be a highlight of this project! How would we go about doing this, if he agrees?
Kindest regards,
Julie
Julie Muretta, Ph.D.
Materials Testing Laboratory Manager
Center for Advanced Materials Processing (CAMP)
(406) 496-4808 | jmuretta@mtech.edu
[Montana Technological University]<https://urldefense.us/v3/__https://www.mtech.edu/__;!!G_uCfscf7eWS!YgUaDWSDN... >
________________________________
From: matt.newville--- via Ifeffit
Investigating further, it seems that the problem might instead be that
you are putting too much faith in the default values for the various
parameters used to process the data. I mean this in the sense of the
third paragraph of this page:
https://urldefense.us/v3/__https://bruceravel.github.io/demeter/documents/At...https://urldefense.us/v3/__https:/bruceravel.github.io/demeter/documents/Ath...
In short, you need to be more mindful of the values of the various
processing parameters. I am skeptical of the value of E0. The values
of the normalization parameters are certainly incorrect for this
measurement, as is clear from the green and purple lines. And when I
click the orange normalization button, sure enough ... it plots the data
inverted.
Playing around just a bit with the parameters explained here:
https://urldefense.us/v3/__https://bruceravel.github.io/demeter/documents/At...https://urldefense.us/v3/__https:/bruceravel.github.io/demeter/documents/Ath...
and setting them to sensible values for your data completely fixes the
problem.
Professorial advice: don't just trust things, make sure you understand
what is happening with your data.
B
On 7/24/25 16:28, Muretta, Julie via Ifeffit wrote:
Hello, First of all, thank you all so very much for offering this
platform to address XAS data processing!! It is wonderful to know it is
available. I am having a problem using Athena "Linear Combination
Fitting" with x-ray fluorescence
ZjQcmQRYFpfptBannerStart
This Message Is From an External Sender
This message came from outside your organization.
ZjQcmQRYFpfptBannerEnd
Hello,
First of all, thank you all so very much for offering this platform to
address XAS data processing!! It is wonderful to know it is available.
I am having a problem using Athena "Linear Combination Fitting" with x-
ray fluorescence data from SSRL. Last year, we collected sulfur K-edge
XANES data at SSRL, beamline 4-3 and processed them using SixPack
(averaging 5 sweeps and normalization) and then used Athena to conduct
linear combination fitting of the XANES region. It worked great!
This year's data are presenting a problem when I get to the LCF step,
however. When I import the sample data .mu file into Athena and plot it
by pressing the orange "E" button, the normalized spectrum looks like it
should (albeit noisy and sometimes not the best data, but that is not
Athena's fault). When I attempt to apply the Linear Combination Fitting
algorithm, fitting a number of spectra from reference samples also
collected _last year and this year_, Athena inverts the sample.mu
spectrum (between -1 and 0 rather than 0 and 1). It does not invert old
or new reference sample spectra. When I try this with old data, using
old and new reference sample spectra, I do not have this problem. With
the inverted sample spectrum, it often does not find a fit, but
sometimes it does.
Attached is an example Athena project file, the .mu file, and a plot of
the output of a test fit, for your reference.
I am hoping someone can please help me figure out why this is happening.
I cannot see anything wrong, based on my limited experience, but
hopefully it is something I have done wrong that can be easily corrected.
Thank you in advance,
Julie
*Julie Muretta, Ph.D.*
/Materials Testing Laboratory Manager/
/Center for Advanced Materials Processing (CAMP)/
_(406) 496-4808_ | jmuretta@mtech.edu
_Montana Technological University <https://urldefense.com/v3/__https://
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cA8TPa7rlyGu5Vmwp--j7WUFcufVPj1XStOTpvP1kNOf8HO7A1eqt_eFg-
C5Pa8ui9EE_-0t6oRf1MKw_luMhQCZfKEoU_0S$__;Lw!!P4SdNyxKAPE!
EsJaL2BxJwKvOZafj458aUdip_eUgtx-
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-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 6BM (BMM) Building 743, Room 114 Upton NY, 11973 Homepage: https://urldefense.us/v3/__http://bruceravel.github.io/home/__;!!G_uCfscf7eW...https://urldefense.us/v3/__http:/bruceravel.github.io/home/__;!!G_uCfscf7eWS... Beamline: https://urldefense.us/v3/__https://www.bnl.gov/ps/beamlines/beamline.php?r=6...https://urldefense.us/v3/__https:/www.bnl.gov/ps/beamlines/beamline.php?r=6-... Software: https://urldefense.us/v3/__https://github.com/bruceravel__;!!G_uCfscf7eWS!cT...https://urldefense.us/v3/__https:/github.com/bruceravel__;!!G_uCfscf7eWS!cTL... Demeter: https://urldefense.us/v3/__http://bruceravel.github.io/demeter/__;!!G_uCfscf...https://urldefense.us/v3/__http:/bruceravel.github.io/demeter/__;!!G_uCfscf7...
participants (4)
-
bnguyen -
matt.newville＠gmail.com -
Muretta, Julie -
Ravel, Bruce