Yepp, 


well known bug in Athena -> 

- either patch Athena

- save the files in eV

- or use larch as Mat showed 

best regards

Stefan

Am 28.06.2022 um 09:33 schrieb Gleb Pokrovski <gleb.pokrovski@get.omp.eu>:

Hi,
If I'm not mistaken, it is a bug of athena 026,
you may easily fix it yourself as Bruce nicely explained below.
don't need to downgrade to 025, I think.
best regards,
Gleb



-------- Forwarded Message --------
Subject:  Re: [Ifeffit] Import Error
Date:  Sat, 6 Apr 2019 14:16:35 +0000
From:  Ravel, Bruce <bravel@bnl.gov>
Reply-To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
To:  ifeffit@millenia.cars.aps.anl.gov <ifeffit@millenia.cars.aps.anl.gov>



I did not remember when you asked the other day, but it occurred to me that your data-in-keV problem was reported a few months ago.

https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2019-January/009688.html

I have not yet made a new Windows release with the fix. However, it is not too hard to apply the fix by editing a small amount of Athena's source code.


I think this is the easiest way to explain the small changes. Find the
file "lib/Demeter/Data.pm" underneath the location on your computer that
the software was installed. Look at this link:

https://github.com/bruceravel/demeter/commit/1b586b88d36336cad00b13d73913ebdb48b1d132#diff-74dd62af0fb82fb27595c1edcf73041f

Make the indicated change at line 22 (i.e. add $EPSILON6 to the argument
list of qw().)

Make the indicated changes around 885 (i.e. add the two lines before the
while block and alter the argument of the greater-than comparison in the
first line of the while block).

The change at line 871 is irrelevant and has no impact on Athena's operations.

That should do it. You can then drop the edited file into place on any
other computer.

B



On 04/05/2019 10:33 AM, Clark Adam Hugh (PSI) wrote:
Dear Bruce and Lucy

Thanks for your work around Lucy, it works perfectly but still doesn't explain the behavior I am observing.

Bruce what other information would be useful to diagnose the problem I am currently having? I have attached two figures, one showing the import window with the setting I have been using, specifically that I am not using the rebin feature. The second figure shows the difference in the pre-edge region between importing the data with eV and keV units for the energy column to demonstrate clearly that resampling is occurring when importing with data that has an energy column of KeV.

Many Thanks
Adam Clark

__________________________________________
Paul Scherrer Institut
Adam Hugh Clark
WLGA/129
Forschungsstrasse 111
5232 Villigen PSI
Schweiz

Telefon: +41 56 310 41 51
E-Mail: adam.clark@psi.ch
-----Original Message-----
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Subject: Ifeffit Digest, Vol 194, Issue 4

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Today's Topics:

1. Data Import Bug (Athena 0.9.26) (Clark Adam Hugh (PSI))
2. Re: Data Import Bug (Athena 0.9.26) (Ravel, Bruce)
3. Re: Data Import Bug (Athena 0.9.26) (Lucy M Mottram)


----------------------------------------------------------------------

Message: 1
Date: Fri, 5 Apr 2019 11:33:13 +0000
From: "Clark Adam Hugh (PSI)" <adam.clark@psi.ch>
To: "ifeffit@millenia.cars.aps.anl.gov"
<ifeffit@millenia.cars.aps.anl.gov>
Subject: [Ifeffit] Data Import Bug (Athena 0.9.26)
Message-ID:
<BDFF4FC62383D24DA3EF530480A33EA70B616536@MBX214.d.ethz.ch>
Content-Type: text/plain; charset="us-ascii"

Dear Mailing List

I have recently come across a data import error when using Athena version 0.9.26. When importing data there appears to be a resampling which significantly reduces the resolution of the data. Attached is an example dataset with an energy step of 0.5 eV on the Cu K edge. When importing with Athena 0.9.26 this data is significantly resampled resulting in an energy resolution on the edge of 1.5 eV which can either be seen by plotting or by exporting and inspecting the datafile. Using version 0.9.25 resolves this issue entirely. The data itself appears to actually be visible correctly during the import process (the import tab shows the data listed correctly when choosing which columns to import).

Is there a setting somewhere within Athena 0.9.26 that sets the default behavior to resample the imported data?

Thanks
Adam Clark

__________________________________________
Paul Scherrer Institut
Adam Hugh Clark
WLGA/129
Forschungsstrasse 111
5232 Villigen PSI
Schweiz

Telefon: +41 56 310 41 51
E-Mail: adam.clark@psi.ch
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Message: 2
Date: Fri, 5 Apr 2019 12:18:01 +0000
From: "Ravel, Bruce" <bravel@bnl.gov>
To: "ifeffit@millenia.cars.aps.anl.gov"
<ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Data Import Bug (Athena 0.9.26)
Message-ID: <83c1d066-e0dc-9c37-6d9c-ca806d641c7d@bnl.gov>
Content-Type: text/plain; charset="Windows-1252"


Unfortunately, I don't observe what you are describing.

Grasping at straws here, but are you inadvertently using this import feature?

http://bruceravel.github.io/demeter/documents/Athena/import/preproc.html#rebinning-quick-scan-data

B

On 04/05/2019 07:33 AM, Clark Adam Hugh (PSI) wrote:
Dear Mailing List

I have recently come across a data import error when using Athena
version 0.9.26. When importing data there appears to be a resampling
which significantly reduces the resolution of the data. Attached is an
example dataset with an energy step of 0.5 eV on the Cu K edge. When
importing with Athena 0.9.26 this data is significantly resampled
resulting in an energy resolution on the edge of 1.5 eV which can
either be seen by plotting or by exporting and inspecting the
datafile. Using version 0.9.25 resolves this issue entirely. The data
itself appears to actually be visible correctly during the import
process (the import tab shows the data listed correctly when choosing which columns to import).

Is there a setting somewhere within Athena 0.9.26 that sets the
default behavior to resample the imported data?

Thanks

Adam Clark

__________________________________________
Paul Scherrer Institut
Adam Hugh Clark
WLGA/129
Forschungsstrasse 111
5232 Villigen PSI
Schweiz

Telefon: +41 56 310 41 51
E-Mail: adam.clark@psi.ch



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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: http://bruceravel.github.io/home/
Beamline: https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
Software: https://github.com/bruceravel
Demeter: http://bruceravel.github.io/demeter/



------------------------------

Message: 3
Date: Fri, 5 Apr 2019 14:18:58 +0100
From: Lucy M Mottram <lmmottram1@sheffield.ac.uk>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Data Import Bug (Athena 0.9.26)
Message-ID:
<CAJ7D-QF6+DZ8QjXG-4L1Gj4NrzuEoVauTkT0AnLERJkymrMZ-w@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear Adam and Mailing List,

I've checked and found some of my data has a similar problem, I don't know how to solve this using settings in Athena, however as a workaround I have found that if I convert the energy in my raw data file from KeV to Ev before importing it into Athena (using excel) it appears that re-sampling issue does not occur. Hopefully that helps in the short term and gives a clue to what is going wrong with the import.

All the best
Lucy Mottram

On Fri, 5 Apr 2019 at 12:35, Clark Adam Hugh (PSI) <adam.clark@psi.ch>
wrote:

Dear Mailing List



I have recently come across a data import error when using Athena
version 0.9.26. When importing data there appears to be a resampling
which significantly reduces the resolution of the data. Attached is an
example dataset with an energy step of 0.5 eV on the Cu K edge. When
importing with Athena 0.9.26 this data is significantly resampled
resulting in an energy resolution on the edge of 1.5 eV which can
either be seen by plotting or by exporting and inspecting the
datafile. Using version 0.9.25 resolves this issue entirely. The data
itself appears to actually be visible correctly during the import
process (the import tab shows the data listed correctly when choosing which columns to import).



Is there a setting somewhere within Athena 0.9.26 that sets the
default behavior to resample the imported data?



Thanks

Adam Clark



__________________________________________
Paul Scherrer Institut
Adam Hugh Clark
WLGA/129
Forschungsstrasse 111
5232 Villigen PSI
Schweiz

Telefon: +41 56 310 41 51
E-Mail: adam.clark@psi.ch
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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:    http://bruceravel.github.io/home/
  Beamline:    https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:    https://github.com/bruceravel
  Demeter:     http://bruceravel.github.io/demeter/

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-- 
Dr. Gleb S. Pokrovski
Geosciences Environnement Toulouse
GET - UMR 5563 of CNRS, University of Toulouse III
14 avenue  Edouard Belin , F- 31400 TOULOUSE, France
e-mail: gleb.pokrovski@get.omp.eu
phone: 33-5-61-33-26-18 , fax: 33-5-61-33-25-60
On 28/06/2022 08:52, Samy Ould-Chikh wrote:
Hello Weronika,
 
I had a similar issue looking at data from the BM30 beamline.
Downgrading Athena version from  0.9.26 down to 0.9.25 solved the problem.
Although you still need to specify keV when importing.
 
 
Best Regards,
Samy Ould-Chikh
 
KAUST Catalysis Center
Bldg.3,Level 4, #4231
4700 King Abdullah University of Science & Technology
Thuwal 23955-6900
Kingdom of Saudi Arabia
 
Tel: +966 12 8084486
 
 
 
From: Ifeffit <ifeffit-bounces@millenia.cars.aps.anl.gov> On Behalf Of Matt Newville
Sent: Tuesday, June 28, 2022 7:22 AM
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] data plotting
 
Hi Weronika,
 
I think that the problem is due to the fact that the data file stores data in keV so that the small increments in energy at the pre-edge look like very, very small changes if the energy is assumed to be in eV.    So, I think you may just need to specify that the data has energy units of keV rather than eV.
 
When I read your Fe_Kedge_falconX.... file into XAS Viewer, I also had to tell it that it was XAS data in keV, but then it read in just fine.  If I zoom in on the pre-edge peaks it shows:
 
  
<image001.png>
 
 
I think that agrees with what you see.
 
 
On Mon, Jun 27, 2022 at 8:40 PM Ofierska Weronika Lucja <weronika.ofierska@erdw.ethz.ch> wrote:

Dear all, 

I am a new user of Athena and encountered some issues with data plotting. 

While plotting the uXAS data for Fe K pre-edge the quality of plotting is somehow less sharp compared to the actual data I plotted using other graphical tool (see below) 

<image002.png>

vs what I get from Athena 

<image003.png>

As you can see the resolution of the pre-edge in Athena is so poor I cannot resolve the Fe2+/Fe3+ ratio as the peak for Fe3+ is not visible. (I plotted Bruce's data from lepidocrocite to see if it's a common problem and it seems that his data look much better than mine). During my time on synchrotron we actually spent a lot of time to resolve best resolution on the pre edge, so it's not a acquisition problem. 

 

Does anyone have any idea how to fix this? 

I am attaching the project file and txt file (plot FluoRT2 column) with the original data. 

 

Thank you for your help, 

Weronika Ofierska 


 
-- 
--Matt Newville <newville at cars.uchicago.edu> 630-327-7411

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