[Ifeffit] Difficulty with normalization of XAS spectra

Sat Apr 13 13:41:39 CDT 2024

No worries...data actually has 0.1 eV steps...a bit finer than I would 
use for Fe, but not grossly oversampled.

For comparison between these data sets , you might try just subtracting 
the y value of the 1st point (ok..in data file 1st point is NAN)...maybe 
average of the first 3 - 5 points...then divide by the value of the last 
point (or avg of a few).
This will allow you to compare data sets on reasonable scale and look 
for changes.

-R.

On 2024-04-13 10:41 a.m., jesse walters wrote:
> Dear Robert, Apologies, the large h5 files were how the data were sent 
> to me. I figured out how to export a single csv file, which is 
> attached. Unfortunately, these data were collected without my input 
> and I am trying to help the student make
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> Dear Robert,
>
> Apologies, the large h5 files were how the data were sent to me. I 
> figured out how to export a single csv file, which is attached. 
> Unfortunately, these data were collected without my input and I am 
> trying to help the student make the data usable if possible. For my 
> own projects I collected Fe K edge XAS spectra from 7000 to 7350 eV. I 
> have not seen all the data from the session, but I believe the data 
> were only collected over the range 7100 to 7150 eV for all analyses. I 
> guess these are not useable?
>
> Cheers,
> Jesse
>
> On Sat, Apr 13, 2024 at 7:17 PM Robert Gordon 
> <moyie.institute at gmail.com> wrote:
>
>     Two things: 1. This is a volunteer community. Asking us to
>     download a massive file and parse through it to find a data file
>     is not a reasonable request. Pick an example and attach it as a
>     txt file (energy, mu(E) or E, I0, IF ). In fact, since
>     ZjQcmQRYFpfptBannerStart
>     This Message Is From an External Sender
>     This message came from outside your organization.
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>     Two things:
>
>     1. This is a volunteer community. Asking us to download a massive
>     file and parse through it to find a data file is not a reasonable
>     request. Pick an example and attach it as a txt file (energy,
>     mu(E) or E, I0, IF ). In fact, since the graph looks like the data
>     were grossly over-sampled for XANES, you might want to sieve it to
>     a more reasonable step size such as 0.1 to 0.3 eV through the
>     edge. That will also help with file size.
>
>     2. If the graph you attached is representative of the data, the
>     data were not collected over a large enough energy range for
>     normalisation. Next time, try +/- 100 - 200 eV below and above the
>     edge (maybe 250 above).
>
>     -R.
>
>     On 2024-04-10 5:22 a.m., jesse walters wrote:
>>     Hi all, I have some spectra collected by a collaborator,
>>     Francesco Ressico, a PhD student at Uni Bologna,  (see attached
>>     .h5 file below) and we are having trouble normalizing the Fe K
>>     edge spectra. The data are for serpentine group minerals
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>>     Hi all,
>>
>>     I have some spectra collected by a collaborator, Francesco
>>     Ressico, a PhD student at Uni Bologna,  (see attached .h5 file
>>     below) and we are having trouble normalizing the Fe K edge
>>     spectra. The data are for serpentine group minerals and were
>>     collected in fluorescence mode. In the attached file, the correct
>>     X array value is 'energy_enc', the data type is 'xas', and the y
>>     array should be 'mu_fluo_det0'. The spectra are already
>>     normalized for the incoming beam energy (although this can also
>>     be done using 'flou_det0/i0'). There are multiple spectra in the
>>     file, any one of them can be chosen to test the procedure.
>>
>>     After loading the spectra, I am able to plot the raw spectra
>>     correctly (see attached). But when I try to normalize the pre and
>>     post edge regions and plot the normalized spectra, the software
>>     only gives a blank plot. I have tried changing the normalization
>>     type, polynomial type, range, etc for both the pre and post edge,
>>     but nothing seems to work. I also tested different spectra, but
>>     with similar results.
>>
>>     Does anyone have suggestions for how these data can be normalized?
>>
>>     The h5 file is too large, so here is a dropbox link
>>     https://urldefense.us/v3/__https://www.dropbox.com/scl/fi/d8k5s67vli0mq97ac520y/COR21_79_Xastransect_79_F1_THC.h5?rlkey=33ragg4p6x9rx65t9yvi5kewe&dl=0__;!!G_uCfscf7eWS!dcAIi3TTGN9d52IHU2K-pKiCEIZLi2wcrteKHRuCLDYpksIvgA0jwzrgeW_VC3t8LPIgcz9GYRSDukE9KV1keBVLwhyKueiVnIEhymk$ 
>>     <https://urldefense.us/v3/__https://www.dropbox.com/scl/fi/d8k5s67vli0mq97ac520y/COR21_79_Xastransect_79_F1_THC.h5?rlkey=33ragg4p6x9rx65t9yvi5kewe&dl=0__;!!G_uCfscf7eWS!btLKhnEiyp5gMQfSDnHdxqgt2ie5vcVHW7e142vokJ-wEX6zZSIOcAyHsf5THg9ZlyyIsx7Vfm27ycKWAQg1_cysDdnW65aCQA$>
>>
>>     Sincerely,
>>     Jesse Walters
>>
>>     -- 
>>     Jesse B. Walters
>>     Ambizione Fellow
>>     Institut für Geologie
>>     Universität Bern
>>
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> -- 
> Jesse B. Walters
> Ambizione Fellow
> Institut für Geologie
> Universität Bern
>
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