[Ifeffit] Difficulty with normalization of XAS spectra

Sat Apr 13 13:49:44 CDT 2024

Note: divide by the value of the adjusted last point(s) after 
subtracting the 1st point(s).

On 2024-04-13 11:41 a.m., Robert Gordon wrote:
> 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
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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!YGLPZRfbpIk6ZteLVfKt43wxk6ly4oKR2FPeQbb-zvenUSgWF0SjIHcCoS8JM32dUY3V-Tl6gh_wW7d2NYJXaO-XGtitCMQaajXaqHI$ 
>>>     <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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