Re: [Ifeffit] Difficulty with normalization of XAS spectra

Dear Matt, Thank you so much for your help! That was quick! We will let you know if there are still any issues. Sincerely, Jesse Walters On Mon, Apr 15, 2024 at 7:14 PM Matt Newville wrote:

Hi Jesse, OK, I think this is now fixed in the development version. If you're up for it, you can install the latest version (updated daily) by finding the Python for your xraylarch installation (maybe C: \Users\yournamae\xraylarch\bin\python) ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization.

ZjQcmQRYFpfptBannerEnd Hi Jesse,

OK, I think this is now fixed in the development version. If you're up for it, you can install the latest version (updated daily) by finding the Python for your xraylarch installation (maybe C:\Users\yournamae\xraylarch\bin\python) and doing

python -m pip install https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/xraylarch/downl... https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/xraylarch/downl...

On Sat, Apr 13, 2024 at 10:29 AM 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 ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization.

ZjQcmQRYFpfptBannerEnd 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!ZC4-5KvLgBq25OQy3GS0S-NDebFeI4z3apDpc6uWrQBOB5PK8y-B5sagqadtvM0m5P8jx8YFiMavbW0CZo-9SYSA3tGKrYhLqA$ 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 _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/listinfo... https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/listinfo... Unsubscribe: https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/options/... https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/options/...

-- --Matt Newville https://urldefense.us/v3/__http://cars.uchicago.edu__;!!G_uCfscf7eWS!eo1MYVG...

...

630-327-7411

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-- Jesse B. Walters Ambizione Fellow Institut für Geologie Universität Bern