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 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.

ZjQcmQRYFpfptBannerEnd 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 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!fBIOzph-Db3ioZGTdqQZ83ckH_bkFR9tjSSpr359OiRFNixZF62emsiEQqIS4y25emWz1jQZvQjSeNOMPzqwDKMCy1IZOJZ65g$ 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

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 ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd 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 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. ZjQcmQRYFpfptBannerEnd 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 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!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

_______________________________________________ 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/...

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-- 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... Unsubscribe:https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/options/...