date:20240413

Re: [Ifeffit] Difficulty with normalization of XAS spectra

2024-04-13 Thread Robert Gordon

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
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=0__;!!G_uCfscf7eWS!YGLPZRfbpIk6ZteLVfKt43wxk6ly4oKR2FPeQbb-zvenUSgWF0SjIHcCoS8JM32dUY3V-Tl6gh_wW7d2NYJXaO-XGtitCMQaajXaqHI$

Re: [Ifeffit] Difficulty with normalization of XAS spectra

2024-04-13 Thread Robert Gordon

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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This message came from outside your organization.
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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
wrote:

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.

-R.

On 2024-04-10 5:22 a.m., jesse walters wrote:

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=0__;!!G_uCfscf7eWS!dcAIi3TTGN9d52IHU2K-pKiCEIZLi2wcrteKHRuCLDYpksIvgA0jwzrgeW_VC3t8LPIgcz9GYRSDukE9KV1keBVLwhyKueiVnIEhymk$

Sincerely,
Jesse Walters

--
Jesse B. Walters

Ambizione Fellow
Institut für Geologie
Universität Bern

Re: [Ifeffit] Difficulty with normalization of XAS spectra

2024-04-13 Thread jesse walters

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=0__;!!G_uCfscf7eWS!fBIOzph-Db3ioZGTdqQZ83ckH_bkFR9tjSSpr359OiRFNixZF62emsiEQqIS4y25emWz1jQZvQjSeNOMPzqwDKMCy1IZOJZ65g$
>  
> 
>
> Sincerely,
> Jesse Walters
>
> --
> Jesse B. Walters
> Ambizione Fellow
> Institut für Geologie
> Universität Bern
>
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Re: [Ifeffit] Difficulty with normalization of XAS spectra

2024-04-13 Thread Robert Gordon

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=0__;!!G_uCfscf7eWS!Y2vfGwfONNMo1aLgkAnnXaF5bQ8shgtgTi51NUeYhIeIHAvFmLRm9we3b2lAA2ZANf1WrgLChlCGWCg0N--jlHp3IM5xIQjzyaIPkA4$

Sincerely,
Jesse Walters

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

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Re: [Ifeffit] Difficulty with normalization of XAS spectra

Re: [Ifeffit] Difficulty with normalization of XAS spectra

Re: [Ifeffit] Difficulty with normalization of XAS spectra

Re: [Ifeffit] Difficulty with normalization of XAS spectra

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