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Today's Topics:

   1. Re: Re. Larch Energy Calibration (Mangold, Stefan (IPS))
   2. Re: Larch Energy calibration (Matt Newville)


----------------------------------------------------------------------

Message: 1
Date: Tue, 9 Mar 2021 11:20:38 +0000
From: "Mangold, Stefan (IPS)" <stefan.mangold@kit.edu>
To: "Schoepfer, Valerie" <valerie.schoepfer@usask.ca>
Cc: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Re. Larch Energy Calibration
Message-ID: <45116D6C-9314-4822-8E1B-7FB929333D72@kit.edu>
Content-Type: text/plain; charset="utf-8"

Dear Valerie,


The reason why I'm currently not using Larch for my data-evaluation chain is, that I didn?t found some features (like energy calibration; not as I use it; like Calibration of references, absorption and fluorescence spectra in one group) in Larch, which I need for my data evaluation process. They might be there, but I didn?t found them.

for the XANES data evaluation your energy region might be a bit to short to fit a good background to the data. Anyway you have to fine-tune the parameters to reach a good background fit in the XANES region. While the automatic process in Athena produces quite good results for a lot of absorption edges, one has to be careful not add artefacts to the data in the XANES.

Best regards

Stefan


> Am 08.03.2021 um 14:17 schrieb Schoepfer, Valerie <valerie.schoepfer@usask.ca>:
>
> Hi Chris and Adam,
>
> I'm actually looking at Mo, so the energy range is from about 19800 through 20200 eV on a Si(220) monochromator.  (But thank you for your Fe offer!)
> The standards seem to be all from the Canadian Light Source, but going as far back as 2013...
> I'm not looking to make the LCF perfect at this point, but it does seem like the deeper I go, the less confident I am that I have the correct standards.
>
> I'm doing alright in Athena with respect to the process, its just that I can't get Larch to align properly. I'll probably just use Athena for data prep, Larch just seemed nice to learn. 
> But then in Athena I run into trouble with incorrect standards. One thing after another, you know?
>
> Thanks-
> Valerie
>
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> Subject: Ifeffit Digest, Vol 217, Issue 3
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> Today's Topics:
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>   1. Re: Larch energy calibration (Matt Newville)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 3 Mar 2021 18:38:24 -0600
> From: Matt Newville <newville@cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Larch energy calibration
> Message-ID:
>        <CA+7ESbrGYtdjidL4X+rCUEi+DfmL3dUyG-R2R-FHffeqshSGTQ@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Valerie,
>
> On Tue, Mar 2, 2021 at 10:48 AM Schoepfer, Valerie < valerie.schoepfer@usask.ca> wrote:
>
>> Hi,
>>
>>
>>
>> I am using Larch XAS Viewer for the first time to analyze some Mo
>> XANES data. It is fairly straightforward, however I am running into
>> problems with energy calibration, which leads to problems with Linear
>> Combination Fitting.
>>
>>
>>
>> Right now, which is likely wrong, I?m calibrating the energy of a
>> standard to the theoretical edge, then auto-aligning the samples to the standard.
>> But how do reference foils fit in here? Reference foils don?t seem to
>> be tied to the sample like they are in Athena. Should I be manually aligning?
>>
>>
>>
>> Is there a general guidance or work flow?
>>
>
> It's possible that I do not fully understand the question or that this answer will veer a bit off the topic of your question.
>
> For sure, energies need to be aligned properly for any multi-spectra comparison or linear method to work well. But it should be that you will have groups of spectra that all share a consistent energy calibration, say from the same beamline/beamtime.
>
> If you do have a reference channel for every measurement, you can compare those reference channels.  Ideally, these will not vary for every
> measurement - that would indicate a serious problem.   So, I think you
> should be able to group spectra together as uniformly calibrated (hopefully all data from a day or more of beamtime at a particular beamline) and then make sure that the different groups of spectra.  Does that seem reasonable?
>
> I have to admit that at my beamline I don't often have the luxury or need to run a reference foil for every scan, so we calibrate consistently ahead
> of time.  I'm sure that leads to a bias in the software.   I guess I forgot
> that Athena had the ability to read and tie a second spectrum as a "reference" and use that to auto-apply calibration.
>
> Is it generally necessary to calibrate many spectra individually, or do people find that doing them in a few large groups is sufficient?
>
> --Matt
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------------------------------

Message: 2
Date: Tue, 9 Mar 2021 07:27:59 -0600
From: Matt Newville <newville@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Larch Energy calibration
Message-ID:
        <CA+7ESbq=PMvfg9tdHgyxZpEv+rxTyfRsKSN3q0ANaTnUO87azA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Valerie,

Sorry for the delay.

On Fri, Mar 5, 2021 at 10:06 AM Schoepfer, Valerie <
valerie.schoepfer@usask.ca> wrote:

> Hi Matt,
>
> The backstory is that I'm trying to find which standards will define my
> samples, so I am pulling standards from different beamlines and years to
> get a basic linear combination fit, to run new standards myself when I have
> more beamtime.
>
> I'm able to do it in Athena- where you more or less:
> 1. Assign E0 to the first peak in the first derivative of your standard
> reference foil.
> 2. Calibrate one standard reference foil to the theoretical edge energy.
> 3. Ensure E0 is right/adjust E0 for all samples and sample foils.
> 4. Align reference foils to the standard reference foil, because the foil
> will pull the sample with it.


> But in Larch, maybe I'm unsure about the groups function?  I'm not
> convinced the reference foils 'follow' the sample spectra.
> If the reference and samples aren't tied together, how do you align
> samples when your energies are off because of different beamlines or years
> or people not as careful to calibrate the beamline energy?
> My first thought was using the first derivative peak of your sample, but
> if your edge energy shifts because of oxidation state changes, what do you
> use then?
>

It is true that Larch's XAS Viewer does not really expose the concept of
each spectrum having its own reference channel.  I guess that reflects my
own bias that if each spectrum in a set of measurements really needs its
own reference, there is a serious problem with the measurements - like, the
monochromator needs fixing.  (Aside: if the energy drifts significantly
from scan to scan, how do we know how to align the energies?).  It probably
also reflects my reality that most of the work I do is in fluorescence and
on samples that will have no transmission, and are done on a beamline where
an "elf-like" scatter measurement is not practical.

But, for sure, if you measure sets of data at different beamlines or even
at the same beamline but weeks apart, you may need to apply energy shifts
to get those *sets* of data to be aligned.   Admittedly, if you're pulling
in standard spectra from many sources, this can be a little tedious but (in
principle) only needs to be done once.

In Larch's XAS Viewer, you can go to the Data->Recalibrate Energy menu to
bring up a window for aligning one spectrum to another.  So, if you have
two sets of data and have measured the same calibrant (say, Mo foil) at
both, you can read in the foil spectra and align them:  Select the data
group for the spectrum from "new foil" and auto-align that to the spectrum
of the "good foil".    With that energy shift (this dialog only does a
constant energy shift, not an angular offset or lattice-spacing offset)
determined, you can apply that shift to any number of Selected Groups, say
all the spectrum measured along with "new foil" spectrum.

Does that seem workable for what you're trying to do?

I guess that if you have a reference channel measured for each spectrum,
you could also read those reference spectra in and see how much their edge
positions vary, assess the variation in those positions, identify outliers,
and so forth.

--Matt
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