�� I'm just agreeing with Matt's comment.


Too fine a spacing does not help you due to typical broadening from imfp or thermal sources [or structural disorder].


And the difference between operation of ifeffit and larch in this context is pretty interesting.


--------------------------------------------------------------------------------------
Christopher Chantler, Professor, FAIP, Fellow American Physical Society
Editor-in-Chief, Radiation Physics and Chemistry
Chair, International IUCr Commission on XAFS
President, International Radiation Physics Society
School of Physics, University of Melbourne
Parkville Victoria 3010 Australia
+61-3-83445437 FAX +61-3-93474783

From: Ifeffit <ifeffit-bounces@millenia.cars.aps.anl.gov> on behalf of ifeffit-request@millenia.cars.aps.anl.gov <ifeffit-request@millenia.cars.aps.anl.gov>
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Subject: Ifeffit Digest, Vol 170, Issue 21
 
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Today's Topics:

   1. Re: Ifeffit Digest, Vol 170, Issue 19 (Matt Newville)
   2. Fwd:  Ifeffit Digest, Vol 170, Issue 19 (Matt Newville)
   3. Looking for EXAFS data of Ni2+ ion in aqueous solution (Van Vu)


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

Message: 1
Date: Thu, 20 Apr 2017 21:18:39 -0500
From: Matt Newville <newville@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Ifeffit Digest, Vol 170, Issue 19
Message-ID:
        <CA+7ESbpEWenMLpspnYAXT4j2T1LkjAaYua59XcGebLpteKTyWg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Chris,

On Thu, Apr 20, 2017 at 5:02 PM, Christopher Thomas Chantler <
chantler@unimelb.edu.au> wrote:

> Note that in general any and every smoothing operation reduces the
> information content of the data and its ability to reveal structure.
>

Well, maybe.  If one has mu(E) measured every 0.01 eV over an 600 eV EXAFS
scan to k=12A^-1, one does not really 60,000 independent measures of the
structure.  Yuji's data wasn't that absurd, but it did have close to 4000
measurements for the full EXAFS spectrum out to k=18^-1.  And to be clear,
there is not anything wrong with that, it's just a matter of how you decide
to treat it.

As the plots attached in Yuji's original message and my replies show, the
resulting chi(k) definitely has is amplitude suppressed when doing a simple
boxcar average of data onto the 0.05 Ang^-1 grid (Athena with Ifeffit).
But when using cubic spline interpolation (Larch), the amplitude of the
EXAFS oscillations are not noticeably suppressed, though the high frequency
noise is also much higher.  Applying a Savitzky-Golay filter prior to the
cubic spline interpolation did not appreciably suppress the EXAFS
oscillations though the high frequency noise was reduced.

Very finely-spaced energy data might reveal is at much higher R than we can
hope to model with EXAFS.  A k-grid of 0.05 Ang^-1 can give frequencies to
31Ang, and so is probably accurate to 16Ang without significant signal
loss.   That is, out to k=18Ang^-1, you really only need 360 samples, but
you'd like these as noise-free as possible.  Having 3600 measurements on a
grid of 0.005 Ang^-1  might give you data out to 160Ang in principle, but
the photo-electron tends to not cooperate.

--Matt
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Message: 2
Date: Thu, 20 Apr 2017 22:33:14 -0500
From: Matt Newville <newville@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: [Ifeffit] Fwd:  Ifeffit Digest, Vol 170, Issue 19
Message-ID:
        <CA+7ESbopsw1P-9hZyyQ+yobHCcH++COHOCyg2z-GExADn3L7EA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Matthew,


On Thu, Apr 20, 2017 at 5:34 PM, Matthew Marcus <mamarcus@lbl.gov> wrote:

> Does Athena use a histogramming method for Fourier filtering?


The autobk() in Ifeffit does.  That is, the background mu0(E) and chi(E)
are found at all input energy points.  This is converted to chi(k) at k for
all energy points, and then a boxcar average is applied to give chi(k) on
the standard 0.05 k-grid.  As shown earlier, this diminishes the noise and
also the amplitude of chi(k), especially at higher frequencies.

In Larch, the cubic spline for the background mu0(E)  is found at all input
energy points, but then evaluated at the values on the uniform k-grid.
.

> That's what I use.  The idea is that to grid the data we don't interpolate
> but take averages over the data appearing within the bin,


 OK, but that boxcar average will blur the data.    I definitely see this
with QXAFS (well "continuous") where I can scan continuously but bin the
measurements into 0.05Ang-1 bins -- that *does* reduce the amplitude
compared to binning into 0.02 Ang^-1 bins and compared to step scans, where
one measures at fixed energies, not slewing over an energy range.

The data from SPRing8 was much finer spaced than EXAFS needs -- and boxcar
averaging to 0.05 Ang^-1 does blur the data.


> with interpolation only when there aren't any points within a bin. For
> those, you have to bridge across a gap.  This is the best idea I've come up
> with for using data which may be tabulated more finely than the k-grid of
> the Fourier filtering process (typically dk=0.05A^-1).
>

Putting the spline through all the energy points does use all the data to
predict the value on the 0.05 Ang^-1 grid, and avoids blurring the data.
Yes, the result can be noisier, but it does not suppress the oscillations.


> Something I've used in a XANES context but never tried for EXAFS is a
> convolution with a kernel whose width depends on energy, such that it
> matches the sharpest credible feature.  See Manceau, A., Marcus, M. A.,
> Lenoir, T. (2014) Estimating the number of pure chemical components in a
> mixture by X-ray absorption spectroscopy. J. Synchrotron Radiat.
> 21,1140-1147,
> specifically the SI.


I've read that paper, but I don't think I looked at the SI.  Will do.


> The notion is that no real feature can be narrower than the combination of
> the core-hole lifetime and instrumental broadening or the EXAFS wiggle
> corresponding to the maximum reasonable path length.  This is done
> by transforming the data from E-space to a space in which a constant step
> in the abscissa corresponds to this energy-dependent minimum credible
> feature width.  Of course, in EXAFS this is mostly a constant width in k,
> so some kind of smoothing would work if it's a constant kernel in k.


 That's sort of what a Fourier filter does, for example zero all the data
above R>10 and transform back to k.

S-G smoothing assumes uniform tabulation so unless your data were taken on
> a uniform k-grid, it doesn't really do the right thing.
>

The S-G smoothing does appear to help even if the data are not strictly
uniform (see example posted earlier where the data was very finely spaced
in energy, but not uniformly).    I did forget about the uniformity
requirement, but I think that for the purposes here (smooth very fine
slightly noisy data before fitting the cubic spline) it's probably not a
disaster.

I would agree that this filter is designed to reduce high-frequency noise
is largely cosmetic, and is not really going to help reduce the noise in
the frequency range of the data we actually care about.  In fact, for me
the main point would be that the S-G filter does *not* greatly alter the
frequencies we care about, whereas boxcar averaging most certainly does.



> A problem with this method is that it drops off the very information you
> need to see what your noise floor is.


Yes, that's a good point.  Removing the obvious high-frequency noise gives
the impression that there is no low-frequency noise, which is not correct.



> I put this out there only for those who insist on smoothing.  I use my
> data un-smoothed for EXAFS analysis, knowing that the treatment of noise
> and sampling finer than the k-bin is not really right.
>



> I don't really see the usefulness of smoothing for XANES or EXAFS
> analysis, though it might be OK for display if not overdone.
>

Yes, I agree -- not smoothing chi(k) is the best approach.  But if you do
smooth, use Savitzky-Golay on the uniform chi(k).


--
--Matt
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Message: 3
Date: Fri, 21 Apr 2017 20:01:05 +0700
From: Van Vu <vuxxx047@umn.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: [Ifeffit] Looking for EXAFS data of Ni2+ ion in aqueous
        solution
Message-ID:
        <CAEDZ6XA66edg1-baDhBnjvzwQSBGD8RS3jmcA7wzmhYSne-N7w@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear everyone,
I am looking for XAS data of Ni2+ ion in aqueous solution that contains
EXAFS data in the k range of 0-12 (Angstrom-1) or so for an undergraduate
student project. I was wondering if anyone would be willing to share the
data with me?
Many thanks in advance.
Best,
Van

On Fri, Apr 21, 2017 at 5:02 AM, Christopher Thomas Chantler <
chantler@unimelb.edu.au> wrote:

> Note that in general any and every smoothing operation reduces the
> information content of the data and its ability to reveal structure. Also,
> many of the smoothing algorithms change the data point values at vertices,
> so change the data prior to analysis.
>
>
> Hence in general avoid unless you know exactly the physical cause
> requiring smoothing.
>
>
> Best wishes
>
>
> ------------------------------------------------------------
> --------------------------
> Christopher Chantler, Professor, FAIP, Fellow American Physical Society
> Editor-in-Chief, Radiation Physics and Chemistry
> Chair, International IUCr Commission on XAFS
> President, International Radiation Physics Society
> School of Physics, University of Melbourne
> Parkville Victoria 3010 Australia
> +61-3-83445437 FAX +61-3-93474783
> chantler@unimelb.edu.au
> <https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdAITgSrfUpfDAUV5oUH1LFYBcz08w8xvHMJoosZRdagfQM.&URL=mailto%3achantler%40unimelb.edu.au>
> chantler@me.com
> <https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdAITgSrfUpfDAUV5oUH1LFYBcz08w8xvHMJoosZRdagfQM.&URL=mailto%3achantler%40me.com>
> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html
> <https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdAITgSrfUpfDAUV5oUH1LFYBcz08w8xvHMJoosZRdagfQM.&URL=http%3a%2f%2foptics.ph.unimelb.edu.au%2f%7echantler%2fxrayopt%2fxrayopt.html>
> http://optics.ph.unimelb.edu.au/~chantler/home.html
> <https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdAITgSrfUpfDAUV5oUH1LFYBcz08w8xvHMJoosZRdagfQM.&URL=http%3a%2f%2foptics.ph.unimelb.edu.au%2f%7echantler%2fhome.html>
>
> ------------------------------
> *From:* Ifeffit <ifeffit-bounces@millenia.cars.aps.anl.gov> on behalf of
> ifeffit-request@millenia.cars.aps.anl.gov <ifeffit-request@millenia.
> https://protect-au.mimecast.com/s/GN1VBvt6aeV8I1?domain=cars.aps.anl.gov>
> *Sent:* Friday, 21 April 2017 3:00:01 AM
> *To:* ifeffit@millenia.cars.aps.anl.gov
> *Subject:* Ifeffit Digest, Vol 170, Issue 19
>
> Send Ifeffit mailing list submissions to
>         ifeffit@millenia.cars.aps.anl.gov
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://protect-au.mimecast.com/s/krZOBlimO6EJCD?domain=millenia.cars.aps.anl.gov
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> Today's Topics:
>
>    1. Re: The difference of EXAFS oscillation when using Athena and
>       when using Larch (Yuji Mahara)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 20 Apr 2017 19:47:20 +0900
> From: "Yuji Mahara" <mahara.yuji@e.mbox.nagoya-u.ac.jp>
> To: "'XAFS Analysis using Ifeffit'"
>         <ifeffit@millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] The difference of EXAFS oscillation when using
>         Athena  and when using Larch
> Message-ID: <003501d2b9c3$7c75c560$75615020$@e.mbox.nagoya-u.ac.jp>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Matt
>
>
>
> Thank you for your reply.
>
> I confirmed that chi (k) becomes smooth by the Savitzky-Goley method by
> doing the attached lar file.
>
>
>
> I will try on various conditions from now.
>
> I may also ask if there is something I do not understand.
>
> Thank you for your help again!
>
>
>
> Bests,
>
> Yuji Mahara
>
>
>
>
>
> From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov
> <ifeffit-bounces@millenia.cars.aps.anl.gov>] On Behalf Of Matt Newville
> Sent: Thursday, April 20, 2017 5:26 AM
> To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] The difference of EXAFS oscillation when using
> Athena and when using Larch
>
>
>
> Hi Yuji,
>
> The attached larch script (a modification of your script but note: not
> python, so you may have to add a bunch of '_larch=mylarch' arguments) to
> show the effects of smoothing with Savitzky-Golay and of interpolating onto
> a "classic XAFS energy grid".   You might want to play around with this
> different options.  It definitely seems that none of these methods are
> systematically over-smoothing the data and reducing the amplitudes of the
> oscillations -- one more reason to use Larch instead of Ifeffit.  But it
> also seems like smoothing this data with a Savitzky-Golay fitler is helpful.
>
> Also attached are plots showing k- and R-space generated from the attached
> script.
>
>
>
> --Matt
>
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