Does Athena use a histogramming method for Fourier filtering? 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, 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).
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. 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. 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.
A problem with this method is that it drops off the very information you need
to see what your noise floor is. 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.
mam
On 4/20/2017 3:02 PM, Christopher Thomas Chantler 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
chant...@unimelb.edu.au
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*Subject:* Ifeffit Digest, Vol 170, Issue 19
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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.y...@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-boun...@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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