[Ifeffit] The difference of EXAFS oscillation when using Athena and when using Larch

Mon Apr 17 21:52:19 CDT 2017

Hi Yuji,

On Mon, Apr 17, 2017 at 12:22 PM, Yuji Mahara <mahara.yuji at e.mbox.nagoya-u.
ac.jp> wrote:

> Dear Matt
>
>
>
> Thank you very much for your quick reply.
>
>
>
> I attached three files: a raw data obtained from SPring-8 in Japan
> (PdO.q), .chik file obtained using Athena based on PdO.q (PdO.q.chik), and
> a python script I actually analyzed with Larch (EXAFSanalaysis.py).
>
> (When opening PdO.q with Athena we use the plugin named "PFBL12C".)
>
>
>
> If you put three files in the same directory and run “EXAFSanalysis.py”,
> you can see the previous PdO.png.
>
>
>
> I am looking forward to hearing from you.
>

Thank you very much for the nice report.  I can reproduce what you see, and
looked into this a bit more.  The energy data you have is very finely
spaced (the mu and energy arrays have 3991 energy points), leading to some
question about how to convert that finely spaced energy data to the chi(k)
grid of 0.05 Ang^-1.

In both Ifeffit and Larch, the autobk() function determine an array for
mu0(E) and chi(E) at all the energy data points provided.  But to use
later, chi(k) needs to be put onto evenly spaced values of k, with a step
size of 0.05 Ang^-1 being both common and appropriate for EXAFS.

For your data (see a modified version of your script, attached), there are
30 energy points between 15.0 and 15.10 Ang^-1.  It's not obvious how to
best use those data to give the value chi(k) at k=15.05.

The autobk() function in Ifeffit essentially does a boxcar average, taking
those ~15 data points closest to k=15.05 and averaging them with equal
weighting.

The autobk function in Larch takes the spline function of mu0(E) and
evaluates that at the k-values of the grid, essentially doing a
cubic-splice interpolation of the surrounding points to give the value at a
particular k.

I think this difference in interpolation explains the difference in chi(k)
and chi(R) you see -- the Ifeffit data is smoother and so lower amplitude
at high R.  The high frequency "noise" has been filtered out by the boxcar
average.   The data processed by Larch does not impose this filter, so the
data retains the higher-frequency components.

The attached plot (from the the attached modified version of your
EXAFSAnalysis.py) includes the data processed with your script, with Athena
using the Larch backend, and with Athena using the Ifeffit backend.  There
are slight differences at low-R -- I didn't worry too much about setting
clamps.

I don't have a strong opinion, but think preserving the noise / high
frequency parts of the data is probably preferred.  You can smooth it with
a variety of methods either before or after background subtraction (and
Larch comes with a few common smoothing algorithms including boxcar
averaging, convolution and the Savitzky-Golay method).

When I do continuous XAFS, I bin the data to energy points selected to be
spaced 0.05Ang^-1 apart.  That effectively boxcar averages the data at the
point of collection.   I don't know that there is always a single best way
to do that averaging/smoothing, but it would be interesting to hear the
approach others take and seeing how we might be able to unify and/or
simplify that part of the data reduction.

--Matt

>
>
> Best,
>
>
>
> Yuji
>
>
>
> *From:* Ifeffit [mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] *On
> Behalf Of *Matt Newville
> *Sent:* Tuesday, April 18, 2017 12:45 AM
> *To:* XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> *Subject:* Re: [Ifeffit] The difference of EXAFS oscillation when using
> Athena and when using Larch
>
>
>
> Hi Yuji,
>
> On Mon, Apr 17, 2017 at 9:49 AM, Yuji Mahara <
> mahara.yuji at e.mbox.nagoya-u.ac.jp> wrote:
>
> Dear All,
>
>
>
> I am Yuji Mahara at Nagoya University, Japan.
>
>
>
> I am using Athena in Demeter 0.9.24 package and Larch 0.9.33 on windows
> 10.
>
> At that time, I am worrying about the difference of EXAFS oscillation when
> using Athena and when using Larch.
>
>
>
> k3-weighted Pd K-edge EXAFS and Fourier transform EXAFS spectrum for PdO
> bulk are shown in attached file(PdO.png).
>
> When XAFS raw data is read using Athena and EXAFS oscillation is obtained,
> EXAFS spectrum is smooth and noise is small. On the other hand, using
> Larch, noise is noticeable in k space.
>
> This phenomenon occurred when analyzing other XAFS data as well.
>
>
>
> I tried to analyze XAFS data by Athena and Larch with the almost same
> conditions.
>
> Does this difference of EXAFS results arise from the difference in
> autobk's algorithm between Athena and Larch?
>
> The analysis conditions are shown below.
>
> If someone knows this reason, please let me know.
>
>
>
> There may be subtle differences in the results from autobk() from Ifeffit
> and autobk() from Larch, but they should not be very big.   If I recall
> correctly, the meaning of the values for the "clamps" is different between
> the two, but I don't think that accounts for the changes you're seeing.
>
> Like you say, the differences seem to be more about the noise in the data
> which is much more noticeable in the data processed with Larch than with
> Athena, as if the data is being smoothed or interpolated differently.  if
> the data is very finely spaced or binned in some unexpected way from a
> QXAFS collection, that might help explain the difference, though I'm not
> sure of that or what behavior would be preferred.
>
> Is it possible to post one of the data files?
>
> --Matt
>
>
>
> Best regards,
>
>
>
> Yuji Mahara
>
> ******************************************
> ■ Yuji Mahara
> Nagoya University(Japan)  D3
> Graduate School of Engineering
> Furo-cho, Chikusa-ku, Nagoya-shi, Aichi, 466-8603, Japan
> ・Phone : +81-52-789-3192
> ・E-mail : mahara.yuji at e.mbox.nagoya-u.ac.jp
> ******************************************
>
>
>
> #####Analysis condition of Athena #####
>
>
>
> e0 à[ set e0 to a fraction of the edge step] à 24355.9037323484
> <%28903%29%20732-3484>
>
> Normalization order: 3
>
> Pre-edge range: from -150 to -60 eV
>
> Normalization range: from 150 to 1100 eV
>
> Rbkg: 1
>
> k-weight used by spline: 2
>
> Spline clamp: low=None, high=Strong
>
> Spline range in k: from 0 to 17
>
> Fourier transform k-range: from 3 to 15, dk=0.5, window=’hanning’
>
>
>
> #####Analysis condition of Larch #####
>
>
>
> dat.e0 = 24355.9037323484 <%28903%29%20732-3484> ß e0 was estimated by
> Athena
>
> pre_edge(dat.e, dat.mu, group=dat, e0=dat.e0, pre1=-150, pre2=-60,
> norm1=150, norm2=1100, nnorm=2, _larch=mylarch)
>
> autobk(dat.e, dat.mu, group=dat, e0=dat.e0, rbkg=1, nclamp=5, clamp_lo=0,
> clamp_hi=24, kstep=0.05, kmin=0, kmax=17, kweight=2, win='hanning',
> _larch=mylarch)
>
> xftf(dat.k, dat.chi, group=dat, kmin=3, kmax=15, dk=0.5, window='hanning',
> kweight=3, _larch=mylarch)
>
>
>
> #########################
>
>
>
>
>
>
>
>
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