[Ifeffit] data after rebinning look worse in k-space than before?

Matt Newville newville at cars.uchicago.edu
Fri Jun 29 09:59:56 CDT 2018


Hi Everyone,

Thanks for the discussion and example data and code!  By itself, Larch was
definitely not handling these datasets gracefully, and now it is doing a
much better job.  There were lots of different topics discussed, but I'd
like to make a few comments:

First, I do not understand the objection to rebinning QXAFS data that is
heavily oversampled in energy.  I think this is necessary.  When I do
continuous XAFS scans (still at ~1 sec per energy, so maybe not "Quick"
anymore), I set up a "normally gridded XAFS scan" and then use that to set
triggers and scan at approximately constant energy velocity so that each
bin of energy is centered on the target energy.  That is, I don't get 8000
values, only ~400 on a nearly-normal EXAFS grid. To be clear, we do this
for convenience, so that the binning is done in the motor controller and
detector hardware, not in post-processing software.  But, there should be
no difference, and like Carlo and Edmund point out, doing it in software
does add flexibility in how the data is treated. As long as the final
energy grid is fine enough relative to energy resolution and/or EXAFS
resolution (so, ~0.05Ang^-1), I think this is fine.
But, whether done in hardware or software, binning *will* happen with
QXAFS.

Interpolation and smoothing could work, but these introduce questions of
how much and which data to use for the interpolation or smoothing.  For
sure, smoothing with Savitzky-Golay followed by simple interpolation could
work.   But, when Larch/Ifeffit/Athena treat data by default, they use a
simple  interpolation and do work to use all the data points in finely
spaced data.  Instead, they use only the 2 or 3 nearest energy values and
do linear or quadratic interpolation with those limited data, assuming the
data is accurate.  That does not work so well for heavily oversampled and
so results in artificially noisy data, as shown below (see especially the
Ru example).

I'm still digesting Matthew's code. I think it is close in spirit to what I
have, but I have not tested it numerically.

For rebinning in Larch and its in-active-development XAS_Viewer, here's
what I have so far (full code at
https://github.com/xraypy/xraylarch/blob/master/plugins/xafs/rebin_xafs.py#L52),
based on playing around with data from Carlo and Edmund:

  Step 1: make "standard XAFS grid" array of energy, with XANES steps of
~0.5 eV or better and EXAFS steps of 0.05 Ang^-1
  Step 2: identify segments in original energy array for each value in the
new energy array.
  Step 3: for each energy value in the new array:
               a) if the segment has 2 or few energy values, do linear
interpolation.
               b) otherwise, take either the mean value ("boxcar") or
centroid of mu for the segment.
               c) estimate the uncertainty as the standard deviation of the
mu for that segment.

I know most of the discussion here was about EXAFS, but I am also slightly
concerned about rebinning introducing systematic shifts at the edge, just
in case this data is used as XANES. Because of this, I use a hybrid
solution of doing rebinning when there are enough original data points (3
or more), and doing linear interpolation when there are 3 or fewer points.
I think Matthew's code does that too....

I thought that using the centroid might improve the noise, but it seemed to
have a tiny (1.e-7) effect, at least on the data looked at so far.  Also,
so far, I'm calculating the uncertainty in mu due to the rebinning, but not
doing anything with that yet.

With this and other fixes for sorting and removing duplicate data, Larch
XAS Viewer now does an OK job with Carlo's and Edmund's data. Attached are
two plots showing data as originally imported without rebinning, and after
rebinning.  The unbinned data look really, really noisy.  For Carlo's
fluorescence data at Fe K edge (1 scan only), rebinning helps a lot.  For
Edmund's 8000+ dataset for Ru in transmission, not-rebinning is a complete
disaster, and rebinning is a huge improvement.

Let me know if you have any more suggestions on how to do this better or
questions about this,


On Thu, Jun 28, 2018 at 8:19 AM Edmund Welter <edmund.welter at desy.de> wrote:

> Dear Matt,
>
> attached you will find a recent data file which is showing the problem and
> two plots of the data (A RuO2 powder sample on Scotch tape) in the file.
> One plot is showing the Chi(k) with and without rebinning the other one
> just mue(E) with and without rebinning. It seems it is no good to convert
> previously rebinned data to k-space. the rebinned mue(E) looks okay and the
> original data converted to k-space does also look ok.
>
> I produced the plots with Athena 0.9.24 (I know not the most recent
> version) under WIN 7 with IFEFFIT as backend. I wasn't able yet to
> reproduce this on my office desktop using LINUX and the most recent dathena
> and Larch, because of some trouble with reading the data file... No idea
> yet, might be worse another thread or might be something stupid on my site.
>
> Cheers,
>
> Edmund
>
> On 27.06.2018 20:31, Matt Newville wrote:
>
> HI Ilya, Edmund, Carlo,
>
> Ilya and/or Carlo: can you post some example unbinned data?  As it turns
> out, I am adding a rebinning feature in the Larch XAS Viewer GUI that
> should be ready for a ready-to-try release very soon (for IIT XAFS School
> and XAFS2018).
>
> This seems like a good chance to test these procedures out.
>
> My approach for this is to this is to make a "normal XAFS energy grid" of
> ~5 eV steps, 0.25 eV steps, 0.05 Ang^-1 steps that the downstream
> processing needs, and then do one of two strategies -- maybe there should
> be more?:
>  a) do a straight interpolation onto this array -- that is probably the
> "noisy" result.
>  b) assign each energy point in the original data to one of these energy
> bins, and take the average of all the points in each bin.
>
> I'd also like to try using energy-weighted mean (centroid).  Probably most
> of the data is so finely spaced that this won't make much difference, but
> it might be a good option.   It might be able to help compensate for energy
> jitter, assuming that the recorded energy (probably from an encoder) is
> more accurate than the requested energy.
>
> It's also interesting to think about doing a Savitzky-Golay smoothing,
> though that might require knowing if the data points are actually uniform
> in mono angle or mono energy.  It also makes it easy to over-do the
> smoothing, and so a little trickier to prevent bad results.
>
> Do you (or anyone else) have any suggestions for how to best re-bin this
> kind of data?
>
> --Matt
>
>
> On Wed, Jun 27, 2018 at 10:15 AM Carlo Segre <segre at iit.edu> wrote:
>
>>
>> Yes, we measure fast and have taken as many as 20000 points.   The
>> problem
>> is not in the shifts that you mention.  This is normal and expected.  the
>> problem is specificallly in the rebinning algorithm in Demeter.  It seems
>> to be different than the one in the old Horae package.  I have done a
>> test
>> of this and I attache a coule of figures that show the difference.
>>
>> I have used 10 continuous scans for this test.  The data were taken at
>> the
>> MRCAT beamline, Sector 10 at the APS.  The data are for the Fe K-edge and
>> there are about 3400 points per scan with a point density of about 0.35
>> eV/step.  I used both versions of Athena and performed the following
>> steps
>> to give the data groups shown in the plots
>>
>> new_athena.png
>>   Fe_new_rebin_merge - (blue) all 10 scans rebinned at input and then
>>                        merged
>>   Fe_new_merge       - (red) all 10 scans merged only
>>   Fe_new_merge_rebin - (green) all 10 scans merged then rebinned
>>
>> old_athena.png
>>   Fe_old_rebin_merge - (blue) all 10 scans rebinned at input and then
>>                        merged
>>   Fe_old_merge       - (red) all 10 scans merged only
>>   Fe_old_merge_rebin - (green) all 10 scans merged then rebinned
>>
>> comp_athena.png
>>   Fe_old_rebin_merge - (blue)
>>   Fe_new_rebin_merge - (red)
>>
>> It is clear that the new Athena (Demeter) is not rebinning the same way
>> as
>> the old one (Horae).  The contrast is particularly evident with the last
>> plot. The new rebinning algorithm is introducing more noise.  For the
>> moment, I recommend only merging and perhaps smoothing if you can
>> tolerate
>> a bit of amplitude reduction.
>>
>> I have been thinking that it might even be better to have the data
>> acquisition software do the rebinning on the fly so the data does not
>> have
>> to be manipulated in Athena.  I am not sure if this is a good idea yet
>> but
>> I think it would help my users.
>>
>> Carlo
>>
>>
>> On Wed, 27 Jun 2018, Edmund Welter wrote:
>>
>> > Dear Carlo,
>> >
>> > do you also measure as fast as possible in the sense that for two
>> consecutive
>> > scans the points on the energy axis are not at the same positions? This
>> is
>> > what happens at my beamline. The differences are typically very small
>> but
>> > there are differences and one should not just add all the first points
>> and
>> > all the second points and so on because they are not necessarily
>> exactly at
>> > the same energy. Sometimes the beamline computer is doing something
>> else in
>> > parallel (whatever that might be) and the distance between points A and
>> B is
>> > significantly larger than the distance between B and C.
>> >
>> > So, the problem is, at which point does it make sense to merge several
>> > spectra of the same sample? I presume that Athena is taking care of
>> this when
>> > I use it to merge spectra, but it can only do so by interpolating the
>> points
>> > in the spectrum onto a common grid before summing up the spectra.
>> >
>> > The best solution might be to rebin/interpolate the spectra onto a
>> fixed grid
>> > before they are imported into Athena (or any other program), depends on
>> what
>> > Athena is exactly doing when it is rebinning data.
>> >
>> > Another aspect is that Athena is not very happy about 8600
>> points/spectrum
>> > anyway, at least as long as it using Ifeffit.
>> >
>> > Cheers,
>> >
>> > Edmund
>> >
>> >
>> >
>> > On 27.06.2018 15:14, Carlo Segre wrote:
>> >>
>> >>
>> >> Hi Ilya:
>> >>
>> >> We always take data in this mode at APS Sector 10 and I have also find
>> that
>> >> the rebinning function is not working satisfactorily at this time.  I
>> find
>> >> that for the current version of the software it is better to merge
>> your
>> >> data and let IFEFFIT interpolate to the dk=0.05 grid that it uses.
>> >>
>> >> Carlo
>> >>
>> >>
>> >> On Wed, 27 Jun 2018, Ilya Sinev wrote:
>> >>
>> >>> Hi all,
>> >>>
>> >>>
>> >>>
>> >>> I have a question regarding the chi(k) function isolation and
>> rebinning
>> >>> processes. I have some data recorded in ?quasi channel-cut? modus,
>> i.e.
>> >>> with
>> >>> the mono constantly moving and the data points collected with the
>> highest
>> >>> possible rate. With 180 sec measurement in yields to a spectrum of
>> ca.
>> >>> 8600
>> >>> point, which obviously needs to be rebinned. The rebinned data,
>> however,
>> >>> does not look good in k-space even if multiple data are merged.
>> Moreover,
>> >>> I
>> >>> have an impression that the raw spectrum in k-space does not have
>> those
>> >>> 8000+ points anymore but significantly less. Is there any reduction
>> of the
>> >>> data points number that is not seen (e.g. as a preparation step for
>> FT)?
>> >>> Since the unbinned data has higher quality, does it then make more
>> sense
>> >>> to
>> >>> keep using it for EXAFS analysis?
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> Thank you
>> >>>
>> >>> Ilya Sinev
>> >>>
>> >>>
>> >>>
>> >>>
>> >>
>> >
>> > _______________________________________________
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>> > Ifeffit at millenia.cars.aps.anl.gov
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>> >
>>
>> --
>> Carlo U. Segre -- Duchossois Leadership Professor of Physics
>> Interim Chair, Department of Chemistry
>> Director, Center for Synchrotron Radiation Research and Instrumentation
>> Illinois Institute of Technology
>> Voice: 312.567.3498            Fax: 312.567.3494
>> segre at iit.edu   http://phys.iit.edu/~segre   segre at debian.org
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>
>
> --
> --Matt Newville <newville at cars.uchicago.edu> 630-252-0431
>
>
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-- 
--Matt Newville <newville at cars.uchicago.edu> 630-252-0431
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