Hi Matt:
I'll send the data I used for the figures directly to you.
Carlo
On Wed, 27 Jun 2018, 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 <se...@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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Carlo U. Segre -- Duchossois Leadership Professor of Physics
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Director, Center for Synchrotron Radiation Research and Instrumentation
Illinois Institute of Technology
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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
se...@iit.edu http://phys.iit.edu/~segre se...@debian.org
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