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

Carlo Segre segre at iit.edu
Wed Jun 27 13:34:43 CDT 2018


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 <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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>>
>> --
>> 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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>
>
>

-- 
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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