[Ifeffit] Basic questions about the preliminary data processing in Athena

Robert Gordon ragordon at alumni.sfu.ca
Fri Jul 27 12:55:34 CDT 2018

HI Haifeng,

Suppose you measure Fe foil three times, and all three scans overlap. 
They are aligned.
But suppose the edge positions are at 7116 eV instead of 7112 eV. The 
calibration is off.
You can adjust to it, but, as Carlo mentioned, it is really an angle 
correction, not simply a
shift in energy. It is better to have an accurate calibration to begin 
with, then aligned and
calibrated would be the same.

Note: Choice of target calibration can differ - some use the X-ray data 
booklet values
and some use the Kraft  et al. values

Just state which calibration you are using when presenting/publishing.


On 2018-07-27 10:32 AM, Haifeng Li wrote:
> Hi, Robert,
> Thanks for your help.
> One more question. What is the real difference between calibration and 
> alignment? Do they have specific meaning?
> Thanks,
> Haifeng
> On Sun, Jul 22, 2018 at 5:45 PM, Robert Gordon <ragordon at alumni.sfu.ca 
> <mailto:ragordon at alumni.sfu.ca>> wrote:
>     Hi Haifeng,
>     Here's my take on what you described:
>     Two sample to be studied at the same edge using the same
>     reference. Three scans on A and three on
>     B are done with simultaneous reference.
>     First: compare the three reference scans for A. If they agree,
>     then compare the data scans. If they also look
>     similar (i.e. no evidence of changing in the beam), you can merge
>     the three data scans
>     on A right away. If the references don't agree, then you determine
>     by how much they differ (how much a correction
>     would be needed to bring them into alignment) and apply that same
>     correction to the data before merging.
>     It is not meaningful to merge data that is not aligned. (If the
>     sample scans show changes from scans 1  to 3,
>     then you need to rethink how to do the measurements)
>     Repeat for B.
>     Now compare the merged (corrected beforehand if necessary)
>     references for A and B. If they agree,
>     you can compare data for A and B (merged) directly. If they do
>     not, determine how much one reference
>     differs from the other and apply that same correction to, say, B,
>     that brings its reference into alignment with
>     A's reference, and then compare A and B
>     You align the references between samples to the same value in
>     order to do a meaningful comparison
>     between them. If you report energy positions of features in your
>     near-edge spectra, the reader
>     would need to know to what energy those positions are referenced.
>     When possible, I recommend references that have tabulated edge
>     values (i.e. metal foils). A reference
>     need not be the same edge as the one being studied. For arsenic,
>     as an example, the gold L3-edge is
>     quite close to the As K-edge and serves as a good reference. If
>     not possible to use a metal foil, use a
>     reference that another interested researcher could readily obtain
>     or has used. This allows for
>     comparison of reproducibility. If your reference looks nothing
>     like literature, you may have a problem
>     with the beamline or in how you processed the data. This should be
>     one of the first things you
>     check when you start taking data at the beamlne.
>     You should also note how the beamline was calibrated when you did
>     the measurements.
>     regards,
>     Robert
>     On 2018-07-22 1:21 PM, Haifeng Li wrote:
>>     Dear ALL,
>>     I am a beginner in Athena. Recently I got the spectra and I am
>>     confusing about the data calibration and alignment. The manual
>>     shows that calibrate the reference data of one scan and align
>>     other reference data to that calibrated one.
>>     Here I want to show examples. I have two samples A and B, Each
>>     sample has three scans with the corresponding reference data. For
>>     sample A, 1st scan is calibrated and the other two scans are
>>     aligned to 1st scan. Then merge them into merged A. The same
>>     procedures for sample B and get merged B. If I want to compare
>>     XANES of sample A and B, do I need to align the merged reference
>>     data between A and B? If so, why? My understanding is that all
>>     scans (original data and merged data) in sample A and B are
>>     calibrated to standard edge energy. Why do they need to align?
>>     I appreciate your help.
>>     Thanks,
>>     Haifeng
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