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

Robert Gordon ragordon at alumni.sfu.ca
Sun Jul 22 17:45:54 CDT 2018

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 


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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