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

[Robert Gordon]

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

http://xdb.lbl.gov/
and some use the Kraft  et al. values
https://aip.scitation.org/doi/abs/10.1063/1.1146657

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

-R.


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

[Bruce Ravel]

On 07/27/2018 01:32 PM, Haifeng Li wrote:
What is the real difference between calibration and alignment? Do they 
have specific meaning?



In Athena, calibration means to determine a value for e0 shift such that 
a particular point in the data is specified to be a particular energy. 
Then the value for E0 is set to that particular energy.  Thus, 
calibration changes both e0 and e0 shift for the group being calibrated.


For example, set the E0 shift such that the first inflection point in 
copper is made to be 8979 eV.  Then set the value for E0 in the 
background removal to 8979.


In Athena alignment is the process by which one data group is given an 
e0 shift value such that it lines up with another data group.  This is 
to compensate for some scan-to-scan variability in the behavior of the 
monochromator.  Often, but not always, alignment is done using a 
zero-valent (or some other) reference which is measured simultaneously 
with the actual sample.  In Athena, the alignment tool DOES NOT change 
the value of e0, but certainly does change the value of e0 shift for the 
group being aligned.  The alignment tool does not change either e0 or e0 
shift for the alignment standard.


Whether you want to do one, the other, both, or neither depends upon the 
beamline and the type of data ensemble you have measured.


This /is/ explained in the user manual.

B


--
 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Lead Beamline Scientist, 06BM (BMM)
 Building 743, Room 114
 Upton NY, 11973

 Homepage:http://bruceravel.github.io/home/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
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Re: [Ifeffit] Basic questions about the preliminary data processing in Athena

[Haifeng Li]

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 
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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[Ifeffit] Demeter Installation Mac server error

[Laurane Léost]

Dear all,

I would like to install Demeter on Mac device.

I followed all the instructions with "Installing Demeter on the Mac" in 
the website. But in the terminal window, when i write : "sudo port 
install xorg-server demeter", this message appears : "Error: Port 
xorg-server not found".


Did someone had already receive this type of message? Or know a way to 
install the program.


Thanks for your help.


--
Laurane Léost

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