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

[Haifeng Li]

Hi, Carlo,

Thanks for your physical explanation for the calibration.

I have another question. I measured the same element at different
beamlines. So if I want to compare different samples measured at different
beamlines, how should I do for this situation given the possible different
calibration methods? I know alignment is very important and just shifting
the energy by calibrating would have issue.

Here I mean different calibration methods is dedicated for my element
ruthenium Ru with E0 of 22117 eV. The derivative curve show it has two
peaks. One beamline used the first one for calibration. The other used the
second. Another used the middle number between the two peaks by claiming
that the peaks stand for oxidation state with one peak for one oxidation
state and multiple peaks for multiple oxidation states. Here for Ru metal
with one oxidation state, since the main peak splits into two, the middle
energy between the two peaks was chose as the E0. Attached is the file of
Ru foil for more information. I do not know which one should be right. In
the manual, it shows choosing the first maximum point as the edge energy.
How should I choose the edge energy? Maybe I think too much. It does not
matter as the calibration is consistency.

The reference data from different calibration methods can be aligned very
well. This is another confusing part. Does the calibration would affect the
alignment?

Thanks in advance.

Haifeng


On Mon, Jul 23, 2018 at 10:48 AM, Carlo Segre  wrote:

>
> The calibration should be done at the beamline with a foil.  Once that is
> done, then you don't really want to change it.  Remember that just shifting
> the energy is not actually the correct way to do a shift.  The energy shift
> is a non-linear function of the angle (Bragg's Law) and so when you shift
> energy you are really distorting Chi(k) since that is also a non-linear
> function of energy (E^1/2).  Yes, it is usually a small effect but I prefer
> not to apply too many shifts in energy if possible.
>
> I assume that the calibrate function is the same as the align except the
> E-shift is left at zero and a correction is applied permanently to the data.
>
> Carlo
>
>
> On Mon, 23 Jul 2018, Haifeng Li wrote:
>
> Hi, Carlo,
>>
>> Thanks for your answer.
>>
>> I may ask you more questions. Why you do not recommend to calibrate the
>> data? Calibration is used to find the E0 and match it to the literature
>> data. What is the real difference between calibration and alignment?
>>
>> Thanks,
>>
>> Haifeng
>>
>> On Sun, Jul 22, 2018 at 5:30 PM, Carlo Segre  wrote:
>>
>>
>>> Hello Haifeng:
>>>
>>> Personally, I would not calibrate the data but merely align the
>>> references
>>> of A2 and A3 to the reference of A1 and similarly align B2 and B3
>>> references to that of B1.  Once merged, you can then aligh the reference
>>> of
>>> the merged B samples to that of the merged A samples.
>>>
>>> If you keep the references then you can always align data taken at a
>>> leter
>>> time to these data sets.  If the energy of your reference is a small bit
>>> off from the tabulated value, that is OK as long as all the data being
>>> compared has aligned references.
>>>
>>> Carlo
>>>
>>>
>>> On Sun, 22 Jul 2018, 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


 --
>>> 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: 312.567.3498Fax: 312.567.3494
>>> se...@iit.edu   http://phys.iit.edu/~segre   se...@debian.org
>>> ___
>>> Ifeffit mailing list
>>> Ifeffit@millenia.cars.aps.anl.gov
>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>>>
>>>
>>
> --
> Carlo U. Segre -- Duchossois Leadership Professor of Physics
> Interim Chair, Department of Chemistry
> Director, Center for Sy

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

[Carlo Segre]

The calibration should be done at the beamline with a foil.  Once that is 
done, then you don't really want to change it.  Remember that just 
shifting the energy is not actually the correct way to do a shift.  The 
energy shift is a non-linear function of the angle (Bragg's Law) and so 
when you shift energy you are really distorting Chi(k) since that is also 
a non-linear function of energy (E^1/2).  Yes, it is usually a small 
effect but I prefer not to apply too many shifts in energy if possible.


I assume that the calibrate function is the same as the align except the 
E-shift is left at zero and a correction is applied permanently to the 
data.


Carlo

On Mon, 23 Jul 2018, Haifeng Li wrote:


Hi, Carlo,

Thanks for your answer.

I may ask you more questions. Why you do not recommend to calibrate the
data? Calibration is used to find the E0 and match it to the literature
data. What is the real difference between calibration and alignment?

Thanks,

Haifeng

On Sun, Jul 22, 2018 at 5:30 PM, Carlo Segre  wrote:



Hello Haifeng:

Personally, I would not calibrate the data but merely align the references
of A2 and A3 to the reference of A1 and similarly align B2 and B3
references to that of B1.  Once merged, you can then aligh the reference of
the merged B samples to that of the merged A samples.

If you keep the references then you can always align data taken at a leter
time to these data sets.  If the energy of your reference is a small bit
off from the tabulated value, that is OK as long as all the data being
compared has aligned references.

Carlo


On Sun, 22 Jul 2018, 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



--
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: 312.567.3498Fax: 312.567.3494
se...@iit.edu   http://phys.iit.edu/~segre   se...@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: 312.567.3498Fax: 312.567.3494
se...@iit.edu   http://phys.iit.edu/~segre   se...@debian.org
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Re: [Ifeffit] Basic questions about the preliminary data processing in Athena

[Haifeng Li]

Hi, Carlo,

Thanks for your answer.

I may ask you more questions. Why you do not recommend to calibrate the
data? Calibration is used to find the E0 and match it to the literature
data. What is the real difference between calibration and alignment?

Thanks,

Haifeng

On Sun, Jul 22, 2018 at 5:30 PM, Carlo Segre  wrote:

>
> Hello Haifeng:
>
> Personally, I would not calibrate the data but merely align the references
> of A2 and A3 to the reference of A1 and similarly align B2 and B3
> references to that of B1.  Once merged, you can then aligh the reference of
> the merged B samples to that of the merged A samples.
>
> If you keep the references then you can always align data taken at a leter
> time to these data sets.  If the energy of your reference is a small bit
> off from the tabulated value, that is OK as long as all the data being
> compared has aligned references.
>
> Carlo
>
>
> On Sun, 22 Jul 2018, 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
>>
>>
> --
> 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: 312.567.3498Fax: 312.567.3494
> se...@iit.edu   http://phys.iit.edu/~segre   se...@debian.org
> ___
> Ifeffit mailing list
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Re: [Ifeffit] Basic questions about the preliminary data processing in Athena

[Robert Gordon]

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

[Carlo Segre]

Hello Haifeng:

Personally, I would not calibrate the data but merely align the references 
of A2 and A3 to the reference of A1 and similarly align B2 and B3 
references to that of B1.  Once merged, you can then aligh the 
reference of the merged B samples to that of the merged A samples.


If you keep the references then you can always align data taken at a leter 
time to these data sets.  If the energy of your reference is a small bit 
off from the tabulated value, that is OK as long as all the data being 
compared has aligned references.


Carlo

On Sun, 22 Jul 2018, 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



--
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: 312.567.3498Fax: 312.567.3494
se...@iit.edu   http://phys.iit.edu/~segre   se...@debian.org
___
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[Ifeffit] Basic questions about the preliminary data processing in Athena

[Haifeng Li]

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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