Re: [Ifeffit] [Ext] Dumb question

2023-02-17 Thread Robert Gordon 
OK...my first impulse would be to plot the full unnormalised XANES on the
same graph so you can see the features grow in or change.
If there are a large number of scans, maybe only plot every 3rd or 4th or
such. You might find a better point to examine for time dependence
than the one you had used.

Sorry...I'm not clear on the type of experiment. Is it something where the
concentration should be increasing, like dissolving in solution,
or a chemical change - concentration of target element is constant, but
chemical form changes, so features in the XANES are changing
or shifting.

In the datafile, are there column headings? Do any of them indicate a dead
time corrected value?
You may need to ask the person who collected the data or the beamline if
such a correction is warranted.

More generally, how much background in X-ray work do you have? Have you had
a course on it?
Do you know how dead time arises for a solid state detector?

If you are looking at the increasing concentration scenario, as the signal
rises, the detector has to reset before counting more.
The higher the signal, the more time spent resetting instead of counting -
the time over which the detector is live is less than
the real time over which you are integrating. A strong white line feature
could be a bad choice for
monitoring over time in this regard without the correction. Look at other
features. Is there a pre-edge feature you could use?
Even the pre-edge background could be indicative of concentration
saturation.

If it is the chemical change scenario, then just look for when it stops
changing.

Sorry if this is vague. Hope it helps.

-R.




On Fri, Feb 17, 2023 at 11:16 AM Roberta Candela  wrote:

> Yes I think that would be the plot. I currently haven’t been normalizing
> anything as I was just trying to see if I could get a rough draft. I
> haven’t done any background removal it was essentially just the raw data.
> As far as the features go I am not sure? I wasn’t trying to target a
> specific feature. The fluorescence was measured using a solid state
> detector but I’m not sure about the dead time. Is that information that is
> contained in xdi files? I wasn’t at this particular beam time so I have
> only the file to work off of.
> Thank you so much for the detailed response!
> -B
>
>
> Sent from Yahoo Mail for iPhone
> 
>
> On Thursday, February 16, 2023, 2:50 PM, Robert Gordon <
> ragor...@alumni.sfu.ca> wrote:
>
> So your goal is to plot If/I0 versus time for a given energy in the XANES.
> Are you exporting normalised XANES or just If/I0?
> Are you doing background removal from the pre-edge?
>
> Is another feature underlying this targeted feature also disappearing or
> changing? i.e. you are not watching a feature
> increase from zero but instead changing from one to another? ...or seeing
> a background increase as well?
>
> Was the fluorescence measured using a solid state detector? Did the
> deadtime of the detector increase significantly
> as the signal from the sample increased (and no deadtime correction
> applied) ?
>
> -R.
>
>
>
> Ifeffit mailing list
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Re: [Ifeffit] [Ext] Dumb question

2023-02-17 Thread Roberta Candela 
Yes I think that would be the plot. I currently haven’t been normalizing 
anything as I was just trying to see if I could get a rough draft. I haven’t 
done any background removal it was essentially just the raw data. As far as the 
features go I am not sure? I wasn’t trying to target a specific feature. The 
fluorescence was measured using a solid state detector but I’m not sure about 
the dead time. Is that information that is contained in xdi files? I wasn’t at 
this particular beam time so I have only the file to work off of.Thank you so 
much for the detailed response!-B

Sent from Yahoo Mail for iPhone


On Thursday, February 16, 2023, 2:50 PM, Robert Gordon  
wrote:

So your goal is to plot If/I0 versus time for a given energy in the XANES. Are 
you exporting normalised XANES or just If/I0?Are you doing background removal 
from the pre-edge?

Is another feature underlying this targeted feature also disappearing or 
changing? i.e. you are not watching a feature 
increase from zero but instead changing from one to another? ...or seeing a 
background increase as well?
Was the fluorescence measured using a solid state detector? Did the deadtime of 
the detector increase significantlyas the signal from the sample increased (and 
no deadtime correction applied) ?
-R.



On Thu, Feb 16, 2023 at 10:53 AM Roberta Candela  wrote:

Ha no worries! It would be Ifinal over time (to my vague understanding). I’m 
trying to show that the sample was saturated by looking above the fluorescence 
k-alpha line (or I guess it’s called the white line?) because the intensity 
should increase and then level off once it’s saturated. This is a xanes scan 
but we were doing fluorescence instead of transmission since it was a dilute 
sample. Did that answer the question? My apologies I’m very new and I’m sure im 
referring to things incorrectly. 


Sent from Yahoo Mail for iPhone


On Thursday, February 16, 2023, 12:45 PM, Carlo Segre  wrote:

Hi Robert:
What, exactly are you interested in plotting?  It is not quite clear from your 
message.  Is it the Io as a function of time during a scan?  Is it the XANES 
scans as a function of time for a reaction?
Carlo
On Thu, Feb 16, 2023 at 11:59 AM Roberta Candela  wrote:

Hi all, I am attempting to graph a simple plot of intensity vs time for some 
supplemental info on a paper (from XAFS data from beamtime). I thought it 
should be simple enough since I can export I0 and If from Athena and I know the 
run time and time per data point but I can’t get anything that looks remotely 
like the logarithmic graph it should be. Am I missing some big fundamental 
point for why this isn’t possible? My apologies if this is way too vague!/I 
feel like I’m missing something super obvious Thank you for your time!Sincerely 
-B


Sent from Yahoo Mail for iPhone
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-- 
Carlo U. Segre (he/him) -- Duchossois Leadership Professor of PhysicsProfessor 
of Materials Science & EngineeringDirector, Center for Synchrotron Radiation 
Research and InstrumentationIllinois Institute of TechnologyVoice: 312.567.3498 
           Fax: 312.567.3494se...@iit.edu   http://phys.iit.edu/~segre   
se...@debian.org
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Re: [Ifeffit] [Ext] Dumb question

2023-02-16 Thread Robert Gordon 
So your goal is to plot If/I0 versus time for a given energy in the XANES.
Are you exporting normalised XANES or just If/I0?
Are you doing background removal from the pre-edge?

Is another feature underlying this targeted feature also disappearing or
changing? i.e. you are not watching a feature
increase from zero but instead changing from one to another? ...or seeing a
background increase as well?

Was the fluorescence measured using a solid state detector? Did the
deadtime of the detector increase significantly
as the signal from the sample increased (and no deadtime correction
applied) ?

-R.



On Thu, Feb 16, 2023 at 10:53 AM Roberta Candela  wrote:

> Ha no worries! It would be Ifinal over time (to my vague understanding).
> I’m trying to show that the sample was saturated by looking above the
> fluorescence k-alpha line (or I guess it’s called the white line?) because
> the intensity should increase and then level off once it’s saturated. This
> is a xanes scan but we were doing fluorescence instead of transmission
> since it was a dilute sample.
> Did that answer the question? My apologies I’m very new and I’m sure im
> referring to things incorrectly.
>
>
>
> Sent from Yahoo Mail for iPhone
> 
>
> On Thursday, February 16, 2023, 12:45 PM, Carlo Segre 
> wrote:
>
> Hi Robert:
>
> What, exactly are you interested in plotting?  It is not quite clear from
> your message.  Is it the Io as a function of time during a scan?  Is it the
> XANES scans as a function of time for a reaction?
>
> Carlo
>
> On Thu, Feb 16, 2023 at 11:59 AM Roberta Candela  wrote:
>
> Hi all, I am attempting to graph a simple plot of intensity vs time for
> some supplemental info on a paper (from XAFS data from beamtime). I thought
> it should be simple enough since I can export I0 and If from Athena and I
> know the run time and time per data point but I can’t get anything that
> looks remotely like the logarithmic graph it should be. Am I missing some
> big fundamental point for why this isn’t possible? My apologies if this is
> way too vague!/I feel like I’m missing something super obvious
> Thank you for your time!
> Sincerely
> -B
>
>
> Sent from Yahoo Mail for iPhone
> 
> ___
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>
>
>
> --
> Carlo U. Segre (he/him) -- Duchossois Leadership Professor of Physics
> Professor of Materials Science & Engineering
> 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] [Ext] Dumb question

2023-02-16 Thread Roberta Candela 
Ha no worries! It would be Ifinal over time (to my vague understanding). I’m 
trying to show that the sample was saturated by looking above the fluorescence 
k-alpha line (or I guess it’s called the white line?) because the intensity 
should increase and then level off once it’s saturated. This is a xanes scan 
but we were doing fluorescence instead of transmission since it was a dilute 
sample. Did that answer the question? My apologies I’m very new and I’m sure im 
referring to things incorrectly. 


Sent from Yahoo Mail for iPhone


On Thursday, February 16, 2023, 12:45 PM, Carlo Segre  wrote:

Hi Robert:
What, exactly are you interested in plotting?  It is not quite clear from your 
message.  Is it the Io as a function of time during a scan?  Is it the XANES 
scans as a function of time for a reaction?
Carlo
On Thu, Feb 16, 2023 at 11:59 AM Roberta Candela  wrote:

Hi all, I am attempting to graph a simple plot of intensity vs time for some 
supplemental info on a paper (from XAFS data from beamtime). I thought it 
should be simple enough since I can export I0 and If from Athena and I know the 
run time and time per data point but I can’t get anything that looks remotely 
like the logarithmic graph it should be. Am I missing some big fundamental 
point for why this isn’t possible? My apologies if this is way too vague!/I 
feel like I’m missing something super obvious Thank you for your time!Sincerely 
-B


Sent from Yahoo Mail for iPhone
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-- 
Carlo U. Segre (he/him) -- Duchossois Leadership Professor of PhysicsProfessor 
of Materials Science & EngineeringDirector, Center for Synchrotron Radiation 
Research and InstrumentationIllinois Institute of TechnologyVoice: 312.567.3498 
           Fax: 312.567.3494se...@iit.edu   http://phys.iit.edu/~segre   
se...@debian.org
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Re: [Ifeffit] [Ext] Dumb question

2023-02-16 Thread Carlo Segre 
Hi Robert:

What, exactly are you interested in plotting?  It is not quite clear from
your message.  Is it the Io as a function of time during a scan?  Is it the
XANES scans as a function of time for a reaction?

Carlo

On Thu, Feb 16, 2023 at 11:59 AM Roberta Candela  wrote:

> Hi all, I am attempting to graph a simple plot of intensity vs time for
> some supplemental info on a paper (from XAFS data from beamtime). I thought
> it should be simple enough since I can export I0 and If from Athena and I
> know the run time and time per data point but I can’t get anything that
> looks remotely like the logarithmic graph it should be. Am I missing some
> big fundamental point for why this isn’t possible? My apologies if this is
> way too vague!/I feel like I’m missing something super obvious
> Thank you for your time!
> Sincerely
> -B
>
>
> Sent from Yahoo Mail for iPhone
> 
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-- 
Carlo U. Segre (he/him) -- Duchossois Leadership Professor of Physics
Professor of Materials Science & Engineering
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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