Re: [Ifeffit] Bug Report importing file.

2016-07-25 Thread Bruce Ravel 

On 07/24/2016 03:55 AM, Samy Ould-Chikh wrote:

I have some issue to import a file in Athena: just a simple x-y column (.txt 
attached with this email).

Ti K-edge.
Data range in the file  : 4916.30 up to 5436.88 eV.
Issue: only data up to 5260 eV are imported (see screenshot: bug-importation).

Version: Demeter 0.9.24
System: Windows 7 Professional SP1

Well, I hope it's just not me not being able to find a proper way to import the 
file...


I have a hard time imagining the need for an XAFS scan with 12000 data 
points.  That will usually provides a point density that about an order 
of magnitude below the core-hole lifetime, maybe 2.  In your case, it 
corresponds to about 0.04 eV steps, which seems silly to me.  While I'm 
quite open to being convinced otherwise, I cannot believe that setting 
up a scan this way is actually necessary.


But, more to the point, I think it is very unprofessional of the 
beamline staff to send you home with data in a format that is so hard to 
use.


Athena does a pretty good job of importing data in all the crazy-ass 
formats that beamlines around the world use.  But it's not really fair 
to expect that she can handle anything you can throw at her.  If a 
beamline presents data in a format that is not easy to interpret, it 
should provide tools for converting the data to a format that can 
reasonably be interpreted.


In your case, the beamline should provide you with a way to rebin the 
data either onto a more coarse grid or onto something like a 
"conventional" EXAFS grid.


So ... what I recommend, if you want to use Athena (*), is that you find 
some way to rebin your data onto a grid that fits within the 8192 limit. 
 Athena's rebinning tool uses a simple box car average -- that would 
suit your data just fine.


If you don't know what a box car average is, a google search for "box 
car average excel", "box car average matlab", "box car average python", 
etc... should provide a hint.  Once you do that, Athena should behave 
without surprises.


B

(*) Or use Athena with Larch.  Larch does not have the 8192 limit.  But 
you should still process the data onto a sensible grid.


B


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

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Building 743, Room 114
 Upton NY, 11973

 Homepage:http://bruceravel.github.io/home/
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
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Re: [Ifeffit] Bug Report importing file.

2016-07-24 Thread Robert Gordon 

According to
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2013-August/006762.html
limit is 8192

It is possible to rebin the data in Athena...in multiple steps...what it 
first imports, then export, then
attach the missing higher E data, re-import, rebin...using a near edge 
step size of 0.2 eV, 0.05 invAng
in the EXAFS and 2 eV in the pre-edge, these two steps were sufficient 
to reduce the data size to 555 points.


The match between original and rebin does show some small differences 
but I didn't deglitch first.




I don't like the steps in the original mu(E) either - rounding off too soon,
or is it there at this level in the raw data?
...discrete noise/quantization error at the 1:800 level versus 
'traditional exafs' 10^6 counts (1:1000)


On 7/24/2016 1:15 AM, Samy Ould-Chikh wrote:

Just a quick idea on why I cannot import the .txt file attached with previous 
email.

I realized that the files contain 11948 points ! (it's QEXAFS data).
Athena might have an hard limit of 8200 points that may be imported in a single 
file.


Best Regards,
Samy Ould-Chikh

KAUST Catalysis Center
Bldg.3,Level 4, #4231
4700 King Abdullah University of Science & Technology
Thuwal 23955-6900
Kingdom of Saudi Arabia

Tel: +966 12 8084486
E-mail: samy.ouldch...@kaust.edu.sa
Website:  http://kcc.kaust.edu.sa/Pages/Home.aspx





-Original Message-
From: Samy Ould-Chikh
Sent: Sunday, July 24, 2016 10:56 AM
To: XAFS Analysis using Ifeffit 
Subject: Bug Report importing file.

Hello,

I have some issue to import a file in Athena: just a simple x-y column (.txt 
attached with this email).

Ti K-edge.
Data range in the file  : 4916.30 up to 5436.88 eV.
Issue: only data up to 5260 eV are imported (see screenshot: bug-importation).

Version: Demeter 0.9.24
System: Windows 7 Professional SP1

Well, I hope it's just not me not being able to find a proper way to import the 
file...


Best Regards,
Samy Ould-Chikh

KAUST Catalysis Center
Bldg.3,Level 4, #4231
4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom 
of Saudi Arabia

Tel: +966 12 8084486
E-mail: samy.ouldch...@kaust.edu.sa
Website:  http://kcc.kaust.edu.sa/Pages/Home.aspx





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original recipient. If you are not the intended recipient or have received this 
message in error, please notify me immediately and delete this message from 
your computer system. Any unauthorized use or distribution is prohibited. 
Please consider the environment before printing this email.

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Re: [Ifeffit] Bug Report importing file.

2016-07-24 Thread Samy Ould-Chikh 
Just a quick idea on why I cannot import the .txt file attached with previous 
email.

I realized that the files contain 11948 points ! (it's QEXAFS data).
Athena might have an hard limit of 8200 points that may be imported in a single 
file.


Best Regards,
Samy Ould-Chikh

KAUST Catalysis Center
Bldg.3,Level 4, #4231
4700 King Abdullah University of Science & Technology
Thuwal 23955-6900
Kingdom of Saudi Arabia

Tel: +966 12 8084486
E-mail: samy.ouldch...@kaust.edu.sa
Website:  http://kcc.kaust.edu.sa/Pages/Home.aspx





-Original Message-
From: Samy Ould-Chikh
Sent: Sunday, July 24, 2016 10:56 AM
To: XAFS Analysis using Ifeffit 
Subject: Bug Report importing file.

Hello,

I have some issue to import a file in Athena: just a simple x-y column (.txt 
attached with this email).

Ti K-edge.
Data range in the file  : 4916.30 up to 5436.88 eV.
Issue: only data up to 5260 eV are imported (see screenshot: bug-importation).

Version: Demeter 0.9.24
System: Windows 7 Professional SP1

Well, I hope it's just not me not being able to find a proper way to import the 
file...


Best Regards,
Samy Ould-Chikh

KAUST Catalysis Center
Bldg.3,Level 4, #4231
4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom 
of Saudi Arabia

Tel: +966 12 8084486
E-mail: samy.ouldch...@kaust.edu.sa
Website:  http://kcc.kaust.edu.sa/Pages/Home.aspx





This message and its contents including attachments are intended solely for the 
original recipient. If you are not the intended recipient or have received this 
message in error, please notify me immediately and delete this message from 
your computer system. Any unauthorized use or distribution is prohibited. 
Please consider the environment before printing this email.

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