Re: [Ifeffit] Athena: Data cannot be imported by using plugin PFBL12C

[Matt Newville]

I have to admit I find this all sort of disappointing.

First, the  PFBL12C is a really poor way to represent EXAFS data.  It uses
a hard-to-parse and hard-to-interpret format and has many unlabeled
columns.  It appears to include this really odd notion that recording
"angle" is somehow better than recording energy, and saves a
ridiculuously over-sampled spectrum that needs smoothing because of the
high noise per recorded point.   It is, in short, a really poor way to
represent EXAFS data.  We've seen it for many years, we've written papers
and published supported code for better representations of EXAFS data.
 Still, we get questions about using data recorded in such files.  Data
files this complex need a way to convert them into something useful.

Second, the limitations you are seeing are due to using the outdated,
no-longer-supported (for several years now actually) Ifeffit library.
These data can be read and processed without problem with Larch, the
replacement for Ifeffit.

Stop using Ifeffit.  Use Larch instead.  Really.

An example script to use larch for your `fail.dat` file is listed below.
It is somewhat complicated because the raw data file is such a poor
representation of EXAFS data.

--Matt

# larch script to read, smooth and process data in the horrible PFBL12C
format
# read raw data, extract angle, i0, sum of fluorescence
datafile = 'fail.dat'
rawdat = read_ascii(datafile)

def degrees2eV(angle, dspace=1.63747):
from scipy.constants import hbar, c, e
hbarc = 1.e10*hbar*c/e
return (pi*hbarc/dspace) / sin(angle*pi/180.0)
#enddef

rawdat.angle  = rawdat.data[0, :]  # angle in degrees.  yikes!
rawdat.energy = degrees2eV(rawdat.angle)
rawdat.i0 = rawdat.data[42, :]
rawdat.fluor  = rawdat.data[3:42, :].sum(axis=0)

# smooth data with Savitzky-Golay (data is ~evenly sampled in angle)
smoothed   = group(energy=rawdat.energy)
smoothed.i0= savitzky_golay(rawdat.i0,5, 1)
smoothed.fluor = savitzky_golay(rawdat.fluor, 5, 1)

newplot(smoothed.energy, rawdat.fluor, win=3)
plot(smoothed.energy, smoothed.fluor, zorder=50, linewidth=4, win=3)

### create "normal" XAFS energies, finely spaced over edge,
### but spaced evenly in k for the EXAFS

e0= 8980.0  # nominal Cu K edge
emin  = smoothed.energy.min()
emax  = smoothed.energy.max() - 5.0
epre1 = e0 - 20.0
epre2 = e0 + 20.0
kmin  = etok(20.0)
kmax  = etok(emax-e0)

def make_range(start, stop, step):
npts = max(2, 1 + int(0.1 + abs(stop-start)/abs(step)))
return linspace(start, stop, npts)
#enddef

en_new = concatenate((make_range(emin, epre1, 5),
  make_range(epre1+0.5, epre2-0.5, 0.5),
  e0 + ktoe(make_range(kmin, kmax, 0.05

# now interpolate smoothed data onto this energy grid
dat   = group(energy=en_new, filename=datafile)
dat.i0= interp(smoothed.energy, smoothed.i0,dat.energy)
dat.fluor = interp(smoothed.energy, smoothed.fluor, dat.energy)
dat.mu= dat.fluor / dat.i0

# run autobk
autobk(dat, rbkg=0.8, kweight=1)

# plot data
plot_mu(dat, show_norm=True)
plot_chik(dat, kweight=1, win=2)

###
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Re: [Ifeffit] Athena: Data cannot be imported by using plugin PFBL12C

[Robert Gordon]

Hi Yuri,

You are probably running into the memory limit. This has been discussed  
a number of times

on this mailing list, e.g.:

https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03931.html

https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg05673.html

Bruce's answer in the 2nd link provides some suggestions.

Note, if I delete 1500 rows or so from your fail file, I am able to 
import it.
This seems to be similar to the success.dat file which also appears to 
be truncated.


Using a column labelled '20' as Io seems to work


-R.

On 11/14/2017 12:59 AM, 平岡　裕治 wrote:

Dear all,

I tried to import a data of multi-element detector at SPring-8 by using
plugin PFBL12C to Athena, but it was not successful.
if the number of rows in the file is about 2000[success.dat], it can be
successfully imported. But for the data over about 4000 rows[fail.dat],
it seems that several data at first of both converted energy and
intensity are substituted by 0. column6.png shows intensity of ch6 vs
energy_attained and I0.png shows intensity of I0 vs energy_attained. you
can see this behavior. As a result, intensity cannot divide by I0, and
data cannot be imported.

if someone knows approach to solve this, could you teach me.

Best regards,
Yuji Hiraoka



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Re: [Ifeffit] current-amp recommendation

[Carlo Segre]

HI Matthew:

One possibility is the Caen quad amplifier that they made for BPMs.

http://www.caenels.com/products/tetramm/

Carlo

On Tue, 14 Nov 2017, Matthew Marcus wrote:

I've gotten involved with a project in which stabilization of the position of 
a monochromatic, soft X-ray beam is needed.  The
offending frequencies seem to be vibration frequencies like 57 and 116Hz.  We 
have in mind to use a thin Au film with a gap in the
middle, measuring the drain current from the films, much as people normally 
use the jaws of slits.  Now, I'd like to find a couple
of current amplifiers which are small enough so that they can be connected 
with very short cables to the BNC connectors on the
air-side of this detector, and which would have decent frequency response and 
low noise with inputs of the order of 0.1-1nA.
Although this topic is outside the realm of XAFS analysis with IFEFFIT, I 
figure that people on this group might have some

good experience.

mam
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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] current-amp recommendation

[Bruce Ravel]

Hi Matthew,

At NSLS-II, we use a solution developed here at BNL for quad BPMs and 
other current-measurement operations.  (I am using it for ion chambers 
at my beam line.)


It is a box developed in the Instrumentation Division with a current 
amplifier, an A2D converter, and a microprocessor all inside a box 
that's about the size of a box of Pop Tarts.  It has 4 SMA input 
channels and a single gain for all four channels.  SMA to BNC cables are 
readily available from all the standard vendors.  The output is an 
ethernet cable.  The microprocessor runs a small debian system and 
starts an EPICS IOC and a DHCP client on boot.  the 4 current get 
exposed as 4 PVs and the IOC does a lot of useful statistics on the fly.


Seems to work pretty well.

You could contact Pete Siddons.  (Search for Siddons at the BNL website. 
 When I tried it, the second hit was his staff page.)


B

On 11/14/2017 03:16 PM, Matthew Marcus wrote:
I've gotten involved with a project in which stabilization of the 
position of a monochromatic, soft X-ray beam is needed.  The
offending frequencies seem to be vibration frequencies like 57 and 
116Hz.  We have in mind to use a thin Au film with a gap in the
middle, measuring the drain current from the films, much as people 
normally use the jaws of slits.  Now, I'd like to find a couple
of current amplifiers which are small enough so that they can be 
connected with very short cables to the BNC connectors on the
air-side of this detector, and which would have decent frequency 
response and low noise with inputs of the order of 0.1-1nA.
Although this topic is outside the realm of XAFS analysis with IFEFFIT, 
I figure that people on this group might have some

good experience.

 mam
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--
 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/
 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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[Ifeffit] current-amp recommendation

[Matthew Marcus]

I've gotten involved with a project in which stabilization of the position of a 
monochromatic, soft X-ray beam is needed.  The
offending frequencies seem to be vibration frequencies like 57 and 116Hz.  We 
have in mind to use a thin Au film with a gap in the
middle, measuring the drain current from the films, much as people normally use 
the jaws of slits.  Now, I'd like to find a couple
of current amplifiers which are small enough so that they can be connected with 
very short cables to the BNC connectors on the
air-side of this detector, and which would have decent frequency response and 
low noise with inputs of the order of 0.1-1nA.
Although this topic is outside the realm of XAFS analysis with IFEFFIT, I 
figure that people on this group might have some
good experience.

mam
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Re: [Ifeffit] Consult a few questions about XAS data analysis

[fred.mosselmans]

Hi Jun,

Two points so Bruce doesn't get two upset. If you included the Athena project 
you used for the lcf and maybe an excel file of the results you got, then 
someone could
Check what you did, as it is there is almost no way to offer an opinion on that.

Bruce gave a course at Dimaond several years ago now, but most of what he shows 
is relatively as true as it was the day he said it. The videos can be found 
here.
http://www.diamond.ac.uk/Beamlines/Spectroscopy/Techniques/XAS.html

The VLC media player works well with them.

Regards
Fred



J.F.W. Mosselmans
Principal Beamline Scientist I18
Diamond Light Source Ltd
Diamond House
Harwell Campus
Didcot
OX11 0DE

P + 44 1235 778568
M + 44 7785510211
E fred.mosselm...@diamond.ac.uk
orcid.org/-0001-6473-2743

[cid:image002.png@01D27563.28EDA240]


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Re: [Ifeffit] Consult a few questions about XAS data analysis

[desmau]

Le 14.11.2017 15:32, Zhang, Guanghui a écrit :

Jun,
You can find many of Bruce's presentations on XAS through this link.
http://bruceravel.github.io/XAS-Education/ [1]

Bruce also wrote a very nice Artemis user's guide. I would suggest
you to take a look.
https://bruceravel.github.io/demeter/documents/Artemis/index.html [2]


Good luck!

--

Regards,
Guanghui

At 2017-11-14 14:21:38, "Jun Ge"  wrote:


Hi Bruce

I'm a learner for XAS data analysis because of the need of
scientific research.

I have been to SLAC in San Francisco three times last year and
collected some XAS data of samples and models in Beamline 7-3. This
summer, I began to learn how to analyze these XAS data.

My professor used to use WinXAS to analyze data. But this time he
asked me to learn Athena. He thinks use two different softwares can
double check the result.

After the data pro-processing, including background remove and data
normalization, etc., I save each spectrum in the form .txt.

However,

IN THE SAME ENERGY RANGE AND SAME FILE OF SAMPLE AND MODELS, THE
RESULT OF LCF PERFORMED BY WINXAS AND ATHENA WAS TOTALLY DIFFERENT!
I try to solve this problem for a long time but no progress was
made. So I turn to you and Ressler (the author of WinXAS) for help.
I guess may be the algorithm is different between your Athena with
WinXAS, but I'm not sure. With great experience in XAS data
analysis, I think it's easy for you to solve this problem, isn't

it?


By the way, I DON'T KNOW HOW TO FIT THE COORDINATION NUMBER IN
ANOTHER SOFTWARE CALLED ARTEMIS in the software package of Demeter.
I was told by Artemis that the coordination number can only be a
number not alphabet. So I have no idea how to do this (yeah, I'm
really a noob orz). And I don't know how to set the parameter more
correctly to run a excellent Feff fit. So could you please help me?




Finally, I WANT TO LEARN XAS DATA ANALYSIS SYSTEMATICALLY. SO COULD
YOU PLEASE RECOMMEND ME SOME REFERENCES LIKE BOOKS OR PAPERS?

Anyway, thanks a lot for your help and your precious time!

Sincerely,
Jun Ge



Links:
--
[1] http://bruceravel.github.io/XAS-Education/
[2] https://bruceravel.github.io/demeter/documents/Artemis/index.html


--
Morgane DESMAU

Doctorant/PhD student
Institut de Physique du Globe de Paris
Équipe de Géochimie des Eaux
1, rue Jussieu - 75238 Paris cedex 05

Mail: des...@ipgp.fr
Phone: +33 1 83 95 77 33
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Re: [Ifeffit] Consult a few questions about XAS data analysis

[Zhang, Guanghui]

Jun,
You can find many of Bruce's presentations on XAS through this link.
http://bruceravel.github.io/XAS-Education/


Bruce also wrote a very nice Artemis user's guide. I would suggest you to take 
a look.
https://bruceravel.github.io/demeter/documents/Artemis/index.html




Good luck!


--

Regards,
Guanghui






 

At 2017-11-14 14:21:38, "Jun Ge"  wrote:

Hi Bruce


I'm a learner for XAS data analysis because of the need of scientific research.


I have been to SLAC in San Francisco three times last year and collected some 
XAS data of samples and models in Beamline 7-3. This summer, I  began to learn 
how to analyze these XAS data. 


My professor used to use WinXAS to analyze data. But this time he asked me to 
learn Athena.  He thinks use two different softwares can double check the 
result.


After the data  pro-processing, including background  remove and data 
normalization, etc., I save each spectrum in the form .txt.  However, in the 
same energy range and same file of sample and models, the result  of LCF 
performed by WinXAS and Athena was totally different! I try to solve this 
problem for a long time but no progress was made. So I turn to you and Ressler 
(the author of WinXAS) for help. I guess may be the algorithm is different 
between your Athena with WinXAS, but I'm not sure. With great experience in XAS 
data analysis, I think it's easy for you to solve this problem, isn't it?


By the way, I don't know how to fit the Coordination Number in another software 
called Artemis in the software package of Demeter.  I was told by Artemis that 
the coordination number can only be a number not alphabet. So I have no idea 
how to do this (yeah, I'm really a noob orz). And I don't know how to set the 
parameter more correctly to run a excellent Feff fit.  So could you please help 
me? 


Finally, I want to learn XAS data analysis systematically. So could you please 
recommend me some references like books or papers?


Anyway, thanks a lot for your help and your precious time!




Sincerely,
Jun Ge___
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