Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 12

9 Sep 2008

      Hi,
AFIK, in Athena it is not possible - you can do it quickly in other
programs, like excel, origin etc... and save/export it in the same
format you have in file
in Athena you can only choose E0
cheers
kicaj
...
-----Original Message-----
From: ifeffit-bounces@millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf
Of Khalid, Syed
Sent: Tuesday, September 09, 2008 4:08 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 12
That is correct: It is a QEXAFS scan of Ni foil as a
function of time.
Please see the data attached as a .txt file.
The first column is time, second I0, and third It.
I can plot this in Athena, time appears at energy axis.
I can set the first derivative to 8333.0 eV ( changing X-axis
from time to energy ). If I have another known energy point of
Ni scan ( which is not a problem ) then I can convert the time
axis to correct energy axis and proceed with normal analysis.
Is that possible?
-----Original Message-----
From: ifeffit-bounces@millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of
ifeffit-request@millenia.cars.aps.anl.gov
Sent: Tuesday, September 09, 2008 9:23 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Ifeffit Digest, Vol 67, Issue 12
Send Ifeffit mailing list submissions to
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Today's Topics:
1. Re: ODP:  enrgy-axis-expansion (Bruce Ravel)
  2. Re: ODP: enrgy-axis-expansion (Matt Newville)
  3. Re: Bugs in Athena under Windows (Matt Newville)
  4. Noise level in XANES spectrum (Pushan Shah)
  5. Re: ODP:  enrgy-axis-expansion (Zajac, Dariusz)
  6. Re: Noise level in XANES spectrum (Zajac, Dariusz)
  7. Re: Ifeffit Digest, Vol 67, Issue 11 (Khalid, Syed)
----------------------------------------------------------------------
Message: 1
Date: Mon, 8 Sep 2008 16:59:08 -0400
From: Bruce Ravel 
Subject: Re: [Ifeffit] ODP:  enrgy-axis-expansion
To: "XAFS Analysis using Ifeffit" 
Message-ID: <200809081659.08948.bravel@bnl.gov>
Content-Type: text/plain;  charset="utf-8"
On Monday 08 September 2008 16:40:47 Zajac, Dariusz wrote:
...
I do not clearly understood what you mean. could you explain it more
precisely? do you want to replace the x scale from energy to
time? if
you want only set the edge energy use E0
Apparently (and Khalid or Anatoly should correct me if I am
wrong), they are collecting data as a function of time in
quick scan mode.  They then have the problem of converting
time to energy.  If the mono speed is recorded somehow
incorrectly, then there is an accordian effect throughout the
data. I think that Khalid wants to be able to adjust this
accordian effect to correct the energy scale of teh data.
B
--
Bruce Ravel  ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A,
X23A2  Building 535A  Upton NY, 11973
My homepage:    http://xafs.org/BruceRavel
EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
------------------------------
Message: 2
Date: Mon, 8 Sep 2008 16:18:55 -0500
From: "Matt Newville" 
Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion
To: "XAFS Analysis using Ifeffit" 
Message-ID:

Content-Type: text/plain; charset=ISO-8859-1
Hi Khalid,
I agree with Dariusz: I do not understand the question.  I
have a hard time believing it is "the beamline cannot provide
data as a function of energy, can Athena do this for me
automatically?" (if it is, the
answer is definitely 'No!').    Could you explain what you're trying
to do?
--Matt
------------------------------
Message: 3
Date: Mon, 8 Sep 2008 16:24:45 -0500
From: "Matt Newville" 
Subject: Re: [Ifeffit] Bugs in Athena under Windows
To: "XAFS Analysis using Ifeffit" 
Message-ID:

Content-Type: text/plain; charset=ISO-8859-1
Timna,
Posting a project would definitely help here, as would clarify
"since the last two versions ..." to say explicitly which
versions do and do not work.  My suspicion is that this
related to the bug noted last week (and possibly another
recent vague report of "not working") that is due to the
latest version of athena -for-windows being hard-linked to
pre-final-release of the ifeffit dll which is making athena's
ifeffit session get stuck in an unresponsive state.
I believe the only cure is a new version of athena.  Again, if
you could post a project that demonstrates the problem, that
would be most helpful.
--Matt
------------------------------
Message: 4
Date: Tue, 09 Sep 2008 15:48:51 +1000
From: "Pushan Shah" 
Subject: [Ifeffit] Noise level in XANES spectrum
To: 
Message-ID: <48C69AE2.0BBD.0060.0@gse.mq.edu.au>
Content-Type: text/plain; charset=US-ASCII
Hello Everyone,
I have a general question regarding noise level of XANES
spectrum. I have collected XANES data for an element which is
present in ppm level in my samples.
Some samples are exhibiting varying degree of noise in XANES
spectrum.
Is the noise level of XANES spectrum would be proportional or
consistent with the concentration of the sample? As XANES
spectra for some of my samples with relatively higher
concentration of this element are exhibiting greater level of
noise than those with relatively lower concentrations.   Will
sample matrix play any role in the noise level?
Thanks and I appreciate your help.
regards,
Pushan
------------------------------
Message: 5
Date: Tue, 9 Sep 2008 10:03:46 +0200
From: "Zajac, Dariusz" 
Subject: Re: [Ifeffit] ODP:  enrgy-axis-expansion
To: "Bruce Ravel" ,	"XAFS Analysis using Ifeffit"

Message-ID: <35E004AD6290A7438FCA34BBF325F4161148AA@ADXV2.win.desy.de>
Content-Type: text/plain;	charset="us-ascii"
hi
so, I think, in case of converting time scale to energy - this
should be supported by beamline (beamline scientist)
somehow... if there is any nonlinearity of the converion
factor (Anatoly  - what whould happened if D parameter is
time/energy dependent?) I think only reference spectra can
help -  do you have it Syed? if you have all needed parameters
the calibration can be relatively quickly done in some other
programs, also in macro (for many files) but that's my
speculations kicaj
...
-----Original Message-----
From: ifeffit-bounces@millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf
Of Bruce Ravel
Sent: Monday, September 08, 2008 10:59 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion
On Monday 08 September 2008 16:40:47 Zajac, Dariusz wrote:
...
I do not clearly understood what you mean. could you explain it more
precisely? do you want to replace the x scale from energy to
time? if
you want only set the edge energy use E0
Apparently (and Khalid or Anatoly should correct me if I am
wrong), they are collecting data as a function of time in
quick scan mode.  They then have the problem of converting
time to energy.  If the mono speed is recorded somehow
incorrectly, then there is an accordian effect throughout the
data. I think that Khalid wants to be able to adjust this
accordian effect to correct the energy scale of teh data.
B
--
Bruce Ravel  ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A,
X23A2  Building 535A  Upton NY, 11973
My homepage:    http://xafs.org/BruceRavel
EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
------------------------------
Message: 6
Date: Tue, 9 Sep 2008 10:12:42 +0200
From: "Zajac, Dariusz" 
Subject: Re: [Ifeffit] Noise level in XANES spectrum
To: "XAFS Analysis using Ifeffit" 
Message-ID: <35E004AD6290A7438FCA34BBF325F4161148AB@ADXV2.win.desy.de>
Content-Type: text/plain;	charset="us-ascii"
Hi Pushan,
can you tell more about the experiment and the way of data collecting?
how did you measure your samples? which method did you use?
what kind of
samples do you have?
the answer of your question is not stricted, but generaly I would say
that the noise level should be independent of the samples, did you
change something on the beamline or program between
samples/measurements? e.g. sample time, no. of repeats, you moved in
/out detector, amplification gain, etc....
kicaj
...
-----Original Message-----
From: ifeffit-bounces@millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf
Of Pushan Shah
Sent: Tuesday, September 09, 2008 7:49 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Noise level in XANES spectrum
Hello Everyone,
I have a general question regarding noise level of XANES
spectrum. I have collected XANES data for an element which is
present in ppm level in my samples.
Some samples are exhibiting varying degree of noise in XANES
spectrum.
Is the noise level of XANES spectrum would be proportional or
consistent with the concentration of the sample? As XANES
spectra for some of my samples with relatively higher
concentration of this element are exhibiting greater level of
noise than those with relatively lower concentrations.   Will
sample matrix play any role in the noise level?
Thanks and I appreciate your help.
regards,
Pushan
_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
------------------------------
Message: 7
Date: Tue, 9 Sep 2008 09:22:14 -0400
From: "Khalid, Syed" 
Subject: Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 11
To: 
Message-ID:
  <55C249AA18FE564E86564FEB2412D45BEFD18B@exchangemb1.bnl.gov>
Content-Type: text/plain;	charset="iso-8859-1"
Anatoly: I will try your approach:
Same problem I can address in a different way.
Suppose the energy is not linear in case of a Pt-L3 scan.
We can set Pt-L3 edge at known 11564 eV. Scanning all the way to
L2 edge and say we find it 200 eV off (exaggerating), can we set
in Athena the L2 edge at known 13273 eV, while the L3 edge is still
at 11564 eV?
-----Original Message-----
From: ifeffit-bounces@millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of
ifeffit-request@millenia.cars.aps.anl.gov
Sent: Monday, September 08, 2008 4:44 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Ifeffit Digest, Vol 67, Issue 11
Send Ifeffit mailing list submissions to
  ifeffit@millenia.cars.aps.anl.gov
To subscribe or unsubscribe via the World Wide Web, visit
  http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
or, via email, send a message with subject or body 'help' to
  ifeffit-request@millenia.cars.aps.anl.gov
You can reach the person managing the list at
  ifeffit-owner@millenia.cars.aps.anl.gov
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Ifeffit digest..."
Today's Topics:
1. FW: enrgy-axis-expansion (Khalid, Syed)
  2. Re: enrgy-axis-expansion (Bruce Ravel)
  3. Re: enrgy-axis-expansion (Anatoly Frenkel)
  4. Re: enrgy-axis-expansion (Bruce Ravel)
  5. ODP:  enrgy-axis-expansion (Zajac, Dariusz)
----------------------------------------------------------------------
Message: 1
Date: Mon, 8 Sep 2008 13:46:47 -0400
From: "Khalid, Syed" 
Subject: [Ifeffit] FW: enrgy-axis-expansion
To: 
Message-ID:
  <55C249AA18FE564E86564FEB2412D45BEFD187@exchangemb1.bnl.gov>
Content-Type: text/plain;	charset="iso-8859-1"
-----Original Message-----
From: Khalid, Syed
Sent: Monday, September 08, 2008 12:21 PM
To: 'ifeffit@millenia.cars.aps.anl.gov'
Subject: enrgy-axis-expansion
It is X-axis, sorry my typo. How to expand or shrink
in an EXAFS spectrum, using Athena.
Syed Khalid
725D, National Synchrotron Light Source
Brookhaven National Laboratory
Upton, NY 11973
Ph: 631-344-7496
FAX: 631-344-3238
e-mail: khalid@bnl.gov
------------------------------
Message: 2
Date: Mon, 8 Sep 2008 13:51:12 -0400
From: Bruce Ravel 
Subject: Re: [Ifeffit] enrgy-axis-expansion
To: XAFS Analysis using Ifeffit 
Message-ID: <200809081351.12614.bravel@bnl.gov>
Content-Type: text/plain;  charset="iso-8859-1"
On Monday 08 September 2008 12:20:47 Khalid, Syed wrote:
...
Is it possible in Athena to change the y-axis (energy
scale) at two different energy points of an EXAFS scan?
I have a Ni foil spectrum as a function of time.
The edge can be set at 8333.0 eV, and I want to
to assign higher energy to a known feature in the Ni scan.
I am not 100% certain I understand the question, but I think the
question is about the calibration dialog.  That is, you want to assign
an energy shift, but not referenced to the edge energy position.
Why can't you just set the energy shift by hand on Athena's main page?
B
--
Bruce Ravel  ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY, 11973
My homepage:    http://xafs.org/BruceRavel
EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
------------------------------
Message: 3
Date: Mon, 8 Sep 2008 13:59:42 -0400
From: "Anatoly Frenkel" 
Subject: Re: [Ifeffit] enrgy-axis-expansion
To: "'XAFS Analysis using Ifeffit'"

Message-ID: <20080908175744.9B7E429C12@fe6.prod.mis.yu.edu>
Content-Type: text/plain; charset="us-ascii"
Khalid, what you can do is to note how much the higher energy
(at energy E1)
feature is shifted from what you think it should be (let's say
by the amount
of D eV), provided that you fixed the lower energy point to
what you wanted
(say, E0). Then, you should transfer the data into a
spreadsheet and apply
linear scaling:
E --> E0 + (E-E0)*D
It will ensure that in the range between E0 and E1 the data
are linearly
stretched or compressed, depending on the sign of D.
Anatoly
=
_____
From: Khalid, Syed [mailto:khalid@bnl.gov]
Sent: Monday, September 08, 2008 12:21 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] enrgy-axis-expansion
Is it possible in Athena to change the y-axis (energy
scale) at two different energy points of an EXAFS scan?
I have a Ni foil spectrum as a function of time.
The edge can be set at 8333.0 eV, and I want to
to assign higher energy to a known feature in the Ni scan.
Syed Khalid
725D, National Synchrotron Light Source
Brookhaven National Laboratory
Upton, NY 11973
Ph: 631-344-7496
FAX: 631-344-3238
e-mail: khalid@bnl.gov
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Ifeffit mailing list
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