[Ifeffit] Re: Ifeffit Digest, Vol 5, Issue 1
Carlo U. Segre
segre at iit.edu
Thu Jul 3 15:05:00 CDT 2003
I totally agree. This can lead to big problems in the data. We
accidentally tried it once and then made sure that the <If/Io> average was
performed instead.
Carlo
On Thu, 3 Jul 2003, Grant Bunker wrote:
> I would second Matt's reservations about averaging I0 for different XAFS
> scans. The main reason we record I0 is to compensate for fluctuations in
> I0, which are mirrored in If (statistically they are highly correlated)
> so the ratio If/I0 eliminates the variation (as long as the detector chain
> is linear).
>
> In short <If/I0> is not equal to <If>/<I0> where < > indicates the
> average.
>
> thanks - grant
>
> On Thu, 3 Jul 2003 ifeffit-request at millenia.cars.aps.anl.gov wrote:
>
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> > Today's Topics:
> >
> > 1. Re: your mail (Matt Newville)
> > 2. merging I0 (Bruce Ravel)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Wed, 2 Jul 2003 16:20:47 -0500 (CDT)
> > From: Matt Newville <newville at cars.uchicago.edu>
> > Subject: [Ifeffit] Re: your mail
> > To: jshokes at sunchem.chem.uga.edu
> > Cc: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> > Message-ID:
> > <Pine.LNX.4.44.0307021605120.12464-100000 at millenia.cars.aps.anl.gov>
> > Content-Type: TEXT/PLAIN; charset=US-ASCII
> >
> > Hi Jacob,
> >
> > Jacob Shokes (jshokes at chem.uga.edu) wrote:
> >
> > > I had a question I was hoping you could help me with. I have imported a
> > > bunch of ASCII type files into Athena and averaged them all together. The
> > > ASCII files contain the Energy, detector file, I0, I1, and I2. After I
> > > average the files together, I want to save the file and export it as an
> > > ASCII file. I understand how to do this, but when I do it I only obtain
> > > the Energy, [detector/IO], and background in column three (like it states
> > > in the manual). Now what I want to do, is extract the averaged I0 column
> > > from the process. Is there anyway to do this or will I just have to
> > > average I0 in another software. Any help with this would be appreciated.
> >
> > Sorry for the delay - I was away at the EXAFS conference, and am
> > still catching up on email. I hope it's OK that I forward this
> > question to the ifeffit mailing list, as others might have similar
> > questions, and Bruce Ravel might have a better answer.
> >
> > I believe you'd have to average all the I0 values yourself, and that
> > athena cannot do this easily. Bruce might correct me on this....
> > It would be possible to do this using the Ifeffit commands directly
> > (including in the athena command window), something like this:
> >
> > read_data(mydat.001, group=a001, label='energy if i0')
> > read_data(mydat.002, group=a002, label='energy if i0')
> > read_data(mydat.003, group=a003, label='energy if i0')
> > ave.energy = (a001.energy + a002.energy + a003.energy ) / 3
> > ave.if = (a001.if + a002.if + a003.if ) / 3
> > ave.i0 = (a001.i0 + a002.i0 + a003.i0 ) / 3
> > write_data(file= ave.dat, ave.energy, ave.if, ave.i0)
> >
> > In most cases I don't think you really want to do this, or use an
> > averaged I0 signal. For EXAFS data in transmission or fluorescence
> > (or electron yield), log(I0/I1) or IF/I0 can be averaged and merged,
> > but averaging I0 may not be meaningful. On the other hand, you might
> > be looking for typical I0 count rates, and the variations in I0, in
> > which case such averages might be useful.
> >
> > Hope that helps,
> >
> > --Matt
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Wed, 2 Jul 2003 17:55:43 -0400
> > From: Bruce Ravel <ravel at phys.washington.edu>
> > Subject: [Ifeffit] merging I0
> > To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> > Cc: jshokes at sunchem.chem.uga.edu
> > Message-ID: <200307021755.43883.ravel at phys.washington.edu>
> > Content-Type: text/plain; charset="us-ascii"
> >
> >
> > Hi folks,
> >
> > As Matt suggested, I will take a stab at this question.
> >
> > > > I had a question I was hoping you could help me with. I have imported a
> > > > bunch of ASCII type files into Athena and averaged them all together. The
> > > > ASCII files contain the Energy, detector file, I0, I1, and I2. After I
> > > > average the files together, I want to save the file and export it as an
> > > > ASCII file. I understand how to do this, but when I do it I only obtain
> > > > the Energy, [detector/IO], and background in column three (like it states
> > > > in the manual). Now what I want to do, is extract the averaged I0 column
> > > > from the process. Is there anyway to do this or will I just have to
> > > > average I0 in another software. Any help with this would be appreciated.
> >
> > > I believe you'd have to average all the I0 values yourself, and that
> > > athena cannot do this easily. Bruce might correct me on this....
> > > It would be possible to do this using the Ifeffit commands directly
> > > (including in the athena command window), something like this:
> >
> > Matt's suggeted sequence of raw ifeffit commands is certainly a fine
> > way of doing what Jacob asked for. Averaging I0 alone is not
> > something I had in mind when I designed Athena's basic interface
> > features, but it should be possible.
> >
> > As is the case when one tries to explain a sequence of mouse clicks,
> > this will be rather wordy. Sorry....
> >
> > As all Athena users know, the first thing that happens when you import
> > a data file is to interact with the file selection dialog:
> >
> > http://leonardo.phys.washington.edu/~ravel/software/exafs/images/athena/columns.png
> > Athena remembers which columns were used to make the numerator and
> > denominator of the expression that constructs mu(E) from the column
> > data. (Note that the ability to make detector groups is lost once the
> > data are saved to a project file. Making detector groups is something
> > that must be done during the session in which the raw data are
> > imported.)
> >
> > In the Group menu is a option for "Make detector groups". This will
> > make entries in the Data groups list for the numerator and denominator
> > used to make the original data group.
> >
> > So my solution to Jacob's problem was to import data files one-by-one.
> > Each time, I made the detector groups. Once all the data was imported
> > and the detector groups were made, I marked the denominator groups (my
> > test data were all transmission, so I0 was in the denominator). Then,
> > in principle, one could select "Merge marked data in mu(E)" from the
> > Merge menu and have the merged I0 data that Jacob was looking for.
> >
> > *In principle*. In fact, there is a bug in the current version of
> > Athena and the merge of the I0 data failed. That bug will, however,
> > be fixed soon. Once that is done, it will be possible, albeit
> > inconvenient, to merge I0 data as Jacob wants. You may wish to try
> > working through the procedure that I described to understand how the
> > detector group feature of Athena works, even if the final step will
> > fail in the current version.
> >
> > B
> >
> > P.S. I am pretty certain that this will be fixed in time for the next
> > release of Athena and that the next release will be before Friday the
> > 11th.
> >
> >
> > --
> > Bruce Ravel ----------------------------------- ravel at phys.washington.edu
> > Code 6134, Building 3, Room 222
> > Naval Research Laboratory phone: (1) 202 767 5947
> > Washington DC 20375, USA fax: (1) 202 767 1697
> >
> > NRL Synchrotron Radiation Consortium (NRL-SRC)
> > Beamlines X11a, X11b, X23b, X24c, U4b
> > National Synchrotron Light Source
> > Brookhaven National Laboratory, Upton, NY 11973
> >
> > My homepage: http://feff.phys.washington.edu/~ravel
> > EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
> >
> >
> > ------------------------------
> >
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> > End of Ifeffit Digest, Vol 5, Issue 1
> > *************************************
> >
>
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--
Carlo U. Segre -- Professor of Physics
Associate Dean for Special Projects, Graduate College
Illinois Institute of Technology
Voice: 312.567.3498 Fax: 312.567.3494
segre at agni.phys.iit.edu http://www.iit.edu/~segre
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