[Ifeffit] Re: Ifeffit Digest, Vol 5, Issue 1

Thu Jul 3 14:25:13 CDT 2003

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:
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>    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
> *************************************
>