[Ifeffit] Importing Multiple Data Sets into Athena

[John Hayes]

Hi Bruce,

Thank you for your reply. I find your lack of faith...disturbing, but
understand your concerns about the data I sent as they were just test files
we collected when we were setting up the beam. However, I do not think the
abridged range is the cause of the problem, as I wasl having issues
importing real data as well (i.e. -150 eV pre-edge and k=12 post edge).
These spectra files are attached, along with the error log file and the
dathena.log file that was recorded when importing these files.

Thanks for your time!

John


On Wed, Feb 20, 2013 at 8:27 AM, Bruce Ravel <bravel at bnl.gov> wrote:

>
> John,
>
> I think the problem is different from what you presume.
>
> You have measured a *very* short data range.  The archive post you
> cite is not really relevant.  This one is:
>
>
> http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03717.html
>
> There are two issues that need addressing given the data you provided.
>
> Issue #1: As I explain in that mailing list posting, you are doing
>   yourself no favors measuring data in a range from -40 to +70 or so.
>   Such data are almost impossible to normalize consistently and
>   defensibly.
>
> Issue #2: Your data point out some shortcomings in Athena.  Athena
>   should deal more gracefully when given ridiculous input like your
>   much-too-short data files.  Here is a short list of things that
>   Athena is doing wrongly:
>
>     1. The default values for the pre-edge line are both allowed to be
>        outside the data range.  This is actually the primary cause of
>        your problems.  Because both pre-edge parameters are before the
>        beginning of the data, the determination of the pre-edge line
>        fails.  Trying to plot the pre-edge line or normalized data,
>        then also fails.  This problem is exacerbated by the fact that
>        you are measuing Mo.  For such a heavy element, the default
>        value for the upper bound of the pre-edge region is -45.  Your
>        data begin at about -38.
>
>     2. As long as the data are flagged as being XANES data (something
>        Athena does to avoid wasting time attempting to find a
>        background function for very short data range), it is not
>        possible to recover from problem 1.  I had to change the data
>        type [1] to mu(E) in order to correctly compute the pre-edge
>        line.
>
>     3. Athena provides no feedback that the source of the problem is
>        extremely short data range and poor choice of pre- and/or
>        post-edge line parameters.  Athena should do some sanity
>        checking and complain about the potential problem.
>
> I will attempt to address the problems Athena has with data like this
> for the next release.
>
> You should reconsider your measurement strategy the next time you go
> to the synchrotron.
>
> B
>
>
> [1]
>
> http://bruceravel.github.com/demeter/aug/ui/glist.html#informationaboutitemsinthegrouplist
>
>
>
>
>
>
> On Tuesday, February 19, 2013 03:33:26 PM John Hayes wrote:
> > Hello,
> >
> > I am having some issues when importing multiple data sets into Athena.
> When
> > I try to import more than one file at a time only the reference sample
> data
> > from the first file are imported and the subsequent files do not import
> the
> > reference data (only a straight line is imported). There is an error that
> > is reported, and I have saved the error log [log.txt] and attached it in
> > the zip file (as well as the dathena.log file and some sample spectra
> > files). The spectra files are of the Mo K-edge and the reference is an Mo
> > foil. These spectra were collected using the HXMA beamline, and as such,
> I
> > am using the HXMA plug-in to import the data. The relevant columns for
> the
> > reference are:
> >
> > col 2: energy
> > col 6: I1
> > col 7: I2
> >
> > I searched the archive and found what I think is a similar issue (link:
> > www.mail-archive.com/ifeffit at millenia.cars.aps.anl.gov/msg03454.html),
> and
> > hope I'm not over-reporting the error (sorry in advance if I am), but the
> > previous report seemed somewhat different, in that there was an issue
> with
> > the wrong edge being chosen for the test and ref data (best I can tell).
> I
> > do have the work around of importing each file individually, so this is
> no
> > more than an inconvenience, but I thought I'd report it and see if maybe
> > someone had some up with a more elegant solution.
> >
> > I am currently using version 9.14 on a 64-bit windows platform.
> >
> > Thanks in advance for any advice or help the community can provide!
>
>
> --
>
>  Bruce Ravel  ------------------------------------ bravel at bnl.gov
>
>  National Institute of Standards and Technology
>  Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
>  Building 535A
>  Upton NY, 11973
>
>  Homepage:    http://xafs.org/BruceRavel
>  Software:    https://github.com/bruceravel
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>



-- 
John Hayes

The Grosvenor Group
Dept. of Chemistry
University of Saskatchewan

Two fish are in a tank. One turns to the other and says, "You man the guns,
I'll drive."
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