[Ifeffit] Importing Multiple Data Sets into Athena

[Bruce Ravel]

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