[Ifeffit] Unable to export flattened normalized XANES spectra from Athena 0.9.24

Bruce Ravel bravel at bnl.gov
Wed Dec 9 13:34:13 CST 2015

On 12/09/2015 11:49 AM, Jeff Catalano wrote:
> I think I have identified the sequence of events to produce a missing
> nbkg column. The attached text file (cubes1_test.txt) is a simple two
> column energy vs. mu(E) data with no header. It is for Si XANES data
> collected at the CLS, and the Si content of this samples was low, hence
> the noise and poor pre-edge region. When reading this text data into
> Athena (1st column E, 2nd column mu), Athena sets this to datatype:
> XANES. See the attached Athena file, I did not change the default
> normalization settings for this example to keep things simple. If I
> export norm(E) from this Athena project (see attached
> cubes1_test_initial.nor), nbkg is missing. If I convert the data to
> mu(E) via Group > Change Data Type then the nbkg column appears (see
> attached cubes1_test_muE.nor). Changing data type back to XANES does not
> remove nbkg, it is still there (not attached, file looks the same as
> cubes1_test_initial.nor). The missing column seems to be associated with
> the importing process for the short energy range involved in my data.

Thanks, Jeff.  I was making a mistake in handling the output arrays
for data marked as being XANES data

I just pushed a fix to the repository which handles that in a sensible

This fix will find its way into the next release of the Windows
installer.  Until then, you will find that the norm(E) files are
missing the "normalized background" column and that the "flattened
background" column is filled with weird numbers, and that the mu(E)
files are missing the background column.  The corrected behavior,
which will be in the next Windows installer, puts all zeros in those
columns.  That assures that the column structure for mu(E) and norm(E)
files will be the same for any data group, regardless of whether it is
flagged as XANES data.

Thanks for the bug report.  Athena is much better thanks to useful bug
reports from users.


  Bruce Ravel  ------------------------------------ bravel at bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Building 535A
  Upton NY, 11973

  Homepage:    http://bruceravel.github.io/home/
  Software:    https://github.com/bruceravel
  Demeter:     http://bruceravel.github.io/demeter/

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