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

Jeff Catalano catalano at levee.wustl.edu
Wed Dec 9 08:24:15 CST 2015

Hi Bruce,

I appreciate the reply. It looks like what I want is the flattend column 
of data, which is not column 2 in the version 0.9.24 norm(E) files, it 
is column 3. I was unaware both flattened and unflatten normalized data 
were exported in the file. In Athena 0.8 if "Flatten normalized data" 
was selected then column 2 was this flattened data in a norm(E) file. I 
had no idea that the export format for norm(E) files changed in version 
0.9. To make sure I have this correct, below are the column labels from 
norm(E) files exported from Athena 0.8.061 and Athena 0.9.24:

0.8.061: #  energy norm bkg_norm der_norm
0.9.24: #   e         norm        flat        fbkg nder        nsec

I have plotting code that expects columns 1 and 2 and I was unaware that 
flattened data is now output separately (in column 3). In version 0.8 a 
flattened normalized spectra was outputted if the box was checked, and 
if it was unchecked then column 2 was the unflattened data, from what I 
can tell. Can you please confirm that I understand this correctly?

I admit that I had not looked at the documentation before writing since 
I understood the Athena 0.8 file format and had not anticipated a format 
change in the new version.  It clearly would have been informative to 
look at the current documentation! Of course, as you note that the 
columns listed in the documentation for norm(E) files are wrong, with 
the current output format being columns 1 4 2 3 6 7 from what is listed 
in the documentation (column 5 does not appear in my file). Should this 
be looked at?  I actually would prefer the column order that is listed 
in the documentation. The file format is clearly not what you intended.

Thank you,

On 12/8/2015 9:15 PM, Bruce Ravel wrote:
> Here's what the manual has to say
> http://bruceravel.github.io/demeter/aug/output/column.html
> Looking at the code, however, it seems the document has swapped 
> columns 2/3 and columns 4/5.  I think what you are looking for is in 
> column 4, not column 2.  If that's right, I'll treat this as a 
> documentation bug.  If that is not the case, then I'll prod you for 
> more information so I can understand the software bug.
> In either case, thanks for the report.
> Cheers,
> B
> On 12/08/2015 06:09 PM, Jeff Catalano wrote:
>> I am looking for some help with a possible error on my part or bug
>> associated with exporting normalized mu(E) spectra from Athena 0.9.24
>> 64-bit on Windows 10 Pro 64-bit. I have some Si XANES data with a
>> challenging background shape that is well removed through careful
>> normalization in Athena, as long as the "Flatten normalized data" option
>> is checked. When I save the current group as norm(E), what is saved is
>> the non-flattened normalized data. The checkbox for flattening the data
>> has no effect on what is exported despite changing what is plotted. I
>> have verified this by comparing the files exported the the flatten box
>> checked or unchecked. I have tried this with multiple data files loaded
>> in multiple formats (raw beamline data, simple two-column E and mu data,
>> PRJ files) and the effect is always the same. It is also unaffected by
>> the normalization ranges I select. No matter what options I select
>> Athena 0.9.24 will only save non-flattened norm(E) data.
>> This behavior is different from what I remember, and I have verified
>> that in version 0.8 of Athena the exported norm(E) was the flattened
>> data, provided that the flatten box was checked (of course). I have been
>> unable to determine if I have any errors in the settings in version
>> 0.9.24 but all parameters that I can find are identical in both 0.9.24
>> and 0.8. I have also uninstalled and reinstalled Athena 0.9.24 and the
>> effect is still the same. Has anyone else noticed this problem? Is this
>> a bug?
>> Thank you,
>> Jeff

Jeffrey G. Catalano, Associate Professor
Department of Earth and Planetary Sciences
Washington University
1 Brookings Drive, Campus Box 1169
Saint Louis, MO 63130

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