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

[Bruce Ravel]

On 12/09/2015 09:24 AM, Jeff Catalano wrote:
> 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:

You are correct.  Some of the details about the program in its current
form are different from the version of Athena for which development
stopped over 8 years ago.

It, of course, helps when the documentation is correct. So I fixed
that this morning. The norm(E) output file is now described correctly
at http://bruceravel.github.io/demeter/aug/output/column.html


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

That's surprising. The third column should be the normalized
background function. I don't understand how the "nbkg" column is not
written to the file. That might suggest some other bug or some
problem with your data.

I'd need to see a project file to understand how and why that's
happening.  Possibly the original data as well.


> 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 don't see how supporting your "plotting code" is my responsibility.
The program works the way it works.  Aside from the misstatement in
the documentation which you pointed out -- and I am very grateful for
that -- the document does a fair job of explaining the program.

> 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!

<cough><cough> .....

> 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.

As I said above, I would need an actionable bug report to understand
why the "nbkg" column is missing in your case.  That's a behavior that
I've not seen before.

Some hints on how to make an actionable bug report:
http://bruceravel.github.com/demeter/pods/bugs.pod.html

B


> Thank you,
> Jeff
>
> 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
>>>
>>
>>
>
>


-- 
  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/