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@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/