Hi Bruce,
I realize that you stopped development on the prior version a long time
ago, but I only made the switch to version 0.9 a couple of years ago,
and thus was a long-time user of prior versions. I don't think users
expect a file format [e.g., norm(E)] to change over time. I note this to
make clear why I did not consider that the same data could be in a
different column when saving norm(E) files in version 0.8 and 0.9. Users
certainly should read documentation to understand how new features work
(like multi-electron excitation removal), but if we have used a program
for many years and are exporting the same file type as we always have
then it is not instinctive to expect the format to have changed.
You misunderstood my comment about my plotting code. I never asked you
to support how I plot data using saved files. I only noted this because
it is how I discovered the problem I was having. I will plot column 4
from now on (more on this below).
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.
I appreciate you taking the time to look into this. As a long-time user
of your software I am grateful for access to such a useful tool for data
processing and analysis.
Jeff
Post by Bruce RavelPost by Jeff CatalanoHi 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
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
Post by Jeff Catalano0.8.061: # 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.
Post by Jeff CatalanoI 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.
Post by Jeff CatalanoI 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> .....
Post by Jeff CatalanoOf 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.
http://bruceravel.github.com/demeter/pods/bugs.pod.html
B
Post by Jeff CatalanoThank you,
Jeff
Post by Bruce RavelHere'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
Post by Jeff CatalanoI 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
USA
http://aqgeochem.wustl.edu/