John,
I now understand the nature of the problem you observed. In fact, I
suspect I can now explain the problem that Scott reported a couple
months ago.
One of the things about doing PCA on a subset of the data in a project
file is that I have to somehow keep track of which set of data groups
have been included in the PCA so that I can know which data groups
should be reconstructed and which could be objects of a target
transform. I did a very stupid thing that resulted in easily loosing
track of which data groups were in the PCA.
I think I will have this fixed in the next release. Until then, I can
suggest a work-around.
In the case of the project file you sent me, simply remove all the
reference spectra from the project, then rerun the PCA. In general,
if you reorganize the group list
(http://bruceravel.github.io/demeter/aug/ui/glist.html#reorganizingthegrouplist)
so that the groups in the PCA are all at the top of the group list,
you will not trigger my silly bug.
As always, thanks for reporting this problem. As I often say,
whatever quality the software has is thanks to the generous
participation of its users.
B
On 07/25/2013 10:56 AM, Ravel, Bruce wrote:
Hi John,
Firstly, I should apologize for a very slow response.
Unfortunately, you posted your problem with PCA right before I went
on travel for a while. Back home, I have finally worked my way to
this item on my to do list.
I am seeing the same problem you report on my own computer. Don't
know what the problem is yet, but I'll work on it. I'll keep you
posted and hopefully it will get resolved for the next release.
Cheers,
B
Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY, 11973
Homepage: http://xafs.org/BruceRavel
Software: https://github.com/bruceravel
________________________________________
From: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of John Hayes [ginger.jesus@usask.ca]
Sent: Wednesday, July 03, 2013 6:43 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] DAthena crashes when reconstructing data from PCA
Hi all,
I seem to be having some trouble with Athena crashing during the reconstruction step for some of my data when doing PCA analysis, and was wondering if anyone might have some insight. I I have attached a project file with the spectra in question (I realize they probably aren't normalized as well as they could be) and the dathena.log file, which is similar to Dr. Calvin's reported error log, aside from the PATH information. However, this is not an issue with Parallels, as I am using a 64 bit version of Windows 7.
Here, the issue I have is when reconstructing any of the files starting with TMF08-03 (in the attached "Combined - tailings.prj" project file). I am able to reconstruct all of the TMF08-01 files, and I have also successfully tried PCA/reconstruction on the files from the Au cyanobacteria example, so I do not believe it is an issue with my computer. To the extent that it may be an error with the TMF08-03 files, I have tried to re-import/re-work all the data, but this does not solve the problem, so it does not seems like the data itself is to blame. Perhaps the file names are presenting issues for Athena? (i.e. it might be confused if it is a standard or a sample?)
Any help on this issue is greatly appreciated. I apologize in advance for any omitted information or poor error reporting on my part, and thank you for your patience and support with this issue.
Cheers!
John
--
John Hayes
The Grosvenor Group
Dept. of Chemistry
University of Saskatchewan
“Somebody told me it was frightening how much topsoil we are losing each year, but I told that story around the campfire and nobody got scared.”
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--
Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY, 11973
Homepage: http://xafs.org/BruceRavel
Software: https://github.com/bruceravel
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