Re: [Ifeffit] DAthena crashes when reconstructing data from PCA -- Update

Hi, Thanks for your reply Bruce! I look forward to the next release, and the workaround is working for me currently. I do have one more question about PCA in Athena. I have noticed that when I changed the order of the data groups the calculated eigenvalues change when the first group on the list changes. The changes are very small and not significant, but based on my (very limited) knowledge of PCA, it would seem that the order of the data would not matter. (More specifically, it would not seem that only the first column should dictate the eigenvectors/values.) Are these discrepancies caused by single-value decomposition algorithm or are the PCA eigenvalues/eigenvectors inherently dependent on the order of the data groups? Again, the values generated are not significantly different, and this is more a question arising from curiosity. Thanks in advance for any information the community can provide! Cheers! John On Mon, Jul 29, 2013 at 7:48 AM, Bruce Ravel wrote:

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#** reorganizingthegrouplisthttp://bruceravel.github.io/demeter/aug/ui/glist.html#reorganizingthegroupli... ) 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 ______________________________**_________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.**gov http://millenia.cars.aps.anl.**gov/mailman/listinfo/ifeffithttp://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- 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.”