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

[John Hayes]

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 <bravel at bnl.gov> 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#**
> reorganizingthegrouplist<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 at 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 at millenia.cars.**aps.anl.gov<ifeffit-bounces at millenia.cars.aps.anl.gov>[
>> ifeffit-bounces at millenia.**cars.aps.anl.gov<ifeffit-bounces at millenia.cars.aps.anl.gov>]
>> on behalf of John Hayes [ginger.jesus at 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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>> Ifeffit at millenia.cars.aps.anl.**gov <Ifeffit at millenia.cars.aps.anl.gov>
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>>
>>
>
> --
>  Bruce Ravel  ------------------------------**------ bravel at 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
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>



-- 
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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