[Ifeffit] Athena: Target transform function not working

John Hayes ginger.jesus at usask.ca
Thu Oct 17 14:55:42 CDT 2013

Hi Bruce,

No worries on the delay, I totally understand. I've followed your
instructions and the Target Transform function is now working. Thanks for
the fix!


On Thu, Oct 17, 2013 at 1:28 PM, Bruce Ravel <bravel at bnl.gov> wrote:

> On 10/02/2013 01:00 PM, John Hayes wrote:
>> I am trying to use Athena to do some PCA work and am having trouble
>> getting the target transform analysis to work. When I click the target
>> transform button no TT coefficients are produced and only a residual
>> that is shaped like the original spectrum to be transformed is plotted.
>> This seems to happen for all of my standards. (For my data in norm3.prj
>> I am doing the PCA on all the spectra that start with TMF and trying to
>> target transform the other spectra.)
>> I have also tried this with the cyanobacteria data in the XAS-Education
>> folder (also attached) to ensure it wasn't just a problem with my data.
>> I am still have the same problems with this file as well. The
>> dathena.log file and screenshot come from trying to target transform
>> using this file.
> Hi John,
> Sorry it took me so long to address this.  As I mentioned in my last
> email, I didn't do much work on the software during the ridiculous
> US government shutdown which left me furloughed.
> This was just a bit of sloppiness on my part.  While trying to make
> some improvements to the PCA part of Demeter, I simply left the target
> transform function in a non-wroking state.  Sorry 'bout that.
> It will be fixed in the next release.  If you would like to apply the
> fix imemdiately, you can do so by hand.  Do the following:
>   1. Download
>      https://raw.github.com/**bruceravel/demeter/master/lib/**
> Demeter/PCA.pm<https://raw.github.com/bruceravel/demeter/master/lib/Demeter/PCA.pm>
>   2. Save that as
>      C:\strawberry\perl\site\lib\**Demeter\PCA.pm
>   3. Download
> https://raw.github.com/**bruceravel/demeter/master/lib/**
> Demeter/UI/Athena/PCA.pm<https://raw.github.com/bruceravel/demeter/master/lib/Demeter/UI/Athena/PCA.pm>
>   4. Save that as
>      C:\strawberry\perl\site\lib\**Demeter\UI\Athena\PCA.pm
> Both of those will overwrite existing files.
> Be careful that your browser does not change the filename to
> PCA.tt.txt or some such.  The filenames should be exactly as shown.
> Note that both files are called PCA.pm, although they live in
> different folders.  Don't get them confused -- they may not be
> swapped.
> B
> --
>  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
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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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