Hi Bruce, thanks for your response..I think that my problem is in the specification of energy unit and/or the numerator/denominator. In the project I sent, I imported the files specifying energy as "k" and nothing for numerator/denominator. The plotter would then display the EXAFS as k2 weighted and I found that I couldn't change the plot display. in a later attempt at importing data, I still specified energy as "k" but then checked "chi" for the numerator. The result is still strange...the data will be imported, but when I try to change k-weighting and replot, I can't re-plot. I can plot the data in "R" or "q" space, but can't ever go back to k... anyway, here is the screen shot you requested. The data are sixpack generated, I would think totally compatible. thanks for the help, andrea [image: Inline image 1] ________________________________________ Andrea L. Foster, PhD U.S. Geological Survey, GMEG Science Center 345 Middlefield Rd., MS 901 Menlo Park, CA 94025 650-329-5437 (t) 650-329-5491 (f) On Sat, Sep 13, 2014 at 12:20 PM, Bruce Ravel wrote:

Andrea,

Your project file is horribly, unrecoverably broken. A project file in that state is unusual in the sense that I do not know how you got there and I do not know how to replicate it.

To understand what went awry, I would have to know more about how you got to that point. For starters, it would help to see the data that you imported into Athena to begin with. A screenshot of the state of the column selection dialog right before clicking the OK button would probably help also. I'll probably have more questions after that.

Bottom line, you found a neat, new (to me) way of breaking my program. Clearly the work of an experienced EXAFS person!! :P

On 09/12/2014 08:51 PM, Foster, Andrea wrote:

...

Hello all,

I am an experienced EXAFS person, but not having a lot of luck using Athena.

I am trying to set up an Athena project for linear combo fitting.

I can get the data + model compounds imported, and I can save a project file. However, after saving and closing the file, the next time I try to open, I am asked to re-import the data from the project file (I think this is a normal part of Athena)... Inline image 4

...but when I try to select importing as chi(k) instead of u(E), I get the following message

This is certainly not related to the problem with the project file, but I want to point out that the box in the project selection dialog is labelled "Plot as", not "Import as". Its purpose is to display the data in different ways to help you decide what data you might want to import. Data is always imported from a project file in the same manner as it was imported from the raw data file regardless of how you choose to plot it before clicking the import selection button.

B

Inline image 2>

...

after "ok-ing" this message away, I can't get any farther. Importing the data as u(E) doesn't give the appropriate results.

I am also attaching the aforementioned project file.

thanks for any help with this, andrea

________________________________________ Andrea L. Foster, PhD U.S. Geological Survey, GMEG Science Center 345 Middlefield Rd., MS 901 Menlo Park, CA 94025 650-329-5437 (t) 650-329-5491 (f)

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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://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Bruce, attached are some data files... btw looking through Athena manual I did find lots of helpful instructions on import, but not specifically on how to import chi(k) files. if you could let me know how to do it, that would be great! ________________________________________ Andrea L. Foster, PhD U.S. Geological Survey, GMEG Science Center 345 Middlefield Rd., MS 901 Menlo Park, CA 94025 650-329-5437 (t) 650-329-5491 (f) On Mon, Sep 15, 2014 at 12:12 PM, Bruce Ravel wrote:

Could I have a data file or two? That way so I could try to walk through what you did. I need to be able to reproduce the problem here in front of myself in order to have a hope of fixing it.

It is certainly true that Athena is not completely reliable noticing that chi(k) data is chi(k) data. You certainly should make sure the data type is set correctly.

Thanks for taking the time to report the problem. B

On 09/15/2014 03:02 PM, Foster, Andrea wrote:

...

Hi Bruce,

thanks for your response..I think that my problem is in the specification of energy unit and/or the numerator/denominator. In the project I sent, I imported the files specifying energy as "k" and nothing for numerator/denominator. The plotter would then display the EXAFS as k2 weighted and I found that I couldn't change the plot display.

in a later attempt at importing data, I still specified energy as "k" but then checked "chi" for the numerator. The result is still strange...the data will be imported, but when I try to change k-weighting and replot, I can't re-plot. I can plot the data in "R" or "q" space, but can't ever go back to k...

anyway, here is the screen shot you requested. The data are sixpack generated, I would think totally compatible.

thanks for the help, andrea

Inline image 1

________________________________________ Andrea L. Foster, PhD U.S. Geological Survey, GMEG Science Center 345 Middlefield Rd., MS 901 Menlo Park, CA 94025 650-329-5437 (t) 650-329-5491 (f)

On Sat, Sep 13, 2014 at 12:20 PM, Bruce Ravel mailto:bravel@bnl.gov> wrote:

Andrea,

Your project file is horribly, unrecoverably broken. A project file in that state is unusual in the sense that I do not know how you got there and I do not know how to replicate it.

To understand what went awry, I would have to know more about how you got to that point. For starters, it would help to see the data that you imported into Athena to begin with. A screenshot of the state of the column selection dialog right before clicking the OK button would probably help also. I'll probably have more questions after that.

Bottom line, you found a neat, new (to me) way of breaking my program. Clearly the work of an experienced EXAFS person!! :P

On 09/12/2014 08:51 PM, Foster, Andrea wrote:

Hello all,

I am an experienced EXAFS person, but not having a lot of luck using Athena.

I am trying to set up an Athena project for linear combo fitting.

I can get the data + model compounds imported, and I can save a project file. However, after saving and closing the file, the next time I try to open, I am asked to re-import the data from the project file (I think this is a normal part of Athena)... Inline image 4

...but when I try to select importing as chi(k) instead of u(E), I get the following message

This is certainly not related to the problem with the project file, but I want to point out that the box in the project selection dialog is labelled "Plot as", not "Import as". Its purpose is to display the data in different ways to help you decide what data you might want to import. Data is always imported from a project file in the same manner as it was imported from the raw data file regardless of how you choose to plot it before clicking the import selection button.

B

Inline image 2> after "ok-ing" this message away, I can't get any farther. Importing the data as u(E) doesn't give the appropriate results.

I am also attaching the aforementioned project file.

thanks for any help with this, andrea

__________________________________________ Andrea L. Foster, PhD U.S. Geological Survey, GMEG Science Center 345 Middlefield Rd., MS 901 Menlo Park, CA 94025 650-329-5437 (t) 650-329-5491 (f)

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-- Bruce Ravel ------------------------------__------ bravel@bnl.gov mailto: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://bruceravel.github.io/__home/ http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/__demeter/ http://bruceravel.github.io/demeter/ _________________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.__gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.__gov/mailman/listinfo/ifeffit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- 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://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

On 09/15/2014 03:39 PM, Foster, Andrea wrote:

Bruce, attached are some data files...

btw looking through Athena manual I did find lots of helpful instructions on import, but not specifically on how to import chi(k) files. if you could let me know how to do it, that would be great!

Andrea, The data were helpful. Thanks. The thing I discovered is that Athena was making a number of mistakes related to importing chi(k) data. The reason for this (this is not an excuse, just an explanation of what happened) is that I assume that Athena users will start from raw data so she's much better tested when starting from raw data. Import of chi(k) data was kind of an afterthought for me and, therefore, rather poorly tested. I think I have put Athena in a better state with respect to importing chi(k) data. I even found and fixed a rather serious problem with the LCF tool after importing chi(k) data. I think that which was your original motivation for sufffering through Athena's many shortcomings :) I need to do some testing on Windows and then I'll need to build a pre-release package for you to try. All of that will take a few days. But I'll get there. Thanks for your patience and thanks for reporting the problem in the first place. Demeter would be much much worse were it not for patient people reporting their problems using the codes. Cheers, B -- 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://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

There's a combination-fit program on the ALS 10.3.2 website https://sites.google.com/a/lbl.gov/microxas-lbl-gov/software . mam On 9/17/2014 9:55 AM, Foster, Andrea wrote:

Bruce, thanks for your help...look forward to seeing new version.

FYI I especially am interested using the "combinatorics" module of Athena's LCF to test the uniqueness of some fits.I have a set of 30 models and PCA tells me that a max of 5 models should explain the dataset. I have been using SixPack for the fits, but it doesn't currently have the option to specify testing the limited set of the permutations that I need (I want to test every possible combination of 5 model compounds out of my set of 30 models).

andrea

________________________________________ Andrea L. Foster, PhD U.S. Geological Survey, GMEG Science Center 345 Middlefield Rd., MS 901 Menlo Park, CA 94025 650-329-5437 (t) 650-329-5491 (f)

On Tue, Sep 16, 2014 at 1:36 PM, Bruce Ravel mailto:bravel@bnl.gov> wrote:

On 09/15/2014 03:39 PM, Foster, Andrea wrote:

Bruce, attached are some data files...

btw looking through Athena manual I did find lots of helpful instructions on import, but not specifically on how to import chi(k) files. if you could let me know how to do it, that would be great!

Andrea,

The data were helpful. Thanks.

The thing I discovered is that Athena was making a number of mistakes related to importing chi(k) data. The reason for this (this is not an excuse, just an explanation of what happened) is that I assume that Athena users will start from raw data so she's much better tested when starting from raw data. Import of chi(k) data was kind of an afterthought for me and, therefore, rather poorly tested.

I think I have put Athena in a better state with respect to importing chi(k) data. I even found and fixed a rather serious problem with the LCF tool after importing chi(k) data. I think that which was your original motivation for sufffering through Athena's many shortcomings :)

I need to do some testing on Windows and then I'll need to build a pre-release package for you to try. All of that will take a few days. But I'll get there.

Thanks for your patience and thanks for reporting the problem in the first place. Demeter would be much much worse were it not for patient people reporting their problems using the codes.

Cheers, B

-- Bruce Ravel ------------------------------__------ bravel@bnl.gov mailto: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://bruceravel.github.io/__home/ http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/__demeter/ http://bruceravel.github.io/demeter/ _________________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.__gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.__gov/mailman/listinfo/ifeffit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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