Re: [Ifeffit] Plotting chi(R) from FEFF in XAS Viewer (Larch) with
Dear Matt and Carlo and Liam,
I agree with Matt and Carlo that phase corrected plots are not a great idea, I
think they lead people to forget that they are not looking at a radial
distribution function and encourages people to think they can read distances
off a plot of the amplitude of the FT of overlapping sine waves reliably.
Thanks
Fred
J F W Mosselmans
Principal Beamline Scientist I20
Diamond Light Source
Harwell Campus
Didcot
OX11 0DE
01235 778568
fred.mosselm...@diamond.ac.uk
07419362123
Message: 1
Date: Tue, 13 Dec 2022 16:53:03 -0600
From: Matt Newville
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Plotting chi(R) from FEFF in XAS Viewer (Larch)
with phase correction
Message-ID:
Content-Type: text/plain; charset="utf-8"
Hi Liam,
Yes, this is not currently available. It would not be hard to enable, but I
am not sure it is a great thing to do. I admit that I sort of find that
phase-correction plots need a lot of explanation, and so are prone to causing
confusion. They might be useful for Pt metal, but they cannot really be
correct for multi-atomic systems. Well, I guess "correct" is not the only
consideration ;).
I guess I would ask if there are suggestions and input from people teaching
XAFS on whether phase corrections (and probably a handful of other "tricks"
or analysis variations) are actually useful or just confusing.
On Tue, Dec 13, 2022 at 7:58 AM Liam Nagle-Cocco wrote:
> Dear all,
>
> In Artemis it is possible to plot chi(R) for FEFF-fit, with the phase
> corrected - i.e. bond length corrected for deltaR. This is shown in
> this screenshot below ("Use this path for phase corrected plotting").
> Is this possible in XAS Viewer?
>
>
> Liam Nagle-Cocco *(he/his)*
>
> PhD Student in Condensed Matter Physics | Cavendish Laboratory
>
> Welfare Officer 2022-2023 | Jesus College MCR
> ___
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
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>
--
--Matt Newville 630-327-7411
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Re: [Ifeffit] Plotting chi(R) from FEFF in XAS Viewer (Larch) with phase correction
Hi Liam,
Yes, this is not currently available. It would not be hard to enable, but
I am not sure it is a great thing to do. I admit that I sort of find that
phase-correction plots need a lot of explanation, and so are prone to
causing confusion. They might be useful for Pt metal, but they cannot
really be correct for multi-atomic systems. Well, I guess "correct" is not
the only consideration ;).
I guess I would ask if there are suggestions and input from people teaching
XAFS on whether phase corrections (and probably a handful of other "tricks"
or analysis variations) are actually useful or just confusing.
On Tue, Dec 13, 2022 at 7:58 AM Liam Nagle-Cocco wrote:
> Dear all,
>
> In Artemis it is possible to plot chi(R) for FEFF-fit, with the phase
> corrected - i.e. bond length corrected for deltaR. This is shown in this
> screenshot below ("Use this path for phase corrected plotting"). Is this
> possible in XAS Viewer?
>
>
> Liam Nagle-Cocco *(he/his)*
>
> PhD Student in Condensed Matter Physics | Cavendish Laboratory
>
> Welfare Officer 2022-2023 | Jesus College MCR
> ___
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>
--
--Matt Newville 630-327-7411
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[Ifeffit] Plotting chi(R) from FEFF in XAS Viewer (Larch) with phase correction
Dear all,
In Artemis it is possible to plot chi(R) for FEFF-fit, with the phase corrected
- i.e. bond length corrected for deltaR. This is shown in this screenshot below
("Use this path for phase corrected plotting"). Is this possible in XAS Viewer?
[cid:b58a0f44-1946-4c60-a12e-c1e0bfa50100]
Liam Nagle-Cocco (he/his)
PhD Student in Condensed Matter Physics | Cavendish Laboratory
Welfare Officer 2022-2023 | Jesus College MCR
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Re: [Ifeffit] Plotting flattened feffit simulation results
Hi Matt, I think the “turn of the pre-edge baseline” option would be useful in cases like mine where one would like to plot the “experimental” E(k) as well as its Fourier transform. If it’s easy to do, why not offer a checkbox to run off the pre-edge subtraction? In any case, thanks for thinking about the problem. Cheers, Paul From: Ifeffit on behalf of Matt Newville Reply-To: XAFS Analysis using Ifeffit Date: Tuesday, January 29, 2019 13:21 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Plotting flattened feffit simulation results Hi Paul, On Mon, Jan 28, 2019 at 2:57 AM FonsPaul mailto:paul-f...@aist.go.jp>> wrote: Hi All, I have a rather simple question and a reply for either Larch or athena would be welcome. I have calculated a number of structures using DFT and have run feff on each of the appropriate sites and have then averaged the E(k) results. I have no problem reading in the data to athena, however, due to the lack of a pre-edge baseline, it is typically not possible to choose a reasonable “pre-edge” baseline so that I can plot the data for the different structures in “flattened” mode. The “post-edge” baseline works very well with the default values (as there is literally no noise in the spectra). My question is how can I induce athena to plot the E(k) data for the different structures in “flattened” mode. Ultimately, I will end up taking a Fourier transform into real space so I would also like to have a proper baseline so I can compare intensities as well. In effect, the data from feff9 is already normalized. Thanks for any suggestions! Sorry for the trouble. Perhaps we should add a routine that adds a more realistic preedge to the Feff XANES calculations, so that the "normal" pre-edge and normalization steps work better? I would think that simply add a segment of 0s for value below the main edge might wok well enough. That would be easy enough to do --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Plotting flattened feffit simulation results
Hi Paul, On Mon, Jan 28, 2019 at 2:57 AM FonsPaul wrote: > Hi All, > I have a rather simple question and a reply for either Larch or athena > would be welcome. I have calculated a number of structures using DFT and > have run feff on each of the appropriate sites and have then averaged the > E(k) results. I have no problem reading in the data to athena, however, > due to the lack of a pre-edge baseline, it is typically not possible to > choose a reasonable “pre-edge” baseline so that I can plot the data for the > different structures in “flattened” mode. The “post-edge” baseline works > very well with the default values (as there is literally no noise in the > spectra). My question is how can I induce athena to plot the E(k) data for > the different structures in “flattened” mode. Ultimately, I will end up > taking a Fourier transform into real space so I would also like to have a > proper baseline so I can compare intensities as well. In effect, the data > from feff9 is already normalized. Thanks for any suggestions! > Sorry for the trouble. Perhaps we should add a routine that adds a more realistic preedge to the Feff XANES calculations, so that the "normal" pre-edge and normalization steps work better? I would think that simply add a segment of 0s for value below the main edge might wok well enough. That would be easy enough to do --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Plotting flattened feffit simulation results
I thought I would add that perhaps the only way forward is to average the already normalized chi(k) spectra that feff also outputs, however, it still would be nice to be able to see simulated that that can be compared to experimental E(k). From: Ifeffit on behalf of FonsPaul Reply-To: XAFS Analysis using Ifeffit Date: Tuesday, January 29, 2019 8:13 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Plotting flattened feffit simulation results Thank you for reply. I am calculating structures (aka coordinates that are used for input to feff) in DFT and ultimately I simply wish to transform the k-space plot to r-space. However, I would like to plot the E(k) data for “cosmetic” reasons and the flattening is an issue there. An improper “pre-edge” subtraction will also affect the relative intensities of the Χ(R)(r) data as well so I guess my request is not entirely for cosmetic reasons. Presumably the E(k) data in feff is already normalized (I didn’t check). From: Ifeffit on behalf of Chris Patridge Reply-To: XAFS Analysis using Ifeffit Date: Monday, January 28, 2019 20:18 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Plotting flattened feffit simulation results Hello, You said you averaged in E(k)? Is this reciprocal space? Are calculating XANES or EXAFS spectra with Feff? You said you would transform the data to real space so I assume it is EXAFS. I don’t think there is flattened mode in EXAFS. If you clarify what you are calculating that might help. Are you comparing intensities between theory and experimental? The intensities would be very different given that there was no noise in the calculations. Sorry I don’t have answers just questions. Chris Sent from my iPhone On Jan 28, 2019, at 3:57 AM, FonsPaul mailto:paul-f...@aist.go.jp>> wrote: Hi All, I have a rather simple question and a reply for either Larch or athena would be welcome. I have calculated a number of structures using DFT and have run feff on each of the appropriate sites and have then averaged the E(k) results. I have no problem reading in the data to athena, however, due to the lack of a pre-edge baseline, it is typically not possible to choose a reasonable “pre-edge” baseline so that I can plot the data for the different structures in “flattened” mode. The “post-edge” baseline works very well with the default values (as there is literally no noise in the spectra). My question is how can I induce athena to plot the E(k) data for the different structures in “flattened” mode. Ultimately, I will end up taking a Fourier transform into real space so I would also like to have a proper baseline so I can compare intensities as well. In effect, the data from feff9 is already normalized. Thanks for any suggestions! ___ 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 Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Plotting flattened feffit simulation results
Hello, You said you averaged in E(k)? Is this reciprocal space? Are calculating XANES or EXAFS spectra with Feff? You said you would transform the data to real space so I assume it is EXAFS. I don’t think there is flattened mode in EXAFS. If you clarify what you are calculating that might help. Are you comparing intensities between theory and experimental? The intensities would be very different given that there was no noise in the calculations. Sorry I don’t have answers just questions. Chris Sent from my iPhone > On Jan 28, 2019, at 3:57 AM, FonsPaul wrote: > > Hi All, > I have a rather simple question and a reply for either Larch or athena > would be welcome. I have calculated a number of structures using DFT and > have run feff on each of the appropriate sites and have then averaged the > E(k) results. I have no problem reading in the data to athena, however, due > to the lack of a pre-edge baseline, it is typically not possible to choose a > reasonable “pre-edge” baseline so that I can plot the data for the different > structures in “flattened” mode. The “post-edge” baseline works very well with > the default values (as there is literally no noise in the spectra). My > question is how can I induce athena to plot the E(k) data for the different > structures in “flattened” mode. Ultimately, I will end up taking a Fourier > transform into real space so I would also like to have a proper baseline so I > can compare intensities as well. In effect, the data from feff9 is already > normalized. Thanks for any suggestions! > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
[Ifeffit] Plotting flattened feffit simulation results
Hi All, I have a rather simple question and a reply for either Larch or athena would be welcome. I have calculated a number of structures using DFT and have run feff on each of the appropriate sites and have then averaged the E(k) results. I have no problem reading in the data to athena, however, due to the lack of a pre-edge baseline, it is typically not possible to choose a reasonable “pre-edge” baseline so that I can plot the data for the different structures in “flattened” mode. The “post-edge” baseline works very well with the default values (as there is literally no noise in the spectra). My question is how can I induce athena to plot the E(k) data for the different structures in “flattened” mode. Ultimately, I will end up taking a Fourier transform into real space so I would also like to have a proper baseline so I can compare intensities as well. In effect, the data from feff9 is already normalized. Thanks for any suggestions! ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Plotting chi(k) linear combination fit in energy
Thank you, all, for your responses. I think Leslie's suggestion will do the trick for now. I did not realize that changing the fitting space post-fitting would allow me to plot the fit differently. Thanks again! Ellen On Tue, Jul 21, 2015 at 7:01 AM, Bruce Ravel bra...@bnl.gov wrote: On 07/21/2015 08:52 AM, Bruce Ravel wrote: That said, plot this result in norm(E) for a fit in chi(k) is a good and useful idea. I'll put it on my to do list. So is plot in chi(k) for this fit in norm(E), for that matter. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II 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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Plotting chi(k) linear combination fit in energy
On 07/21/2015 08:52 AM, Bruce Ravel wrote: That said, plot this result in norm(E) for a fit in chi(k) is a good and useful idea. I'll put it on my to do list. So is plot in chi(k) for this fit in norm(E), for that matter. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II 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
Re: [Ifeffit] Plotting chi(k) linear combination fit in energy
Leslie had a good suggestion. That would, I think, be close to what you want. There is not a button to automate exactly what you want -- not even one that I've been hiding from Matt all these years. Another way of doing what you want would be to jot down the best fit values for the weights, then use the data summation tool (http://bruceravel.github.io/demeter/aug/process/sum.html) to make that sum of norm(E) spectra. These is no automated interaction between these tools, so you'll have to do the tedious work of setting things up in the summation tool. Another idea would be to jot down the best fit value, then mark the data group and the groups used as the fitting standards, then select Save marked groups as ... norm(E) from the File menu. Import that file into Excel or whatever and use the weights you jotted down. Again, there is no automation to do this. That said, plot this result in norm(E) for a fit in chi(k) is a good and useful idea. I'll put it on my to do list. B On 07/20/2015 10:09 PM, Ellen Daugherty wrote: Sorry that I did not explain that clearly. Matt Newville's interpretation is correct. Ellen On Jul 20, 2015, at 19:41, Matt Newville newvi...@cars.uchicago.edu mailto:newvi...@cars.uchicago.edu wrote: I think Ellen wants to first do a linear combination fit with chi(k) data and then look at what that combination of spectral components would look like for the XANES region. It seems like a fine idea to me. Off the top of my head I don't know the easiest way to do this. I don't think there is a single button for that, but I've been known to miss hidden features in Athena for years. --Matt On Jul 20, 2015 8:16 PM, Scott Calvin scal...@sarahlawrence.edu mailto:scal...@sarahlawrence.edu wrote: Hi Ellen, Either I’m not understanding what you’re trying to do, or what you’re trying to do doesn’t make sense. XANES is generally plotted as mu(E) or norm(E). To get from norm(E) to chi(k), two things must be done: a smooth background must be subtracted from norm(E), and E has to be converted to k. The conversion from E to k is reversible, but the background subtraction is not, since chi(k) is meant to be background independent. You therefore cannot, in principle, plot chi(k) data as norm(E). —Scott Calvin Sarah Lawrence College On Jul 20, 2015, at 7:48 PM, Ellen Daugherty ellen.daughe...@colostate.edu mailto:ellen.daughe...@colostate.edu wrote: Hello, I was unable to find an example of this question in the archive, but please let me know if it has already been addressed. I would like to plot the results of linear combination fits performed in chi(k) in energy space to compare them to XANES fits. When I try to plot the saved fit in energy, I get a message saying: chi data cannot be plotted in energy. Is there any way to do this other than to use Excel to scale the weights of the standards? This would be exhausting to perform for combinatorial fits. I am using Athena in Demeter 0.9.20 on Windows 7. I have attached a sample and a few standards for aid in addressing the issue. Thank you! Ellen -- Ph.D. Candidate Research Assistant, Borch Lab http://borch.agsci.colostate.edu/ Department of Chemistry Colorado State University http://borch.agsci.colostate.edu/group-members/ellen-daugherty/ Sample.norStandard 1.norStandard 2.norStandard 3.nor___ 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 ___ 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 ___ 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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II 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
Re: [Ifeffit] Plotting chi(k) linear combination fit in energy
I think Ellen wants to first do a linear combination fit with chi(k) data and then look at what that combination of spectral components would look like for the XANES region. It seems like a fine idea to me. Off the top of my head I don't know the easiest way to do this. I don't think there is a single button for that, but I've been known to miss hidden features in Athena for years. --Matt On Jul 20, 2015 8:16 PM, Scott Calvin scal...@sarahlawrence.edu wrote: Hi Ellen, Either I’m not understanding what you’re trying to do, or what you’re trying to do doesn’t make sense. XANES is generally plotted as mu(E) or norm(E). To get from norm(E) to chi(k), two things must be done: a smooth background must be subtracted from norm(E), and E has to be converted to k. The conversion from E to k is reversible, but the background subtraction is not, since chi(k) is meant to be background independent. You therefore cannot, in principle, plot chi(k) data as norm(E). —Scott Calvin Sarah Lawrence College On Jul 20, 2015, at 7:48 PM, Ellen Daugherty ellen.daughe...@colostate.edu wrote: Hello, I was unable to find an example of this question in the archive, but please let me know if it has already been addressed. I would like to plot the results of linear combination fits performed in chi(k) in energy space to compare them to XANES fits. When I try to plot the saved fit in energy, I get a message saying: chi data cannot be plotted in energy. Is there any way to do this other than to use Excel to scale the weights of the standards? This would be exhausting to perform for combinatorial fits. I am using Athena in Demeter 0.9.20 on Windows 7. I have attached a sample and a few standards for aid in addressing the issue. Thank you! Ellen -- Ph.D. Candidate Research Assistant, Borch Lab http://borch.agsci.colostate.edu/ Department of Chemistry Colorado State University http://borch.agsci.colostate.edu/group-members/ellen-daugherty/ Sample.norStandard 1.norStandard 2.norStandard 3.nor ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov 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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Plotting chi(k) linear combination fit in energy
Sorry that I did not explain that clearly. Matt Newville's interpretation is correct. Ellen On Jul 20, 2015, at 19:41, Matt Newville newvi...@cars.uchicago.edu wrote: I think Ellen wants to first do a linear combination fit with chi(k) data and then look at what that combination of spectral components would look like for the XANES region. It seems like a fine idea to me. Off the top of my head I don't know the easiest way to do this. I don't think there is a single button for that, but I've been known to miss hidden features in Athena for years. --Matt On Jul 20, 2015 8:16 PM, Scott Calvin scal...@sarahlawrence.edu wrote: Hi Ellen, Either I’m not understanding what you’re trying to do, or what you’re trying to do doesn’t make sense. XANES is generally plotted as mu(E) or norm(E). To get from norm(E) to chi(k), two things must be done: a smooth background must be subtracted from norm(E), and E has to be converted to k. The conversion from E to k is reversible, but the background subtraction is not, since chi(k) is meant to be background independent. You therefore cannot, in principle, plot chi(k) data as norm(E). —Scott Calvin Sarah Lawrence College On Jul 20, 2015, at 7:48 PM, Ellen Daugherty ellen.daughe...@colostate.edu wrote: Hello, I was unable to find an example of this question in the archive, but please let me know if it has already been addressed. I would like to plot the results of linear combination fits performed in chi(k) in energy space to compare them to XANES fits. When I try to plot the saved fit in energy, I get a message saying: chi data cannot be plotted in energy. Is there any way to do this other than to use Excel to scale the weights of the standards? This would be exhausting to perform for combinatorial fits. I am using Athena in Demeter 0.9.20 on Windows 7. I have attached a sample and a few standards for aid in addressing the issue. Thank you! Ellen -- Ph.D. Candidate Research Assistant, Borch Lab Department of Chemistry Colorado State University http://borch.agsci.colostate.edu/group-members/ellen-daugherty/ Sample.norStandard 1.norStandard 2.norStandard 3.nor___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov 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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov 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
Re: [Ifeffit] Plotting chi(k) linear combination fit in energy
Hi Ellen, Either I’m not understanding what you’re trying to do, or what you’re trying to do doesn’t make sense. XANES is generally plotted as mu(E) or norm(E). To get from norm(E) to chi(k), two things must be done: a smooth background must be subtracted from norm(E), and E has to be converted to k. The conversion from E to k is reversible, but the background subtraction is not, since chi(k) is meant to be background independent. You therefore cannot, in principle, plot chi(k) data as norm(E). —Scott Calvin Sarah Lawrence College On Jul 20, 2015, at 7:48 PM, Ellen Daugherty ellen.daughe...@colostate.edumailto:ellen.daughe...@colostate.edu wrote: Hello, I was unable to find an example of this question in the archive, but please let me know if it has already been addressed. I would like to plot the results of linear combination fits performed in chi(k) in energy space to compare them to XANES fits. When I try to plot the saved fit in energy, I get a message saying: chi data cannot be plotted in energy. Is there any way to do this other than to use Excel to scale the weights of the standards? This would be exhausting to perform for combinatorial fits. I am using Athena in Demeter 0.9.20 on Windows 7. I have attached a sample and a few standards for aid in addressing the issue. Thank you! Ellen -- Ph.D. Candidate Research Assistant, Borch Labhttp://borch.agsci.colostate.edu/ Department of Chemistry Colorado State University http://borch.agsci.colostate.edu/group-members/ellen-daugherty/ Sample.norStandard 1.norStandard 2.norStandard 3.nor___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.govmailto:Ifeffit@millenia.cars.aps.anl.gov 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
Re: [Ifeffit] Plotting chi(k) linear combination fit in energy
Ellen, In the LCF tool, after you do the fit in chi, select norm in the fitting space radio button and click the Plot data and sum button. It will plot the current fit's weightings. You can also type in the weighting you would like to plot, if you already have a table of results. After doing this, you can use the Make group from fit button to add it to your project (but you can't transform it like a regular data file, as you noticed, so you might want to write both the xanes and the chi), or you can export it using the Save fit as column data button. Those buttons seem to write the plotted data, so make sure you have first plotted what you want to export. Leslie ** Leslie L. Baker, Ph.D. Research Assistant Professor Department of Geological Sciences and Department of Plant, Soil and Entomological Sciences University of Idaho 875 Perimeter Drive MS 2339 Moscow, ID 83844-2339 208-885-9239 http://scholar.google.com/citations?user=ejpH5p0J From: ifeffit-boun...@millenia.cars.aps.anl.gov ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Ellen Daugherty daughert...@gmail.com Sent: Monday, July 20, 2015 7:09 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Plotting chi(k) linear combination fit in energy Sorry that I did not explain that clearly. Matt Newville's interpretation is correct. Ellen On Jul 20, 2015, at 19:41, Matt Newville newvi...@cars.uchicago.edumailto:newvi...@cars.uchicago.edu wrote: I think Ellen wants to first do a linear combination fit with chi(k) data and then look at what that combination of spectral components would look like for the XANES region. It seems like a fine idea to me. Off the top of my head I don't know the easiest way to do this. I don't think there is a single button for that, but I've been known to miss hidden features in Athena for years. --Matt On Jul 20, 2015 8:16 PM, Scott Calvin scal...@sarahlawrence.edumailto:scal...@sarahlawrence.edu wrote: Hi Ellen, Either I'm not understanding what you're trying to do, or what you're trying to do doesn't make sense. XANES is generally plotted as mu(E) or norm(E). To get from norm(E) to chi(k), two things must be done: a smooth background must be subtracted from norm(E), and E has to be converted to k. The conversion from E to k is reversible, but the background subtraction is not, since chi(k) is meant to be background independent. You therefore cannot, in principle, plot chi(k) data as norm(E). -Scott Calvin Sarah Lawrence College On Jul 20, 2015, at 7:48 PM, Ellen Daugherty ellen.daughe...@colostate.edumailto:ellen.daughe...@colostate.edu wrote: Hello, I was unable to find an example of this question in the archive, but please let me know if it has already been addressed. I would like to plot the results of linear combination fits performed in chi(k) in energy space to compare them to XANES fits. When I try to plot the saved fit in energy, I get a message saying: chi data cannot be plotted in energy. Is there any way to do this other than to use Excel to scale the weights of the standards? This would be exhausting to perform for combinatorial fits. I am using Athena in Demeter 0.9.20 on Windows 7. I have attached a sample and a few standards for aid in addressing the issue. Thank you! Ellen -- Ph.D. Candidate Research Assistant, Borch Labhttp://borch.agsci.colostate.edu/ Department of Chemistry Colorado State University http://borch.agsci.colostate.edu/group-members/ellen-daugherty/ Sample.norStandard 1.norStandard 2.norStandard 3.nor___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.govmailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.govmailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.govmailto:Ifeffit@millenia.cars.aps.anl.gov 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
[Ifeffit] plotting
Thanks everyone for the helpful comments! I'll go with exporting to Origin. A final question. I am now a Mac user, is there a good alternative to Origin? Best, - Eva On Mar 26, 2013, at 2:45 PM, ifeffit-requ...@millenia.cars.aps.anl.gov wrote: Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than Re: Contents of Ifeffit digest... Today's Topics: 1. generating high res figures (Eva Vanamee) 2. Re: generating high res figures (Scott Calvin) 3. Re: generating high res figures (Jason Gaudet) 4. Re: generating high res figures (Christopher Patridge) 5. Re: generating high res figures (Ravel, Bruce) -- Message: 1 Date: Tue, 26 Mar 2013 13:13:17 -0400 From: Eva Vanamee eva.vana...@mssm.edu To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] generating high res figures Message-ID: c2797f03-a481-47c5-8631-b43292f37...@mssm.edu Content-Type: text/plain; charset=us-ascii Hi, I'm in the happy stages of making figures. I'd like to know how to change figure legends, make high resolution figures from a fit, etc. For instance: I saved the session file. Can I go back to a particular fit to make a figure or do I need to rerun it? Can I change the figure legends? I used sample 1 and I want to give it a different name Can I use special characters (e.g. Greek letters)? Can I adjust the resolution for different formats (talk vs. publication)? I am running Demeter 0.9.9.9 under XP. Thanks in advance for the help! - Eva -- Message: 2 Date: Tue, 26 Mar 2013 13:25:01 -0400 From: Scott Calvin scal...@sarahlawrence.edu To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] generating high res figures Message-ID: ccdba9e5-8a56-4438-a0ec-e1a9b3f6c...@slc.edu Content-Type: text/plain; charset=us-ascii Hi Eva, Demeter is not intended to be used to produce publication-quality figures. It's best to export the data, fits, etc., and then use a proper graphing program to generate figures. Even a spreadsheet will do in a pinch, although most of us use dedicated scientific graphing software. --Scott Calvin Sarah Lawrence College On Mar 26, 2013, at 1:13 PM, Eva Vanamee eva.vana...@mssm.edu wrote: Hi, I'm in the happy stages of making figures. I'd like to know how to change figure legends, make high resolution figures from a fit, etc. For instance: I saved the session file. Can I go back to a particular fit to make a figure or do I need to rerun it? Can I change the figure legends? I used sample 1 and I want to give it a different name Can I use special characters (e.g. Greek letters)? Can I adjust the resolution for different formats (talk vs. publication)? I am running Demeter 0.9.9.9 under XP. Thanks in advance for the help! - Eva ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Message: 3 Date: Tue, 26 Mar 2013 13:51:36 -0400 From: Jason Gaudet jason.r.gau...@gmail.com To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] generating high res figures Message-ID: CANMcWtM=do9gr-jsmc--dxepwojaz-78n44mpranv5ujhtm...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 And to do this, use the Artemis Plot dialog box to generate the chart you want (e.g. the data and fit in magnitude R-space), click the Save Next Plot to File button at the very bottom of the dialog box, and click the correct plot button at the top (e.g. R). This lets you save the plot as an ASCII file. -Jason On Tue, Mar 26, 2013 at 1:25 PM, Scott Calvin scal...@sarahlawrence.eduwrote: Hi Eva, Demeter is not intended to be used to produce publication-quality figures. It's best to export the data, fits, etc., and then use a proper graphing program to generate figures. Even a spreadsheet will do in a pinch, although most of us use dedicated scientific graphing software. --Scott Calvin Sarah Lawrence College On Mar 26, 2013, at 1:13 PM, Eva Vanamee eva.vana...@mssm.edu wrote: Hi, I'm in the happy stages of making figures. I'd like to know how to change figure legends, make high resolution figures from a fit, etc. For instance: I saved the session file. Can I go back to a particular fit to make a figure or do I need to rerun
Re: [Ifeffit] plotting
Igor Simon -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Eva Vanamee Sent: Tuesday, March 26, 2013 3:51 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] plotting Thanks everyone for the helpful comments! I'll go with exporting to Origin. A final question. I am now a Mac user, is there a good alternative to Origin? Best, - Eva On Mar 26, 2013, at 2:45 PM, ifeffit-requ...@millenia.cars.aps.anl.gov wrote: Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than Re: Contents of Ifeffit digest... Today's Topics: 1. generating high res figures (Eva Vanamee) 2. Re: generating high res figures (Scott Calvin) 3. Re: generating high res figures (Jason Gaudet) 4. Re: generating high res figures (Christopher Patridge) 5. Re: generating high res figures (Ravel, Bruce) -- Message: 1 Date: Tue, 26 Mar 2013 13:13:17 -0400 From: Eva Vanamee eva.vana...@mssm.edu To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] generating high res figures Message-ID: c2797f03-a481-47c5-8631-b43292f37...@mssm.edu Content-Type: text/plain; charset=us-ascii Hi, I'm in the happy stages of making figures. I'd like to know how to change figure legends, make high resolution figures from a fit, etc. For instance: I saved the session file. Can I go back to a particular fit to make a figure or do I need to rerun it? Can I change the figure legends? I used sample 1 and I want to give it a different name Can I use special characters (e.g. Greek letters)? Can I adjust the resolution for different formats (talk vs. publication)? I am running Demeter 0.9.9.9 under XP. Thanks in advance for the help! - Eva -- Message: 2 Date: Tue, 26 Mar 2013 13:25:01 -0400 From: Scott Calvin scal...@sarahlawrence.edu To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] generating high res figures Message-ID: ccdba9e5-8a56-4438-a0ec-e1a9b3f6c...@slc.edu Content-Type: text/plain; charset=us-ascii Hi Eva, Demeter is not intended to be used to produce publication-quality figures. It's best to export the data, fits, etc., and then use a proper graphing program to generate figures. Even a spreadsheet will do in a pinch, although most of us use dedicated scientific graphing software. --Scott Calvin Sarah Lawrence College On Mar 26, 2013, at 1:13 PM, Eva Vanamee eva.vana...@mssm.edu wrote: Hi, I'm in the happy stages of making figures. I'd like to know how to change figure legends, make high resolution figures from a fit, etc. For instance: I saved the session file. Can I go back to a particular fit to make a figure or do I need to rerun it? Can I change the figure legends? I used sample 1 and I want to give it a different name Can I use special characters (e.g. Greek letters)? Can I adjust the resolution for different formats (talk vs. publication)? I am running Demeter 0.9.9.9 under XP. Thanks in advance for the help! - Eva ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Message: 3 Date: Tue, 26 Mar 2013 13:51:36 -0400 From: Jason Gaudet jason.r.gau...@gmail.com To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] generating high res figures Message-ID: CANMcWtM=do9gr-jsmc--dxepwojaz-78n44mpranv5ujhtm...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 And to do this, use the Artemis Plot dialog box to generate the chart you want (e.g. the data and fit in magnitude R-space), click the Save Next Plot to File button at the very bottom of the dialog box, and click the correct plot button at the top (e.g. R). This lets you save the plot as an ASCII file. -Jason On Tue, Mar 26, 2013 at 1:25 PM, Scott Calvin scal...@sarahlawrence.eduwrote: Hi Eva, Demeter is not intended to be used to produce publication-quality figures. It's best to export the data, fits, etc., and then use a proper graphing program to generate figures. Even a spreadsheet will do in a pinch, although most of us use dedicated scientific graphing software. --Scott Calvin Sarah Lawrence College On Mar 26, 2013, at 1:13 PM, Eva Vanamee eva.vana...@mssm.edu
Re: [Ifeffit] plotting
This list of alternatives is pretty near exhaustive: http://alternativeto.net/software/originlab/ Although I personally use Origin. On Tue, Mar 26, 2013 at 5:07 PM, Scott Calvin scal...@sarahlawrence.eduwrote: Hi Eva, Personally, I'm pretty happy with Pro Fit. It's a commercial product (like Origin) but is much cheaper. It's also got the stupidest name imaginable, since Google will assume you misspelled profit. With that in mind the website is http://www.quansoft.com . If you're willing to spend more, Igor Pro is a good product. --Scott Calvin Sarah Lawrence College P.S. Disclosure: I have no financial relationship with either software producer. On Mar 26, 2013, at 4:50 PM, Eva Vanamee eva.vana...@mssm.edu wrote: Thanks everyone for the helpful comments! I'll go with exporting to Origin. A final question. I am now a Mac user, is there a good alternative to Origin? Best, - Eva ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov 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
Re: [Ifeffit] plotting
I'll second Igor Pro. Jeff Sent from my iPhone On Mar 26, 2013, at 3:57 PM, Bare, Simon R simon.b...@honeywell.com wrote: Igor Simon -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Eva Vanamee Sent: Tuesday, March 26, 2013 3:51 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] plotting Thanks everyone for the helpful comments! I'll go with exporting to Origin. A final question. I am now a Mac user, is there a good alternative to Origin? Best, - Eva On Mar 26, 2013, at 2:45 PM, ifeffit-requ...@millenia.cars.aps.anl.gov wrote: Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than Re: Contents of Ifeffit digest... Today's Topics: 1. generating high res figures (Eva Vanamee) 2. Re: generating high res figures (Scott Calvin) 3. Re: generating high res figures (Jason Gaudet) 4. Re: generating high res figures (Christopher Patridge) 5. Re: generating high res figures (Ravel, Bruce) -- Message: 1 Date: Tue, 26 Mar 2013 13:13:17 -0400 From: Eva Vanamee eva.vana...@mssm.edu To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] generating high res figures Message-ID: c2797f03-a481-47c5-8631-b43292f37...@mssm.edu Content-Type: text/plain; charset=us-ascii Hi, I'm in the happy stages of making figures. I'd like to know how to change figure legends, make high resolution figures from a fit, etc. For instance: I saved the session file. Can I go back to a particular fit to make a figure or do I need to rerun it? Can I change the figure legends? I used sample 1 and I want to give it a different name Can I use special characters (e.g. Greek letters)? Can I adjust the resolution for different formats (talk vs. publication)? I am running Demeter 0.9.9.9 under XP. Thanks in advance for the help! - Eva -- Message: 2 Date: Tue, 26 Mar 2013 13:25:01 -0400 From: Scott Calvin scal...@sarahlawrence.edu To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] generating high res figures Message-ID: ccdba9e5-8a56-4438-a0ec-e1a9b3f6c...@slc.edu Content-Type: text/plain; charset=us-ascii Hi Eva, Demeter is not intended to be used to produce publication-quality figures. It's best to export the data, fits, etc., and then use a proper graphing program to generate figures. Even a spreadsheet will do in a pinch, although most of us use dedicated scientific graphing software. --Scott Calvin Sarah Lawrence College On Mar 26, 2013, at 1:13 PM, Eva Vanamee eva.vana...@mssm.edu wrote: Hi, I'm in the happy stages of making figures. I'd like to know how to change figure legends, make high resolution figures from a fit, etc. For instance: I saved the session file. Can I go back to a particular fit to make a figure or do I need to rerun it? Can I change the figure legends? I used sample 1 and I want to give it a different name Can I use special characters (e.g. Greek letters)? Can I adjust the resolution for different formats (talk vs. publication)? I am running Demeter 0.9.9.9 under XP. Thanks in advance for the help! - Eva ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Message: 3 Date: Tue, 26 Mar 2013 13:51:36 -0400 From: Jason Gaudet jason.r.gau...@gmail.com To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] generating high res figures Message-ID: CANMcWtM=do9gr-jsmc--dxepwojaz-78n44mpranv5ujhtm...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 And to do this, use the Artemis Plot dialog box to generate the chart you want (e.g. the data and fit in magnitude R-space), click the Save Next Plot to File button at the very bottom of the dialog box, and click the correct plot button at the top (e.g. R). This lets you save the plot as an ASCII file. -Jason On Tue, Mar 26, 2013 at 1:25 PM, Scott Calvin scal...@sarahlawrence.eduwrote: Hi Eva, Demeter is not intended to be used to produce publication-quality figures. It's best to export the data, fits, etc., and then use a proper graphing program to generate figures. Even a spreadsheet will do in a pinch, although most of us use dedicated scientific
Re: [Ifeffit] plotting
Hi, Sorry for coming in late in this conversation. I won't disagree that Origin or Igor Pro can be used to make lovely publication-quality graphics -- those are fine choices. The poor quality of the graphics in the older versions of Ifeffit / Horae was always been a disappointment to me. It's certainly reasonable to say that exporting to another program is necessary, but I believe the latest versions should and do have much higher quality graphics. Larch certainly has much better graphics than Ifeffit. See for example: http://xraypy.github.com/xraylarch/xafs/xafsft.html#examples-forward-xafs-fourier-transforms In the on-line docs, the graphics may look mediocre because they are scaled, but if you click on them you will see the PNG file created directly by saving the image from the Plot window (or cut with Ctrl-C and pasted directly into presentation software). Another example (from the feffit chapter): http://xraypy.github.com/xraylarch/_images/feffit_feo_r.png shows the Greek characters and mathematical rendering, generated using latex notation. Depending on what you need, these may publication quality graphs,and they can be copied directly from the Plotting windows into other applications (for example, Ctrl-C to copy to clipboard works). The axis labels (plain text or latex), colors, symbols, line widths, and so on can be adjusted from a Plot Configuration window after the plot is drawn, see http://xraypy.github.com/xraylarch/plotting/index.html#interactive-use-of-the-plot-windows There are many things that cannot be done simply with these plots (figure-in-figure, complex stacking), but in principle, Larch can be used to generate any of the kinds of plots available from the matplotlib library, see http://matplotlib.org/gallery.html Of course, this does requires some scripting to make plots. There are other good, free choices for making high-quality graphics. As others have said, investing some time in learning how to make high quality graphics is worth the effort. Origin or Igor Pro are very good tools, and would be fine choices for learning and not very expensive. But please do not use Excel. It cannot make publication quality graphics. Cheers, --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] plotting
Matt is correct. The graphics in Larch are much better than the graphics in the old version of ifeffit. I may go back to using the command line. Jeff On Mar 26, 2013, at 6:12 PM, Matt Newville newvi...@cars.uchicago.edu wrote: The poor quality of the graphics in the older versions of Ifeffit / Horae was always been a disappointment to me. It's certainly reasonable to say that exporting to another program is necessary, but I believe the latest versions should and do have much higher quality graphics. Larch certainly has much better graphics than Ifeffit. See for example: http://xraypy.github.com/xraylarch/xafs/xafsft.html#examples-forward-xafs-fourier-transforms In the on-line docs, the graphics may look mediocre because they are scaled, but if you click on them you will see the PNG file created directly by saving the image from the Plot window (or cut with Ctrl-C and pasted directly into presentation software). Another example (from the feffit chapter): http://xraypy.github.com/xraylarch/_images/feffit_feo_r.png shows the Greek characters and mathematical rendering, generated using latex notation. Depending on what you need, these may publication quality graphs,and they can be copied directly from the Plotting windows into other applications (for example, Ctrl-C to copy to clipboard works). The axis labels (plain text or latex), colors, symbols, line widths, and so on can be adjusted from a Plot Configuration window after the plot is drawn, see http://xraypy.github.com/xraylarch/plotting/index.html#interactive-use-of-the-plot-windows There are many things that cannot be done simply with these plots (figure-in-figure, complex stacking), but in principle, Larch can be used to generate any of the kinds of plots available from the matplotlib library, see http://matplotlib.org/gallery.html ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] plotting backends in Demeter
Hi, This afternoon I noticed that someone who goes by the handle khuonggit posted a question at David Hughes' gist about installing Demeter on Ubuntu. https://gist.github.com/3959252 I hope he is reading this mailing list. khuonggit asked: I am beginner in EXAFS. I tried to install Demeter in Ubuntu 12.04 64 bit following the guidance here and the installation was successful. However, when I tried to open (d)athena and import some data, the default plotting backend is PGPLOT, not GNUPLOT. Could you please show me how to change it to GNUPLOT ? Good question. In the time since khuonggit posted that question, I have modified the build script to attempt to detect the presence of gnuplot and modify Demeter's configuration accordingly. Hopefully, this will become a non-issue in the future. The plotting backend can be set by hand at any time in any of the GUI programs by editing the preferences. In Athena, choose Preferences from the main menu. In Artemis, choose Edit preferences from the file menu. In Hephaestus, click on the Configure icon at the bottom left. Once at the preferences tool, select Plot then plotwith. Select gnuplot then click Apply and save. B -- Bruce Ravel bra...@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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Plotting Athena mu(E) with pre / post edge lines
Hello all, How do I export absorption data showing the pre edge, post edge, and background function to a text file so I can plot this in origin or excel? Joseph -- Joseph Washington Research Assistant Department of Physics North Carolina State University 431 Riddick Hall Raleigh, NC 27695-8202 email: jswas...@ncsu.edu ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Plotting Athena mu(E) with pre / post edge lines
Joseph, See the FAQ here (scroll down to How do I make publication quality plots...): http://cars9.uchicago.edu/ifeffit/FAQ/HoraeQuestions#head-2536b76fd9a517c8cff6b367d89e9fd03cbf5999 -Rich On Tue, Oct 27, 2009 at 6:33 PM, Joseph Washington breadit...@gmail.comwrote: Hello all, How do I export absorption data showing the pre edge, post edge, and background function to a text file so I can plot this in origin or excel? Joseph -- Joseph Washington Research Assistant Department of Physics North Carolina State University 431 Riddick Hall Raleigh, NC 27695-8202 email: jswas...@ncsu.edu ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov 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
Re: [Ifeffit] Plotting problem
On Wednesday 23 May 2007, Clement Mbudi wrote: Can somebody tell how to get rid of the all marked groups default title when plotting several groups together within Athena environment. The change group label seems to only work for a single group. Similarly, how to change titles of both Y and X axes within Athena ? As we have discussed recently, Athena and Ifeffit are XAS programs with some visualization tools. Those visualization tools were never intended as publication quality plotting tools. Consequently there are lots of parts of the plot over which Athena does not offer any control. For example, there is no way (aside from the zooming tool, I suppose) to set the plotting range on the y axis. Similarly, the title and axis labels are generated automatically. My stock answer for Athena users is to export the data to a proper plotting program when writing an article or preparing a poster. I could be persuaded to create controls for all the things that don't have controls, but I am sceptical that it would add much value to the program as long as we are working with pgplot. If reading all marked groups over and over again -- or any other part of Athena -- is really bugging you, make a suggestion for how you think Athena should work and I'll consider implementing it. B -- Bruce Ravel -- [EMAIL PROTECTED] Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USAfax: (1) 630 252 9793 My homepage:http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Plotting problem
On Wednesday 23 May 2007, Webb, Adam wrote: Hi, In the edit menu there is a handy tool called Display Ifeffit buffer. This shows you the commands that Athena sends to Ifeffit. In fact it is possible to send commands yourself. You just enter it into the entry box at the bottom of the window. In answer to your question. The way that I know is to make a plot and see what the commands are. You can directly copy them into a text editor, make the changes and paste them back into Athena. All the labels, colours etc are there. Adam brings up a really good point here. So good, in fact, that I added a new FAQ question. See number 10 at http://cars9.uchicago.edu/iffwiki/FAQ/HoraeQuestions B Clement Mbudi wrote: Hi there, Can somebody tell how to get rid of the all marked groups default title when plotting several groups together within Athena environment. The change group label seems to only work for a single group. Similarly, how to change titles of both Y and X axes within Athena ? Thanks. Clement Edmonton, AB -- Bruce Ravel -- [EMAIL PROTECTED] Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USAfax: (1) 630 252 9793 My homepage:http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
