Re: [Ifeffit] Plotting chi(R) from FEFF in XAS Viewer (Larch) with

2022-12-14 Thread Mosselmans, Fred (DLSLtd,RAL,SCI)


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 
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Re: [Ifeffit] Plotting chi(R) from FEFF in XAS Viewer (Larch) with phase correction

2022-12-13 Thread Matt Newville
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
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Re: [Ifeffit] Plotting flattened feffit simulation results

2019-01-28 Thread FonsPaul
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

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Re: [Ifeffit] Plotting flattened feffit simulation results

2019-01-28 Thread Matt Newville
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
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Re: [Ifeffit] Plotting flattened feffit simulation results

2019-01-28 Thread FonsPaul
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!
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Re: [Ifeffit] Plotting flattened feffit simulation results

2019-01-28 Thread Chris Patridge
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!
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Re: [Ifeffit] Plotting chi(k) linear combination fit in energy

2015-07-21 Thread Ellen Daugherty
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/
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Re: [Ifeffit] Plotting chi(k) linear combination fit in energy

2015-07-21 Thread Bruce Ravel

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/
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Re: [Ifeffit] Plotting chi(k) linear combination fit in energy

2015-07-21 Thread Bruce Ravel


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___
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--
 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/
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Re: [Ifeffit] Plotting chi(k) linear combination fit in energy

2015-07-20 Thread Matt Newville
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
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Re: [Ifeffit] Plotting chi(k) linear combination fit in energy

2015-07-20 Thread Ellen Daugherty
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___
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Re: [Ifeffit] Plotting chi(k) linear combination fit in energy

2015-07-20 Thread Scott Calvin
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___
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Re: [Ifeffit] Plotting chi(k) linear combination fit in energy

2015-07-20 Thread Baker, Leslie (lba...@uidaho.edu)
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___
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Re: [Ifeffit] plotting

2013-03-26 Thread Bare, Simon R
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
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 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

2013-03-26 Thread Jason Gaudet
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
 


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Re: [Ifeffit] plotting

2013-03-26 Thread Jeff Terry
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

2013-03-26 Thread Matt Newville
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
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Re: [Ifeffit] plotting

2013-03-26 Thread Jeff Terry
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
 


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Re: [Ifeffit] Plotting Athena mu(E) with pre / post edge lines

2009-10-27 Thread Richard Mayes
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
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Re: [Ifeffit] Plotting problem

2007-05-23 Thread Bruce Ravel
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/


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Re: [Ifeffit] Plotting problem

2007-05-23 Thread Bruce Ravel
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/

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