[Ifeffit] plotting

Bare, Simon R Simon.Bare at honeywell.com
Tue Mar 26 15:57:47 CDT 2013


Igor

Simon 


-----Original Message-----
From: ifeffit-bounces at millenia.cars.aps.anl.gov [mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of Eva Vanamee
Sent: Tuesday, March 26, 2013 3:51 PM
To: ifeffit at 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-request at millenia.cars.aps.anl.gov>
 wrote:

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> 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.vanamee at mssm.edu>
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: [Ifeffit] generating high res figures
> Message-ID: <C2797F03-A481-47C5-8631-B43292F375B2 at 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 <scalvin at sarahlawrence.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] generating high res figures
> Message-ID: <CCDBA9E5-8A56-4438-A0EC-E1A9B3F6CB45 at 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.vanamee at 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 at 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.gaudet at gmail.com>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] generating high res figures
> Message-ID:
> 	<CANMcWtM=dO9GR-jSMC--dXEPWojAZ-78N44mPrAnV5ujHtMAmw at 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 <scalvin at sarahlawrence.edu>wrote:
> 
>> 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.vanamee at 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 at millenia.cars.aps.anl.gov
>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> 
>> 
>> _______________________________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> 
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> 
> ------------------------------
> 
> Message: 4
> Date: Tue, 26 Mar 2013 13:25:34 -0400
> From: Christopher Patridge <patridge at buffalo.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] generating high res figures
> Message-ID: <5151DA0E.9090206 at buffalo.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Eva,
> 
> I don't how flexible would consider exporting the fits you have 
> completed and using a plotting software (Excel, Origin, Qplot, 
> sigmaplot, Igor) to generate the number of adjustments you require.
> 
> Chris
> 
> ********************************
> Christopher J. Patridge, PhD
> NRC Post Doctoral Research Associate
> Naval Research Laboratory
> Washington, DC 20375
> Cell: 315-529-0501
> 
> On 3/26/2013 1:13 PM, Eva Vanamee 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 at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> 
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Tue, 26 Mar 2013 18:45:19 +0000
> From: "Ravel, Bruce" <bravel at bnl.gov>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] generating high res figures
> Message-ID:
> 	<47CED3CD722C2A439C0D1D1056B213251F32FEBF at EX10-MB1.BNL.GOV>
> Content-Type: text/plain; charset="iso-8859-7"
> 
> 
> As others said, it is not my intention that A&A be used for publication quality plots, although part of the motivation to make Demeter, as compared to the earlier version, was not make prettier plots.  I, in fact, use screen captures of the plot window regularly in presentations and posters.  But I also do as the others advised -- I export the data to ascii column files and make dedicated plots for my publications.
> 
> Even aside from the fact that I chose not to make Demeter into a fully featured scientific plotting tool, it is wise to spend some time thinking hard about your plots for publication.  Figures are part of the story you are telling in your paper.  It is good for you and good for your reader if you spend the time to make beautiful, expressive plots using a highly capable plotting tool.
> 
>> Can I change the figure legends? I used sample 1 and I want to give it a different name
> 
> Yes.  That's easy.  Group menu -> Rename current group.  Or Shift-ctrl-l.  Or double click on the data group in the group list.
> 
>> Can I use special characters (e.g. Greek letters)?
> 
> Not conveniently.  Strictly speaking, if you observe the weird formatting rules of the underlying plotting tool, you can do so.  For example, if you you change "Sample 1" to "Sample {/Symbol a}" it will be printed in the legend of the plot as "Sample ?".  But then you will have a weirdly named data group in the group list.  (The rest of the Greek characters are made in the same way.  "Sample {/Symbol S}" = "Sample ?" and so on.)
> 
> I have never actually thought about how to make it possible to give a group a sensible name and have special characters plotted in the legend.  It doesn't seem like a high priority, but I could be persuaded.
> 
>> Can I adjust the resolution for different formats (talk vs. publication)?
> 
> Your best bet by FAR is to export the data as ascii column files and use your favorite plotting tool to export into a vector format, such as PDF or SVG.  The beauty of vector formats is that they can rescale without loss of quality.
> 
>> I am running Demeter 0.9.9.9 under XP.
> 
> You might consider upgrading.  There have been a lot of bug fixes and new features since then.   One such feature is the ability to export the most recent plot as a PNG or PDF file.
> 
> B
> 
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