Hi, I wonder if you can help: I'm using Athena to process some XANES data and wish to export the derivative data so that I can use a package such as Excel to prepare the data for publication. However, the derivative data that is presented visually in the graphics window is a much cleaner, smoother data set than the one I get when I export it in either deriv Mu(E) or deriv Norm(E). I tried the smoothing option in Data-Smooth mu(E) with 3 iterations and again with 10 iterations on the interpolative smoothing. Both gave far noisier data than the data shown in the Graphics window. Please can you tell me how to get exported derivative data that will be (more or less) the same as that shown in the graphics window? Basically I' hoping for WYSIWYG if that's possible? Any thoughts or suggestions would be very welcome and thanks for your time. -- Dr. Paul Bingham Postdoctoral Research Associate Immobilisation Science Laboratory Dept. of Engineering Materials University of Sheffield Mappin Street Sheffield S1 3JD UK Email: p.a.bingham@sheffield.ac.uk Direct Line: (0114) 2225473
Paul, By default, Athena smooths derivative data three times before plotting it. This is controlled by the plot->smoothderiv parameter (which can be set in the preferences dialog under the Setting menu). When you export the derivative data, it is not smoothed. So, to reproduce Athena's plot exactly in some other plotting program, you would need to smooth the data using that tool. Not very WISIWYG, I suppose. But it still seems like the right solution. With exported data that is not smoothed, you have the option to smoothing. Exporting data that is smoothed, you do not have the option of unsmoothing! B On Sunday, May 30, 2010 06:47:34 am Paul Bingham wrote:
Hi, I wonder if you can help:
I'm using Athena to process some XANES data and wish to export the derivative data so that I can use a package such as Excel to prepare the data for publication. However, the derivative data that is presented visually in the graphics window is a much cleaner, smoother data set than the one I get when I export it in either deriv Mu(E) or deriv Norm(E). I tried the smoothing option in Data-Smooth mu(E) with 3 iterations and again with 10 iterations on the interpolative smoothing. Both gave far noisier data than the data shown in the Graphics window.
Please can you tell me how to get exported derivative data that will be (more or less) the same as that shown in the graphics window? Basically I' hoping for WYSIWYG if that's possible? Any thoughts or suggestions would be very welcome and thanks for your time.
By default, Athena smooths derivative data three times before plotting it. This is controlled by the plot->smoothderiv parameter (which can be set in the preferences dialog under the Setting menu).
When you export the derivative data, it is not smoothed. So, to reproduce Athena's plot exactly in some other plotting program, you would need to smooth the data using that tool.
Or using the ifeffit command window.... If you open the ifeffit buffer window and look at what happens when you plot the derivative, you'll see something like: set fmgb.smooth = fmgb.xmu set fmgb.smooth = smooth(fmgb.smooth) set fmgb.smooth = smooth(fmgb.smooth) set fmgb.smooth = smooth(fmgb.smooth) newplot(fmgb.energy+0, "1*(deriv(fmgb.smooth)/deriv(fmgb.energy))+0", xlabel="E (eV)", ylabel="smoothed deriv x\gm(E)", fg=black, bg=white, grid, gridcolor="grey82" , xmin=8777.58, xmax=9777.58, style=lines, color="blue", key="\gm", title="cu.xmu") pmarker "fmgb.energy+0", "deriv(fmgb.smooth)/deriv(fmgb.energy)", 8977.58, 9, orange2, 0 (Note: the "fmgb" part will be some other 4 character sequence). And if you click "Save norm(E)" you'll see something like this in the Ifeffit buffer window: set fmgb.der_norm = deriv(fmgb.norm)/deriv(fmgb.energy) set fmgb.ee = fmgb.energy+0 write_data(file="..../cu.xmu.nor", label="energy norm bkg_norm der_norm", $id_line, $id2_line, $param_line_*, $fmgb_title_*, fmgb.ee, fmgb.flat , fmgb.fbkg, fmgb.der_norm ) erase fmgb.ee erase fmgb.bkg_norm fmgb.der_norm This may look like a lot of "code", but you don't need most of it, and can just pare it down to something like set fmgb.deriv = deriv(smooth(smooth(smooth(fmgb.xmu))))/deriv(fmgb.energy) write_data(file="derivplot.dat", fmgb.energy, fmgb.deriv) If you're doing this for many datasets, you could write a macro: macro savederiv group filename set $1.deriv = deriv(smooth(smooth(smooth($1.xmu))))/deriv($1.energy) write_data(file=$2, $1.energy, $1.deriv) end macro And then use that as savederiv fmgb derivplot_group1.dat savederiv xdsa derivplot_group2.dat and so on. It's not WSYWIG, but it is more flexible -- you can easily change how much smoothing is done, for example. Hope that helps, --Matt
Paul,
If you're just wanting to adjust things like fonts and line sizes on the
plot for publication, then you have the option to save the plot as a
metafile from the PGPlot window and import it into PowerPoint. Then convert
the metafile into a drawing object with the "ungroup" feature. From this
point you can change fonts, line shapes, colors, etc. to get the plot how
you want it to look for publication. You can then re-save that slide as a
picture (gif, tiff, metafile, etc) to be imported into the manuscript. This
can get time intensive, but it's an alternative if all you want to do is
adjust fonts and line colors/sizes.
One caveat though, don't change the data! You can easily and unknowingly
change the data if you're not careful (performing an action on one part of
the drawing object without realizing another is highlighted for example) so
always compare the final product to the original to make sure it's the same.
-Rich
On Sun, May 30, 2010 at 6:47 AM, Paul Bingham
Hi, I wonder if you can help:
I'm using Athena to process some XANES data and wish to export the derivative data so that I can use a package such as Excel to prepare the data for publication. However, the derivative data that is presented visually in the graphics window is a much cleaner, smoother data set than the one I get when I export it in either deriv Mu(E) or deriv Norm(E). I tried the smoothing option in Data-Smooth mu(E) with 3 iterations and again with 10 iterations on the interpolative smoothing. Both gave far noisier data than the data shown in the Graphics window.
Please can you tell me how to get exported derivative data that will be (more or less) the same as that shown in the graphics window? Basically I' hoping for WYSIWYG if that's possible? Any thoughts or suggestions would be very welcome and thanks for your time.
-- Dr. Paul Bingham Postdoctoral Research Associate Immobilisation Science Laboratory Dept. of Engineering Materials University of Sheffield Mappin Street Sheffield S1 3JD UK
Email: p.a.bingham@sheffield.ac.uk Direct Line: (0114) 2225473
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
participants (4)
-
Bruce Ravel -
Matt Newville -
Paul Bingham -
Richard Mayes