Hi folks, I was just playing a bit around with some data and it sprang to my mind that sometimes the idea of doing difference file spectra fits would be a nice feature (like XDAP has it). This would be great to identify single contributions of certain scatterers that are close to each other or somehow other produce similar paths. How about including a feature which lets you extract a "new" chi.dat file from the original data minus some paths one has selected? This file could then be further processed. Finally something similar for EASE: I'm still one of those old-fashioned EMACS folks and would like to have something like this at my hands in EASE too. Bruce, what do you think about it? Would it be possible? I'm keen on hearing your ideas about this. Norbert -- Dr. rer. nat. Norbert Weiher (norbertweiher@yahoo.de) Laboratory for Technical Chemistry - ETH Hönggerberg HCI E 117 - 8093 Zürich - Phone: +41 1 63 2 3123
On Tuesday 18 March 2003 06:56 am, Norbert Weiher wrote:
I was just playing a bit around with some data and it sprang to my mind that sometimes the idea of doing difference file spectra fits would be a nice feature (like XDAP has it). This would be great to identify single contributions of certain scatterers that are close to each other or somehow other produce similar paths.
How about including a feature which lets you extract a "new" chi.dat file from the original data minus some paths one has selected? This file could then be further processed.
Subtracting a sum of paths from the data is pretty easy at the level of ifeffit's math expressions. A feature for subtracting an arbitrary sum of paths from the data does not currently exist in Artemis, but I can put it on the todo list. If you choose to fit in original k-space, the residual is basically what you are asking for. You can save the residual function to a file and then treat it as data in a new fitting project.
Finally something similar for EASE: I'm still one of those old-fashioned EMACS folks and would like to have something like this at my hands in EASE too. Bruce, what do you think about it? Would it be possible?
What you are asking for would be a little outside the scope of EASE (though not out of the question). Since that would be a rather low priority chore for me, you would be much better off solving this yourself. Run feffit with the flags for writing the individual path files in k-space turned on. Then write yourself a little perl or python script to read in the data and a number of the k.NNN files and write out the difference spectrum. That should be pretty easy since, if you restrict yourself to the output files from feffit, you can be sure that they are all on the same grid. I bet you could solve that in 20 lines or less of perl ;-) B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Hi Norbert, Bruce,
On Tuesday 18 March 2003 06:56 am, Norbert Weiher wrote:
I was just playing a bit around with some data and it sprang to my mind that sometimes the idea of doing difference file spectra fits would be a nice feature (like XDAP has it). This would be great to identify single contributions of certain scatterers that are close to each other or somehow other produce similar paths.
How about including a feature which lets you extract a "new" chi.dat file from the original data minus some paths one has selected? This file could then be further processed.
Subtracting a sum of paths from the data is pretty easy at the level of ifeffit's math expressions. A feature for subtracting an arbitrary
Like Bruce said, subtracting a partial fit (say, of the first shell) from data, and fitting the residual is possible with ifeffit. It might even be called easy. Similarly, working with the differences between data files is not hard. I'm not sure what XDAP does... Anyway, fitting and then subtracting the contribution from a set of paths (eg, the first shell) so that you can analyze further paths is identical to first fitting the set of paths, then fixing all the parameters to the best fit values to analyze the higher shells. Doing the subtraction emphasizes the rest of the spectra, which can definitely help visualization of the fit to the higher shells. But doing the subtraction does come at a price though. What you're subtracting is 'only' the best-fit, not necessarily the truth and definitely not including the uncertainty in the fit. At the end of the analysis, it's usually best to do a full fit (that is, with all parameters floating) to understand the correlations between variables. Subtracting off a shell makes that impossible, so whiile analyzing differences has definite advantages, it should be done with caution. It is very difficult to subtract uncertainty. --Matt
On Tuesday 18 March 2003 12:41 pm, Matt Newville wrote:
At the end of the analysis, it's usually best to do a full fit (that is, with all parameters floating) to understand the correlations between variables. Subtracting off a shell makes that impossible, so whiile analyzing differences has definite advantages, it should be done with caution.
It is very difficult to subtract uncertainty.
A darn good point! B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
participants (3)
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Bruce Ravel -
Matt Newville -
Norbert Weiher