A question about the new Artemis version
Hello all I just upgraded to the newest horae-031 package It looks to me that the new Artemis version (0.7.001) doesn't have that nice button "use previous background" anymore. If I am not mistaken the button allowed to subtract background fitted previously. Am I? Is it somehow hidden in the new version? Thank you in advance Stanislav
On Wednesday 24 March 2004 02:50 pm, Stanislav Stoupin wrote:
I just upgraded to the newest horae-031 package It looks to me that the new Artemis version (0.7.001) doesn't have that nice button "use previous background" anymore. If I am not mistaken the button allowed to subtract background fitted previously. Am I? Is it somehow hidden in the new version?
I changed how the concept of using background subtracted data is implemented. Like many things with Artemis, it is underdocumented. In the Data menu is a option for "Save background subtracted as chi(k)". This will subtract the background you just performed form the data and save that chi(k) function to a file. The default behavior is to save the new chi(k) file in the project workspace so that it gets inlcuded in the project when the project is saved. Then, Artemis will ask if you want to replace the current data with the background subtracted data. You can say yes or no, as you wish. As you continue working, it is easy to switch between the original data and the background subtracted data because both are stored in the project work space. File menu -> "Project data" -> "Import project data" is a shortcut to all the data stored in the project work space. This underscores one of the advantages of using zip files as project files. It is easy to carry around many data files along with a project and then quickly switch between them without changing the model or stopping and restarting Artemis. FYI. Difference spectra work essentially the same way. The chi(k) containing the data minus a sum of paths is saved to the workspace and you are asked if you want to change from the original data to the difference spectrum. All clear? B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b 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 all, A project we're working on now seems like something that shouldn't be that hard to do in Artemis, but it's proving unwieldly. I was hoping someone could suggest a less cumbersome method: We have data on 11 related samples, plus a standard. All use the same FEFF calculation and paths (about 25 paths or so). Each one was analyzed as a separate project file, and gave us promising results. Now we would like to perform a multiple-data set fit...on all the samples if possible, or some subset if not. There are a couple of reasons for wanting to do this. One is to get a more robust determination of parameters that are universal to all samples, like S02, rather than just depending on the fit from the standard. The other is that one parameter we are fitting (crystallite size) quite properly shows a rather large uncertainty in its fit. But it is clear from playing around that the difference between samples for crystallite size is much better determined. Our plan is to guess crystallite size for one particular sample, and guess a difference from this size for each of the other samples. This should, of course, not yield a significantly different result from just guessing each size. But then we'd like to set the crystallite size for the first sample to its best-fit value. The only purpose for this is to obtain an estimate of the uncertainty in the =relative= crystallite sizes of the samples. OK, so that's the plan, but the implementation is awkward. It seems to me that with the current version of Artemis we have to pretend that there is a separate FEFF calculation for each sample, and we have to enter all the path parameters anew for each sample. There's a lot of nitty-gritty constraints on multiple-scattering paths and such, so that's a lot of data entry. Also, I forget what the current limits are on total number of FEFF paths and total number of samples--are we going to be hitting limits? Basically, I can understand if we simply can't fit this many samples simultaneously with the standard code. That's not a big problem; we can get most of what we want by fitting a subset of the samples. It's the data-entry that's a bit of a pain. For each sample we have to re-enter all of the path and GDS information, and I think we'll get a bloated ZIP file, since presumably the FEFF calculation will be repeated once for each sample even though they are all identical. This doesn't seem like all that unusual a scenario. Does anyone have a good idea of how this should be done in Artemis, or do we just have to bite the bullet and re-enter all the pertinent information for each sample we bring in (and live with the bloated project file). --Scott Calvin Sarah Lawrence College P.S. Thanks to Matt and Bruce again for even making such a thing conceivable. The analysis on this project is being done by a talented freshman without coding experience. It is a tribute to the software (and the student!) that we've been able to get so far so fast.
On Tuesday 30 March 2004 07:03 pm, Scott Calvin wrote:
This doesn't seem like all that unusual a scenario. Does anyone have a good idea of how this should be done in Artemis, or do we just have to bite the bullet and re-enter all the pertinent information for each sample we bring in (and live with the bloated project file).
I think the answer that involves Artemis alone is to bite the bullet. However, you are the second person in the last 18 hours to ask for the ability to clone a feff calculation. (Shelly is the other ;-) Since it has been on my todo list for quite some time and since two of the power-users have asked for it, I suppose it is high time to implement it. FWIW, I don't see project file size as a real problem here. The real problem is the inconvenience of replicating the feff calculation within Artemis and that doing so is error-prone. Another possibility is to use Artemis to set up the one-data-set fit and have it write out the Ifeffit script for that fit. Then use a text editor and a lot of cut-n-paste to turn the one-set fit into a multi-set fit. Then run the script from the command line. B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b 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/
At 09:25 AM 3/31/2004 -0500, you wrote:
I think the answer that involves Artemis alone is to bite the bullet.
However, you are the second person in the last 18 hours to ask for the ability to clone a feff calculation. (Shelly is the other ;-) Since it has been on my todo list for quite some time and since two of the power-users have asked for it, I suppose it is high time to implement it.
Crazy minds think alike... :)
Another possibility is to use Artemis to set up the one-data-set fit and have it write out the Ifeffit script for that fit. Then use a text editor and a lot of cut-n-paste to turn the one-set fit into a multi-set fit. Then run the script from the command line.
That makes sense...we may try to do it that way. --Scott Calvin Sarah Lawrence College
participants (3)
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Bruce Ravel -
Scott Calvin -
Stanislav Stoupin