Hi, If my memory is correct there was a period of time you were taking request for improvements on Athena. This may be too late however I would like to see the LCF function of Athena capable of running multiple models (sequential models e.g. Sample A followed by B, C...) using a similar set of standards. For instances, I may have 25-40 spectra (environmental samples), one set of standards which may be plausible, and currently I have to run the model wait for the LCF model for sample A to finish before starting Sample B. If there was a way to write a script or add the functionality of multiple scans from the same set of standards, I (and maybe others) could set up a computer and leave for several hours instead of returning every 5-30 mins to execute a new LCF model. A conversation was posted about running models with a large number of standards (and whether it was appropriate), similarly running multiple samples is cumbersome. In a related comment I have tried to take advantage of access to high speed computing, but Athena's code does not appear to be capable of taking advantage of increased resources (either RAM and CPU) in order to decrease computational time. All the same thanks (to the many of you working on Ifeffit) for the shareware and all your support. Thanks for your time. Respectfully, Bradley W. Miller, Ph.D. Post Doctoral Fellow Oak Ridge Institute for Science and Education U. S. Environmental Protection Agency National Risk Management Research Laboratory Land Remediation and Pollution Control Division 5995 Center Hill Avenue, Cincinnati, OH 45224-1702 Office: (513) 487-2889 Miller.BradleyW@epa.gov Fax: (513) 569-7879 www.epa.gov www.tinyurl.com/bwmiller The great tragedy of Science—the slaying of beautiful hypothesis by an ugly fact.— Thomas H. Huxley Views or Opinions expressed in this email is solely representative of the sender and does not represents those of the EPA or any other agency.
On Thursday, July 05, 2012 12:15:42 PM BradleyW Miller wrote:
If my memory is correct there was a period of time you were taking request for improvements on Athena.
That period of time includes now and the foreseeable future.
This may be too late however I would like to see the LCF function of Athena capable of running multiple models (sequential models e.g. Sample A followed by B, C...) using a similar set of standards. For instances, I may have 25-40 spectra (environmental samples), one set of standards which may be plausible, and currently I have to run the model wait for the LCF model for sample A to finish before starting Sample B.
I am confused by your terminology, so I am not sure which kind of automation you are asking for. One possibility is that you want to apply a given model (i.e. a given set of standards) fit to a sequence of data sets. That automation is already a feature of Athena. See the attached screenshot. I circled the relevant button. Clicking that will run a sequence of fits using the three standards currently on display in the list on the left. The other possibility is that you want to run a sequence of models (i.e. variable lists of standards) against one or more data sets. That's sort of what the "Fit all combinations" button does, but not exactly. I will have to spend some time thinking about the problem a sequence of specified models applied to a sequence of specified data sets. I don't see an obvious, user-friendly way to implement something with that many details in a GUI application.
If there was a way to write a script or add the functionality of multiple scans from the same set of standards, I (and maybe others) could set up a computer and leave for several hours instead of returning every 5-30 mins to execute a new LCF model. A conversation was posted about running models with a large number of standards (and whether it was appropriate), similarly running multiple samples is cumbersome.
Well, as I have said several times in recent months, the new versions of Athena and Artemis are more than just a visual make-over. I actually rewrote about 95% of the code base to strictly separate presentation from functionality. A&A are now built on an extensive library that I call Demeter. The nice thing about this is that it is now possible to write a one-off script that does /exactly/ what A&A do. That was never easily possible using the old versions of A&A. It's not exactly trivial now, in the sense that you have to write a program and writing a program is often non-trivial. But it is certainly possible and people other than myself have done so. Indeed I test every feature of A&A that doesn't specifically have to do with the arrangement of controls on the screen by writing stand-alone test scripts. Here are the three test scripts I wrote to get linear combination fitting working. There is a script that implements a single fit, one that implements a combinatorial sequence for a single data set, and one that implements the application of a model to a sequence of data sets: https://github.com/bruceravel/demeter/tree/master/examples/recipes/LCF As you can see, they are fairly short and not especially complicated (unless, I suppose, you have never seen perl code before). Using those as a starting point, you could pretty easily implement almost any kind of automation.
In a related comment I have tried to take advantage of access to high speed computing, but Athena's code does not appear to be capable of taking advantage of increased resources (either RAM and CPU) in order to decrease computational time.
This has been discussed recently on the mailing list. Neither Ifeffit nor Demeter was written to make use of threads, so neither can make use of more CPUs. As Matt mentioned the other day, his Larch project will be able to operate as a server which can fork as many instances as you have CPUs. Demeter still won't be able to thread itself among multiple servers, but you will presumably be able to run multiple instances of Demeter-based programs, each pointed at a different instance of a Larch server. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel
Bruce and Scott, Thanks for the response. I thought I had downloaded the latest version of Athena (twice I tried) but looking at the image you sent demonstrates that I have not. Thanks for your time. Respectfully, Bradley W. Miller, Ph.D. Post Doctoral Fellow Oak Ridge Institute for Science and Education U. S. Environmental Protection Agency National Risk Management Research Laboratory Land Remediation and Pollution Control Division 5995 Center Hill Avenue, Cincinnati, OH 45224-1702 Office: (513) 487-2889 Miller.BradleyW@epa.gov Fax: (513) 569-7879 www.epa.gov www.tinyurl.com/bwmiller The great tragedy of Science—the slaying of beautiful hypothesis by an ugly fact.— Thomas H. Huxley Views or Opinions expressed in this email is solely representative of the sender and does not represents those of the EPA or any other agency.
I announce these things on the mailing list. Of course, that means you have to read what gets posted on the mailing list .... http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2012-April/010494.html B On Wednesday, July 11, 2012 04:04:21 PM BradleyW Miller wrote:
Bruce and Scott,
Thanks for the response. I thought I had downloaded the latest version of Athena (twice I tried) but looking at the image you sent demonstrates that I have not.
-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel
Hi Bradley, It seems to me that you can get pretty close to what you're asking for by a combination of "fit marked groups" and "fit all combinations." If you were to take a few representative scans and "fit all combinations" you could discover which constituents were actually present in the set. Then choose those as your standards and "fit marked groups." You could use PCA (newly added to Demeter Athena--yay!) to make this even more robust, by first ascertaining how many constituents are varying between the whole sample set. --Scott Calvin Sarah Lawrence College On Jul 5, 2012, at 12:15 PM, BradleyW Miller wrote: Hi, If my memory is correct there was a period of time you were taking request for improvements on Athena. This may be too late however I would like to see the LCF function of Athena capable of running multiple models (sequential models e.g. Sample A followed by B, C...) using a similar set of standards. For instances, I may have 25-40 spectra (environmental samples), one set of standards which may be plausible, and currently I have to run the model wait for the LCF model for sample A to finish before starting Sample B. If there was a way to write a script or add the functionality of multiple scans from the same set of standards, I (and maybe others) could set up a computer and leave for several hours instead of returning every 5-30 mins to execute a new LCF model. A conversation was posted about running models with a large number of standards (and whether it was appropriate), similarly running multiple samples is cumbersome.
participants (3)
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BradleyW Miller -
Bruce Ravel -
Scott Calvin