Hi folks, In the absence of a real document, I want to write something down to help people get started with Athena. Here goes.... First, Athena, like gifeffit, is an attempt to automate the creation of ifeffit commands. The beauty of ifeffit's command interface is that it is very flexible, both in terms of functional flexibility and in terms of writing wrappers. The annoying part of ifeffit's command interface is that you have to remember a lot of syntax and do a lot of typing. Essentially, Athena does a lot of typing for you. Second, Athena has two features that may not be obvious to folks who have used Mac-xafs or win-xafs or some other extant package. (1) There are no buttons that say "Remove background" or "Fourier transform". There are only buttons that say "Plot in energy" or "plot in R". Athena is clever about keeping track of what needs to be done and doing all necessary analysis steps in the background before plotting. So, if you change the k-weight for the Fourier transform, Athena knows to redo the forward and backward transforms as needed but not to redo the background removal. If you change Rbkg and plot in energy only, the background removal will be done. And so on. (2) You can "mark" groups and perform various actions on single groups or on ensembles of marked groups. So it is easy to plot single groups or ensembles of groups with a few mouse clicks. What's more the analysis steps are taken care of automagically for single groups or for ensembles of groups. Now I am going to describe specific features of Athena: ***** Reading in data Athena reads ASCII data using ifeffit, so all the rules that apply to ifeffit also apply to Athena. Basically, Athena expects that data will be in the form of column data, possibly with headers. Athena can directly read mu(E) or chi(k) data. It can also read raw data straight from the beamline. See http://leonardo.phys.washington.edu/~ravel/software/exafs/images/athena/colu... You can then construct mu(E) data by selecting columns for the numerator and denominator. In the screen-shot, I show selecting It and I0 columns as the numerator and denominator for transmission data. There is a natural log button which should be clicked for transmission data. You can also handle multi-element detector data in a very rudimentary way by selecting multiple numerator columns for fluorescence data. You will notice that there are options in the File menu for reading single or multiple files. This is annoying but necessary. The standard file dialog does not do extended selection, the motif-like file dialog does extended selection but is unfamiliar to most people. Extended selection is very useful -- if you extendedly select a group of identically formatted files, Athena will only give the column selection dialog for the first one. The button labeled "Set preprocessing parameters" is beyond the scope of this post, but may become clear to you once you grok all the features of Athena. ***** Selecting and marking groups Once you have read in some data, you will probably want to plot it. You select a group by clicking on its name in the skinny frame on the right. When you select a group, its name will be highlighted in orange and its parameter values will displayed in the form on the left. When you click on a *red* plotting button, the selected group will be plotted. To the left of the group's name is a little check button. You mark a group by clicking the checkbutton on. When you click a *purple* plot button, all marked groups will be over-plotted. ***** Setting parameter values You can only directly edit the parameters for the selected group because only the selected group has its parameters displayed. There are ways of setting the parameters of other groups to the values of the selected group. In the Group menu is and option for setting the values of all parameters of all other groups to the values of the currently selected group. There is another option for setting all parameters of all marked groups to the values of the currently selected group. There is also fine grained control over setting parameters which is described in the next section. ***** Mouse clicks on labels When you pass the mouse over a label in the frame displaying all the parameter values, you will notice that the text and background change color. This is a visual cue that the text is sensitive to mouse clicks. Clicking the left mouse button on a word that has changed color will display a little bit of text in the echo area at the bottom of the window which explains in a few words the purpose of that parameter. Clicking the right mouse button will pop up a menu which allows you to set that parameter for other groups to the value of the currently selected group. The functions in the Group menu explained above work on all parameters, this right-click function works only on that specific parameter. ***** Plotting options You can independently control how single and marked group plots are made by choosing different options in the Plotting Options section at the lower right hand corner of the window. There is one notecard for each plotting space. Red buttons are for single group plots and purple buttons are for marked group plots. I suggest poking at these buttons to see what kinds of plots you can make. The plot ranges for the x-axis are set in this space as well. You may need to think about these values. For example, the data alignment function (described below) uses the values of Emin and Emax. Typically, you would want to restrict the plot to a few tens of volts above and below the edge so you can see the details of the edge for alignment. ***** Palettes The options in the Edit menu all pop up a new window with notecards which display all sorts of textual information. Perhaps the most useful is the ifeffit buffer which allows you to monitor the communication between Athena and ifeffit. ***** Project files You have the options of saving data in a variety of column formats, including mu(E), norm(E), chi(k), chi(R), and chi(q). You can also save a "project file". Which is an Athena specific which records the state of your Athena session. It will record data and parameters in a big ASCII file that is hard for a human but easy for Athena to read. Athena's project files are different from ifeffit's PAD files. They exploit the object oriented nature of its internal data structures to save the state of an ensemble of groups, even if the data in that ensemble is unrelated one to the other. ***** Deglitching The deglitch menu has two options in it, deglitching and truncating. Deglitching is for removing spurious points throughout the data set, truncating is for removing all data points after a specified point. Deglitching can be done point-by-point or algorithmically. The point-by-point is done by clicking the "Select a point" button, then clicking on the plot. The "remove point" button will then become active. Clicking it will remove the point from the group. The algorithm is a bit more complicated. There are three parameters which set margins above and below the data in a range either in the pre-edge or the post-edge. Any data points which extend outside these margins will be removed. To understand this better, try reading the data file uhup.003 and plying around with the algorithmic deglitching parameters. Eventually you will make it look like this: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/athena/degl... Clicking the "Remove glitches" button will remove the four points outside the margins. ***** Aligning Alignment can be done using raw mu(E), normalized mu(E), or the derivative of mu(E). I think this one is pretty easy to understand. The "Standard" is the fixed reference. The "Other" is the group to be energy shifted. When you click the + or - buttons, the other group's e0 shift is incremented and the two data sets are replotted. See this: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/athena/alig... ***** Merging Merging works on all marked groups. You can merge in any of the plotting spaces. The average and standard deviation of marked groups are calculated. The average, the average + the std. dev., and the average - the std. dev. will be plotted. The standard deviation will be written to output column data and to project files. There is more stuff to explain. I have not discussed macros, plot multipliers, clamps, phase corrections, Cromer-Liberman normalization, hints, the Plot and Mark menus, data preprocessing, detector data, pluck buttons, autobk standards, feff data, and a few other things. But hopefully this is enough to get people started until I write a proper document/tutorial. Regards, B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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/