athena(1)

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💖 athena(1) — interactive XAS data processing 💖

okay bestie, sit down, hydrate, and let me tell you about athena, section 1 of the General Commands Manual. she's an icon, she's a legend, and she is literally about to make your XAS data processing life so much easier. 🧚✨

✨ NAME ✨

athena — interactive XAS data processing. that's it, that's the vibe. 👑

🌸 SYNOPSIS 🌸

athena file...

💅 DESCRIPTION 💅

so this manpage is all about the athena program, which does interactive XAS data processing — and when I say processing I mean the whole glow-up pipeline: converting raw data to mu(E), aligning, merging, deglitching, Fourier transforming, and plotting. 💫

basically, Athena handles all the chores involving XAS data except for quantitative analysis by fitting to theoretical standards. that job belongs to her sister program Artemis, the fitting program. sibling energy fr. 👯

Athena has two interesting and unusual features, and honestly? they're giving main character energy.

  1. There are no buttons for explicitly removing the background from mu(E) data, and no buttons for performing Fourier transforms. the only active buttons on the main window are for plotting. Athena always knows when data requires a background removal or a Fourier transform, and she will perform the necessary analysis steps before displaying the plot. she's just that girl. 💁
  2. It is just as easy to perform analysis and plotting chores on multiple data sets as on an individual data set. Athena automates the most common data processing chores and automatically generates plots of one or more data sets. multitasking queen. 👑

🖥️ SYNOPSIS (yes, again — the layout tour) 🖥️

Athena is a graphical and interactive program written in the perl programming language, using the Tk display engine, the IFEFFIT EXAFS library, and the PGPLOT plotting library. (there's a list of relevant URLs below, don't worry. 🫶)

when Athena starts, you get a window whose layout looks something like this:

       +----------------------------------------+
       |    menubar                             |
       +---------------------------+------------+
       |                           |            |
       |                           |            |
       |                           |   Group    |
       |     Group                 |   List     |
       |    Parameters             |            |
       |                           |            |
       |                           |            |
       |                           +------------+
       |                           | Plot crrnt |
       |                           +------------+
       |                           | Plot mrked |
       |                           +------------+
       |                           |            |
       |                           |   Plot     |
       |                           |  Features  |
       |                           |            |
       |                           |            |
       +---------------------------+------------+
       |    echo area                           |
       +----------------------------------------+

as you import data into Athena, data groups are created and those groups are listed in the section labeled Group List. you select a group as the active one by clicking the left mouse button on its entry in the group list. when selected, the list entry is highlighted with an orange background and the parameters associated with that group are displayed in the large area on the left labeled Group Parameters. 🍊

when you pass the mouse over a label in the group parameters section, you'll notice the label changes color. that's the app telling you a mouse click on that label will have an effect — no cap. clicking the left mouse button will display a hint in the echo area about what that parameter does. for the effect of a right mouse click, see the section on group operations. iykyk. 👀

the view of the group parameters gets replaced when certain features of Athena are used. choosing any of the options from the Data, Align, Diff, or Analysis menus will temporarily replace the group parameters with views of parameters relevant to the chosen task. for example, when the log-ratio option is chosen from the Analysis menu, the view of group parameters is replaced by a view of the interface to Athena's log-ratio/phase-difference analysis. ✨

below the group list are two rows of buttons for plotting data. the red buttons are for plotting the selected data group. the purple buttons are for plotting multiple data groups. these buttons are labeled according to the data space of the plot: E, k, R, and q refer to energy, photoelectron k, real space R, and backtransform k, respectively. 💫

below the plot buttons are a set of tabs for specifying the details of the plots in each space. for each space you can specify the range of the x-axis. for energy plots, you can select whether the background function is plotted along with the data, and whether the data and background are normalized. for k-space plots, you can select the amount of k-weighting. for R- and q-space plots, you can select which part of those complex functions are plotted. there are also tabs for setting up stacked plots and for establishing plot indicators. for a complete discussion, see the section on plotting. 📊

finally, at the bottom of the page is the echo area. Athena uses this area to display hints, brief help messages, warnings, and updates about recently performed analysis or plotting actions. a few features of Athena will prompt the user for a text string — in those situations, the echo area is temporarily replaced by a text string dialog. 💬

throughout Athena the right mouse button serves to post context sensitive menus. these include parameter labels, groups list entries, and other elements on the screen. you should genuinely try clicking the right mouse button in different places to see what useful things might pop up. go on, poke around. 🖱️✨

🔗 REFERENCES 🔗

here are the relevant URLs:

😭 MISSING FEATURES 😭

you betcha! lots! here's a partial list:

  • Principal Component Analysis on the set of marked groups
  • XANES analysis by fitting a sum of scans to an unknown
  • Dead-time and self-absorption corrections
  • Handle dispersive data sets, i.e. data sets wherein the I0 and IT measurements are in separate data files because the data were obtained sequentially
  • Calibrate dispersive data to a trusted standard
  • Handle SPEC files. an independent perl module would be ideal. this is a project some eager contributor could tackle without having to delve into ATHENA's source code. 👀 (calling all volunteers bestie)
  • Alignment of scans using a reference, either of the same edge or of a nearby edge. (any suggestions? the author is lacking a good idea about how to implement this...)
  • Formulas for the energy axis (useful for converting encoder readings to energy values)
  • R and q space records, that is to be able to read and write data in R and q space just as easily as E or k space
  • Internationalization. that is, build a framework for having text strings read from external files and for the language to be a configuration option.
  • Documentation, documentation, documentation
not me listing all of these like a to-do list on the group chat 💀 but fr, this is the wishlist, unedited.

👑 WHAT'S IN A NAME? 👑

Athena was the goddess of wisdom and is also associated with skill and justice. those are all good qualities for a data analysis program! iconic naming choice, honestly. 🏛️✨

⚙️ OPTIONS ⚙️

this program requires no options. zero. none. she simply arrives and slays. 💅

🌈 SEE ALSO 🌈

this program is part of the horae XAS analysis suite, which can be obtained at

http://cars9.uchicago.edu/~ravel/software/

💜 AUTHOR 💜

Bruce Ravel <ravel@phys.washington.edu> (c) 2001 - 2003

Ifeffit is copyright (c) 1992 - 2003 Matt Newville newville@cars.uchicago.edu http://cars9.uchicago.edu/~newville/ifeffit/

okay that's the whole page bestie, go forth and process that data 💖🦋🌸

athena(1) — General Commands Manual, dated June 26, 2006. that's the source and the date, and that's the sign-off. periodt. ✨👑💅

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