Introduction to Athena

ATHENA is an interactive graphical utility for processing EXAFS data. It handles most of the common data handling chores of interest at the beamline or for preparing your data to begin analysis. ATHENA is a graphical front end to Matt Newville's IFEFFIT library written entirely in the Perl programming language and using the Gnuplot program for data display. It is being developed on Linux and tested on various flavors of Windows, but should work on any unix-like, Windows, or Mac operating system.

ATHENA is intended to provide high quality analysis with a highly usable interface. It allows very fine grained control over the processing and plotting of individual data sets while still enabling the processing and visualization of large quantities of data.

Among ATHENA's many, many features, you will find:

• Convert raw data to μ(E)

• File import plugins for reading arbitrary data files

• Process and plot multiple data scans simultaneously

• Merge data as μ(E), normalized μ(E), or χ(k)

• Energy calibration

• Align data scans with or without a reference channel

• Deglitch, truncate, convolve, or smooth μ(E) data

• Self-absorption corrections for fluorescence spectra

• Compute difference spectra

• Fit linear combinations of standards to μ(E), derivative of μ(E), or χ(k) data

• Fit peak functions to XANES data

• Log-ratio/phase-difference analysis

• Background removal using the AUTOBK algorithm

• Forward and backward Fourier transforms

• Save data as μ(E), normalized μ(E), χ(k), χ(R), or back-transformed χ(k)

• Save project files, allowing you to return to your analysis later

• ... and much, MUCH more!

---

 

First Look at ATHENA

When ATHENA first starts, something like the picture below appears on your computer screen. The ATHENA window is divided into several parts. We will discuss each of these parts and give each a name.

At the top of the window is a menu bar. This works much like the menu bar in any program. Much of the functionality in ATHENA is accessed through those menus.

The largest part is the main window, highlighted in the picture above with a red border. The red border does not happen in the real program -- it's there simply to clarify this discussion. The main window is divided into six parts. The top box identifies the file name of the current project file. Below that, are various parameters identifying the current data group.

The next three boxes are used to define the parameters associated with normalization and background removal, forward Fourier transforms, and reverse Fourier transforms. At the bottom of the main window are a couple of parameters associated with plotting.

At the bottom of the screen is the echo area. This very important space is used by ATHENA to communicate with you, the user. This space is used to display informational messages while ATHENA is working on your data, error messages when it runs into trouble, and other kinds of messages.

The large blank area on the right is the group list area. As data are imported into ATHENA, they will be listed in this space. Access to the data already imported is made by clicking in this space.

Above the group list area are the mark buttons The blank space next to the mark buttons is the modified project indicator. This indicator shows when your project has been modified and needs to be saved.

Below the group list area are the plot buttons. Below that are the buttons used to set the k-weighting for use when plotting in k-space or when making a forward Fourier transform. Below that are various other plotting controls in the plotting options section.

After importing several data files, each is made into a data group and listed in the group list. The label and the check button next to it are the main controls for interacting with data in ATHENA.

---

 

Getting help

There is quite a bit of help built right into ATHENA. Typing Control-m or selecting “Document” from the Help menu will display ATHENA's document in a web browser or in the built-in document viewer. The “Document sections” submenu allows you to jump directly to a particular topic. Also, many parts of the program have a button which will take you directly to the part of the document that describes that part of the program.

---

 

Folders and log files

On occasion, it is helpful to know something about how ATHENA writes information to disk during its operations.

working folder

Many of ATHENA's chores involve writing temporary files. Many file type plugins write temporary files after performing some transformation on the original data. GNUPLOT writes temporary files as part of its plot creation. These files are stored in the “stash folder”. On linux (and other unixes) this is $HOME/.horae/stash/. On Windows this is %APPDATA%\demeter\stash.

log files

When ATHENA runs into problems, it attempts to write enough information to the screen that the problem can be addressed. This screen information is what Bruce needs to troubleshoot bugs. On a linux (or other unix) machine, simply run ATHENA from the command line and the informative screen messages will be written to the screen. You can cut-n-paste that text or capture the output by running ATHENA through tee: ~> dathena | tee capture.log

On a Windows machine, it is uncommon to run the software from the command line, so ATHENA has been instrumented to write a run-time log file. This log file is called dathena.log and can be found in the %APPDATA%\demeter folder.

%APPDATA% is C:\Users\<username>\AppDataRoaming\ on Windows 7 and 8.

It is C:\Documents and Settings\<username>\Application Data\ on Windows XP and Vista.

In either case, <username> is your log-in name.