NAME

Artemis - interactive EXAFS data analysis

DESCRIPTION

Artemis is a program for analyzing EXAFS data using theoretical standards from Feff. Artemis includes interfaces to Atoms and Feff as well as forms for defining parameters and applying those parameters to the paths from the Feff calculation. Artemis uses chi(k) as it's input. It does not handle any data processing chores, such as converting raw data to mu(E) or doing background removal. Artemis's sister program Athena is the data processing program.

SYNOPSIS

Artemis 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. (See below for a list of relevant URLs.)

Artemis helps you organize all aspects of a fitting project, including running the Feff calculation, settings parameters for the Fourier transform and fitting of the data, parameterizing the paths from the Feff calculation, running the fit, and plotting the results. The Artemis window is divided into three panels. The largest panel is the space where most of the work happens. Its content is model and depends on the state of the Data and Paths List. This list is in the center, skinny panel. The other skinny panel contains the controls the are used to specify how plots are made.

At the top of the window are the menubar and the project bar. The project bar displays the name of the current project file. It also contains an indicator that tells you if the project has been modified since the last time it was saved. Clicking on the modified indicator will save the project (just like C-s or the ``Save project'' item in the File menu). At the bottom of the screen is the echo area, where Artemis writes all sorts of helpful messages as you use the program.

The Data and Paths list contains a tree-like list of all of the objects that can be manipulated as you use Artemis. When the program starts, two such items are displayed. As you run Feff calculations, import Feff paths and other data sets, and run fits, more items are added to this list. In total, there are five kinds of entries in this list, each of which controls a diffferent aspect of Artemis. These five kinds of list entries are: (1) fitting parameters, (2) data, (3) fits, (4) Feff calculation, or (5) Feff path. When you click on an item in the Data and Paths List, that item will be ``selected'' and ``anchored''. A selected item is highlighted in orange. An anchored item is outlined with a dashed line. Only one item can be anchored. 0, 1, or more items can be selected.

The anchored item determines the mode of the large panel. For instance, when the ``Guess, Def, Set'' item is anchored, the main panel will display a page used for setting the fitting parameters. When a data item is anchored, the main panel will display a page for setting Fourier tranform parameters, the fitting range, and other parameters associated with the data. Many functions in Artemis depend upon the mode of the main panel. Some features are available only in certain modes. Each of the modes is described in its own document section. See SECTIONS OF THE DOCUMENT.

Plots in Artemis are always made using the selected items. To plot, for example, data, a fit, and several individual paths, it is necessary to select each of those items. Many other functions in Artemis also work on the set of selected items.

Anchoring and setting paths is usually done by using the mouse in the Data and Paths List, although there are several other ways of changing the anchor and selection using the mouse or the keyboard. Here is a list of mouse events useful in the Data and Paths List:

Left mouse button: Clicking the left mouse button will clear all selections then select and anchor the item clicked. The main panel will display the page apporpriate to the anchored item.
Center mouse button: Clicking the center mouse button will anchor the item clicked without changing the selection. The main panel will display the page apporpriate to the anchored item.
Right mouse button: Clicking the right mouse button will anchor the item clicked without changing the selection. It will also post a menu of functions appopriate to the item clicked. These menus are the same as the menus in the menubar at the top of the window. The main panel will display the page appopriate to the anchored item.
Control key + left mouse button: Clicking the left mouse button while holding down the control key will add the item clicked to the group of selected items. The anchor is not changed.
Shift key + left mouse button: Clicking the left mouse button while holding down the shift key will select all items between the anchor and the item clicked, inclusively. The anchor is not changed.
Left mouse button + mouse drag: Clicking the left mouse button then dragging the mouse while holding down the button will select all items that you drag the cursor over. The item initially clicked will be anchored and the main panel will display the page appopriate to the anchored item.
Control-k, Control-j: Hitting the k or j keys while holdong the control key will move the anchor to the previous or next item in the list without changing the selection. The main panel will display the page appopriate to the anchored item. These two key sequences, behave differently when the Guess, Def, Set item is anchored. See The Guess, Def, Set page for details
Control-l: Hitting the l key while holding down the control key will put focus on the Data and Path List. This allows you to navigate the list using the arrow keys.

The color and font of the text in the Data and Paths List indicates the status of each item. Any item written in black, upright text is an item that can be plotted. When a data set or Feff path is excluded from the fit, it will be written in brown text. The Guess, Def, Set item and the Feff calculation items are written in italic text. The italic text indicates items that cannot be plotted. Although these non-plotable items can be selected, they will be ignored when a plot is made.

SECTIONS OF THE DOCUMENT

Modal views in the main window: The data parameters || The Guess, Def, Set page || The Atoms page || Feff and it's input file || The Feff interpretation page || Paths and path parameters || The log viewer ||
Input and Output: Importing Athena project data || Output files || Artemis project files ||
Features of Artemis: Plotting in Artemis || Palettes || Using the Data and Paths List || The edit math expression dialog || Quick first shell theory || The Menubar || The preferences dialog ||

REFERENCES

Here are the relevant URLs:

IFEFFIT

  http://cars.uchicago.edu/ifeffit

PGPLOT

  http://www.astro.caltech.edu/~tjp/pgplot/

Perl

  http://www.perl.com

perl/Tk

  http://www.lehigh.edu/~sol0/ptk/

MISSING FEATURES

You betcha!

WHAT'S IN A NAME?

Artemis was the goddess of the hunt, an apt metaphor doing EXAFS analysis. ARTemis is also a pun on the nature of EXAFS analysis that works in English and in the romance languages.

AUTHOR

  Bruce Ravel <bravel@anl.gov> (c) 2001 - 2006
  http://cars.uchicago.edu/~ravel/software/

  Ifeffit is copyright (c) 1992 - 2006 Matt Newville
  newville@cars.uchicago.edu
  http://cars.uchicago.edu/ifeffit/