=head1 NAME

B<Artemis> - interactive EXAFS data analysis

=head1 DESCRIPTION

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

=head1 SYNOPSIS

B<Artemis> is a graphical and interactive program written in the perl
programming language, using the Tk display engine, the B<Ifeffit>
EXAFS library, and the PGPLOT plotting library.  (See below for a list
of relevant URLs.)

B<Artemis> helps you organize all aspects of a fitting project,
including running the B<Feff> calculation, settings parameters for the
Fourier transform and fitting of the data, parameterizing the paths
from the B<Feff> calculation, running the fit, and plotting the
results.  The B<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
B<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 B<Artemis>.  When the
program starts, two such items are displayed.  As you run B<Feff>
calculations, import B<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
B<Artemis>.  These five kinds of list entries are: (1) fitting
parameters, (2) data, (3) fits, (4) B<Feff> calculation, or (5)
B<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 B<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 L<SECTIONS OF THE DOCUMENT>.

Plots in B<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
B<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:

=over 4

=item B<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.

=item B<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.

=item B<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.

=item CB<ontrol 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.

=item B<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.

=item  B<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.

=item B<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 L<The Guess, Def, Set
page|artemis_gds> for details

=item B<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.

=back


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 B<Feff> path is
excluded from the fit, it will be written in brown text.  The Guess,
Def, Set item and the B<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.




=head1 SECTIONS OF THE DOCUMENT


=head2 Modal views in the main window

L<The data parameters|artemis_opparams> ||
L<The Guess, Def, Set page|artemis_gds> ||
L<The B<Atoms> page|artemis_atoms> ||
L<B<Feff> and it's input file|artemis_feffinp> ||
L<The B<Feff> interpretation page|artemis_intrp> ||
L<Paths and path parameters|artemis_path> ||
L<The log viewer|artemis_logview> ||

=head2 Input and Output

L<Importing B<Athena> project data|artemis_athena> ||
Output files ||
B<Artemis> project files ||

=head2 Features of B<Artemis>

L<Plotting in B<Artemis>|artemis_plot> ||
Palettes ||
Using the Data and Paths List ||
L<The edit math expression dialog|artemis_editme> ||
L<Quick first shell theory|artemis_afs> ||
The Menubar ||
The preferences dialog ||


=head1 REFERENCES


Here are the relevant URLs:

=over 4

=item IFEFFIT

  http://cars.uchicago.edu/ifeffit

=item PGPLOT

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

=item Perl

  http://www.perl.com

=item perl/Tk

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

=back

=head1 MISSING FEATURES

You betcha!

=head1 WHAT'S IN A NAME?

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

=head1 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/
