=head1 ARTEMIS: The Data Page

B<ARTEMIS> - The data page

The data page is displayed in B<Artemis>'s main panel when a data item
is anchored in the Data and Paths List.  See L<the main document
section|artemis> for an explanation of anchoring and selecting items
in the Data and Paths List.

The data page is divided into five sections.  At the top is a box
containing the title lines associated with these data.  These are read
from the input data file, but can be edited at any time by the user.
When the data are written to output files, the contents of this box
are written as headers.  Below the titles box is the name of the data
file that was imported.  Below that are four boxes containing groups
of related controls.

=head2 Data toggles

This box contains three toggles that control certain aspects of the
fit.  The first two are only relevant in a multiple data set fit.
When setting up a project containing a multiple data set fit, it is
sometimes useful to exclude an entire data set from the fit without
deleting it from the project.  This can be done with the first
toggle.  When a data set is excluded, it and all items beneath it are
shown in brown text in the Data and Paths List to indicate that they
have been excluded from the fit.

After the fit is complete, B<Artemis> wants to show off her handiwork
and display a plot of the data and the just-finished fit.  In the case
of a multiple data set fit, you might have a preference about which
data set gets plotting.  Click this toggle on for your prefered data
set.

The third toggle tells B<Artemis> to do a corefinement of the
background spline when it performs the fit.  This corefinement is,
effectively, the same operation that was performed by B<Athena> to
remove the background from the data.  The C<rmin> parameter serves the
same purpose as B<Athena>'s C<rbkg> parameter.  When the fit is
performed with the background corefinement, a spline is used to fit
the Fourier components of the data below C<rmin> and the B<Feff> paths
are used to fit the Fourier components between C<rmin> and C<rmax>.
The number of parameters used to determine the spline is the number of
independent points in that portion of the data:
C<2*delta_k*delta_R/pi>, where C<delta_k> is the range of the Fourier
transform and C<delta_R> is the range between 0 and C<rmin>.  The
advantage of doing the background corefinement, other than the
possibility of making the fit look nicer at low R, is that
correlations between the background parameters and the fitting
parameters can be measured.

=head2 Fourier transform and fitting parameters

This box contains the controls used to set the ranges of the forward
Fourier transform and of the fit.  The fit range is also used as the
backward Fourier transform range when a plot is q space is made.  See
L<Pluck buttons> for a discussion of the little quare buttons marked
with a blue x.

Other controls are used to set the functional forms of the Fourier
transform window used in k and R.  The widths of the sills of those
functions are set usng the entry boxes labeled C<dk> and C<dr>.

=head2 k-weight parameters

The controls in this box are used to set the values of k-weight to be
used in the fits.  There are togles for turning on k-weight of 1, 2,
or 3.  There is also a toggle for specifying an arbitrary value of
k-weight.

These are the k-weight values used in the fit but not the k-weight
used to plot the data.  These two purposes of k-weight are handled
independently by B<Artemis>.  See L<Plotting in Artemis|artemis_plot>
for a discussion of the plotting k-weight controls.

People sometimes get confused by the concept of multipl k-weights for
fitting.  The prupose of choosing a low or high value for k-weight is
to attempt to emphasize either the low- or high-k end of the data.
Because different regions of the data are sensitive to different kinds
of parameters, one might choose a low or high value to increase the
precision of measurement of certain parameters.  Doing multiple
k-weight fits is a sort of compromise -- a way of emphasizing both
ends of the data in the fit.

The fit is determined by minimizing a quantity called chi-square.
Chi-square is evaluated by summing the squares of the difference
between the data and the theory.  Since the FT is complex, there is a
real part and an imaginary part.  So chi-square is proporitional to:

         /                                                    \
    sum <   Re[ data(R) - th(R) ]^2 + Im[ data(R) - th(R)]^2   >
     R   \                                                    /

In a multiple k-weight fit, there are simply more terms in the sum.
Let's take a kw=1&3 fit as an example.  This summation is made for the
kw=1 data and theory.  B<And> the summation is made for the kw=3 data
and theory.  The summations are added together and the full sum is
used to evaluate chi-square.

At the end of the day, there is only one set of guess parameters that
have been optimized by the fit.  These guess parameters along with the
set parameters are used to evaluate the def parameters and the path
parameters.  The path parameters are used to evaluate the exafs
equation for each path.  The exafs equations for the paths are summed
up to make the best-fit theoretical C<chi(k)>.  You have a data
C<chi(k)> and a best-fit C<chi(k)>.  Those can then be plotted however
you like -- even using a k-weight that was not used in determining the
fit.

=head2 Other parameters

The last box contains several controls that did not fit into theother
boxes.  There is a menu for selecting the fitting space.  You can
choose to fit the data in any of k, R, or q space.  The default is to
fit in R.

Epsilon is the uncertainty used to evaluate chi-square.  Normally it
is fine to let B<Artemis> use the default value (which is determined
from the RMS value of the data between 15 and 25 angstroms in
R-space).  In some situations, you may find it useful to explicitly
set a value for epsilon.

After the fit, B<Artemis> writes a log file documenting the fit.
Among the information in that log file are the correlations between
all the fitting parameters.  You can set the level below which
B<Artemis> will exclude a correlation from this report.

Finally, there is a menu for selecting the path to use for phase
corrected plots.  This menu contains the first five paths from each
B<Feff> calculation used with the data set.  When a path is selected
for phase corrected plots, the full phase shift of that path -- both
the central atom and scattering atom portions -- will be subtracted
from anything that is Fourier transformed before it is plotted.  If a
path is selected for phase correction and you make a plot of, say, the
data, the fit, and several paths, the selected phase shift will be
subtracted from each item before it is plotted.  Phase correction is
for plotting only.  Fits are always done on non-phase-corrected data.

=head2 Pluck buttons

Several of the controls on this page a have a small button with a blue
x next to them.  These are called pluck buttons and are used for
grabbing values from the plot window.  When you click on one of these
buttons, a prompt will be written to echo area asking you to click on
a pointin the plot.  When you do so, the value that you clicked on
will be inserted into the entry box adjacent to the pluck button.
B<Artemis> is careful not to let you pluck a k-value from a plot in R,
or vice versa.

=head2 Context menus

As you pass the mouse over labels on the data page, the text under the
mouse will change color.  This color change is an indication that mouse
clicks will do something.  A left mouse click on one of these labels
will cause a brief description of that parameter to be displayed in
the echo area.  Many of these descriptions also suggest reasonable
values for the parameter.

Clicking the right mouse button on one of the labels will post a
context menu of useful function.  One such function is restore that
parameter to its default value.  If you have a muliple data set fit,
the other menu options allow you to constrain the parameter between
data sets.

The labels at the top of the boxes are all sensitive to the left mouse
button.  The labels atop the Fourier transform and fit range box and
the k-weights box are also sensitive to the right mouse click.

=over 5

=item

L<Back to the main document|artemis>

=back

