athena - interactive XAS data processing
This manpage documents the athena
program, for interactive XAS data
processing, including converting raw data to mu(E), aligning, merging,
deglitching, Fourier transforming, and plotting. Basically, Athena
intended to handle all chores involving XAS data except for quantitative
analysis by fitting to theoretical standards. Athena
's sister program
is the fitting program.
has two interesting and unusual features. The first is that there
are no buttons for explicitly removing the background from mu(E) data or for
performing Fourier transforms. The only active buttons displayed on the main
window are for plotting. Athena
always knows when data requires a
background removal or a Fourier transform and will perform the necessary
analysis steps before displaying the plot.
The second interesting feature is that it is just as easy to perform analysis
and plotting chores on multiple data sets as on an individual data set.
automates the most common data processing chores and
automatically generates plots of one or more data sets.
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.)
starts, you are presented with 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 will notice that the label changes color.
This indicates that a mouse click on the label will have an effect. Clicking
the left mouse button will display a hint in the echo area as to the function
of that parameter. See the section on group operations for the effect of a
right mouse click.
The view of the group parameters is replaced when certain features of
are used. Choosuing 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
Below the group list are two rows of button 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
, and q
refer to energy
, real space R
, and backtransform k
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
this area to display hints, brief help messages, warnings, and updates about
recently performed analysis or plotting actions. A few features of
will prompt the user for a text string. In those situations, the
echo area is temporarily replaced by text string dialog.
the right mouse button serves to post context
. These include parameter labels, groups list entries,
and other elements on the screen. You should try clicking the right mouse
button in different places to see what usefuls things might pop up.
Here are the relevant URLs:
- Central atom phase shifts
You betcha! Lots! Here's a partial list:
- Principal Component Analysis on the set of marked
- 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 becuase the data were
- 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.
- Alignment of scans using a reference, either of the same
edge or of a nearby edge. (Any suggestions? I am 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
- Documentation, documentation, documentation
Athena was the goddess of wisdom and is also associated with skill and justice.
Those are all good qualities for a data analysis program!
This program requires no options.
This program is part of the horae XAS analysis suite which can be obtained at
Bruce Ravel <firstname.lastname@example.org> (c) 2001 - 2003
Ifeffit is copyright (c) 1992 - 2003 Matt Newville