Provided by: horae_071~svn536-1_all bug


       athena - interactive XAS data processing


       athena  file...


       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  is intended to handle all chores involving XAS data except
       for quantitative analysis by fitting to theoretical standards.   Athena's  sister  program
       Artemis is the fitting program.

       Athena  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.   Athena  automates  the  most
       common data processing chores and automatically generates plots of one or more data sets.


       Athena  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.)

       When  Athena  starts,  you  are  presented with a window whose layout looks something like

              |    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  Athena  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's
       log-ratio/phase-difference analysis.

       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, k, R, and
       q refer to energy, photoelectron k, real space R, and backtransform k, respectively.

       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.  Athena uses  this  area  to  display
       hints,  brief  help  messages,  warnings, and updates about recently performed analysis or
       plotting actions.  A few features of Athena will prompt the user for a  text  string.   In
       those situations, the echo area is temporarily replaced by text string dialog.

       Throughout  Athena  the  right mouse button serves to post context sensitive menus.  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 groups

       *   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 obtained sequentially

       *   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 configuration option.

       *   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 <> (c) 2001 - 2003

       Ifeffit is copyright (c) 1992 - 2003 Matt Newville

                                          June 26, 2006                                 athena(1)