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       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 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
       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,

       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


       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)