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.TH ATHENA 1 "June 26, 2006"
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athena \- interactive \s-1XAS\s0 data processing
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This manpage documents the
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program, for interactive \s-1XAS\s0 data processing, including
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converting raw data to mu(E), aligning, merging, deglitching, Fourier
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transforming, and plotting. Basically, \fBAthena\fR is intended to
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handle all chores involving \s-1XAS\s0 data except for quantitative analysis
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by fitting to theoretical standards. \fBAthena\fR's sister program
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\&\fBArtemis\fR is the fitting program.
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\&\fBAthena\fR has two interesting and unusual features. The first is that
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there are no buttons for explicitly removing the background from mu(E)
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data or for performing Fourier transforms. The only active buttons
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displayed on the main window are for plotting. \fBAthena\fR always knows
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when data requires a background removal or a Fourier transform and
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will perform the necessary analysis steps before displaying the plot.
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The second interesting feature is that it is just as easy to perform
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analysis and plotting chores on multiple data sets as on an individual
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data set. \fBAthena\fR automates the most common data processing chores
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and automatically generates plots of one or more data sets.
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\&\fBAthena\fR is a graphical and interactive program written in the perl
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programming language, using the Tk display engine, the \s-1IFEFFIT\s0 \s-1EXAFS\s0
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library, and the \s-1PGPLOT\s0 plotting library. (See below for a list of
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When \fBAthena\fR starts, you are presented with a window whose layout
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looks something like this:
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\& +----------------------------------------+
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\& +---------------------------+------------+
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\& +---------------------------+------------+
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\& +----------------------------------------+
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As you import data into \fBAthena\fR, \fIdata groups\fR are created and
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those groups are listed in the section labeled `Group List' . You
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select a group as the active one by clicking the left mouse button on
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its entry in the group list. When selected, the list entry is
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highlighted with an orange background and the parameters associated
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with that group are displayed in the large area on the left labeled
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`Group Parameters'. When you pass the mouse over a label in the group
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parameters section, you will notice that the label changes color.
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This indicates that a mouse click on the label will have an effect.
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Clicking the left mouse button will display a hint in the echo area as
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to the function of that parameter. See the section on group operations
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for the effect of a right mouse click.
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The view of the group parameters is replaced when certain features of
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\&\fBAthena\fR are used. Choosuing any of the options from the Data,
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Align, Diff, or Analysis menus will temporarily replace the group
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parameters with views of parameters relevant to the chosen task. For
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example, when the log-ratio option is chosen from the Analysis menu,
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the view of group parameters is replaced by a view of the interface to
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\&\fBAthena\fR's log\-ratio/phase\-difference analysis.
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Below the group list are two rows of button for plotting data. The
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red buttons are for plotting the selected data group. The purple
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buttons are for plotting multiple data groups. These buttons are
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labeled according to the data space of the plot. \fIE\fR, \fIk\fR, \fIR\fR,
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and \fIq\fR refer to \fIenergy\fR, \fIphotoelectron k\fR, \fIreal space R\fR, and
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\&\fIbacktransform k\fR, respectively.
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Below the plot buttons are a set of tabs for specifying the details of
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the plots in each space. For each space you can specify the range of
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the x\-axis. For energy plots, you can select whether the background
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function is plotted along with the data and whether the data and
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background are normalized. For k\-space plots, you can select the
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amount of k\-weighting. For R\- and q\-space plots, you can select which
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part of those complex functions are plotted. There are also tabs for
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setting up stacked plots and for establishing plot indicators. For a
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complete discussion see the section on plotting.
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Finally, at the bottom of the page is the \fIecho area\fR. \fBAthena\fR
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uses this area to display hints, brief help messages, warnings, and
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updates about recently performed analysis or plotting actions. A few
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features of \fBAthena\fR will prompt the user for a text string. In
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those situations, the echo area is temporarily replaced by text string
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Throughout \fBAthena\fR the right mouse button serves to post \fIcontext
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sensitive menus\fR. These include parameter labels, groups list
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entries, and other elements on the screen. You should try clicking
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the right mouse button in different places to see what usefuls things
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.SH "SECTIONS OF THE DOCUMENT"
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.IX Header "SECTIONS OF THE DOCUMENT"
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.IP "Handling data" 4
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.IX Item "Handling data"
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Normalization and background removal ||
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.IP "Data operations" 4
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.IX Item "Data operations"
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Energy calibration ||
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Self-absorption corrections ||
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Dead-time corrections ||
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Calibrating dispersive \s-1XAS\s0 data ||
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Difference spectra ||
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Log\-ratio/phase\-difference analysis ||
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Principal component analysis ||
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Linear fitting of spectra ||
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.IX Item "Using Athena"
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Setting preferences ||
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Binding key sequences ||
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.IX Header "REFERENCES"
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Here are the relevant URLs:
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.IP "\s-1IFEFFIT\s0" 4
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\& http://cars.uchicago.edu/ifeffit
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.IP "\s-1PGPLOT\s0" 4
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\& http://www.astro.caltech.edu/~tjp/pgplot/
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\& http://www.perl.com
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\& http://www.lehigh.edu/~sol0/ptk/
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.IP "Central atom phase shifts" 4
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.IX Item "Central atom phase shifts"
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\& http://leonardo.phys.washington.edu/~ravel/software/feff_tables/
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.SH "MISSING FEATURES"
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.IX Header "MISSING FEATURES"
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You betcha! Lots! Here's a partial list:
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Principle Component Analysis on the set of marked groups
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\&\s-1XANES\s0 analysis by fitting a sum of scans to an unknown
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Dead-time and self-absorption corrections
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Handle dispersive data sets, i.e. data sets wherein the I0 and \s-1IT\s0
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measurements are in separate data files becuase the data were obtained
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Calibrate dispersive data to a trusted standard
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Handle \s-1SPEC\s0 files. An independent perl module would be ideal. This is
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a project some eager contributor could tackle without having to delve
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into \s-1ATHENA\s0's source code.
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Alignment of scans using a reference, either of the same edge or of a
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nearby edge. (Any suggestions? I am lacking a good idea about how to
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Formulas for the energy axis (useful for converting encoder readings
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R and q space records, that is to be able to read and write data in R
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and q space just as easily as E or k space.
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Internationalization. That is, build a framework for having text
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strings read from external files and for the language to be a
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configuration option.
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Documentation, documentation, documentation
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.SH "WHAT'S IN A NAME?"
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.IX Header "WHAT'S IN A NAME?"
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Athena was the goddess of wisdom and is also associated with skill and
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justice. Those are all good qualities for a data analysis program!
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This program requires no options.
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This program is part of the horae XAS analysis suite
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which can be obtained at
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http://cars9.uchicago.edu/~ravel/software/
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\& Bruce Ravel <ravel@phys.washington.edu> (c) 2001 - 2003
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\& Ifeffit is copyright (c) 1992 - 2003 Matt Newville
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\& newville@cars.uchicago.edu
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\& http://cars9.uchicago.edu/~newville/ifeffit/
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debian/athena.1
