Temple of Artemis, Jerash, Jordon
photo by Matthew Marcus
ARTEMIS is an interactive graphical utility for fitting EXAFS
data using theoretical standards from FEFF. ARTEMIS
is a graphical front end to Matt Newville's IFEFFIT library
written entirely in the Perl programming language and using the
PGPLOT graphical library for data display. It is being developed
on Linux and Windows XP, but should work on any Unix or any Windows
operating system. The current version requires IFEFFIT 1.2.5
or later.
- A forms-based interface to setting fitting parameters, contraints
between parameters, and restraints on parameters.
- Co-refinement of multiple data sets.
- Refinement of data sets using multiple k-weightings
- Co-refinement of a background spline with the
EXAFS data and determination of correlations between
the background and the data
- Fit using results of multiple FEFF calculations.
- Plot in k-, R-, or backtransformed k-space
- Plot of the data, the best fit, the background
spline, and individual paths
- Report errorbars and correlations between
variables
- Complete fit history -- review and plot previous fits
in a project and revert a project to a previous fitting model.
- Import data directly from ATHENA project files.
- Interfaces to ATOMS and FEFF
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ARTEMIS is software under development. While
it is working quite well, you are quite likely to find
bugs and other forms of misbehavior. If you download and
use ARTEMIS, I presume that you understand
this and that you will agree to report on your experiences
so that I may further improve the code.
ARTEMIS is free software, as are the things
upon which it depends: Perl,
IFEFFIT,
and PGPLOT.
See the license
for details.
ARTEMIS may have a short remaining lifespan. See
my wiki page on ARTEMIS's shortcomings.
ARTEMIS is only intended to fit EXAFS data.
Her sister program
ATHENA is the data processing program.
Aside from bug fixes, here are things I'd like to do for
ARTEMIS. The items in black text should be done before she
can be called 1.0. Items in grey are
low-priority items for me, either because I see them as relatively
unimportant or because they would be excessively difficult to
implement. Items in reddish-purple won't
happen until after version 1.0. If any of these seems particularly
important to you, let me know .
-
Functionality
- Merging of projects, in the sense of
reading a portion (say a FEFF
calculation or a data set and all its
FEFF calculations) of one project
into another
- An ability to abort a fit.
- Parameter mapping, as in, for example,
Biochemistry 35 (1996)
pp. 9014-9023
- Batch processing, i.e. a meachnism to run fits on a series
of data files using the same model.
- Watch out for excessive memory usage as in
ATHENA.
-
User Interface
- Color coding of reserved words and function
names in path parameter math expressions.
- ATHENA and FEFF interfaces
- Convert PDB (and others) to
`feff.inp' files and vice
versa.
Open Babel might be useful.
-
Path finder enhancements, for instance an ability to
collapse very similar paths into a single path in
ARTEMIS, to turn off degeneracy entirely,
and other features to facilitate complex modeling.
- Data
-
Tweak background removal for data imported from an
ATHENA project file.
-
Import data or feff calculations from the web.
-
Convert a data file into a
`feffNNNN.dat' style
pseudo-path by Fourier filtering. This may be
useful for situations involving hydrogen.
-
Import `feffit.inp' files
correctly, including recursing into include
files.
-
Plotting
-
Multiple component plots in R and q, as in Athena
-
Arrows, text, shapes on plot.
-
Documentation
- More/better in-program documentation.
- User guide, with pix and examples.
- Demo projects
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Main screen. This view shows the data page where Fourier transform
and fit range parameters are set. To the right, you can see the
list of all data and paths used in the project as well as all the
plotting controls.
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Fit history screen. From here you can examine the results of previous fits
and generate reports of fitting and statistical parameters from past fits.
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ATOMS screen. On this page you can enter and manipulate
crystallographic information and generate input data for FEFF.
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FEFF interpretation screen. This screen displays the results of a
FEFF calculation and provides several utilities for plotting and
manipulating the paths from the calculation.
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Path screen. On this page, you set the parameters for each path
included in the fit.
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normatively acceptable about it. It contravened the freedom of speech
and ideas. We [don't] engage in it because it [excludes] people from
ideas.
Eban Moglan, General Counsel, Free Software Foundation