EXAFS Analysis Software: ARTEMIS

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ARTEMIS
0.8.011
20 September, 2007

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Main Page

Downloads

Contributions

Documents

Change Logs

Reporting bugs

Bruce's homepage

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IFEFFIT Homepage

IFEFFIT Wiki

Bruce's Wiki page

IFEFFIT mailing list

IFEFFIT FAQ

xafs.org

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ATHENA

ARTEMIS

HEPHAESTUS

DEMETER

ATOMS

SixPack

WebATOMS

ATOMS database

XAS File Format

EASE

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How is IFEFFIT used by ATHENA and ARTEMIS?

What is IFEFFIT worth to you?

Do you have a question about using WinXAS?

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ATHENA, ARTEMIS, HEPHAESTUS: B. Ravel & M. Newville J. Synchrotron Rad. (2005), 12:4, pp. 537-541.

IFEFFIT: M. Newville J. Synchrotron Rad. (2001) 8, 322-324

ATOMS: B. Ravel J. Synchrotron Rad. (2001) 8, 314-316

FEFF: J.J. Rehr & R.C. Albers, Rev. Mod. Phys. (2000) 72, 621-654

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.	S c r e e n s h o t s
	Fit history screen. From here you can examine the results of previous fits and generate reports of fitting and statistical parameters from past fits.
	ATOMS screen. On this page you can enter and manipulate crystallographic information and generate input data for FEFF.
	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.
	Path screen. On this page, you set the parameters for each path included in the fit.

S i t e m a p	Main Page
	Downloads
	Contributions
	Documents
	Change Logs
	Reporting bugs
	Bruce's homepage

I F E F F I T	IFEFFIT Homepage
	IFEFFIT Wiki
	Bruce's Wiki page
	IFEFFIT mailing list
	IFEFFIT FAQ
	xafs.org

X A S S o f t w a r e	ATHENA
	ARTEMIS
	HEPHAESTUS
	DEMETER
	ATOMS
	SixPack
	WebATOMS
	ATOMS database
	XAS File Format
	EASE

Q & A	How is IFEFFIT used by ATHENA and ARTEMIS?
	What is IFEFFIT worth to you?
	Do you have a question about using WinXAS?