EXAFS analysis

XDI file format

The files automatically exported by Acquaman are plain ASCII files with .dat extension, and they follow the XDI format specification (full format details here, https://iopscience.iop.org/article/10.1088/1742-6596/712/1/012148). The file contains a header with information about the measurement, and columns with data.

Importing Transmission measurements in Athena

To import the data,

  1. Drag the xdi file (1) into Athena (2). A dialog (3) will pop-up with the list of columns.
  2. On the sample column selection (5) select the appropriate columns depending on the type of measurement (see table above). in this case 4 and 5. Remember to select Natural Log for transmission data.
  3. If a reference is used, import it as a ref channel (7), selecting the appropriate columns [5,6 in this example], and select the log (8). In most cases, the ref is the same element as the edge (select Same element if it is), but this is not always the case.

transmission import athena

Importing Fluorescence measurements in Athena

To import the fluorescence data,

  1. do the same as before, but looking at the list of column names (1), select the fluorescence columns (2), and NO natural log (3). The right fluorescence columns can be determined based on the column labels when looking at the file heather, and knowing what those labels mean. See next section for details.
  2. The ref column (4) and other settings (5) should be the same as for transmission.

Columns when data was collected on BioXAS-spectroscopy Main

Fluorescence athena import on Main

Columns when data was collected on BioXAS-Spectroscopy Side

Fluorescence athena import

Tutorial videos


Demeter is a Suite or XAS related programs created by Bruce Ravel. The suite can be found here:  http://bruceravel.gi1thub.io/demeter/, and it contains:

  1. Athena, a XAS experimental data processing application.
  2. Artemis, an EXAFS fitting application
  3. Hephaestus, a periodic table containing X-ray related information for all (or most) chemical elements.

Link to tutorial videos: https://www.diamond.ac.uk/Instruments/Spectroscopy/Techniques/XAS.html

More information: https://github.com/bruceravel/XAS-Education


Xray Larch (https://xraypy.github.io/xraylarch/getting_started.html) is the "evolution" in a sense of the Athena package (Demeter), made by Matt Newville in collaboration with Bruce Ravel (the author of Athena). As of 2021 this is the package that we're recommending for processing data generated by the BioXAS-spectroscopy beamlines.

Tutorial videos: https://www.youtube.com/playlist?list=PLgNIl_xwV_vK4V6CmrsEsahNCAsjt8_Be

CLS EXAFS analysis workshop 2020

Videos from the CLS EXAFS analysis workshop can be found here: https://www.youtube.com/playlist?list=PLCmYaA6Q0hA1HG8f51uv9K9TOH6_3UvOV

Workshop topics include:

Session 1 - Automated XAS data analysis in Python / Larch

Presenter: Dr. Matthew Newville, APS, Argonne National Laboratory, Chicago, IL

Session 2 - FEFF: Advanced applications

Presenters: Dr. Fernando Vila, Dr. Joshua Kas, University of Washington, Seattle, WA

Session 3 - Ab initio XANES calculation with FDMNES

Presenter: Dr. Yves Joly, CNRS, Grenoble, France.

Session 4 - AI and Machine Learning in EXAFS analysis

Presenters:  Dr. Janis Timoshenko, Fritz-Haber Institut, Berlin, Germany