| Larch: Data Analysis Tools for X-ray Spectroscopy

\(\newcommand{\AA}{\unicode{x212B}}\)

# 5. Larix (was XAS Viewer)

The Larix Application gives a graphical user interface (GUI) for the visualization and analyis of X-ray absorption spectroscopy (XAS) data, both XANES and EXAFS. It is deliberately patterned after the Demeter Package (Athena and Artemis programs), and shares many concepts and presentation ideas with these progrqms. As a GUI Program, Larix should seem very “Athena-like” though of course there will be several differences. We hope that many of these differences will be “improvements”. By using Larch for all of its analysis steps, Larix not only provides interactive data visualization, exploration, and analysis of XAS data, but also records those steps as Larch / Python commands that can be saved and reproduced outside of the GUI, say to enable batch processing of large volumes of data.

Larix is still in active development with new features driving much of the development and releases of Larch version for the past few years. At this writing (October, 2023, Larch version 0.9.72), the main feature of Larix are met, though improvements and new featutes continue to be made, and bugs are being fixed as quickly as possible. Ideas for additions and improvements are most welcome. If you find problems with it or unexpected or missing functionality, please let us know. In addition, if you find any features from Athena, Artemis, Sixpack, or other analysis programs that you would like to see in Larix, please let us know.

- 5.1. Larix Overview
  - 5.1.1. Basic Layout, GUI Controls, and XAS Data Management
  - 5.1.2. Data Input and Output
  - 5.1.3. Data Normalization
  - 5.1.4. XANES Analysis
  - 5.1.5. EXAFS Processing
  - 5.1.6. EXAFS Modeling with FEFF
- 5.2. Reading and Saving Data into Larix
  - 5.2.1. Reading Plain text data files, including XDI
  - 5.2.2. Reading Data from Athena Project Files
  - 5.2.3. Reading Spec/Bliss HDF5 Data
  - 5.2.4. Larch Session Files and Larix
  - 5.2.5. Auto-saving Larch Session Files
- 5.3. Pre-edge subtraction and Normalization
- 5.4. Common XAS Processing Dialogs
  - 5.4.1. Energy Calibration and alignment
  - 5.4.2. Deglitching and Truncating Data
  - 5.4.3. Smoothing Data
  - 5.4.4. De-convolving XAS Data
  - 5.4.5. Re-binning XAS Data
  - 5.4.6. Correcting for Over-Absorption in XAS Data
- 5.5. Pre-edge peak fitting
- 5.6. Linear Combination Analysis
- 5.7. Principal Component and Non-negative Factor Analysis
- 5.8. Linear Regression with LASSO and PLS to predict external variable
- 5.9. EXAFS Processing: Background Subtraction
- 5.10. EXAFS Processing: Fourier Transforms
- 5.11. Fitting EXAFS data to Feff Paths