Larch is a open-source library and set of applications for processing and analyzing X-ray absorption and fluorescence spectroscopy data and X-ray fluorescence and diffraction image data from synchrotron beamlines. It aims to be a complete analysis toolkit for X-ray absorption fine-structure spectroscopy (XAFS) including X-ray absorption near-edge spectroscopy (XANES) and extended X-ray absorption fine-structure spectroscopy (EXAFS). It also supports visualization and analysis tools for X-ray fluorescence (XRF) spectra and XRF and X-ray diffraction (XRD) images as collected at scanning X-ray microprobe beamlines.
Larch is written in Python, making heavy use of the excellent scientific python libraries including numpy, scipy, h5py, matplotlib, and provides a Python library for processing and analyzing X-ray spectroscopy and imaging data. There are a few GUI applications written using this library for common data visualization and analysis tasks, notably XAS Viewer, GSE Map Viewer, and XRF Viewer as described in more detail below.
While Larch can be used as a Python library, the applications built with Larch use a Python-like macro language - the “Larch language” - for interactive and batch processing. This macro language is available from an interactive command-line interface through either larch or Larch GUI and intended to be very easy to use for novices while also being complete enough to automate data processing and analysis. Most of the GUIs can generate and save “Larch code” for an analysis session to make reproducible analysis sessions, and to encourage and facilitate a gentle transition to transition from GUI-only analyses to scripted and programmatic analysis of larger data sets. This macro language also allows Larch to be run as a background service that other processes can use Larch as the analysis engine. The popular Demeter XAFS application suite can use Larch in this way.
Larch is distribute under an open-source license that is nearly identical to the BSD license. It is under active and open development centered at the GeoScoilEnviroCARS sector of Center for Advanced Radiation Sources at the University of Chicago has been supported by the US National Science Foundation - Earth Sciences (EAR-1128799), and Department of Energy GeoSciences (DE-FG02-94ER14466). In addition, funding specifically for Larch was granted by the National Science Foundation - Advanced CyberInfrastructure (ACI-1450468).
Table of Larch Applications
These applications installed with Larch, in addition to a basic Python library. Here, GUI = Graphical User Interface, CLI = Command Line Interface, and beta indicates a work in progress. The Feff6L and Feff8L codes are the open-source versions of Feff6 and Feff8, written by the Feff Project, and included with Larch by permission and with license to redistrubute.
XAFS Processing and Analysis: XANES pre-edge peak fitting, linear analysis, PCA/LASSO, EXAFS extraction
simple shell command-line interface
enhanced command-line interface with data browser
XRF Map Viewer for GSECARS X-ray microprobe data.
Display and Analyze XRF Spectra.
Feff 6 EXAFS calculations
Feff 8 EXAFS calculations (no XANES)
1D XRD Viewer
Display and work with 1-D XRD patterns
2D XRD Viewer
Display XRD images
Display RIXS planes, take profiles
Note that the Dioptas program for viewing and calibrating 2-D XRD patterns, written and maintained by Clemens Prescher has been included with earlier versions of Larch. It is no longer included, but we recommend downloading and installing that for working with XRD image data.
Table of Contents¶
- 1. Downloading and Installation
- 2. Getting Started with Larch
- 3. Larch: Motivation and Overview
- 4. Larch GUIs
- 5. XASViewer
- 5.1. Reading Data into XAS Viewer
- 5.2. Common XAS Processing Dialogs
- 5.3. Pre-edge subtraction and Normalization
- 5.4. Pre-edge peak fitting
- 5.5. Linear Combination Analysis
- 5.6. Principal Component and Non-negative Factor Analysis
- 5.7. Linear Regression with LASSO and PLS to predict external variable
- 5.8. EXAFS Processing: Background Subtraction
- 5.9. EXAFS Processing: Fourier Transforms
- 5.10. Fitting EXAFS data to Feff Paths
- 6. GSECARS Mapviewr
- 7. QtRIXS
- 8. Programming with Larch from Python
- 9. Larch Macro Language Tutorial
- 10. Reading and Writing Data
- 10.1. Simple ASCII Column Files
- 10.2. Athena Project Files
- 10.3. Reading HDF5 Files
- 10.4. Reading NetCDF Files
- 10.5. Reading TIFF Images
- 10.6. Working with Epics Channel Access
- 10.7. Reading Scan Data from APS Beamlines
- 10.8. Reading XAFS Data Interchange (XDI) Files
- 10.9. Reading Spec/BLISS files via silx.io.open
- 10.10. Saving and Restoring Larch Groups
- 11. Plotting and Displaying Data
- 12. Fitting and Modeling Data
- 13. XAFS Analysis
- 13.1. XAFS Functions: Overview and Naming Conventions
- 13.2. XAFS: Pre-edge Subtraction, Normalization, and data treatment
- 13.3. XANES Analysis: Linear Combination Analysis, Principal Component Analysis, Pre-edge Peak Fitting
- 13.4. XAFS: Post-edge Background Subtraction
- 13.5. XAFS: Fourier Transforms for XAFS
- 13.6. XAFS: Wavelet Transforms for XAFS
- 13.7. XAFS: Reading and using Feff Paths
- 13.8. XAFS: Fitting XAFS to Feff Paths
- 13.9. XAFS: Computing anomalous scattering factors from XAFS data
- 14. X-ray Databases
- 15. X-ray Fluorescence Analysis
- 16. References