2. Getting Started with Larch¶
Larch provides several tools for working with X-ray spectroscopy data.
First, Larch provides a Python programming library that includes (or, at
least aims to include) all the functionality needed for visualizing,
processing, and analyzing X-ray Absorption and Flourescence spectroscopy
data. Most users will start Larch has a few GUI applications, especially
GSE XRM MapViewer, and
XRF Display for these. In
addition, Larch includes an embedded Python-like macro language for
interacting with data that can be used either from a basic command-line
interface or as a callable service from a different programming language
(so that Athena and Artemis can use Larch instead of the older Ifeffit
library). In fact, most of the Larch GUIs generate and run code in this
“larch macro language” so that it can be recorded for reproducible results
and to assist creating batch scripts and more complicated analysis scripts.
Because of these different levels of access available, it can be somewhat confusing to answer the question “What is Larch?” and slightly overwhelming for new people to know where to get started using it.
2.1. First, install Larch¶
If you are new to Larch, we recommend installing using the binary installer for your operating system listed in the Table of Larch Installers. On the other hand, if you are familiar with Python and want to use Larch as a library see Downloading and Installation for other ways to install Larch into your existing Python environment.
2.2. Second, use Athena, XAS Viewer and/or GSE MapViewer¶
If you are mostly interested in using Larch as a backend for the Athena and Artemis programs for XAFS Analysis, just install Larch and the latest version of Demeter, and Demeter should find and use Larch for EXAFS Analysis, replacing the older Ifeffit library and its many limitations.
Even using Larch instead of Ifeffit, Athena still has some limitations for XAFS Analysis, and development and support for it has declined in recent years. You may be interested in the XAS Viewer program for XAFS processing and visualization. At this writing, XAS Viewer is nearly a complete replacement for Athena, with several improvements in graphics and handling of large data sets. XAS Viewer is especially aimed at XANES Analysis, and so includes robust tools for peak-fitting, and machine-learning methods such as Principal Component Analysis, Partial Least Squares and LASSO regression.
If you are a user of the GSECARS microprobe beamline or have XRF Mapping data from a compatible beamline (XFM at NSLS-II, maybe others), you’ll want to start using the GSE Mapviewer program for reading, displaying, and working with X-ray fluorescence maps. Much of the documentation here discusses commands you can type in the “Larch Buffer”, available from the Mapviewer program for scripting and more detailed access to the data in the XRF map HDF5 files.
If you are a general-purpose user or ready for more control over data analysis for many types of data, the Larch GUI can help you browse through the available commands and data, and provide a good starting point for interactive, exploratory data analysis.
2.3. Third, start scripting with Larch and/or Python¶
Once you’ve done a little bit of GUI or interactive work, you may be ready to write scripts. Such scripts can help you automate repeated tasks and can build and remember more complex analyses. The combination of the high level commands of Larch and the interactive command-line GUI for exploratory data analysis are a great way to get started in writing your own scripts and building up more sophisticated programs.