Table of Contents

• 1. Getting Started with Larch
  • 1.1. First, install Larch
  • 1.2. Second, use Athena, XASViewer and/or GSEMapViewer
  • 1.3. Third, start scripting with Larch and/or Python
• 2. Downloading and Installation
  • 2.1. Single-File Installers
  • 2.2. Install with Python
    • 2.2.1. Using Anaconda Python
    • 2.2.2. Using pip
    • 2.2.3. Source Inxstallation
    • 2.2.4. Optional Python Packages
  • 2.3. Getting Help and Support
  • 2.4. Docs and Examples
  • 2.5. Citing Larch
  • 2.6. Funding and Support
  • 2.7. Acknowledgements
  • 2.8. License
• 3. Larch GUIs
  • 3.1. Basic Larch GUI
• 4. XASViewer
  • 4.1. Reading Data into XAS Viewer
  • 4.2. Common XAS Processing Dialogs
  • 4.3. Pre-edge subtraction and Normalization
  • 4.4. Pre-edge peak fitting
  • 4.5. Linear Combination Analysis
  • 4.6. Principal Component and Non-negative Factor Analysis
  • 4.7. EXAFS Processing: Background Subtraction
  • 4.8. EXAFS Processing: Fourier Transforms
• 5. GSECARS Mapviewr
• 6. QtRIXS
  • 6.1. Reading RIXS data
  • 6.2. Plotting RIXS data
• 7. Larch Language Tutorial
  • 7.1. Getting Started
    • 7.1.1. Larch as a Basic Calculator
  • 7.2. Basic and Complex Data Types
    • 7.2.1. Basic Data Types
    • 7.2.2. Objects and Groups
    • 7.2.3. More Complex Data Structures: Lists, Arrays, Dictionaries
    • 7.2.4. Object identities, copying, and equality vs. identity
  • 7.3. Basic Array Manipulation
    • 7.3.1. Functions for creating arrays
    • 7.3.2. The array dtype – datatype
    • 7.3.3. Basic array manipulation
    • 7.3.4. Slicing and extracting sub-arrays
    • 7.3.5. Array attributes and methods
    • 7.3.6. Mathematical functions for arrays
  • 7.4. Conditional Execution and Flow Control
    • 7.4.1. Conditional Evaluation with if and else
    • 7.4.2. For loops
    • 7.4.3. While loops
  • 7.5. Dealing With Errors
    • 7.5.1. Syntax Errors
    • 7.5.2. Exceptions
    • 7.5.3. Try and Except
    • 7.5.4. Raising your own exceptions
  • 7.6. Writing Functions or Procedures
    • 7.6.1. Def statement
    • 7.6.2. Namespace and “Scope” inside a Procedure
    • 7.6.3. The return statement, and multiple Return values
    • 7.6.4. Keyword arguments
    • 7.6.5. Documentation Strings
  • 7.7. Running Larch Scripts, and Modules
    • 7.7.1. Running a larch script with run()
    • 7.7.2. Importing a Larch Script as a Module
  • 7.8. Builtin Functions
    • 7.8.1. Builtin data values
    • 7.8.2. Larch-Specific Builtin functions
    • 7.8.3. Builtin functions inherited from Python
• 8. Reading and Writing Data
  • 8.1. Simple ASCII Column Files
  • 8.2. Athena Project Files
    • 8.2.1. Reading Athena Project Files
    • 8.2.2. Creating and Writing to Athena Project Files
  • 8.3. Using HDF5 Files
  • 8.4. Reading NetCDF Files
  • 8.5. Reading TIFF Images
  • 8.6. Working with Epics Channel Access
  • 8.7. Reading Scan Data from APS Beamlines
  • 8.8. Reading XAFS Data Interchange (XDI) Files
  • 8.9. Saving and Restoring Larch Groups
• 9. Plotting and Displaying Data
  • 9.1. Line Plots
    • 9.1.1. plot(), newplot(), and oplot()
    • 9.1.2. Plot Examples
    • 9.1.3. Interactive Use of the Plot Windows
    • 9.1.4. Using TeX-like commands for labels and titles
  • 9.2. Image Display and Contour
  • 9.3. Advanced Plotting: using matplotlib
• 10. Fitting and Modeling Data
  • 10.1. Fitting Overview
  • 10.2. Parameters
    • 10.2.1. setting bounds
    • 10.2.2. using algebraic constraints
    • 10.2.3. param_group(): creating a Parameter Group for fitting constraints
    • 10.2.4. fiteval and details about algebraic constraints
    • 10.2.5. working with uncertainties
  • 10.3. minimize() and objective Functions
  • 10.4. Fit Results and Outputs
  • 10.5. Some Builtin Line-shape Functions
  • 10.6. Fit Examples
    • 10.6.1. Example 1: Fitting a Simple Gaussian
    • 10.6.2. Example 2: Fitting XANES Pre-edge Peaks
    • 10.6.3. Example 3: Fitting XANES Spectra as a Linear Combination of Other Spectra
  • 10.7. Simplified Peak Fitting with fit_peak()
    • 10.7.1. Example: Fitting a Gaussian + background with fit_peak()
    • 10.7.2. Example: Fitting a Rectangular function with fit_peak()
    • 10.7.3. Using lmfit.Model
  • 10.8. Advanced Confidence Intervals and Chi-square maps
    • 10.8.1. Confidence interval, Example 1
    • 10.8.2. Confidence interval, Example 2
    • 10.8.3. Chi-square Maps
• 11. XAFS Analysis
  • 11.1. XAFS Functions: Overview and Naming Conventions
    • 11.1.1. Naming conventions for XAFS arrays
    • 11.1.2. Plotting Macros for XAFS
    • 11.1.3. Utility Functions for XAFS
  • 11.2. XAFS: Pre-edge Subtraction, Normalization, and data treatment
    • 11.2.1. The pre_edge() function
    • 11.2.2. Pre-Edge Subtraction Example
    • 11.2.3. The MBACK algorithm
    • 11.2.4. Pre-edge baseline subtraction
    • 11.2.5. Over-absorption Corrections
    • 11.2.6. Spectral deconvolution
  • 11.3. XANES Analysis: Linear Combination Analysis, Principal Component Analysis, Pre-edge Peak Fitting
    • 11.3.1. Pre-edge Peak fitting
    • 11.3.2. Linear Combination Analysis
    • 11.3.3. Principal Component Analysis
    • 11.3.4. PCA example
  • 11.4. XAFS: Post-edge Background Subtraction
    • 11.4.1. The autobk() function
    • 11.4.2. The AUTOBK Algorithm
    • 11.4.3. Examples
  • 11.5. XAFS: Fourier Transforms for XAFS
    • 11.5.1. Overview of XAFS Fourier transforms
    • 11.5.2. Forward XAFS Fourier transforms (\(k{\rightarrow}R\))
    • 11.5.3. Reverse XAFS Fourier transforms (\(R{\rightarrow}q\))
    • 11.5.4. ftwindow(): Generating Fourier transform windows
    • 11.5.5. Catalog of Fourier transform window
    • 11.5.6. Examples: Forward XAFS Fourier transforms
    • 11.5.7. Examples: Reverse XAFS Fourier transforms, Fourier Filtering
  • 11.6. XAFS: Wavelet Transforms for XAFS
    • 11.6.1. cauchy_wavelet()
    • 11.6.2. Wavelet Example
  • 11.7. XAFS: Reading and using Feff Paths
    • 11.7.1. Running Feff
    • 11.7.2. feffpath() and FeffPath Groups
    • 11.7.3. path2chi() and ff2chi(): Generating \(\chi(k)\) for a FeffPath
    • 11.7.4. The _feffdat Group: Full Details of the Feff.Dat File
    • 11.7.5. The EXAFS Equation using Feff and FeffPath Groups
    • 11.7.6. Models for Calculating \(\sigma^2\)
    • 11.7.7. Example: Reading a Feff file
    • 11.7.8. Example: Adding Feff files
    • 11.7.9. Example: Using Path Parameters when adding Feff files
  • 11.8. XAFS: Fitting XAFS to Feff Paths
    • 11.8.1. The Feffit Strategy for Modeling EXAFS Data
    • 11.8.2. Fit statistics and goodness-of-fit meassures for feffit()
    • 11.8.3. The Feffit functions in Larch
    • 11.8.4. feffit_transform() and the Feffit Transform Group
    • 11.8.5. feffit_dataset()
    • 11.8.6. feffit()
    • 11.8.7. feffit_report()
    • 11.8.8. Example 1: Simple fit with 1 Path
    • 11.8.9. Example 2: Fit 1 dataset with 3 Paths
    • 11.8.10. Example 3: Fit 3 datasets with 1 Path each
    • 11.8.11. Example 4: Measuring Coordination number
    • 11.8.12. Example 5: Comparing Fits in different Fit Spaces
    • 11.8.13. Example 6: Testing EXAFS sensitivity to \(Z\)
  • 11.9. XAFS: Computing anomalous scattering factors from XAFS data
    • 11.9.1. Overview of the diffKK implementation
    • 11.9.2. diffKK on L edge data
• 12. X-ray Databases
  • 12.1. X-ray Properties of the Elements
  • 12.2. X-ray Properties of Materials and Chemicals
• 13. X-ray Fluorescence Analysis with Larch
  • 13.1. MCA and ROI objects
  • 13.2. Creating MCA objects
• 14. Programming with Larch from Python
  • 14.1. Larch submodules
• 15. Bibliography