XANES Example

This example demonstrates a complete workflow for processing XANES data using EstraPy. It covers:

  1. Directory setup and data loading
  2. Basic data cleaning and normalization
  3. Pre-edge and post-edge fitting
  4. Noise estimation
  5. Final plotting and export

1. Directory Setup and Data Loading

The tutorial assumes a rigid directory structure for organizing raw and processed data. EstraPy never modifies raw files, and is designed to be fast enough to be frequently re-run as you adjust parameters.

Therefore, we recommend a clean separation between raw data and processing outputs.

    
.
├── analysis           # Analysis folder (contains EstraPy projects and outputs)
│   ├── xanes.estra    # EstraPy project file
│   │
│   └── xanes          # Output folder generated by EstraPy
│       └── xanes.log
│
└── data               # Raw data directory (contains original data files)
    ├── scan_01.xy     # Raw data files (never modified by EstraPy)
    :
    └── scan_09.xy

In this structure:

  • The data folder contains all raw data files (e.g. scan_01.xy, scan_02.xy, …, scan_09.xy). These files are never modified by EstraPy.
  • The analysis folder contains the EstraPy project file (xanes.estra). Once the .estra file is run, it generates a subfolder xanes where all processed data, logs, images and outputs are stored. This separation allows you to freely re-run the .estra file, adjusting parameters as needed, without worrying about overwriting raw data.

1.1. Data structure

Let’s first examine the structure of the raw data files. Each file is a text file with a number of header lines (starting with #) followed by columns of data. In this case, this is the head of one of the files:

# Sample: Fe2O3
# Edge: Fe K-edge

To load the data, we start by creating a new EstraPy project and adding the raw files:

# version 2.0.1

# Let's give a title to the project
%title "XANES Analysis Example"


# Read the input files. The path supports relative paths
# (relative to the .estra file) and glob patterns.
filein "data/scan_*.xy"