PySpline3

PySpline3 is a graphical, cross-platform program for processing X-ray absorption spectroscopy (XAS) and Extended X-ray absorption fine structure (EXAFS) data. It provides an interactive interface for background subtraction, normalization, spline fitting, and Fourier transformation to analyze atomic structure from X-ray absorption measurements.

This is a Python 3 port of the original PySpline by A. Tenderholt.

What PySpline3 Does

PySpline3 processes XAS/EXAFS data through a complete analysis pipeline:

1. Raw Data & Background: Load energy vs. absorption data and fit polynomial backgrounds
2. Normalization & Spline: Remove background and fit splines for edge jump normalization
3. K-space Conversion: Transform to momentum space with windowing functions
4. Fourier Transform: Convert to R-space to reveal atomic coordination structure

The program displays four interactive plot windows that update in real-time as you adjust parameters, allowing you to see immediately how changes affect your final results.

Installation

Prerequisites

PySpline3 requires Python 3.6+ and the following packages so it is probably wise to make a new environment:

pip install PyQt5 numpy PythonQwt

Install PySpline3

1. Clone or download this repository
2. Navigate to the pyspline3 directory
3. Install dependencies as shown above

Running PySpline3

From the pyspline3 directory, run:

python run_pyspline.py

This will open the main PySpline3 interface with four plot windows.

Basic Usage

Loading Data

File → Open or File → Import Raw Data

PySpline3 supports several file formats:

• Legacy .d files: Complete PySpline files with saved parameters
• SSRL .001 files: Multi-column EXAFS Data Collector format
• Simple .dat files: Two-column energy/absorption data

For simple data files, you'll need to specify the absorption edge energy (E0) when prompted.

Processing Workflow

1. Adjust Background (Raw Data window): Drag the vertical markers to set the pre-edge region, adjust polynomial order with spinner
2. Set Spline Segments (Normalized Data window): Drag green markers to position spline knots, adjust segment orders
3. Window K-space Data (EXAFS window): Drag markers to set the k-range for Fourier transform
4. View Results (Fourier Transform window): See the final R-space coordination structure

Saving Results

• File → Save: Save complete PySpline file with all parameters
• File → Export FFT: Export R-space data as text file
• File → Print: Generate publication-ready four-panel plot

File Formats

• .d files: Native PySpline format with embedded processing parameters
• .001 files: SSRL EXAFS Data Collector multi-column format
• .dat files: Simple two-column energy/absorption data
• .fft files: Exported Fourier transform results

Requirements

• Python 3.6+
• PyQt5
• NumPy
• PythonQwt (for plotting widgets)

Platform Notes

• macOS: Uses os._exit() to prevent Qt cleanup segfaults
• Linux/Windows: Standard Qt cleanup should work normally