EPyR Tools Documentation

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EPyR Tools is a comprehensive Python package for Electron Paramagnetic Resonance (EPR) spectroscopy data analysis. It provides a complete toolkit for loading, processing, analyzing, and visualizing EPR data from Bruker spectrometers, with a focus on FAIR (Findable, Accessible, Interoperable, and Reusable) data principles.

From basic data loading to advanced quantitative analysis, EPyR Tools offers professional-grade capabilities for EPR researchers, with comprehensive documentation and interactive tutorials.

Key Features

Data Loading & Formats

  • Bruker File Support: Load BES3T (.dta/.dsc) and ESP/WinEPR (.par/.spc) files seamlessly

  • Automatic Format Detection: Smart file format recognition and parameter extraction

  • FAIR Data Conversion: Export to CSV, JSON, and HDF5 formats with complete metadata

  • Batch Processing: Handle multiple files efficiently

Advanced Analysis

  • Baseline Correction: Multiple algorithms (polynomial, exponential) with signal exclusion

  • Peak Detection: Automatic identification of EPR spectral features

  • g-Factor Calculations: Precise electronic g-factor determination with field calibration

  • Quantitative Integration: Single and double integration for spin quantification

  • Lineshape Analysis: Comprehensive EPR lineshape functions (Gaussian, Lorentzian, Voigt, pseudo-Voigt)

Visualization & Plotting

  • Interactive CLI Plotting: Command-line plotting with measurement tools (epyr-plot --interactive --measure)

  • Delta X/Y Measurements: Click two points to measure precise distances with visual feedback

  • 2D Spectral Maps: Professional publication-quality EPR plots

  • macOS Optimized: Smooth interactive plotting with TkAgg backend

  • Customizable Styling: Flexible plot configuration for different EPR experiments

  • Export Options: High-resolution outputs for publications

Learning & Documentation

  • Interactive Tutorials: Comprehensive Jupyter notebooks (beginner → advanced)

  • Complete API Documentation: Professional Sphinx-generated docs

  • Example Scripts: Ready-to-use Python automation scripts

  • Best Practices Guide: EPR analysis workflows and quality assessment

EPR-Specific Tools

  • Physical Constants: Comprehensive EPR-relevant constants library

  • Isotope Database: Nuclear properties and magnetic parameters

  • Field-Frequency Conversion: Precise EPR measurement calculations

  • Spectrometer Support: Optimized for modern Bruker EPR systems

Quick Start

import epyr

# Load EPR data (opens file dialog if no path given)
x, y, params, filepath = epyr.eprload()

# Apply baseline correction
from epyr.baseline import baseline_polynomial
y_corrected, baseline = baseline_polynomial(y, x_data=x, poly_order=1)

# Convert to FAIR formats (CSV, JSON, HDF5)
from epyr.fair import convert_bruker_to_fair
convert_bruker_to_fair(filepath, output_dir='./fair_data')

# Generate EPR lineshapes for analysis
from epyr.lineshapes import gaussian, lorentzian, Lineshape
B = np.linspace(320, 340, 1000)  # mT
gauss_line = gaussian(B, center=334.8, width=2.0)
lorentz_line = lorentzian(B, center=334.8, width=2.0)

# Or use the unified interface
shape = Lineshape('pseudo_voigt', width=2.0, alpha=0.5)
mixed_line = shape(B, center=334.8)

# Create publication-quality plots
import matplotlib.pyplot as plt
plt.plot(x, y_corrected, 'b-', linewidth=1.5, label='Corrected Data')
plt.plot(B, gauss_line, 'r--', linewidth=1.5, label='Gaussian Fit')
plt.xlabel('Magnetic Field (G)')
plt.ylabel('EPR Signal (a.u.)')
plt.legend()
plt.show()

For interactive plotting with measurement tools from command line:

# Interactive plotting with measurement tools
epyr-plot --interactive --measure

# Load specific file with measurements
epyr-plot spectrum.dsc --interactive --measure --save

Documentation Contents

User Guide

API Reference

Developer Guide

Indices and tables