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PyEIDORS Project Layout

This document is intended for code readers and contributors. For end-user setup and quick demos, start with README.md.

Directory Overview

Core source code

src/
└── pyeidors/                   # Main package
    ├── core_system.py          # High-level EITSystem entry point
    ├── data/                   # Data structures + synthetic/real data helpers
    ├── electrodes/             # Electrodes and stimulation/measurement patterns
    ├── forward/                # Forward solver (Complete Electrode Model)
    ├── inverse/                # Inverse solvers / workflows
    ├── geometry/               # Mesh generation + loading
    ├── visualization/          # Plotting and reporting utilities
    └── utils/                  # Misc utilities

Tests

tests/
├── unit/                       # Unit tests
└── run_all_tests.py            # Test runner

Examples and demos

examples/                       # Example scripts / notebooks
demos/                          # Demo scripts and generated figures
scripts/                        # CLI entry scripts and utilities

Data, meshes, and results (mostly generated)

data/                           # Input datasets (measurements)
eit_meshes/                     # Cached meshes (generated)
results/                        # Generated outputs (figures, npz, csv, metrics)

These folders are large and/or private by default, so the repository uses a whitelist in .gitignore to keep only the small demo artifacts needed for the paper results.

Code Map (file-level)

This section lists the main implementation files and where to look when modifying the project.

  • src/pyeidors/core_system.py: EITSystem orchestration (setup, forward_solve, inverse_solve).
  • src/pyeidors/forward/eit_forward_model.py: Complete Electrode Model forward solver.
  • src/pyeidors/electrodes/patterns.py: stimulation/measurement pattern generation and filtering.
  • src/pyeidors/inverse/jacobian/direct_jacobian.py: direct/adjoint Jacobian computation.
  • src/pyeidors/inverse/jacobian/adjoint_jacobian.py: EIDORS-style adjoint Jacobian utilities.
  • src/pyeidors/inverse/regularization/smoothness.py: regularization operators (including NOSER-style options).
  • src/pyeidors/inverse/solvers/gauss_newton.py: modular Gauss-Newton solver.
  • src/pyeidors/inverse/solvers/sparse_bayesian.py: sparse Bayesian solver implementation (CUQIpy-based).
  • src/pyeidors/inverse/workflows/: higher-level workflows (absolute, difference, sparse Bayesian).
  • src/pyeidors/data/structures.py: shared data structures (PatternConfig, EITData, EITImage, ...).
  • src/pyeidors/data/measurement_dataset.py: loading/validation helpers for real measurement datasets.
  • src/pyeidors/data/synthetic_data.py: synthetic data generation and phantoms.
  • src/pyeidors/geometry/optimized_mesh_generator.py: GMsh mesh generation + electrode placement convention.
  • src/pyeidors/geometry/mesh_loader.py: loading cached meshes and conversion helpers.
  • src/pyeidors/visualization/eit_plots.py: plotting utilities used by demos and scripts.

Recent change highlight

Electrode position convention (Y-axis start)

  • Code: src/pyeidors/geometry/optimized_mesh_generator.py
  • Tests: tests/unit/test_electrode_position_y_axis.py
  • Demo: demos/demo_y_axis_electrodes.py

Contributor workflow

Run tests

python tests/unit/test_electrode_position_y_axis.py
python tests/run_all_tests.py

Add or update paper/demo artifacts

This repository keeps most generated outputs out of Git, and only whitelists the paper/demo artifacts in .gitignore. If you add a new demo, update the allowlist and include a COMMAND.md file in the output directory documenting how it was generated.

Updated: 2025-07-04