BioWaveFDTD is a compact Python package for verified one-dimensional and two-dimensional finite-difference time-domain (FDTD) modeling of electromagnetic propagation and layer-resolved energy transport in biological tissue at 2.45 GHz.
The repository includes the reusable source package, executable examples, the complete automated test suite, a cleaned reproduction notebook, and compact reference datasets. Manuscripts, LaTeX sources, PDFs, historical versions, generated figures, caches, and temporary files are intentionally excluded.
- One-dimensional lossy multilayer FDTD modeling
- Mur and convolutional perfectly matched layer (CPML) boundaries
- Analytical Fresnel and multilayer transfer-matrix comparisons
- Two-dimensional TMz propagation in planar and curved tissue geometries
- Two-dimensional CPML verification and sensitivity checks
- Layer-resolved electric and magnetic fields, Poynting flux, conductive loss, interface coefficients, and standing-wave metrics
Create a virtual environment, then install the package and development dependencies:
python -m venv .venv
source .venv/bin/activate # Windows: .venv\Scripts\activate
python -m pip install --upgrade pip
python -m pip install -e ".[dev]"Alternatively, install the minimum-version runtime, example, and test dependencies from requirements.txt, then install BioWaveFDTD itself:
python -m pip install -r requirements.txt
python -m pip install -e . --no-depsRun the complete test suite from the repository root:
python -m pytest -qThe release archive was created only after the full suite passed: 18 tests passed.
Examples write generated CSV, JSON, report, and figure files under outputs/, which is excluded from version control.
python examples/run_verified_1d.py
python examples/run_boundary_verification.py
python examples/run_2d_extension.py
python examples/run_2d_cpml_verification.py
python examples/run_layer_energy_transport.py
python examples/run_submission_audit.pyThe two-dimensional and submission-audit examples are more computationally intensive than the unit tests. In particular, run_2d_extension.py can spend several minutes writing high-resolution PNG/PDF figures and large field-map CSV files, and run_submission_audit.py performs a multi-parameter CPML sweep.
Open notebooks/BioWaveFDTD_Reproduction.ipynb from the repository root. The notebook contains no saved outputs, private paths, credentials, or Colab-specific metadata.
reference_data/ contains compact input and benchmark tables retained from the software archive. Large field maps, probe time series, generated figures, and other reproducible outputs were removed to keep this GitHub release minimal.
The tissue stack is an idealized verification geometry and is not a patient-specific anatomical model. The software does not claim antenna, SAR, thermal, clinical, or experimental validation.
Citation metadata is provided in CITATION.cff.
BSD 3-Clause License. Copyright (c) 2026 Othman H. Y. Zalloum.