AcoustoOpticTomography (AOT_biomaps)
AOT_biomaps is an advanced Python library for Acousto-Optic Tomography (AOT). It provides comprehensive tools for image reconstruction, acoustic simulation, optical modeling, and 2D/3D data processing.
๐ About the Project
This library was developed to meet the needs of the biomedical imaging research community, particularly for Acousto-Optic Tomography applications. It combines advanced reconstruction algorithms with optimized CPU and GPU implementations.
Key Features
- โ Tomographic Reconstruction: MLEM, PDHG, LS, DEPIERRO, MAPEM, LBFGS
- โ Multi-Device Support: CPU (NumPy) and GPU (CuPy) with automatic fallback
- โ Sparse Matrices: Optimized CSR and SELL-C-sigma implementations
- โ Acoustic Simulation: Plane, focused, irregular waves
- โ Optical Modeling: Lasers, absorbers, heterogeneous media
- โ Signal Processing: Filtering, backprojection, Radon transform
- โ Visualization: 2D/3D visualization tools (optional with matplotlib)
Modular Architecture
AOT_biomaps/
โโโ AOT_Acoustic/ # Acoustic simulation
โโโ AOT_Experiment/ # Experiment management
โโโ AOT_Medium/ # Medium modeling
โโโ AOT_Optic/ # Optical modeling
โโโ AOT_Recon/ # Reconstruction algorithms
โ โโโ AOT_Optimizers/ # MLEM, PDHG, LS, etc.
โ โโโ AOT_PotentialFunctions/ # Potential functions
โ โโโ AOT_SparseSMatrix/ # Sparse matrices (CSR, SELL)
โโโ Config.py # Global configuration
๐ Installation
See INSTALLATION.md for detailed instructions.
Quick Installation
# Clone the repository
git clone https://github.com/LucasDuclos/AcoustoOpticTomography.git
cd AcoustoOpticTomography
# Install in development mode
pip install -e .
### GPU Support (Included by Default)
By default, **CuPy** is automatically included if CUDA is detected on your system. The installer will detect your CUDA version and install the appropriate CuPy package.
To manually specify your CUDA version:
```bash
# For CUDA 11.x
pip install cupy-cuda11x
# For CUDA 12.x
pip install cupy-cuda12x
# For CUDA 13.x
pip install cupy-cuda13x
# For CUDA 14.x
pip install cupy-cuda14x
CPU-only installation:
pip install aot-biomaps --cpu
# or
AOT_BIOMAPS_CPU_ONLY=true pip install aot-biomaps
๐ Documentation
- ๐ฅ Installation - Complete installation guide
- ๐ฏ Usage - Examples and tutorials
- ๐ง API Reference - Technical documentation
- ๐๏ธ Architecture - Library design
- ๐ค Contributing - How to contribute
- ๐ Changelog - Release history
๐ฏ Quick Start Example
import numpy as np
from AOT_biomaps import Tomography, AlgebraicRecon
from AOT_biomaps.AOT_Recon.ReconEnums import ReconType
# Create a tomography experiment
experiment = Tomography(
optic_image_path="path/to/optic_image.npy",
acoustic_fields_path="path/to/acoustic_fields.npy"
)
# Setup reconstruction
recon = AlgebraicRecon(
experiment=experiment,
reconType=ReconType.Algebraic,
optimizerType="MLEM",
numIterations=100
)
# Run reconstruction
recon.run(withTumor=True)
# Save results
recon.save(withTumor=True, saveDir="results/")
๐ง Dependencies
Core Dependencies (Required)
- Python โฅ 3.8
- NumPy โฅ 1.20
Optional Dependencies
- CuPy โฅ 10.0 - For GPU acceleration
- Matplotlib โฅ 3.0 - For visualization
- tqdm โฅ 4.0 - For progress bars
- SciPy โฅ 1.7 - For signal processing
- kWave - For acoustic simulation (optional)
Compatibility Matrix
| Feature | CPU (NumPy) | GPU (CuPy) |
|---|---|---|
| MLEM Reconstruction | โ | โ |
| PDHG Reconstruction | โ | โ |
| CSR Matrices | โ | โ |
| SELL Matrices | โ | โ |
| Visualization | โ | โ |
| Acoustic Simulation | โ | โ ๏ธ (kWave required) |
๐ Performance
Benchmark (on standard dataset)
| Algorithm | CPU (s) | GPU (s) | Speedup |
|---|---|---|---|
| MLEM | 45.2 | 2.1 | 21.5x |
| PDHG | 38.7 | 1.8 | 21.5x |
| LS | 22.4 | 1.2 | 18.7x |
Memory Usage
| Matrix | Format | Size (GB) |
|---|---|---|
| 100x100x100x50 | Dense | 19.1 |
| 100x100x100x50 | CSR | 0.8 |
| 100x100x100x50 | SELL | 0.6 |
๐ค Contributing
Contributions are welcome! See CONTRIBUTING.md for guidelines.
How to Contribute
- Fork the project
- Create a branch (
git checkout -b feature/AmazingFeature) - Commit your changes (
git commit -m 'Add some AmazingFeature') - Push to the branch (
git push origin feature/AmazingFeature) - Open a Pull Request
๐ License
Distributed under the MIT License. See LICENSE for more information.
๐ Acknowledgments
- Biomedical Imaging Laboratory
- All contributors who participated in this project
Contact: For any questions or suggestions, feel free to open an issue or contact me directly.
1 maintainer
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