wasper-bary

wasp is a Rust re-implementation of the Wasserstein representation for Persistence diagrams paper. The original C++ implementation is available in this repository.

Getting Started

Prerequisites

1. Rust: Install the Rust toolchain from rustup.rs.
2. Python: Python 3.8+ is recommended.
3. uv (Recommended): A fast Python package manager. Install with brew install uv or see uv documentation.

Installation & Build

1. Clone the repository:

   git clone https://github.com/Gklajer/wasserstein-for-persistence-tda.git
   cd wasserstein-for-persistence-tda

2. Sync the environment (creates venv and installs all dependencies):

   uv sync

Running the Code

After building the extension, you can run the provided Python scripts from the examples/ directory:

• Barycenter Test: Visualizes the Wasserstein barycenter of two diagrams.

  uv run examples/barycenter_test.py

• Matching Test: Visualizes the optimal matching between two diagrams.

  uv run examples/test_maching.py

• Benchmark: Runs performance benchmarks.

  uv run examples/benchmark.py

Data Preparation

To convert persistence diagrams from VTU format (e.g., from ParaView/TTK) to the CSV format used by this project, you can use the provided conversion script. It handles Birth, Death (including infinite values), and PairType extraction.

uv run scripts/vtu_to_csv.py --input data/VTU --output data/CSV

References

The following additional papers were used in the implementation:

• Progressive Wasserstein Barycenters of Persistence Diagrams
• Geometry Helps to Compare Persistence Diagrams
• Multidimensional Binary Search Trees Used for Associative Searching