DarSIA

Darcy scale image analysis toolbox — an open-source Python library for turning images of porous-media experiments into quantitative physical data.

DarSIA represents an image as an array that also knows its physical extent, acquisition time and coordinate system, and provides:

• I/O for optical photographs, DICOM stacks and simulation output (vtu);
• corrections — colour, illumination, curvature, perspective, drift, deformation;
• restoration — total-variation and H1 denoising;
• segmentation and registration of multi-layered media;
• concentration analysis — tracer / CO2 / mass maps, with pluggable signal models and calibration;
• transport-based distances (Earth Mover's / Wasserstein);
• a configuration-driven workflow system and a Qt GUI that runs it without scripting.

Documentation

https://pmgbergen.github.io/DarSIA — user guide, runnable example gallery, and full API reference.

See the example gallery for more, including CO2 concentration analysis and Wasserstein distances.

Installation

DarSIA needs Python 3.12+ and is installed from a clone (not on PyPI yet, and here using the recommended package manager uv).

git clone https://github.com/pmgbergen/DarSIA.git
cd DarSIA
uv python install 3.12         # installs Python 3.12
uv sync --extra dev            # or: pip install -e ".[dev]"

The installation guide covers the optional petsc4py solvers, a conda environment, the GUI, and building the documentation.

GUI

A Qt desktop application that runs the configuration-driven analysis workflow from a TOML file — set up, calibrate, and batch-process an experiment without writing a driver script.

uv run darsia-install-desktop   # optional: adds a desktop / Start-menu launcher
uv run darsia                   # launch the GUI after desktop installation

See the GUI guide for a full walkthrough.

Citing

If you use DarSIA in your research, we ask you to cite the following publication:

Nordbotten, J. M., Benali, B., Both, J. W., Brattekås, B., Storvik, E., & Fernø, M. A. (2023). DarSIA: An open-source Python toolbox for two-scale image processing of dynamics in porous media. Transport in Porous Media, https://doi.org/10.1007/s11242-023-02000-9

The first release can be also found on Zenodo: 10.5281/zenodo.7515016

Developing DarSIA

DarSIA is an open+source project, and contributions are most welcomed! Code under src/ must pass black (24.10.0), isort and flake8; run the tests with uv run pytest. See the contributor guide and DEVELOPER_NOTES.md.