Tomotok is a framework for the tomographic inversion of fusion plasmas, focusing on inversion methods based on discretisation. It is structured as a namespace package to ease implementation on different experimental devices and various diagnostics.
Documentation built from the development branch of this repository, tracking the latest changes, is available at https://tomotok.github.io/core/.
The core package of the Tomotok namespace implements various discretisation algorithms that are used for tomographic reconstruction of tokamak plasmas. It is a dependency for specific packages that automate database access for a given fusion experimental device.
The package can be installed using pip:
pip install tomotokThe PyPI packages might not contain the most recent features. It is recommended to install the package from source, if you want to use the latest features and do not mind the possibility of backward compatibility issues.
The source code can be found in the repository on GitHub.
The stable branch ensures backward compatibility within the latest major version.
Newest features with not fully guaranteed backward compatibility are implemented in the development branch. Tags follow the versions published on PyPI.
The algorithms accept inputs in the form of numpy.ndarray or scipy.sparse matrix objects, allowing them to run independently of the rest of the package.
There are three main types of algorithms implemented:
- Minimum Fisher Regularisation (MFR)
- Linear algebraic methods (LAME)
- Biorthogonal Basis decomposition (BOB)
Apart from the main inversion methods, some utility features are also included.
A simple synthetic diagnostic framework is implemented for testing the implemented algorithms. It uses regular rectangular nodes and assumes toroidal symmetry, as it is the simplest case often used for inversions of tokamak plasma radiation.
Implemented utility features:
- Geometry matrix computation using numerical integration and a single line of sight approximation
- Smoothing matrix computation, both isotropic and anisotropic (based on magnetic flux surfaces)
- Simple phantom model generators (isotropic and anisotropic)
- Other tools for processing
When used for research purposes, please cite the following paper. To cite specific inversion methods, please refer to the corresponding papers included in the documentation.
"J. Svoboda, J. Cavalier, O. Ficker, M. Imrisek, J. Mlynar and M. Hron, Tomotok: python package for tomography of tokamak plasma radiation, Journal of Instrumentation 16.12 (2021): C12015." DOI 10.1088/1748-0221/16/12/c12015
| Name | Role | Scope | Years |
|---|---|---|---|
| Jakub Svoboda (@skuba31) | Lead Developer | core | 2018 - |
| Jordan Cavalier | Consultant | biorthogonal basis decomposition | 2020 - |
| Ondřej Ficker | Contributor | MFR | 2018 - |
| Martin Imríšek | Consultant | MFR | 2018 - |
| Jan Mlynář | Mentoring | - | 2018 - 2023 |