# TauFactor
TauFactor is an application for calculating tortuosity factors from tomographic data.
- Free software: MIT license
- Documentation: [https://taufactor.readthedocs.io](https://taufactor.readthedocs.io).
<p align="center">
<img src="https://tldr-group.github.io/static/media/tau_example.2c29eaf9.png" alt="TauFactor" width="324" height="324">
</p>
<p align="center">
<a href="https://pypi.python.org/pypi/taufactor">
<img src="https://img.shields.io/pypi/v/taufactor.svg"
alt="PyPI"></a>
<a href="https://taufactor.readthedocs.io/en/latest/?badge=latest">
<img src="https://readthedocs.org/projects/taufactor/badge/?version=latest"
alt="ReadTheDocs"></a>
<a href="https://opensource.org/licenses/MIT">
<img src="https://img.shields.io/badge/License-MIT-yellow.svg"
alt="MIT LICENSE"></a>
<img src="https://github.com/tldr-group/taufactor/actions/workflows/taufactor.yml/badge.svg"
alt="github actions">
</p>
## Requirements
Before installing taufactor, [download the most recent version of PyTorch](https://pytorch.org/get-started/locally/). Ensure you have `pytorch>=1.10` installed in your Python environment.
For example, for a Linux machine with CUDA GPU
```
conda install pytorch pytorch-cuda=11.7 -c pytorch -c nvidia
```
## Quickstart
To install TauFactor via PyPI
```
pip install taufactor
```
To extract effective diffusivity and tortuosity factor from your data:
```python
import taufactor as tau
import tifffile
# load image
img = tifffile.imread('path/filename')
# ensure 1s for conductive phase and 0s otherwise.
# create a solver object with loaded image
s = tau.Solver(img)
# call solve function
s.solve()
# view effective diffusivity and tau
print(s.D_eff, s.tau)
```
## Tests
To run unit tests navigate to the root directory and run
```
pytest
```
## Credits
This package was created by the [tldr group](https://tldr-group.github.io/) at the Dyson School of Design Engineering, Imperial College London.
## TauFactor MATLAB
The package in this repository refers to a Python implementation of the TauFactor solver. There is a deprecated [MATLAB implementation](https://www.mathworks.com/matlabcentral/fileexchange/57956-taufactor), which is no longer maintained.
# History
## 1.1.0 (2023-07-24)
---
- Added comments from reviewers
- Added examples to documentation
- Added API documentation
- Fix test times on comparison
## 1.0.0 (2023-03-23)
---
- Migrated to PyTorch from CuPy
- New convergence criteria
- New documentation style
- CI testing
- Includes TauFactor paper
## 0.1.4 (2022-07-11)
---
- Add TauE solver
- Add triple phase boundary calculations
- Fix cuboids not converging
- Fix convergence messaging
## 0.1.3 (2021-03-25)
---
- Hotfix code in taufactor.py
## 0.1.2 (2021-03-25)
---
- Added multi-phase and periodic solvers and metrics calculations
## 0.1.1 (2021-02-10)
---
- Removed CuPy from requirements and added installation instructions to README
## 0.1.0 (2021-02-08)
---
- First release on PyPI.
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"description": "# TauFactor\n\nTauFactor is an application for calculating tortuosity factors from tomographic data.\n\n- Free software: MIT license\n- Documentation: [https://taufactor.readthedocs.io](https://taufactor.readthedocs.io).\n\n<p align=\"center\">\n<img src=\"https://tldr-group.github.io/static/media/tau_example.2c29eaf9.png\" alt=\"TauFactor\" width=\"324\" height=\"324\">\n</p>\n<p align=\"center\">\n<a href=\"https://pypi.python.org/pypi/taufactor\">\n <img src=\"https://img.shields.io/pypi/v/taufactor.svg\"\n alt=\"PyPI\"></a>\n<a href=\"https://taufactor.readthedocs.io/en/latest/?badge=latest\">\n <img src=\"https://readthedocs.org/projects/taufactor/badge/?version=latest\"\n alt=\"ReadTheDocs\"></a>\n<a href=\"https://opensource.org/licenses/MIT\">\n <img src=\"https://img.shields.io/badge/License-MIT-yellow.svg\"\n alt=\"MIT LICENSE\"></a>\n<img src=\"https://github.com/tldr-group/taufactor/actions/workflows/taufactor.yml/badge.svg\"\n alt=\"github actions\">\n\n</p>\n\n## Requirements\n\nBefore installing taufactor, [download the most recent version of PyTorch](https://pytorch.org/get-started/locally/). Ensure you have `pytorch>=1.10` installed in your Python environment.\n\nFor example, for a Linux machine with CUDA GPU\n\n```\nconda install pytorch pytorch-cuda=11.7 -c pytorch -c nvidia\n```\n\n## Quickstart\n\nTo install TauFactor via PyPI\n\n```\npip install taufactor\n```\n\nTo extract effective diffusivity and tortuosity factor from your data:\n\n```python\nimport taufactor as tau\nimport tifffile\n\n# load image\nimg = tifffile.imread('path/filename')\n# ensure 1s for conductive phase and 0s otherwise.\n\n# create a solver object with loaded image\ns = tau.Solver(img)\n\n# call solve function\ns.solve()\n\n# view effective diffusivity and tau\nprint(s.D_eff, s.tau)\n\n```\n\n## Tests\n\nTo run unit tests navigate to the root directory and run\n\n```\npytest\n```\n\n## Credits\n\nThis package was created by the [tldr group](https://tldr-group.github.io/) at the Dyson School of Design Engineering, Imperial College London.\n\n## TauFactor MATLAB\n\nThe package in this repository refers to a Python implementation of the TauFactor solver. There is a deprecated [MATLAB implementation](https://www.mathworks.com/matlabcentral/fileexchange/57956-taufactor), which is no longer maintained.\n\n\n# History\n\n## 1.1.0 (2023-07-24)\n\n---\n\n- Added comments from reviewers\n- Added examples to documentation\n- Added API documentation\n- Fix test times on comparison\n\n## 1.0.0 (2023-03-23)\n\n---\n\n- Migrated to PyTorch from CuPy\n- New convergence criteria\n- New documentation style\n- CI testing\n- Includes TauFactor paper\n\n## 0.1.4 (2022-07-11)\n\n---\n\n- Add TauE solver\n- Add triple phase boundary calculations\n- Fix cuboids not converging\n- Fix convergence messaging\n\n## 0.1.3 (2021-03-25)\n\n---\n\n- Hotfix code in taufactor.py\n\n## 0.1.2 (2021-03-25)\n\n---\n\n- Added multi-phase and periodic solvers and metrics calculations\n\n## 0.1.1 (2021-02-10)\n\n---\n\n- Removed CuPy from requirements and added installation instructions to README\n\n## 0.1.0 (2021-02-08)\n\n---\n\n- First release on PyPI.\n",
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