Quantification of segmented pore-scale images

This notebook takes a segmennted pore-scale image and calculates the 4 Minkowski functionals:

1. Volume
2. Surface area
3. Mean Curvature
4. Total integral curvature/ Euler characteristic

The Minkowski functionals are described in detail in this manuscript: https://doi.org/10.1016/j.softx.2021.100823

There is also an example for calculating the maximum inscribed sphere in 2D.

Recommended steps for running the notebook.

1. Download and install vscode: https://code.visualstudio.com/

2. Download and install python: https://www.python.org/downloads/ (download version 3.10.11)

3. Install the python extension in vscode. In vscode, click the extensions icon in the sidebar and search for "python"

4. Open a new folder (link it the folder containing the contents of this repository, wherever that is on your computer)

5. Create a virtual enviornment. In vscode click View>Terminal and enter the code below:

   python -m venv myenv

   Then for Mac enter:

   source myenv/bin/activate

   or for Windows:

   myenv\Scripts\activate   

6. Install the necessary packages by typing this in the terminal:
   

   pip install -r requirements.txt

   NB. must be in the folder where the requirements.txt file is. Alternatively, you can install the packages individually e.g. pip install numpy.

7. Now open the notebook and begin!