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https://github.com/cspurin/quantification_porescale_images

Notebook for calculating the Minkowski functionals for a segmented pore scale image

https://github.com/cspurin/quantification_porescale_images

Science Score: 13.0%

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Notebook for calculating the Minkowski functionals for a segmented pore scale image

Basic Info
  • Host: GitHub
  • Owner: cspurin
  • Language: Jupyter Notebook
  • Default Branch: main
  • Homepage:
  • Size: 17.1 MB
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  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 2 years ago · Last pushed over 2 years ago
Metadata Files
Readme

README.md

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: bash python -m venv myenv Then for Mac enter: bash source myenv/bin/activate
    or for Windows: bash myenv\Scripts\activate

  6. Install the necessary packages by typing this in the terminal:
    bash 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. 8. Now open the notebook and begin!

Owner

  • Name: Catherine Spurin
  • Login: cspurin
  • Kind: user
  • Company: Stanford University

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