https://github.com/benjaminjack/spatial_structure
https://github.com/benjaminjack/spatial_structure
Last synced: 2 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/benjaminjack/spatial_structure
- Owner: benjaminjack
- Created: 2016-10-20T06:36:09.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2017-04-10T19:48:19.000Z (about 8 years ago)
- Last Synced: 2025-01-25T13:44:38.040Z (4 months ago)
- Language: Python
- Size: 715 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# Spatially-structured models of phage infection
The scripts in this repository implement two different models of phage infecting bacteria on a plate. See `latex/notes.pdf` for a complete description of each model.
## Dependencies
The Python scripts were written for Python3. They both require NumPy, a module for efficient numerical operations. Assuming you have Python3 installed, you can install it with `pip3` using the following command:
```
pip3 install numpy
```
For making heatmap animations, matplotlib is required. It can also be installed with `pip3`:
```
pip3 install matplotlib
```
## Converting `matplotlib`-generated PNGs to an animated gif
If you have a directory of numbered PNGs (e.g. 1.png, 2.png, 3.png, etc.), navigate to inside of that directory, and use the following ImageMagick command to convert the PNGs to an animated GIF:
```
convert -delay 15 -loop 0 `ls | sort -n` ../test.gif
```