Python Cellular Automata

Python implementation of the cellular automata model corresponding to Lange, Schmied et. al.

Overview

• test/ - contains various scripts/notebooks for testing purposes
• cellularautomaton.py - the Automata. Used to run experiments
• parameters.py - contains parameters for the automata
• multiverse.[sh|ps1] - runs multiverse
• plot.py - generates plots for multiverse (also works if -n = 1)
• requirements.txt - list of dependencies. Install with pip install -r requirements.txt or conda install -c conda-forge --file requirements.txt

Options

Automata (cellularautomaton.py)

usage: cellularautomaton.py [-h] [--box] [--colonial] [--dt DT] [--gridsize GRIDSIZE] [--movementspeed MOVEMENTSPEED] [--seed SEED] [--symmetric] [--experimental] [--tmax TMAX] [--multiverse MULTIVERSE]
                            [--real REAL] [--expdata EXPDATA] [--output OUTPUT] [--exportcsv] [--exporthdf] [--plot] [--plothist]

optional arguments:
  -h, --help            show this help message and exit
  --box                 Run box experiment
  --colonial            Run colonial experiment
  --dt DT               Time step width (in min, default: 6)
  --gridsize GRIDSIZE   Grid edge size (default: 256 for Colonial and 12 for Box experiment)
  --movementspeed MOVEMENTSPEED, -v MOVEMENTSPEED
                        Specify movement speed of cells (in µm/h)
  --seed SEED, -s SEED  Simulation seed
  --symmetric           Toggle symmetric/asymmetric proliferation (asymmetric by default)
  --experimental        Enable experimental features
  --tmax TMAX           Maximum time (in days, default: 8 for Colonial and 15 for Box experiment)
  --multiverse MULTIVERSE
                        Specify multiverse id of current simulation
  --real REAL           Specify realisation index of current simulation
  --expdata EXPDATA     Path to experimental data
  --output OUTPUT, -o OUTPUT
                        Specify output directory
  --exportcsv           Export colony development history to csv
  --exporthdf           Export colony development history to hdf5
  --plot                Create and save plots during experiment (final stage only)
  --plothist            Save plots during colony development

Multiverse (multiverse.[sh|ps1])

usage: multiverse.[ps1|sh] [-n] <Number of Realisations> [-box|--box] [-plot|--plot]

options:
  -n NUMBER             Specify number of Realisations (.ps1 only, in .sh use it without -n)
  --box                 Specify that experiment is of type box (different plot output)
  --plot                Create and save plots after run finished 

Examples

It's easiest to run all modules using the module syntax from the root directory of the project (CellularAutomataPython).

Single Run

Run colonial experiment, 12 days, calculate every 6 min:

python -m src.cellularautomaton --colonial --dt 6 --tmax 10 --plot --exportcsv

Multiverse Run

• .\multiverse.ps1 -n 20 -plot on Windows
• ./multiverse.sh 20 --plot on *nix

Plotting

Note: --plot is optional for Multiverse. Alternatively, you can always generate plots manually afterward by calling the plot script:

python -m src.utils.plot --path /path/to/multiversum_xxxxx --expdata /path/to/cellularautomata_experimentaldata/Puliafito_2012_01_17 --output pdf [--box].

Options:

• --output: Specify output format. Default: png. Other options: pdf, svg.

Generated Plots

Development of cell count, colony area, cell area distribution (single run):

Cell culture (by density) and growth history collage (single run):

Development of colony area, cell density (multiverse):

Performance