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Source code for the artice

Recurrent amplification of grid-cell activity

by Tiziano D'Albis and Richard Kempter

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REQUIREMENTS

All source code is in Python language and was tested in the following environmnent:

• Python 2.7.15
• Matplotlib 2.2.3
• NumPy 1.15.1
• Scipy 1.2.1
• Pandas 0.24.2
• Psutils 5.6.3
• Pytables 3.5.2

The easiest way to run the code is to create an Anaconda environment using the file conda_env.yml provided in the root folder of this package. This can be done with the command:

conda env create -f conda_env.yml

This will create a new conda environment named grid_amp. Note that this environment may contain more packages then actually needed (i.e., it provides more than the minimal set of required dependencies).

USAGE

0. Before starting make you have to create a file called config.json in the project root. The file contains the paths on your local machines where the simulation results (RESULTS_PATH) and the figures (FIGURES_PATH) are going to be saved. Here is an example:

{
  "RESULTS_PATH": "/home/tiziano/grid_amp/results",
  "FIGURES_PATH": "/home/tiziano/grid_amp/figures"
}

2D MODEL

1. Run the script amp_paper_2d_main.py. This generates and saves to disk all the required simulation data to be plotted. Note: if you need only a subset of the result you can easily filter out simulations in the main section of the program.

2. Run the snippet of code that generates the required figure. The script amp_paper_2d_fig_main.py contains the code to generate Figure 1 The script amp_paper_2d_fig_temporal.py contains the code to generate Figures 2 and 3 The script amp_paper_2d_fig_grid_index.py contains the code to generate Figure 8 The script amp_paper_2d_fig_noise.py contains the code to generate all the remaining figures of the 2D model

3. Find the generated figures saved as SVG and PNG in the selected target folder (see FIGURES_PATH in config.json)

1D MODEL

1. Run the script amp_paper_1d_plots.py to generate all figures related to the 1D model

2. Find the generated figures saved as SVG and PNG in the selected target folder (see FIGURES_PATH in config.json)

TECHNICAL NOTE

This project imports an external git repository (grid_utils) using ``git subtree''. For a tutorial see: http://atlassianblog.wpengine.com/2013/05/alternatives-to-git-submodule-git-subtree/