## Source code for the artice
# Recurrent amplification of grid-cell activity
## by Tiziano D'Albis and Richard Kempter
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).
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:
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`)
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`)
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/