_________________________________________________________________________________ ## Source code for the artice # Recurrent amplification of grid-cell activity ## by Tiziano D'Albis and Richard Kempter ___________________________________________________________________________________ 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/