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Hex-maze

This repo provides a set of functions to generate, plot, and calculate info about hex maze configurations and optimal barrier change sequences for the hex maze behavioral task used by the Berke Lab at UCSF. It also provides databases of valid maze configurations and their attributes.

Step 1. Fork and clone the repository

To contribute to this project, you first need to fork the repository to your own GitHub account. This creates a copy of the project where you can make changes. Do this by clicking the "Fork" button at the top-right corner of the repository page and following the instructions.

Once you have forked the repository, you need to clone it to your local machine to start working on it.

  1. Open a terminal or command prompt.

  2. Clone your forked repository using the following command (replacing {your-github-username} with your username):

    git clone https://github.com/{your-github-username}/Hex-maze.git

  3. Navigate to the newly created Hex-maze directory.

    cd Hex-maze

Step 2. Install dependencies

  1. First, make sure you are in the repo inside a terminal or command prompt (Step 3 above).

  2. To install all necessary dependencies for this project, run the following command:

    pip install -r requirements.txt

Step 3. Start the tutorials

Navigate to the Tutorials/ folder and begin with the Getting_Started.ipynb notebook.

Tutorials/ also includes the following tutorial notebooks:

These 3 are also provided for reference:

Note that some of these tutorials are currently in progress, LMK if you need one asap and I'll make it a priority!

Step 4: Explore and use the databases!

This repo provides the following databases of valid maze configurations and barrier change sequences for the hex maze task:

Database of hex maze configurations

maze_configuration_database contains 55,896 possible hex maze configurations with the following attributes:

  • 9 barriers
  • no unreachable hexes
  • path lengths between reward ports are between 15-25 hexes
  • all critical choice points are >=6 hexes away from a reward port
  • there are a maximum of 3 critical choice points
  • there are no straight paths >6 hexes to a reward port (including port hex)
  • there are no straight paths >6 hexes in the middle of the maze

This database also provides information about each maze configuration:

  • length of the optimal path(s) between each pair of reward ports
  • lists of hexes defining the optimal path(s) between those reward ports
  • number of choice points, and which hexes are choice points
  • number of cycles (where the rat can start and end at the same hex without turning around) and lists of hexes defining those cycles
  • a set of other mazes isomorphic to this maze (representing reflections and rotations of the maze)

This database is provided in both csv (.csv) and pickle (.pkl) format - csv is better to explore in excel, but pickle is preferable for loading and working with in jupyter notebooks (csv tends to load everything as a string).

This database was generated using the Generate_Hex_Maze_Database.ipynb notebook available in the Tutorials/ folder.

Database of mazes for barrier change experiments

The Barrier_Sequence_Databases/ folder contains multiple databases of barrier sequences (consecutive maze configurations that differ by the movement of a single barrier).

  • barrier_sequence_database contains 3126 barrier sequences that are 4-6 mazes long, and is a good place to start.
  • single_choice_point contains 3720 barrier sequences >= 3 mazes long where all mazes in the sequence have a single choice point.

The Barrier_Sequence_Database_Search.ipynb notebook in the Tutorials/ folder has more information about the other available databases, and how to search these databases for a barrier sequence that fits your criteria.

Custom databases can be generated using the Generate_Custom_Barrier_Sequence_Database.ipynb notebook available in the Tutorials/ folder.

Database of mazes for probability change experiments

Maze_Databases/probability_change_mazes contains a database of mazes good for probability change experiments. These mazes are grouped such that all mazes in a group differ by at least 10 hexes on optimal paths.

This database was generated using the Generate_Probability_Change_Database.ipynb notebook available in the Tutorials/ folder.

Database of mazes for early stages of training

Maze_Databases/training_maze_database contains a database of mazes good for training. There are 5-6 barriers and all paths are the same length (either 15 or 17 hexes).

This database was generated using the Generate_Training_Maze_Database.ipynb notebook available in the Tutorials/ folder.

Other info

Hex maze functions

hex_maze_utils.py provides all of the functions for hex maze related tasks.

All of these functions are (hopefully) well documented (if not, let me know!!).

A tutorial for the most useful functions can be found at Tutorials/Hex_Maze_Functions.ipynb. For functions without tutorials, you can view the documentation running help(function_name), or just by scrolling through the hex_maze_utils.py file.

dev

The dev folder is my sandbox/trashcan for things I'm currently working on or have abandoned. You can ignore it :)