# Mouse Simulation

## Installation Guide

1. Install the necessary dependencies: pyquaternion, scipy(1.8.1), numpy(1.2..0), pytorch, pyyaml(6.0), (open ai) gym, cython(0.29.32), pandas, colorama (0.4.5), matplotlib

- Note: To ensure proper installation versions (of those specified), pip install the farms_muscle library before installing the rest of the dependencies

2. Clone this respository

3. To install the mouse model libraries git clone the following repository into the top directory: 

    - [pybullet](https://github.com/bulletphysics/bullet3) 

    - [farms_pylog](https://gitlab.com/farmsim/farms_pylog.git)

    - [farms_container](https://gitlab.com/farmsim/farms_container.git)

    - [farms_muscle](https://gitlab.com/farmsim/farms_muscle.git)

4. Navigate to "/bullet3/examples/SharedMemory/SharedMemoryCommands.h"

    - Change the integers in lines(33-34) "#MAX_DEGREE_OF_FREEDOM 128" and "#MAX_NUM_SENSORS 256" to 512

5. Go to the root of the four cloned repos and type 

    ```

    pip install -e .

    ```

## Simulation

1. To begin training, enter the scripts folder and run:

    ```

    python main.py --visualize True

    ``` 

2. To view a trained model, run:

    ```

    python main_trained.py

    ```

## Logistics

The data we used to train the mouse is readily available on under the data folder. Any scripts/demos to train/run the simulation are under the scripts folder. Any scripts to analyze the neural activity is found under the Data_Analysis folder.