Dewan Lab PID Analysis

This repository contains the python package required to read, repackage, and graph data collected using the Dewan Lab's PID setup. This package currently only supports the 'new' Bpod-based PID setup files, but will eventually be updated to be backwards compatible with the older Arduino-based PID setup H5 files.

Installation

Note: It is recommended to use the included environment.yaml file to install the package. However, the package can also be installed manually if desired.

Anaconda / Conda / Mamba

Ensure you have a working installation of Anaconda. We recommend using mamba which is included in miniforge.

1. Download the environment.yaml file from this repository
2. Run the command mamba env create -f [PATH_TO_FILE]/environment.yaml to automatically install the package and all required dependencies

Manually

1. Clone the repository and navigate into the directory
2. Run pip install . within the cloned repository to install the package in the currently active python environment

Alternative Install: You can run pip install git+https://github.com/OlfactoryBehaviorLab/PID_Analysis.git to download the package directly from GitHub without the need to clone it.

Using the Package

Note: If using Anaconda/Conda/Mamba, be sure to activate the PID environment by running conda activate PID

To run the package, simply open a terminal and run python -m pid_analysis and select the .mat file(s) to process.