drosophila-courtship

An app and python package for the tracking, classification, and analysis of fly behaviors.

Repo Structure

|-courtship
    |-app         # code for generating GUI
    |-ml          # code for creating feature matrices and behavioral classifiers
    |-stats       # code for calculating stats about flies and their behaviors
    |-plots       # code for generating plots

|-docs        # sphinx docs
|-tests       # tests

Installation

1. Clone and navigate to this repo in a terminal
2. Setup an environment using:

conda env create -f environment.yml

3. Activate environment:

activate courtship  # or 'source activate courtship'

4. Install drosophila-courtship:

python setup.py install

Documentation

Note: the documentation is currently being updated, but the API should be complete.

Using a terminal, navigate into the docs folder of this repo, then call make:

make html

This will generate an html file with all of the most recent documentation. This should be located in 'docs/build/html/index.html'.

Video Requirements

The GUI is optimized to work with videos that are 640x480 pixels (width x height).

All videos should also be in .fmf format (FlyMovieFormat). To convert from .mp4/.avi/.mov/etc to .fmf format, consider using the ffmpeg2fmf video conversion tool available from here.