FishPy

What is this

This is the code I wrote for my PhD project in university of Bristol. The code produced these results:

• https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009394

This is not meant to be used easily as I am the only contributer. I will work on making it more user-friendly but this is what I could do for now.

IMHO, the package is good in terms of these feaures,

1. Getting 2D coordinates and orientations of a large amount of fish from a 2D video.
2. Reconstructing the 3D locations from matched 2D coordinates from multiple views (with water refraction correction).
3. Linking positions into trajectories, for both 2D and 3D data.
4. Calculating spatial & temporal correlation functions.

Install the package

1. Download the code with command git clone --recursive https://github.com/yangyushi/FishPy.git. It is important to include the --recursive option, so that the eigen and pybind11 will be downloaded.
2. Change the content in build.sh accordingly, then execute ./build.sh to build the python modules. This step is hard.
3. [optional] Add the full path of folder FishPy/lib to the PYTHONPATH, so that the module can be imported in Python.
4. [optional] Add the full path of folder FishPy/bin to the PATH, to use the scripts in bin folder.

Dependencies

C/C++

• cplex (you need to download the source code and compile. Also you need to install its Python API.)

Python

• opencv-python-headless
• numba
• pandas
• pillow
• joblib
• trackpy
• numpy
• scipy
• matplotlib
• tensorflow (optional)