fish-simulator 0.0.10

Simulate zebrafish swim from tail angle tracking data

Zebrafish Tail Animator

Python toolbox to transform zebrafish tracking data to tail animations

Description

zf_animator is a Python package used to create visualisation of how swimming data looks from high-speed tracking data. The typical data used should be the tail angle along segments of the tail. The package will convert these tail angles to x- y- coordinates, and interpolate many more points along the range of tracked tail segments. These sets of coordinates will then transform slices of the zebrafish image, producing a stack of .png files that can be rendered into an mp4 file.

Package installation

This package can be installed via pip

pip install fish-simulator

Alternatively, you can download and locally install the package.

cd path/to/save/package
git clone clone-latest-tag [e-mail]:ThomasMullen/fish_simulator.git
cd ./fish_simulator
python3 setup.py bdist_wheel sdist
pip install ./dist/fish_simulator-<latest_tag>.tar.gz

Requires ffmpeg

Installation instructions

To convert the .png files to an .mp4 animation requires ffmpeg to be installed on the running computer. This can be install in Ubuntu in the terminal:

sudo apt install ffmpeg

Or with OS X can be installed:

brew install ffmpeg

Check it is installed by running which ffmpeg in the terminal. More details can be found here.

Dependencies

Default Fish image

Example

Default image simulation

This will use warp the default repo .png and stack the generated images into an .mp4.

from fish_simulator.simulator import make_image_simulation, make_video
make_image_simulation(data=tail_angle_data, upsample=4, f_path="dir/to/save/png_files")
make_video(png_dir="dir/to/save/png_files", vid_fname="file/path/of/generated_vid.mp4")

Generate a simulation of the fish tail posture

from fish_simulator.simulator import make_posture_simulation, make_video
make_posture_simulation(data=tail_angle_data, n_segments=30, png_dir="dir/to/save/png_files")
make_video(png_dir="dir/to/save/png_files", vid_fname="file/path/of/generated_vid.mp4")

Key Functions