trackPath: Track an animal's movement across a series of still frames

In gunpowder78/pathtrackr: Video Tracking and Analysis of Animal Movement

Description

This function is the core of the pathtrackr package. It takes a series of jpegs (extracted from a video) as inputs and tracks an animal's movement across frames. A list is returned containing the xy co-ordinates of the animal in each frame, as well as summary statistics. The returned list can be called for plotting and further functions in the pathtrackr package.

Usage

trackPath(dirpath, xarena, yarena, fps = 30, box = 1, jitter.damp = 0.9)

Arguments

dirpath	a character string specifying a directory containing only jpeg files extracted from a video
xarena	an integer specifying the arena width in mm; this value is used for distance and velocity calculations, an incorrect value will not cause an error but will result in inaccurate calculations
yarena	an integer specifying the arena height in mm; this value is used for distance and velocity calculations, an incorrect value will not cause an error but will result in inaccurate calculations
fps	an integer specifying the frame rate at which jpegs were extracted from a video; this value is used for distance and velocity calculations, an incorrect value will not cause an error but will result in inaccurate calculations
box	an integer specifying the size of the tracking box relative to the initial animal selection box; a larger box size will help prevent the animal being lost (useful for fast moving animals) but will also increase sensitivity to background and lighting changes (default 1)
jitter.damp	a value between 0.5 and 1. Reduces noise in the animal's track, useful if the animal's track is very jittery, which may overestiamte path length. A value of 1 indicates no jitter damping, 0.5 indicates extreme damping and is unlikely to be useful

Details

trackPath tracks an individual animal's movement across a series of still frames. The function utilises a focusing box to limit the search area for the animal relative to its previous position. This makes trackPath relatively robust to background lighting changes, extraneous backgroud movement and jpeg noise. It can handle a dark animal on a light background and vice versa, as well as heterogenous backgrounds where the animal is at times darker and lighter than the background.

Value

A list containing a matrix of xy co-ordinates of the animal in each frame, a matrix of movement data including the distance, velocity and trajectories of movement between frames, and summary statistics.

gunpowder78/pathtrackr documentation built on May 28, 2019, 8:54 p.m.