Automated detection of foot contacts, aerial phases, and visibility of bird

These codes were written by Daniel Hasse and were used, in combination with other methods, to perform an automated large-scale study (over one million frames) on the fluctuations of the CoM’s mechanical energy in several bird species (quail, oystercatcher, northern lapwing, pigeon, and avocet) during treadmill locomotion. see Andrada, E. et al. Mixed gaits in small avian terrestrial locomotion. Sci. Rep. 5, 13636; doi: 10.1038/srep13636 (2015). for more information events.R includes: Touch-down detection: we found that when the pixel values of the leg of every frame are projected onto the x-axis, the obtained 1D-curve display at TD a maximal bimodality. We measured the bimodality value of the 1D-curve by comparing it to a normal distribution of same mean and variance using histogram intersection distance. Frames in which a TD event occurs are then found by identifying all local maxima of the bimodality score over all frames (Andrada et. al., Mixed gaits in avian locomotion, in review, Fig. 5). Aerial phase: for each frame of a trial, we computed the minimum distance between the lowest point of the legs and the bottom of the image. Afterwards, a threshold was used to classify each frame as "aerial phase" or "stance phase" based on its leg height. For each sequence, the threshold was estimated automatically in such a way that only frames in which the legs are substantially higher than the median leg height are classified as "aerial phase" (Andrada et. al., Mixed gaits in avian locomotion, in review. Supplementary Information, Fig. S1). visibility.R includes: Visibility: to account for cases in which the birds left the field of view, for every frame of each trial we computed the number of pixels in which the bird is visible ('bird-pixels'). % of congruity was computed, only when the measured number of bird-pixel during all frames of a stance phase was higher than 80% of the maximal computed number of bird-pixels of the complete trial.