create_overlays: Function to create a new video with the extracted...

In pennekampster/bemovi: BEMOVI, software for extracting BEhaviour and MOrphology from VIdeos

Description

A function to overlay the extracted trajectories onto the original video, using plots created in R and then processed in ImageJ; two visualization types are available

Usage

create_overlays(to.data, merged.data.folder, raw.video.folder,
  temp.overlay.folder, overlay.folder, width, height, difference.lag,
  type = "traj", predict_spec = F, contrast.enhancement = 0, IJ.path,
  memory = 512)

Arguments

to.data	path to the working directory
merged.data.folder	directory where the global database is saved
raw.video.folder	directory with the raw video files
temp.overlay.folder	temporary directory to save the overlay created with R
overlay.folder	directory where the overlay videos are saved
width	width of the raw video
height	height of the raw video
difference.lag	numeric value specifying the offset between two video frames to compute the difference image
type	string indicating the visualization type (i.e. 'label' or 'traj'): either the overlay is showing the trajectory ID and outlines the detected particle (type='label') or the whole trajectory remains plotted (type='traj').
predict_spec	logical If TRUE, the Master.RData file must have a column called predict_spec, indicating the species to which the trajectory belongs
contrast.enhancement	numeric value to increase the contrast of the original video
IJ.path	path to ImageJ folder, containing the 'ij.jar' executable
memory	numeric value specifying the amount of memory available to ImageJ (defaults to 512)

pennekampster/bemovi documentation built on May 25, 2019, 12:46 a.m.