check_threshold_values: Function to assist finding good thresholds used for the...

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

Description

This function creates an ImageJ macro that can be helpful for checking the thresholds specified in the user section; the macro will be saved in the ImageJ macro directory in the working directory and then automatically opened in ImageJ. Depending on the video size, it might take some time to open the video and the thresholding menu. The default thresholds values should be adjusted in the ImageJ macro, until appropriate values are found. These values should then be used in the R functions / script, e.g., when calling the Locate_and_measure_particles function.

Usage

check_threshold_values(to.data, raw.video.folder, ijmacs.folder,
  vid_select = 0, difference.lag, thresholds, IJ.path, memory = 512)

Arguments

to.data	path to the working directory
raw.video.folder	directory with the raw video files
ijmacs.folder	directory where the check_trehsolds macro is saved
vid_select	video selected to find appropriate thresholds; default is the first video
difference.lag	numeric value specifying the offset between two frames of a video
thresholds	Numeric vector containing the min and max threshold values
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.