generateTraj: Generate a 'TrajectorySet' object with corrected y-values

In Ayan1/Cell-Trajectory-Analysis: Functions for biological trajectory analysis and video processing

Description

Returns a TrajectorySet so that the y value is the distance from the bottom of the Frames object, not from the top

Usage

generateTraj(particles, L = 26, R = 3, epsilon1 = 0, epsilon2 = 0,
  lambda1 = 1, lambda2 = 0, penaltyFunction = penaltyFunctionGenerator(),
  include.area = FALSE, frames)

Arguments

particles	A ParticleSet object
L	Maximum number of pixels an object can move in two consecutive frames
R	Linkrange, i.e. the number of consecutive frames to search for potential candidate links
epsilon1	A numeric value, to be used in the formula. Jitter for allowing angular displacements
epsilon2	A numeric value, to be used in the formula. Jitter for allowing spatial displacements
lambda1	A numeric value. Multiplicative factor for the penalty function
lambda2	A numeric value. Multiplicative factor applied to the angular displacement
penaltyFunction	A function structured in such a way to be applied as penalty function in the linking
include.area	Logical, whether to include also area change of the particles in the cost function calculation
frames	The Frames object that the ParticleSet object is derived from
verboseOutput	Logical, whether the output should report additional intermediate steps. For debugging use mainly.
prog	Logical, whether the a progress bar should be shown during the tracking phase
include.intensity	Logical, whether to include also intensity change of the particles in the cost function calculation

Value

A TrajectorySet object

Author(s)

Ayan Bandyopadhyay, Bellarmine College Prep 11/26/2015

Examples

library(flowcatchR)
platelets <-particles(channel.Frames(MesenteriumSubset,"red"))
trajSet <- generateTraj(platelets,
                       L=26, R=3,
                       epsilon1=0, epsilon2=0,
                       lambda1=1, lambda2=0,
                       penaltyFunction=penaltyFunctionGenerator(),
                       include.area=FALSE, MesenteriumSubset)

Ayan1/Cell-Trajectory-Analysis documentation built on May 5, 2019, 9:23 a.m.