update.particles: Update identified particles.

In trackdem: Particle Tracking and Demography

Description

Apply trained artificial neural network to particleStat object.

Usage

## S3 method for class 'particles'
update(object, neuralnet, pca = TRUE, colorimages = NULL, sbg = NULL, ...)

Arguments

object	Object of class 'nnTrackdemObject'.
neuralnet	Trained neural net obtained from testNN
pca	Logical. By default TRUE, indicating that a principal component analysis is performed on the predictors.
colorimages	An array with the original full color images, in order to plot on the original images, obtained by loadImages. By default the original color images are used.
sbg	Images subtracted from background, as obtained by subtractBackground. By default, the original subtracted images are used.
...	further arguments passed to or from other methods.

Value

Data frame class 'particles', containing updated particle statistics (excluding particles that have been filtered out by the neural net).

Author(s)

Marjolein Bruijning, Caspar A. Hallmann & Marco D. Visser

Examples

## Not run: 
dir.create("images")
## Create image sequence
traj <- simulTrajec(path="images",
                    nframes=30,nIndividuals=20,domain='square',
                    h=0.01,rho=0.9,movingNoise=TRUE,
                    parsMoving = list(density=20, duration=10, size=1,
                                      speed = 10, colRange = c(0,1)),
                    sizes=runif(20,0.004,0.006))
## Load images
dir <- "images"
allFullImages <- loadImages (dirPictures=dir,nImages=1:30)
stillBack <- createBackground(allFullImages,method="mean")
allImages <- subtractBackground(stillBack)
partIden <- identifyParticles(allImages,threshold=-0.1,
                                   pixelRange=c(3,400))
nframes <- 3
frames <- order(tapply(partIden$patchID,partIden$frame,length),
                decreasing=TRUE)[1:nframes]
mId <- manuallySelect(particles=partIden,frame=frames)
finalNN <- testNN(dat=mId,repetitions=10,maxH=4,prop=c(6,2,2))
partIdenNN <- update(particles=partIden,neuralnet=finalNN)

## End(Not run)

trackdem documentation built on Sept. 25, 2021, 1:07 a.m.