runBatch: Batch analysis

In trackdem: Particle Tracking and Demography

Batch analysis

Description

runBatch analyzes all image sequences in a specified directory. Use this function when settings have been optimized previously on a single or selection of movies/image sequences.

Usage

runBatch(
  path,
  settings = NULL,
  dirnames = NULL,
  nImages = 1:30,
  pixelRange = NULL,
  threshold = -0.1,
  qthreshold = NULL,
  select = "dark",
  nn = NULL,
  incThres = NULL,
  plotOutput = FALSE,
  plotType = "trajectories",
  L = 20,
  R = 2,
  weight = c(1, 1, 1),
  autoThres = FALSE,
  perFrame = FALSE,
  methodBg = "mean",
  frames = NULL,
  saveAll = FALSE
)

Arguments

path	A character vector of path name that contains all directories with image sequences.
settings	Object of class 'tracked' containing all optimized settings in attributes, as obtained from trackParticles. Alternatively, settings can be specified using arguments described below.
dirnames	If not all image sequences should be analyzed, specify which files to use as a character string.
nImages	See loadImages
pixelRange	See identifyParticles
threshold	See identifyParticles
qthreshold	See identifyParticles
select	See identifyParticles
nn	Name of artificial neural net if apply it to images. Default is NULL, resulting in no neural net being applied.
incThres	Minimum number of frames that a particle must be present. By default, automated estimate is used.
plotOutput	Default is FALSE. Set TRUE to plot results.
plotType	Default is 'trajectories'. Other options are 'sizes' and 'animation'.
L	See trackParticles
R	See trackParticles
weight	See trackParticles
autoThres	See identifyParticles
perFrame	See identifyParticles
methodBg	See createBackground
frames	See identifyParticles
saveAll	Logical. Set TRUE to save for each image sequence the full object obtained from loadImages. Default is FALSE.

Value

Dataframe with estimated population size for each image sequence.

Author(s)

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

See Also

loadImages, createBackground, subtractBackground, identifyParticles, trackParticles.

Examples

## Not run: 
## Simulate 3 image sequences
wd <- getwd()
folders <- paste0(rep("images",3),1:3)
populations <- c(15,25,50)
dir.create("./batchTest")
setwd("./batchTest")
for(i in 1:length(folders)){
  dir.create(folders[i])
  traj <- simulTrajec(path=folders[i],
                      nframes=30,nIndividuals=populations[i],
                      h=0.01,rho=0.9,
                      sizes=runif(populations[i],0.004,0.006))
}
setwd(wd)
batchpath <- "./batchTest"
results <- runBatch(path=batchpath,
                    nImages=1:30,threshold=-0.1,select='dark',
                    pixelRange=c(1,100),L=50,R=3,
                    incThres=10)
results

## End(Not run)

trackdem documentation built on May 29, 2024, 7:43 a.m.