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## linkSkippedFrames-methods
##' @name linkSkippedFrames
##' @aliases linkSkippedFrames
##' @title linkSkippedFrames
##' @rdname linkSkippedFrames-methods
##' @docType methods
##'
##' @description link trajectories skipped (or do not appear for) a number of
##' frames
##' @usage
##' linkSkippedFrames(trackll, tolerance, maxSkip, cores = 1)
##'
##' @param trackll A list of track lists.
##' @param tolerance Distance tolerance level measured in pixels after the
##' frame skip.
##' @param maxSkip Maximum number of frames a trajectory can skip.
##' @param cores Number of cores used for parallel computation. This can be
##' the cores on a workstation, or on a cluster. Tip: each core will be
##' assigned to read in a file when paralleled.
##' @return linked trackll
##' @details
##' Given user input for a tolerance level to limit how far the next point
##' after the skip can deviate from the last point in pixel distance
##' and a maximum number of frame skips possible, all trajectories falling
##' within these parameters are automatically linked, renamed, and ordered
##' accordingly.
##' For a maxSkip example, if the maxSkip for a trajectory ending in frame 7
##' was 3, the next linked trajectory can start up to a maximum frame of 11.
##'
##' Although not required, in order for the output to have a frame record
##' column (recommended), the input must have one as well.
##'
##' The naming scheme for each linked track is as follows:
##'
##' [Last five characters of the file name].[Start frame #].[Length].[Track #].
##' [# of links]
##'
##' Track List: [full name of input file]
##'
##' Track: [Last five characters of the file name].[Start frame].[Length].
##' [Track].[# of links].
##' [Index in overall list (will differ from Track # when merging)]
##'
##' (Note: The last five characters of the file name, excluding the extension,
##' cannot contain '.')
##' @examples
##' folder=system.file('extdata','SWR1',package='sojourner')
##' trackll=createTrackll(folder=folder, input=3)
##' #Basic function call of linkSkippedFrames
##' trackll.linked <- linkSkippedFrames(trackll, tolerance = 5, maxSkip = 10)
##' @export linkSkippedFrames
###############################################################################
#### .linkSkippedFrames ####
.linkSkippedFrames = function(track.list, tolerance, maxSkip) {
# Get abbreviated file name
file.name = getTrackFileName(track.list)
# Confirmation text of function call
cat("\nLinking", file.name, "...\n")
# Instantiate empty linked track list
track.list.linked = list()
# Instantiate frame/length/linknum list for track naming
frame.list = list()
length.list = list()
linknum.list = list()
# Instantiate starting frame of the last trajectory, max frame after
# skips, and index
lastTrajFrame = getStartFrame(track.list, length(track.list))
maxFrame = maxSkip + 1
trajectoryIndex = 1
# Extract file sub-name from given track list
file.subname = substr(names(track.list[1]), 1, gregexpr(pattern = "\\.",
names(track.list[1]))[[1]][1] - 1)
# Loop through each new linked trajectory
repeat {
# Extract first trajectory in track list into data frame temp for
# linking trajectories
temp <- track.list[[1]]
# Record the start amd last frame of the starting trajectory from track
# name
startFrame = getStartFrame(track.list, 1)
lastFrame = getStartFrame(track.list, 1) + nrow(temp) - 1
# Delete the extracted first trajectory from track list and shift list
# to replace The first trajectory in the track list is the next
# trajectory after the data frame temp
track.list[[1]] <- NULL
# Record the last X and Y coordinate values of data frame temp
lastX = temp[[1]][[nrow(temp)]]
lastY = temp[[2]][[nrow(temp)]]
# Set link counter to 0;
linkCounter = 0
# Instantiate index i and loop through trajectories in track list to
# look for frame skips
i = 1
repeat {
# If the starting frame of the trajectory is beyond the maximum
# skips possible or the last frame, break
nextFrame = getStartFrame(track.list, i)
if (i > length(track.list) || nextFrame > lastFrame + maxFrame) {
break
}
# Record the first X and Y coordinate values of trajectory
nextX = track.list[[i]][[1]][[1]]
nextY = track.list[[i]][[2]][[1]]
# Check if the distance difference between the first coordinate of
# trajectory and the last coordinate of temp are within the set
# tolerance
if (sqrt((lastX - nextX)^2 + (lastY - nextY)^2) <= tolerance) {
# Update lastFrame
lastFrame = getStartFrame(track.list, i) +
nrow(track.list[[i]]) - 1
# Append trajectory to temp
temp <- rbind(temp, track.list[[i]])
# Delete trajectory from track list and shift
track.list[[i]] <- NULL
# Recalculate last X and Y coordinate values of appended data
# frame temp
lastX = temp[[1]][[nrow(temp)]]
lastY = temp[[2]][[nrow(temp)]]
# Increment link counter
linkCounter = linkCounter + 1
} else {
# Increment index to next trajectory if nothing is found
i = i + 1
}
}
# Add start frame to frame list
frame.list[[length(frame.list) + 1]] <- startFrame
# Add track length to length list
length.list[[length(length.list) + 1]] <- nrow(temp)
linknum.list[[length(linknum.list) + 1]] <- linkCounter
# Append data frame temp of the fully linked trajectory into
# track.list.linked and increment index
track.list.linked[[trajectoryIndex]] <- temp
trajectoryIndex = trajectoryIndex + 1
# Break if the track list of decreasing length is empty
if (length(track.list) == 0) {
break
}
}
# Name track list: [File name from input].[Start frame
# #].[Length].[Track #].[# of links]
names(track.list.linked) = paste(file.subname, frame.list, length.list,
c(seq_along(track.list.linked)), linknum.list, sep = ".")
# Return linked track list and confirmation text
cat("\n", Reduce("+", linknum.list), "links found in", file.name, "\n")
return(track.list.linked)
}
#### linkSkippedFrames ####
linkSkippedFrames = function(trackll, tolerance, maxSkip, cores = 1) {
# detect number of cores
max.cores = parallel::detectCores(logical = TRUE)
if (cores == 1) {
link.trackll = lapply(trackll, function(x) {
.linkSkippedFrames(track.list = x, tolerance = tolerance,
maxSkip = maxSkip)
})
} else {
# parallel excecute above block of code
if (cores > max.cores)
stop("Number of cores specified is greater than maxium: ",
max.cores)
cat("Initiated parallel execution on", cores, "cores\n")
# use outfile='' to display result on screen
cl <- parallel::makeCluster(spec = cores, type = "PSOCK", outfile = "")
# register cluster
parallel::setDefaultCluster(cl)
# pass environment variables to workers
parallel::clusterExport(cl, varlist = c(".linkSkippedFrames",
"tolerance", "maxSkip"), envir = environment())
link.trackll = parallel::parLapply(cl, trackll, function(x) {
.linkSkippedFrames(track.list = x, tolerance = tolerance,
maxSkip = maxSkip)
})
# stop cluster
cat("\nStopping clusters...\n")
parallel::stopCluster(cl)
}
cat("\nProcess complete.\n")
return(link.trackll)
}
#### Extra and useless functions ####
findMaxLinks = function(track.list, maxTolerance = 10, maxMaxSkip = 500) {
minLength = length(track.list)
minTolerance = maxTolerance
minSkip = maxMaxSkip
cat("Searching...")
for (i in seq_len(maxTolerance)) {
for (j in seq_len(maxMaxSkip)) {
length = length(linkSkippedFrames(track.list, tolerance = i,
maxSkip = j))
if (length < minLength) {
minLength = length
minTolerance = i
minSkip = j
}
}
}
cat(paste("For the maximum number of links,",
"with minimum tolerance and then minimum skips:"))
cat("\nTolerance =", minTolerance)
cat("\nSkips =", minSkip)
cat("\nLength =", minLength)
}
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