R/linkSkippedFrames.R

In sheng-liu/sojourner: Statistical analysis of single molecule trajectories

## 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)
}