R/JoinIntervals.R

In kevin-allen/relectro: Analysis of electrophysiological data

#' Join two sets of intervals using an AND logic
#' 
#' To be included in the output interval, the time period needs to be included in both set of time intervals.
#' Adjacent s1-e1 or s2-e2 will be joined together by default
#'  
#' @param s1 Numeric vector containing the start times of the first set of intervals
#' @param e1 Numeric vector containing the end times of the first set of intervals
#' @param s2 Numeric vector containing the start times of the second set of intervals
#' @param e2 Numeric vector containing the end times of the second set of intervals
#' @return matrix containing the start and end of the resulting intervals. First col is the start times. Second col is end times.
#' @examples 
#' s1<-c(0,20000)
#' e1<-c(500,25000)
#' s2<-c(250,24000)
#' e2<-c(600,30000)
#' joinIntervalsAND(s1,e1,s2,e2)
joinIntervalsAND<-function(s1,e1,s2,e2){
  ## check args
  if(length(s1)!=length(e1))
    stop("unequal length of first intervals")
  if(length(s2)!=length(e2))
    stop("unequal lenght of the second intervals")
  if(any(s1>e1))
    stop("problem with chronology of the first set of intervals")
  if(any(s2>e2))
    stop("problem with chronology of the first set of intervals")
  res<-.Call("joinIntervalsAND_cwrap",
        as.integer(s1),
        as.integer(e1),
        length(s1),
        as.integer(s2),
        as.integer(e2),
        length(s2))
  if(!is.null(res)) colnames(res)<-c("start","end")
  return(res)
}


#' Get a logical vector to know if time points are within a series of intervals
#' 
#' Only time points that are within the limit of the interval will return TRUE.
#' For example time point 2 is not in the interval 2 4.
#' Only 3 would return TRUE in this case.
#' 
#' @param x Integer vector representing time points
#' @param s Integer vector representing the start of intervals
#' @param e Integer vector representing the end of intervals
#' @return Logical, whether the time points are within the intervals
timeWithinIntervals<-function(x,s,e){
  if(length(s)!=length(e))
    stop("unequal length of s and e")
  if(length(x)==0)
    stop("length of x is 0")
  index<-as.logical(.Call("resWithinIntervals",
                          length(s),
                          as.integer(s),
                          as.integer(e),
                          length(x),
                          as.integer(x)))
  return(index)
}


#' Remove time that falls outside of intervals from time stamps
#' 
#' The time outside the intervals is removed from the time stamps
#' Only the intervals before a given timestamps are considered
#' 
#' It assumes that all the spikes are within the intervals
#' 
#' @param x Integer vector representing time points
#' @param s Integer vector representing the start of intervals
#' @param e Integer vector representing the end of intervals
#' @return Numeric, timestamps without the time ouside the intervals
removeTimeOutsideIntervalsFromTimeStamps<-function(x,s,e){
  if(length(s)!=length(e))
    stop("unequal length of s and e")
  if(length(x)==0)
    stop("length of x is 0")
  if(any(!timeWithinIntervals(x,s,e)))
    stop("Timestamps outside intervals")
  
  timeStamps<-as.numeric(.Call("removeTimeOutsideIntervalsTimeStamps",
                          length(s),
                          as.integer(s),
                          as.integer(e),
                          length(x),
                          as.integer(x)))
  return(timeStamps)
}

#' Generate equally spaced time points within a series of intervals
#' 
#' 
#' @param min Numeric indicating the smallest time point
#' @param max Numeric indicating the maximal time point
#' @param by Numeric indicating the spacing between timepoints
#' @param s Integer vector representing the start of intervals
#' @param e Integer vector representing the end of intervals
#' @return Numeric, equally spaced timestamps when only considering the time within intervals
equallySpacedTimePointsWithinIntervals<-function(min,max,by,s,e){
  if(length(s)!=length(e))
    stop("unequal length of s and e")
  if(length(min)!=1)
    stop("length of min should be 1")
  if(length(max)!=1)
    stop("length of min should be 1")
  if(length(by)!=1)
    stop("length of min should be 1")
  if(min<0)
    stop("min should not be negative")
  if(max<=min)
    stop("max should be larger than min")
  if(by<=0)
    stop("by should be larger than 0")
  if(max-min<by)
    return(min)
  
  
  timeStamps<-as.numeric(.Call("equallySpacedTimePointsWithinIntervals",
                               as.integer(min),
                               as.integer(max),
                               as.integer(by),
                               length(s),
                               as.integer(s),
                               as.integer(e)
                               ))
  return(timeStamps)
}