1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
# track_mean_speed <- function(x,framerate=30,pxsize=100){
#   #speed um/ms
#
#   #scale to um
#   x$X <- (x$X*pxsize)/1000
#   x$Y <- (x$Y*pxsize)/1000
#
#   #apply function for every track (column V4)
#   meansp <- ddply(x,.variables = "track",.fun= function(x) {
#     speed <- 0
#     for (i in 2:nrow(x)){
#       speed <- speed + (x$X[i]-x$X[i-1])^2+(x$Y[i]-x$Y[i-1])^2/((x$frame[i]-x$frame[i-1])*framerate)
#     }
#     speed <- speed/nrow(x)
#   })
#   names(meansp) <- c("trackid","speed")
#   return(meansp)
# }
#
# TRACK_MEAN_SPEED <- function(x,framerate=30,pxsize=100){
#   UseMethod("TRACK_MEAN_SPEED")
# }
#
# TRACK_MEAN_SPEED.default <- function(x,framerate=30,pxsize=100){
#   stop("TRACK_MEAN_SPEED requires data frame")
# }
#
# TRACK_MEAN_SPEED.data.frame <-  function(x,framerate=30,pxsize=100){
#   track_mean_speed(x,framerate,pxsize)
#
# }
#
# TRACK_MEAN_SPEED.list <-  function(x,framerate=30,pxsize=100){
#   llply(x,function(x){
#     TRACK_MEAN_SPEED(x,framerate,pxsize)
#   })
# }


#According to Reuter et al.
#Filter tracks in bound vs unboud via a threshold, analyse both groups separately
#Calculate CDF of r^2, one can fit this distribution with multiple exponents to extract D coefficients
#Make 2D (difference) histograms by defining mobile vs immobile segments

track_stat <- function(x,framerate=30,pxsize=100){

  x$X <- (x$X*pxsize)/1000
  x$Y <- (x$Y*pxsize)/1000
  out <- ddply(x,.variables = "track",.fun= function(x) {
    speed <- 0
    for (i in 2:nrow(x)){
      speed <- speed + (x$X[i]-x$X[i-1])^2+(x$Y[i]-x$Y[i-1])^2/((x$frame[i]-x$frame[i-1])*framerate)
    }
    speed <- speed/nrow(x)

    coord <- cbind(x$X,x$Y)
    # use pricipal component analysis on X and Y coordinates to get eigenvectors: major and minor axis
    D <- princomp(coord)
    angle <- atan2(D$loadings[2,1],D$loadings[1,1])
    #calculate convex hull and futher statistics
    y <- chull(coord)
    area <- pracma::polyarea(coord[rev(y),1], coord[rev(y),2])
    perimeter <- pracma::poly_length(coord[rev(y),1], coord[rev(y),2])
    D_chull <- princomp(coord[y,])


    #return(data.frame("sd"=((sd(x$X)+sd(x$Y))/2)*2.35,"N"=nrow(x),"channel"=1))
    # return(data.frame(,"N"=nrow(x),"channel"=1))
    return(data.frame("N"=nrow(x),"meanX"=mean(x$X),"meanY"=mean(x$Y),"meanspeed"=speed ,
                      "sd"=((sd(x$X)+sd(x$Y))/2),"sdpri"=((D$sdev[1]+D$sdev[2])/2),"major"=D$sdev[1],"minor"=D$sdev[2],
                      "width"=(max(D$scores[,1])-min(D$scores[,1])),"ratio"=(D$sdev[1]/D$sdev[2]),"angle"=angle,
                      "chull_area"=area,"chull_perimeter"=perimeter,"chull_major"=D_chull$sdev[1],"chull_minor"=D_chull$sdev[2]))
  })

  return(out)
}

TRACK_STAT <- function(x,framerate=30,pxsize=100){
  UseMethod("TRACK_STAT")
}

TRACK_STAT.default <- function(x,framerate=30,pxsize=100){
  stop("TRACK_STAT requires data frame")
}

TRACK_STAT.data.frame <-  function(x,framerate=30,pxsize=100){
  track_stat(x,framerate,pxsize)

}

TRACK_STAT.list <-  function(x,framerate=30,pxsize=100){
  llply(x,function(x){
    TRACK_STAT(x,framerate,pxsize)
  })
}


segment_stat <- function(x){

  get_angle <- function(x){
    seg_angle <- vector()
    for(i in 1:(nrow(x)-2)){
      A <- as.numeric(x[i,2:3])
      B <- as.numeric(x[i+1,2:3])
      C <- as.numeric(x[i+2,2:3])
      AB <- B-A
      CB <- C-B
      dAB <- sqrt((B[1]-A[1])^2+(B[2]-A[2])^2)
      dBC <- sqrt((C[1]-B[1])^2+(C[2]-B[2])^2)
      seg_angle <- c(seg_angle,(acos((AB%*%CB)/(dAB*dBC))*180/pi))


    }
    seg_angle <- c(-1,seg_angle,-1)
    return(seg_angle)
  }

  result <- ddply(x,.variables = "track",function(x){
  if(nrow(x)>4){x$angle <- get_angle(x)}else{
    x$angle<- 0
  }
  x$disp_squared <- x$displacement^2
  x$disp_squared[x$displacement==-1] <- -1
  return(x)
  }
  )
  return(result)
}

SEGMENT_STAT <- function(x){
  UseMethod("SEGMENT_STAT")
}

SEGMENT_STAT.default <- function(x){
  stop("SEGMENT_STAT requires data frame")
}

SEGMENT_STAT.data.frame <-  function(x){
  segment_stat(x)

}

SEGMENT_STAT.list <-  function(x){
  result <- llply(x,function(x){
    SEGMENT_STAT(x)
  })
  return(result)
}