DSC <- function(x,y){

  x <- as.array(x)

  y <- as.array(y)

  tt <- sum( x &  y)

  tf <- sum( x & !y)

  ft <- sum(!x &  y)

  ff <- sum(!x & !y)

  tab = matrix(c(ff, tf, ft, tt), ncol=2)

  n = list(c("FALSE", "TRUE"), c("FALSE", "TRUE"))

  dimnames(tab) = n

  tab = as.table(tab)

  DSC = 2*tab[2,2] / (2*tab[2,2] + tab[1,2] + tab[2,1])

  return(DSC)

}

#' Dice Similarity Coefficient Calculation

#'

#' Calculate the Dice similarity coefficient (DSC) for two iterations of lung templates

#'

#' @param template0 Initial template mask. Right lung = 1, left lung = 2, non-lung = 0

#' @param template1 New template mask. Right lung = 1, left lung = 2, non-lung = 0

#' @param sides Calculate DSC on right and/or left lungs. Overall DSC is given by default.

#'

#' @return DSC on whole lung, right lung and left lung.

#' @export

calculate_DSC <- function(template0, template1, sides = c("right","left")){

  # Overall DSC

  x <- template0 > 0

  y <- template1 > 0

  DSC_overall <- DSC(x,y)

  if ("right" %in% sides){

    x <- template0 == 1

    y <- template1 == 1

    DSC_right <- DSC(x,y)

  }else{DSC_right = NULL}

  if ("left" %in% sides){

    x <- template0 == 2

    y <- template1 == 2

    DSC_left <- DSC(x,y)

  }else{DSC_left = NULL}

  return(list(DSC_overall = DSC_overall,

              DSC_right = DSC_right,

              DSC_left = DSC_left))

}