R/reland.R

In jinyung/otolith: Identification of fish otolith using digital images

#' Re-arrage semi-landmark configuration
#' 
#' @description To flip or change the order of semi-landmark configuration
#' @param landdata semi-landmarks data generated from \code{\link{equaldist}} 
#'   functions. A matrix/dataframe consists of two columns of x and y
#'   coordinates
#' @param type character of \code{"ori"}, \code{"rev"}, \code{"flip"}, or
#'   \code{"fliprev"} to set the configuration of the semi-landmarks. See
#'   details.
#' @return matrix of xy coordinates of re-arranged semi-landmarks data.
#' @details There are four possible configurations of semi-landmark sampling for
#'   any set of otolith, depending on the side of the otolith and the initial 
#'   orietation of the image. This function can be used to standardize the
#'   sampling of semi-landmarks.
#'  
#' \code{type} argument change the semi-landmarks as if the otolith image was
#' taken from different end on the left (\code{"rev"}), or as if the otolith is
#' from the other side (\code{"flip"}), or as if the otolith is from the other
#' side and image taken from different end on the left (\code{"fliprev"}).
#' \code{"ori"} do nothing on the semi-landmarks.
#' @export

reland <- function (landdata, type = c("ori", "rev", "flip", "fliprev")) {
  type <- match.arg(type)
  nd <- dim(landdata)[1] / 2
  landdatanew <- landdataF <- landdataFN <- 
    array(data = NA,  dim = c(dim(landdata)[1], 2))
  landdataF <- landdata
  landdataF[, 1] <- -landdataF[, 1] # flipping
  landdataFN[1, ] <- landdataF[nd + 1, ]
  landdataFN[nd + 1, ] <- landdataF[1, ]
  landdataFN[2:nd, ] <- landdataF[nd:2, ]
  landdataFN[(nd + 2):(nd * 2), ] <- landdataF[(nd * 2):(nd + 2), ]
  if (type == "ori") {
    landdatanew <- landdata
  } else if (type == "flip") {
    landdatanew <- landdataFN
  } else {
    if (type == "fliprev")
      landdata <- landdataFN
    else if (type == "rev")
      landdata <- landdata
    else
      stop("incorrect type, please choose from \"ori\", \"rev\", \"flip\" or \"fliprev\"")
    landdatanew[1, ] <- landdata[nd + 1, ]
    landdatanew[nd + 1, ] <- landdata[1, ]
    landdatanew[2:nd, ] <- landdata [(nd + 2):(nd * 2),  ]
    landdatanew[(nd + 2):(nd * 2), ] <- landdata [2:nd, ]
  }
  return(landdatanew)
}