R/readtext.ij.r

In LeafArea: Rapid Digital Image Analysis of Leaf Area

#' File management
#'
#' Read multiple tab-delimited text files with a leaf area and perimeter value (one text file for each original JPEG image file) generated by ImageJ.
#'
#' @importFrom utils read.delim
#' @exportPattern "."
#' @param path Path to the target directory
#' @return
#'  A list of data frame of leaf area for each image
#'  \item{area}{Leaf area of the image (cm2)}
#' @author Masatoshi Katabuchi \email{mattocci27@gmail.com}
#' @seealso \code{\link{run.ij}}, \code{\link{resmerge.ij}}
#' @examples
#' #prepare example files
#' data(leafdata)
#' tf <- paste(tempdir(), "/", sep = "")
#' for (i in 1:7){
#' 	write.table(leafdata[[i]],paste(tf,names(leafdata)[i],sep=""),sep="\t")
#' }
#' 
#' #list of files
#' list.files(tf)
#' 
#' readtext.ij(tf)
#' 
#' unlink(list.files(tf))

readtext.ij <- function(path){
  file.list <- list.files(path)
  file.list <- file.list[grep(".txt$", file.list)]
  if (length(file.list[-grep("macro|bat", file.list)] != 0)){
    file.list <- file.list[-grep("macro|bat", file.list)]
  }

  size <- length(0)
  file.name <- length(0)

  data <- list()

  temp.slash <- substr(path, nchar(path), nchar(path))
    if (temp.slash != "/" & temp.slash != "\\"){
      path <- paste(path, "/", sep = "")
    }

  for (i in 1:length(file.list)){
    temp <- read.delim(paste(path, file.list[i], sep = ""))
    data[[i]] <- data.frame(Area = temp$Area)
    # data[[i]] <- read.delim(paste(path,file.list[i],sep=""))
    names(data)[i] <- paste(file.list[i])
   }
  return(data)
}