R/read_tree_pc.R

In lmterryn/ITSMe: Individual Tree Structural Metrics

#' Read a tree point cloud
#'
#' Reads a tree point cloud file of txt, las/laz or ply format and returns the tree
#' point cloud as a data.frame with 3 columns (X,Y,Z).
#'
#' Reading the txt, las/laz and ply files is based on
#' \code{\link[data.table]{fread}}, \code{\link[lidR]{readTLSLAS}} and
#' \code{\link[Rvcg]{vcgPlyRead}} respectively. Sampling is based on
#' \code{\link[base]{sample}} and is mainly a useful tool to reduce the amount
#' of points for quicker plotting.
#'
#' @param path A character with the path to the tree point cloud file. File can
#'   be \emph{txt}, \emph{las}, \emph{laz} or \emph{ply} format. The 3D coordinates have to
#'   be in the first three columns in case of a \emph{txt} file.
#' @param samplefactor A numeric value ranging from 0 to 1 (default=1). This
#'   determines the amount of points that are sampled from the point cloud. 1 to
#'   sample 100 percent of the points and for example 0.5 to sample 50 percent
#'   of the points.
#'
#' @return The tree point cloud as a data.frame (nx3) with X, Y, and Z
#'   coordinates in the first, second and third column respectively.
#'
#' @export
#'
#' @examples
#' \dontrun{
#' # Read a tree point cloud file of the txt format
#' pc_txt <- read_tree_pc(PC_path = "path/to/point_cloud.txt")
#' # Read a tree point cloud file of the ply format
#' pc_ply <- read_tree_pc(PC_path = "path/to/point_cloud.ply")
#' # Read a tree point cloud file of the las/laz format
#' # and subsample to 20 percent of the points
#' pc_las <- read_tree_pc(PC_path = "path/to/point_cloud.las", 0.2)
#' }
read_tree_pc <- function(path, samplefactor = 1) {
  extension <-
    utils::tail(strsplit(path, split = ".", fixed = T)[[1]], 1)
  if (extension == "txt") {
    txt <- data.table::fread(path)
    pc <- data.frame(txt[, 1:3])
    colnames(pc) <- c("X", "Y", "Z")
  } else if (extension %in% c("las", "laz")) {
    las <- lidR::readTLSLAS(path)
    pc <- data.frame("X" = las$X,
                     "Y" = las$Y,
                     "Z" = las$Z)
  } else if (extension == "ply") {
    ply <- Rvcg::vcgPlyRead(path, updateNormals = TRUE, clean = TRUE)
    pc <-
      data.frame("X" = ply$vb[1,],
                 "Y" = ply$vb[2,],
                 "Z" = ply$vb[3,])
  } else {
    print("This extension is not recognized. Try txt, las/laz or ply format")
    pc <- c()
  }
  if (samplefactor != 1) {
    pc <- pc[sample(
      nrow(pc),
      size = floor(nrow(pc) * samplefactor),
      replace = FALSE,
      prob = NULL
    ),]
  }
  return(pc)
}