#' Read .las or .laz files
#'
#' Reads .las or .laz files into an object of class \link[=LAS-class]{LAS}. If several files are read at
#' once the returned LAS object is considered as one LAS file. The optional parameters enable the user
#' to save a substantial amount of memory by choosing to load only the attributes or points of interest.
#' LAS formats 1.0 to 1.4 are supported. Point Data Record Format 0 to 10 are supported.\cr\cr
#' `readLAS` is the original function and always works. Using one of the `readALS` or `readTLS` functions
#' adds information to the returned object to register a point-cloud type. Registering the correct point
#' type improves the performance of some functions by enabling users to select an appropriate spatial index.
#' See \link[=lidR-spatial-index]{spatial indexing}. Notice that by legacy and for backwards-compatibility reasons,
#' `readLAS()` and `readALS()` are equivalent because lidR was originally designed for ALS and thus the
#' original function `readLAS()` was (supposedly) used for ALS. Reading a TLS dataset with `readLAS()` instead
#' of `readTLS()` is perfectly valid but less powerful.
#'
#'
#' **Select:** the 'select' argument specifies the data that will actually be loaded. For example,
#' 'xyzia' means that the x, y, and z coordinates, the intensity and the scan angle will be loaded.
#' The supported entries are t - gpstime, a - scan angle, i - intensity, n - number of returns,
#' r - return number, c - classification, s - synthetic flag, k - keypoint flag, w - withheld flag,
#' o - overlap flag (format 6+), u - user data, p - point source ID, e - edge of flight line flag,
#' d - direction of scan flag, R - red channel of RGB color, G - green channel of RGB color,
#' B - blue channel of RGB color, N - near-infrared channel, C - scanner channel (format 6+),
#' W - Full waveform.
#' Also numbers from 1 to 9 for the extra bytes data numbers 1 to 9. 0 enables all extra bytes to be
#' loaded and '*' is the wildcard that enables everything to be loaded from the LAS file. \cr
#' Note that x, y, z are implicit and always loaded. 'xyzia' is equivalent to 'ia'.\cr\cr
#' **Filter:** the 'filter' argument allows filtering of the point cloud while reading files.
#' This is much more efficient than \link{filter_poi} in many ways. If the desired filters are known
#' before reading the file, the internal filters should always be preferred. The available filters are
#' those from `LASlib` and can be found by running the following command: `readLAS(filter = "-help")`.
#' (see also \link[rlas:read.las]{rlas::read.las}). From `rlas` v1.3.6 the transformation commands
#' can also be passed via the argument filter.
#'
#' @template section-fwf
#'
#' @param files characters. Path(s) to one or several a file(s). Can also be a
#' \link[=LAScatalog-class]{LAScatalog} object.
#' @param select character. Read only attributes of interest to save memory (see details).
#' @param filter character. Read only points of interest to save memory (see details).
#'
#' @return A LAS object
#'
#' @export
#'
#' @examples
#' LASfile <- system.file("extdata", "Megaplot.laz", package="lidR")
#' las = readLAS(LASfile)
#' las = readLAS(LASfile, select = "xyz")
#' las = readLAS(LASfile, select = "xyzi", filter = "-keep_first")
#' las = readLAS(LASfile, select = "xyziar", filter = "-keep_first -drop_z_below 0")
#'
#' # Negation of attributes is also possible (all except intensity and angle)
#' las = readLAS(LASfile, select = "* -i -a")
#' @md
readLAS = function(files, select = "*", filter = "")
{
  if (filter == "-h" | filter == "-help")
  {
    rlas:::lasfilterusage()
    return(invisible())
  }

  UseMethod("readLAS", files)
}


#' Read a .las or .laz file header
#'
#' Reads a .las or .laz file header into an object of class \link[=LASheader-class]{LASheader}.
#' This function strictly reads the header while the function \link{readLAS} can alter the header to
#' fit the actual data loaded.
#'
#' @param file characters. Path to one file.
#' @return A LASheader object
#' @export
#' @examples
#' LASfile <- system.file("extdata", "Megaplot.laz", package="lidR")
#' header = readLASheader(LASfile)
#'
#' print(header)
#' plot(header)
#'
#' \dontrun{
#' plot(header, mapview = TRUE)}
readLASheader = function(file)
{
  header <- rlas::read.lasheader(file)
  return(LASheader(header))
}

#' @export
readLAS.LAScatalog = function(files, select, filter)
{
  if (missing(select)) select <- opt_select(files)
  if (missing(filter)) filter <- opt_filter(files)

  return(readLAS(files@data$filename, select, filter))
}

#' @export
readLAS.LAScluster = function(files, select = NULL, filter = NULL)
{
  if (!is.null(select)) warning("Argument 'select' is not used with a LAScluster. Use opt_select() with the LAScatalog instead.", call. = FALSE)
  if (!is.null(filter)) warning("Argument 'filter' is not used with a LAScluster. Use opt_filter() with the LAScatalog instead.", call. = FALSE)

  if (!all(file.exists(files@files)) && all(files@alt_dir != "")) {
    for (alt_dir in files@alt_dir) {
      paths <- paste0(alt_dir, basename(files@files))
      if (all(file.exists(paths))) break
    }
    files@files <- paths
  }

  if (!all(file.exists(files@files))) stop("File not found", call. = FALSE)

  buffer <- X <- Y <- NULL

  las <- readLAS(files@files, files@select, files@filter)
  st_crs(las) <- st_crs(files)
  las@index <- files@index

  las@data[["buffer"]] <- rep(LIDRNOBUFFER, npoints(las))

  if (files@buffer > 0)
  {
    ext     <- st_bbox(files)
    ybottom <- ext$ymin
    ytop    <- ext$ymax
    xleft   <- ext$xmin
    xright  <- ext$xmax
    xc      <- files@center$x
    yc      <- files@center$y
    r       <- (files@width - 2*files@buffer)/2

    if (files@shape == LIDRCIRCLE)
    {
      las@data[(X - xc)^2 + (Y - yc)^2 > r^2, buffer := LIDRBUFFER]
    }
    else
    {
      las@data[Y < ybottom, buffer := LIDRBOTTOMBUFFER]
      las@data[X < xleft,   buffer := LIDRLEFTBUFFER]
      las@data[Y >= ytop,    buffer := LIDRTOPBUFFER]
      las@data[X >= xright,  buffer := LIDRRIGHTBUFFER]
      las@data[(X >= xright) & (Y < ybottom), buffer := LIDRBOTTOMBUFFER]
    }

    # We found a region with no actual data. The points all belong in the buffer
    # Return empty point cloud
    if (fast_countequal(las@data[["buffer"]], LIDRNOBUFFER) == 0)
      las <- filter_poi(las, buffer == LIDRNOBUFFER)
  }

  return(las)
}

#' @export
readLAS.character = function(files, select = "*", filter = "")
{
  assert_is_a_string(select)
  assert_is_a_string(filter)
  return(streamLAS(files, ofile = "", select, filter))
}

streamLAS = function(x, ofile, select = "*", filter = "", filter_wkt = "")
{
  UseMethod("streamLAS", x)
}

streamLAS.LAScluster = function(x, ofile, select = "*", filter = "", filter_wkt = "")
{
  las = streamLAS(x@files, ofile, x@select, x@filter, filter_wkt)

  # Automatically remove files that are empty
  if (ofile != "")
  {
    header = rlas::read.lasheader(ofile)

    if (header$`Number of point records` == 0)
    {
      file.remove(ofile)
      return(NULL)
    }
  }

  return(las)
}

streamLAS.character = function(x, ofile, select = "*", filter = "", filter_wkt = "")
{
  # Compatibility with rlas that no longer supports WKT string to filter polygons
  geom = list()
  if (utils::packageVersion("rlas") >= "1.8.0")
  {
    if (is.character(filter_wkt) && filter_wkt[1] != "")
    {
      geom = sf::st_as_sfc(filter_wkt)
      geom = extract_polygons(geom)
    }
  }

  assert_all_are_existing_files(x)

  islas <- tools::file_ext(x) %in% c("las", "laz", "ply", "LAS", "LAZ", "PLY")

  if (any(!islas)) stop("File(s) are not las or laz")

  ifiles <- normalizePath(x)

  if (ofile != "")
  {
    dir = dirname(ofile)
    if (!dir.exists(dir)) dir.create(dir, recursive = TRUE)
  }

  header <- rlas::read.lasheader(ifiles[1])

  # More than one file we need to check the compatibility
  if (length(ifiles) > 1)
  {
    for (file in ifiles)
    {
      temp.header <- rlas::read.lasheader(file)

      if (temp.header[["Point Data Format ID"]] != header[["Point Data Format ID"]] )
        warning("Different files have different Point Data Format ID and are incompatible. Some attribute may have been discarded or zeroed", call. = FALSE)

      if (temp.header[["X scale factor"]] != header[["X scale factor"]] )
        warning("Different files have different X scale factors and are incompatible. The first file has precedence and data were rescaled.", call. = FALSE)

      if (temp.header[["Y scale factor"]] != header[["Y scale factor"]] )
        warning("Different files have different Y scale factors and are incompatible. The first file has precedence and data were rescaled.", call. = FALSE)

      if (temp.header[["Z scale factor"]] != header[["Z scale factor"]] )
        warning("Different files have different Z scale factors and are incompatible. The first file has precedence and data were rescaled.", call. = FALSE)

      if (rlas::header_get_epsg(header) != rlas::header_get_epsg(temp.header))
        warning("Different files have diferent CRS and are incompatible. The CRS of the first file has been retained.", call. = FALSE)
    }
  }

  if (utils::packageVersion("rlas") >= "1.8.0") {
    data <- rlas:::stream.las(ifiles, ofile, select, filter, geom)
  } else {
    data <- rlas:::stream.las(ifiles, ofile, select, filter, filter_wkt)
  }

  if (is.null(data))
    return(invisible())

  if (nrow(data) > 0)
  {
    # If the number of files read is > 1 header bbox will not be in accordance with the data. Update the header.
    if (length(ifiles) > 1 || filter != "")
      header <- rlas::header_update(header, data)
  }

  # Remove extrabytes in the header if not loaded

  extrabytes <- names(header[["Variable Length Records"]][["Extra_Bytes"]][["Extra Bytes Description"]])

  if (!is.null(extrabytes))
  {
    for (extrabyte in extrabytes)
    {
      if (!extrabyte %in% names(data))
      {
        header[["Variable Length Records"]][["Extra_Bytes"]][["Extra Bytes Description"]][[extrabyte]] <- NULL
      }
    }

    if (length(header[["Variable Length Records"]][["Extra_Bytes"]][["Extra Bytes Description"]]) == 0)
    {
      header[["Variable Length Records"]][["Extra_Bytes"]] <- NULL
    }
  }

  return(LAS(data, header, check = TRUE, index = NULL, no_attr_name_check = TRUE))
}
