Use a CHM raster to detect individual trees

raster2trees() is an all-in-one function to process a CHM raster and return a spatial data frame of tree crown polygons and points. The order of operations is:

• Perform individual tree detection using lidR::locate_trees() with the lidR::lmf() algorithm

• Delineate tree crowns using ForestTools::mcws()

Note, this function does not estimate DBH for the detected trees and only returns tree location, crown area, and height information. To estimate tree DBH from the detected tree heights see trees_dbh().

Usage

raster2trees(
  chm_rast,
  outfolder,
  ws = itd_ws_functions()[["log_fn"]],
  min_height = 2,
  min_crown_area = 0.1,
  tempdir = tempdir()
)

Arguments

chm_rast

raster. A raster from terra or starsrepresenting a canopy height model

outfolder

string. The path of a folder to write the crown vector data to

ws

numeric or function. Length or diameter of the moving window used to detect the local maxima in the units of the input data (usually meters). If it is numeric a fixed window size is used. If it is a function, the function determines the size of the window at any given location on the canopy. By default function takes the height of a given pixel as its only argument and return the desired size of the search window when centered on that pixel.

min_height

numeric. Set the minimum height (m) for individual tree detection

min_crown_area

numeric. Set the minimum crown area (m2) for individual tree detection

tempdir

string. Directory to write intermediate files. Intermediate files are only created for large rasters too big to fit in memory.

Value

Returns a spatial data frame of individual tree crown vectors detected using the CHM. The tree top point coordinates are located in the tree_x and tree_y columns. The process also writes two .gpkg files to the outfolder directory: chm_detected_crowns.gpkg and chm_detected_tree_tops.gpkg

References

https://r-lidar.github.io/lidRbook/itd.html

Examples

 if (FALSE) { # \dontrun{
 f <- paste0(system.file(package = "cloud2trees"),"/extdata/chm.tif")
 crowns_sf <- raster2trees(chm_rast = terra::rast(f), outfolder = tempdir())
 crowns_sf %>% class()
 crowns_sf %>% dplyr::glimpse()
 crowns_sf %>% ggplot2::ggplot() + ggplot2::geom_sf(ggplot2::aes(fill=tree_height_m))
 } # }