R: Individual Tree Segmentation Algorithm

watershed {lidR}

R Documentation

Individual Tree Segmentation Algorithm

Description

This function is made to be used in segment_trees. It implements an algorithm for tree segmentation based on a watershed or a marker-controlled watershed.

Simple watershed is based on the bioconductor package EBIimage. You need to install this package to run this method (see its github page). Internally, the function EBImage::watershed is called.
Marker-controlled watershed is based on the imager package and has been removed because imager is an orphaned package.

Usage

watershed(chm, th_tree = 2, tol = 1, ext = 1)

mcwatershed(chm, treetops, th_tree = 2, ID = "treeID")

Arguments

`chm`	RasterLayer. Image of the canopy. Can be computed with grid_canopy or read from an external file.
`th_tree`	numeric. Threshold below which a pixel cannot be a tree. Default is 2.
`tol`	numeric. Tolerance see ?EBImage::watershed.
`ext`	numeric. see ?EBImage::watershed.
`treetops`	`SpatialPointsDataFrame`. Can be computed with find_trees or read from an external shapefile.
`ID`	character. If the `SpatialPointsDataFrame` contains an attribute with the ID for each tree, the name of this column. This way, original IDs will be preserved. If there is no such data trees will be numbered sequentially.

Details

Because this algorithm works on a CHM only there is no actual need for a point cloud. Sometimes the user does not even have the point cloud that generated the CHM. lidR is a point cloud-oriented library, which is why this algorithm must be used in segment_trees to merge the result into the point cloud. However, the user can use this as a stand-alone function like this:

 chm = raster("file/to/a/chm/")
 ttops = find_trees(chm, lmf(3))
 crowns = watershed(chm)()

Examples

## Not run: 
LASfile <- system.file("extdata", "MixedConifer.laz", package="lidR")
poi <- "-drop_z_below 0 -inside 481280 3812940 481320 3812980"
las <- readLAS(LASfile, select = "xyz", filter = poi)
col <- pastel.colors(250)

chm <- grid_canopy(las, res = 0.5, p2r(0.3))
ker <- matrix(1,3,3)
chm <- raster::focal(chm, w = ker, fun = mean, na.rm = TRUE)
las <- segment_trees(las, watershed(chm))

plot(las, color = "treeID", colorPalette = col)

## End(Not run)