lidR - add vegetation classification to unique trees

Question

I have done a individual tree segmentation using lidR and the resulting LAS file now has been classified so that all points belonging to a tree have a unique treeID. So far so good!

But before writing the LAS file I would like to add High, Medium and Low vegetation to the trees as well. So for example if a tree have a height of let say 5 meter it should be classified as Low vegetation (classification = 3) and between 5 to 10 meters should be classified to Medium vegetation (classification = 4) and so on. I cant figure out how to do it, is this possible using lidR?

Answer 1

There is no such built-in tools in lidR but we can use data.table native syntax.

1. Segmentation using the example in the manual

LASfile <- system.file("extdata", "MixedConifer.laz", package="lidR")
las <- readLAS(LASfile, select = "xyzc", filter = "-drop_z_below 0")
las <- segment_trees(las, li2012(R = 3, speed_up = 5))
plot(las, color = "treeID")

2. Define a function to attribute a class to each tree (here I chose thresholds to generate a good looking picture).

vegetation_class = function(Z)
{
  mz = max(Z) 
  if (mz < 10)
    return(LASLOWVEGETATION)
  else if (mz >= 10 & mz < 22)
    return(LASMEDIUMVEGETATION)
  else
    return(LASHIGHVEGETATION)
}

3. Apply this function by treeID. The former classification is preserved for points that are not trees

las@data[!is.na(treeID), Classification := vegetation_class(Z), by = treeID]
plot(las, color = "Classification")