Extract the filename from a chunk when processing a LAScatalog

Question

I'm using the R packages lidR and TreeLS to process lidar data and I made a function that takes in a single LAS file and splits out a shapefile, it looks like this:

lasfile = 'tile_1.las'
las = readLAS(lasfile)

stemdetection = function(las, ...)
{
  UseMethod("stemdetection", las)
}

stemdetection.LAS = function(las, vox, dens, n, rad)
{
  thin = tlsSample(las, voxelize(vox))
  map = treeMap(thin, map.hough(hmin = 0.25, hmax = 16, hstep = 0.5, pixel_size = 0.05, max_radius = rad, min_density = dens))
  tls = stemPoints(las, map)#classify stem points
  seg = stemSegmentation(tls, sgmt.ransac.circle(n))#extract measures
  cs <- crs(tls)
  thin <- NULL
  map <- NULL
  coordinates(seg) = cbind(seg$X, seg$Y)
  output <- writeOGR(seg, td, paste(tools::file_path_sans_ext(basename(lasfile)), "_stems", sep=""), driver="ESRI Shapefile", overwrite_layer=TRUE)
  return(output)
}

I'm trying to change the function to work on a LAScatalog but having some issues with getting the name of each las file (chunk). Here is one example of what I tried:

stemdetection.LAScluster = function(las, vox, dens, n, rad)
{
  las <- readLAS(las, select = 'xyzi')# Read the LAScluster
  if (is.empty(las)) return(NULL)              # Exit early (see documentation)

  thin = tlsSample(las, voxelize(vox))
  map = treeMap(thin, map.hough(hmin = 0.25, hmax = 16, hstep = 0.5, pixel_size = 0.05, max_radius = rad, min_density = dens))
  tls = stemPoints(las, map)#classify stem points
  seg = stemSegmentation(tls, sgmt.ransac.circle(n))#extract measures
  cs <- crs(tls)
  thin <- NULL; map <- NULL ; tls = NULL
  coordinates(seg) = cbind(seg$X, seg$Y)
  output <- writeOGR(seg, td, paste(tools::file_path_sans_ext(basename(ctg@data$File)), "_stems", sep=""), driver="ESRI Shapefile", overwrite_layer=TRUE)
  return(output)
}

stemdetection.LAScatalog = function(las, vox, dens, n, rad)
{
  catalog_apply(las, stemdetection, vox = vox, dens = dens, n = n, rad = rad)
}

Is there a way to append the filename to the LAS object while (or after) performing the readLAS function?

Thanks in advance!

Answer 1

There is no (documented) way to get the filename because it does not make sense in the general case. A chunk can be a single file or can be built out of several files and in this case the filename is meaningless. Sometime some chunks may be smaller than a file and thus several chunks share the same filename.

You don't need to call any write*() function. the LAScatalog processing engine already manage that for you. Your code should look like

stemdetection.LAScluster = function(las, vox, dens, n, rad)
{
  bbox <- raster::extent(las)
  las <- readLAS(las) # no select = 'xyzi' it is not considered
  [...]
  coordinates(seg) = cbind(seg$X, seg$Y)

  seg <- raster::crop(seg, bbox) # code to remove the buffer
  return(seg)
}

stemdetection.LAScatalog = function(las, vox, dens, n, rad)
{
  options = list(need_buffer = TRUE, automerge = TRUE)
  catalog_apply(las, stemdetection, vox = vox, dens = dens, n = n, rad = rad, .options = options)
}

Then you can use the engine options

opt_select(ctg) <- "xyzi"
opt_chunk_buffer(ctg) <- 10
opt_chunk_size(ctg) <- 0
opt_output_files(ctg)<- "/path/to/folder/{ORIGINALFILENAME}_stem"

out <- stemdetection(ctg, ...)