Originally posted by kulpojke May 5, 2022
I am using the lidR package to do some tree segmentation on a set of 561 km² tiles using the LAScatalog engine and the futures library for parallelization. I have successfully created the DTM, but when I attempt to normalize I get an error.
I have read this thread already and it did not solve my problem.
I am running inside of a container (rocker/tidyverse:4.2) with the following:
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
future_1.25.0
lidR_4.0.0
Here is the code:
# import libraries
library(lidR)
library(future)
plan(multisession)
# define some paramaters, currently using ft :(
chunk_size <-1000 # chunk size
buff <- 50 # buffer size
resolution <-2 # raster resolution
# (1) path to data
path <- '/data'
# make las catalog
ctg <- readLAScatalog(path)
# set disk storage option by assigning a filename template to a function
opt_output_files(ctg) <- paste0(tempdir(), "/{XCENTER}_{YCENTER}_{ID}")
# create index files (lax) to index points within laz files. speeds up reads.
lidR:::catalog_laxindex(ctg)
# set the chunk buffer ofr ctg
opt_chunk_buffer(ctg) <- buff
# set the chunk size for ctg
opt_chunk_size(ctg) <- chunk_size
# make dtm
opt_output_files(ctg) <- paste0(tempdir(), "/{XCENTER}_{YCENTER}_{ID}_dtm")
dtm <- rasterize_terrain(ctg, resolution, tin())
# in my Rmd I plot the dtm here and it looks right
# normalise ctg
opt_output_files(ctg) <- paste0(tempdir(), "/{XCENTER}_{YCENTER}_{ID}_norm")
ctg_norm <- normalize_height(ctg, dtm)
During the normalization I get the following warning, then error:
Processing [-----------------] 0% (0/1152) eta: ?sWarning: There are 3 points flagged 'withheld'.
Processing [-----------------] 0% (1/1152) eta: 4hError: NULL value passed as symbol address
After reading this thread. I tried disabling multisession and using set_lidr_threads,
# import libraries library(lidR) library(future) #plan(multisession) get_lidr_threads()
but the problem persists. Any insights would be greatly appreciated.
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