normalize_height causes "NULL value passed as symbol address"

[kulpojke]

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.

[Jean-Romain]

It looks more like a bug than a question. In the thread you are mentioning the op never gave me a reproducible example. So far it has never been reproduced. Is it reproducible with a small dataset from the package?

[kulpojke]

I will try it with a smaller dataset. I just tried to download the dataset used in section 14 of the book and got a 404 error. Can you suggest a good example dataset? Otherwise I'll just grab a smaller 3DEP dataset.

[kulpojke]

Here is a version that uses a smaller dataset that it first downloads. I was unable to reproduce the original error though because I ran into another error first. Now at the dtm <- rasterize_terrain(ctg, resolution, tin()) step I get:

Processing [=====>-------------]  25% (1/4) eta:  2sError: object 'paths' not found

I have changed nothing other than the data (and the download steps obviously).
Here is the revised code.

library(lidR)
library(future)
#plan(multisession)
get_lidr_threads()

# define globals, currently using ft :(
chunk_size <-1000            # chunk size 
buff <- 50                   # buffer size
resolution <-2               # raster resolution

# --------Downloading data code -----------------------------------------------
# make a place to put the laz files
path <- './laz'
dir.create(path)

# download list
urls <- list("https://rockyweb.usgs.gov/vdelivery/Datasets/Staged/Elevation/LPC/Projects/OR_RogueSiskiyouNF_2019_B19/OR_RogueRiverSiskiyouNF_B1_2019/LAZ/USGS_LPC_OR_RogueSiskiyouNF_2019_B19_10TDM7456.laz",
             "https://rockyweb.usgs.gov/vdelivery/Datasets/Staged/Elevation/LPC/Projects/OR_RogueSiskiyouNF_2019_B19/OR_RogueRiverSiskiyouNF_B1_2019/LAZ/USGS_LPC_OR_RogueSiskiyouNF_2019_B19_10TDM7457.laz",
             "https://rockyweb.usgs.gov/vdelivery/Datasets/Staged/Elevation/LPC/Projects/OR_RogueSiskiyouNF_2019_B19/OR_RogueRiverSiskiyouNF_B1_2019/LAZ/USGS_LPC_OR_RogueSiskiyouNF_2019_B19_10TDM7556.laz",
             "https://rockyweb.usgs.gov/vdelivery/Datasets/Staged/Elevation/LPC/Projects/OR_RogueSiskiyouNF_2019_B19/OR_RogueRiverSiskiyouNF_B1_2019/LAZ/USGS_LPC_OR_RogueSiskiyouNF_2019_B19_10TDM7557.laz")

# download the files
for (url in urls) {
  destfile <- paste0('./laz/', basename(url))
  download.file(url, destfile)
}

# --------------- Original portion of code below --------------------------

# 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 for ctg
opt_chunk_buffer(ctg) <- buff

# set the chunk size for ctg
opt_chunk_size(ctg) <- chunk_size

# set output location
opt_output_files(ctg) <- paste0(tempdir(), "/{XCENTER}_{YCENTER}_{ID}_dtm")

# make dtm. ERROR happens here now
dtm <- rasterize_terrain(ctg, resolution, tin())

# set output location
opt_output_files(ctg) <- paste0(tempdir(), "/{XCENTER}_{YCENTER}_{ID}_norm")

# normalise ctg
ctg_norm <- normalize_height(ctg, dtm)

[kulpojke]

I appreciate your help by the way.

[Jean-Romain]

#580