r-lidar-lab/lidrviewer

An OpenGL point cloud viewer for R able to handle several millions of points

This is a point cloud viewer for R. The first goal of this package is to be an alternative backend to display point clouds in the lidR package in replacement of rgl. It is fully supported but one may consider that this package is under development (it works good enough to me but still have bugs).

rgl is an awesome package but has some difficulties displaying large point clouds. The lidRviewer package is able to display large point clouds consisting of several million points. So far I have tried it with over 30 million points and the display window remained fluid (smoothly pan, zoom and rotate).

Advantage of lidRviewer:

• Can easily handle more than 20 million points while rgl can struggle displaying a tenth of that.
• Is much more memory efficient. It allocates only a small amount of additional memory while rgl may require gigabytes of memory.

Drawbacks

• Blocks the R session. If the viewer windows is open, you can't use R for anything else. You must close the viewer windows first.
• Can only display point clouds. No other feature. This is only a point cloud displayer so not intended as a replacement for rgl

Installation

GNU/Linux

sudo apt-get install libsdl2-dev freeglut3-dev

devtools::install_github("r-lidar-lab/lidRviewer")

Windows

devtools::install_github("r-lidar-lab/lidRviewer")

MacOS

brew install sdl2 mesa mesa-glu

devtools::install_github("r-lidar-lab/lidRviewer")

Usage

library(lidR)
LASfile <- system.file("extdata", "Megaplot.laz", package="lidR")
las <- readLAS(LASfile)
plot(las, backend = "lidRviewer")

• Rotate with left mouse button
• Zoom with mouse wheel
• Pan with right mouse button

How it works

Displaying huge point clouds in real time is a complex task. Advanced techniques often rely on Octrees to selectively display points within the camera field of view. These techniques are smart but not really appropriate for my low memory usage requirements. Considering how R stores data, constructing an Octree would require a full copy of the point cloud. This package uses some very naive optimization to render large point clouds in pseudo-real time:

• When users rotate/pan/zoom it only displays a maximum of 2 million points, which allows for smooth, fluid movement of the display.
• When the program finds a few milliseconds of free time between two events it progressively densifies the point cloud until the entire point cloud is displayed. This allows the user to rotate/pan/zoom again before the end of the rendering.
• It uses a pointer to the R memory and does not create any copy. The memory allocated for the rendering is therefore reduced to a few megabytes independently of the point cloud size.

So far it works well on my tests and the package can display as many points as the user wants (I stopped my tests after 35 million points [~1GB]).

Benchmark

On a core i7 with 11 million points.

Package	Time (s)	Alloc mem	Fluid
rgl	15-20	1.2 GB	no
lidRviewer	< 1	1.0 MB	yes

'Time' is the time taken to open the Windows. 'Alloc mem' is the extra memory allocated by the call. 'Fluid' means you can rotate and zoom freely.

lidrviewer's Issues

Usage of id option in plot function

Hi,

great work. It is indeed very performing. I am just struggling to use the id option. Your example perfectly works. I am now trying to apply it to a LiDAR point cloud and would like to colourize the Z values with height colours. But somehow it is not clear to me how to use the "id" option in this case, except generating random colours. Also the regular specifications of color palettes does not work as used in rgl.

Could put an example for a LiDAR data set and rainbow(50) or height.colours(50) ?

Thanks, a lot.

alternatives

Hi,
I would love to use lidRviewer, but unfortunately I dont have admin rights on my maschine.
Is there any way to use it without admin rights?
Or are you aware of any possible alternatives? (E.g. stream it to QGIS pointcloud viewer)

SDL and OpenGL not found on MacOS

Hi there, I tried to install lidRviewer on my system:

platform       x86_64-apple-darwin17.0     
arch           x86_64                      
os             darwin17.0                  
system         x86_64, darwin17.0          
status                                     
major          4                           
minor          0.5                         
year           2021                        
month          03                          
day            31                          
svn rev        80133                       
language       R                           
version.string R version 4.0.5 (2021-03-31)
nickname       Shake and Throw   

I got the following error. Is there a known work-around?

> devtools::install_github("Jean-Romain/lidRviewer")
Downloading GitHub repo Jean-Romain/lidRviewer@HEAD
✓  checking for file ‘/private/var/folders/dl/t0tty2rx6n3ft5qmnht_v8rnpg83bb/T/RtmpwS9MDT/remotese1fa29c262ab/Jean-Romain-lidRviewer-01bcf48/DESCRIPTION’ ...
─  preparing ‘lidRviewer’:
✓  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘lidRviewer_0.2.0.tar.gz’
   Warning: invalid uid value replaced by that for user 'nobody'
   Warning: invalid gid value replaced by that for user 'nobody'
   
* installing *source* package ‘lidRviewer’ ...
** using staged installation
** libs
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c camera.cpp -o camera.o
In file included from camera.cpp:1:
./camera.h:4:10: fatal error: 'SDL/SDL.h' file not found
#include <SDL/SDL.h>
         ^~~~~~~~~~~
1 error generated.
make: *** [camera.o] Error 1
ERROR: compilation failed for package ‘lidRviewer’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/lidRviewer’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/dl/t0tty2rx6n3ft5qmnht_v8rnpg83bb/T//RtmpwS9MDT/filee1faac9d188/lidRviewer_0.2.0.tar.gz’ had non-zero exit status

Rgl is still default viewer

Hi JR,
I'm playing a bit with the 1.4.1 on a old dual core ( 64bit, 4gb RAM) with Ubuntu.
I tried to simply load and display the pointcloud (appr. 500Mb, 7.5M points) but RStudio opens it with rgl by default and not with this viewer.
I installed the necessary libs as described in the initial page and no error is reported. Any idea where to look for the issue? I'm definitely not experienced with ubuntu.

lidRviewer 1.0.0 announcement

The devel branch contains the version 1.0.0 which is complete redesign of the package. @H4estu @caiohamamura @ptompalski @liamirwin may I ask you to test it and provide feedback. It is designed to efficiently display arbitrarily large in-memory point clouds, with tested cases including over 130 million points.

remotes::install_github("r-lidar-lab/lidRviewer", ref = "devel" )

Usage

Use library(lidRviewer) after library(lidR) to overide the default rgl plot function from lidR.

library(lidR)
library(lidRviewer)
LASfile <- system.file("extdata", "Megaplot.laz", package="lidR")
las <- readLAS(LASfile)
plot(las)

• Rotate with left mouse button
• Zoom with mouse wheel
• Pan with right mouse button
• Keyboard r or g or b to color with RGB
• Keyboard z to color with Z
• Keyboard i to color with Intensity
• Keyboard c to color with Classification
• Keyboard + or - to change the point size
• Keyboard l to enable/disable eyes-dome lightning

`color="RGB"` doesn’t work

Hello,

plot(las1, color="RGB", backend = "lidRviewer") return the following stacktrace :

Erreur dans lidRviewer::plot_xyzrgb(x@data$X, x@data$Y, x@data$Z, x@data$R,  : 
  'id' must contain integers
9. stop("'id' must contain integers")
8. lidRviewer::plot_xyzrgb(x@data$X, x@data$Y, x@data$Z, x@data$R,
x@data$G, x@data$B, args$size) à <text>#1
7. eval(parse(text = "lidRviewer::plot_xyzrgb(x@data$X, x@data$Y, x@data$Z, x@data$R, x@data$G, x@data$B, args$size)"))
6. eval(parse(text = "lidRviewer::plot_xyzrgb(x@data$X, x@data$Y, x@data$Z, x@data$R, x@data$G, x@data$B, args$size)"))
5. lasplot(x, bg, idcolor, pal, clear_artifacts, axis, legend, args,
add, voxel, breaks)
4. plot.LAS(x, y, ..., color = color, pal = pal, bg = bg, breaks = breaks,
nbreaks = nbreaks, backend = backend, clear_artifacts = clear_artifacts,
axis = axis, legend = legend, add = add, voxel = voxel, NAcol = NAcol,
mapview = mapview)
3. .local(x, y = y, ...)
2. plot(las1, color = "RGB", backend = "lidRviewer")
1. plot(las1, color = "RGB", backend = "lidRviewer")

It works with backend="rgl" or with color="Classification", color="Intensity", etc. Only the combo color="RGB", backend = "lidRviewer" return the error.

Error in match.arg(backend) : 'arg' should be one of “rgl”

This is on Windows 10 x64 architecture.
Installed SDL using script (source("https://raw.githubusercontent.com/Jean-Romain/lidRviewer/master/sdl.R")) as admin
Installed lidRviewer devtools::install_github("Jean-Romain/lidRviewer").

plot(las) with rgl works (barely).

plot(las, backend = "lidRviewer")
Error in match.arg(backend) : 'arg' should be one of “rgl”

I installed lidR from the standard CRAN repository. With "lidRviewer" failing in the argument check for the backend parameter, maybe a different lidR install is needed?

Compatability

Hello, will this be made compatible with R version 4.2.2? currently says it is "not available with this version of R"

SDL2 compatibility

Fedora has moved to SDL2, and the current version of sdl.h is in /usr/include/SDL2 instead of /usr/include/SDL
(SDL2-devel.x86_64 2.26.2-1.fc36)

A symbolic link fixed that, but unfortunately SDL_BUTTON_WHEELUP and SDL_BUTTON_WHEELDOWN are not part of the current includes. I imagine there's a new specification, but I'm not familiar with SDL.

camera.cpp: In member function ‘void Camera::OnMouseButton(const SDL_MouseButtonEvent&)’:
camera.cpp:162:29: error: ‘SDL_BUTTON_WHEELUP’ was not declared in this scope; did you mean ‘SDL_BUTTON_MIDDLE’?
162 | else if ((event.button == SDL_BUTTON_WHEELUP) && (event.type == SDL_MOUSEBUTTONDOWN))
| ^~~~~~~~~~~~~~~~~~
| SDL_BUTTON_MIDDLE
camera.cpp:169:29: error: ‘SDL_BUTTON_WHEELDOWN’ was not declared in this scope
169 | else if ((event.button == SDL_BUTTON_WHEELDOWN) && (event.type == SDL_MOUSEBUTTONDOWN))
| ^~~~~~~~~~~~~~~~~~~~
make: *** [/usr/lib64/R/etc/Makeconf:177: camera.o] Error 1
ERROR: compilation failed for package ‘lidRviewer’

system can't find i386

source("https://raw.githubusercontent.com/Jean-Romain/lidRviewer/master/sdl.R")
Downloading and installing SDL headers...

• SDL headers downloaded
• SDL headers uncompressed
• SDL headers installed
  Downloading and installing SDL dll (x64)...
• SDL dll downloaded
• SDL dll uncompressed
• SDL dll installed
  Downloading and installing SDL dll (i386)...
• SDL dll installation skipped
  Installation of the SDL library: okWarning message:
  In normalizePath(path.expand(path), winslash, mustWork) :
  path[1]="D:/R/Rsetup/R-4.1.2/bin/x64/../i386/": 系统找不到指定的文件。

Cannot install due to SDL.h not being found

Hi!

I'm running into the following error when attempting install:

devtools::install_github("Jean-Romain/PointCloudViewer")
Downloading GitHub repo Jean-Romain/PointCloudViewer@master
✔  checking for file ‘/tmp/Rtmp8mfSL5/remotes67d83df20d72/Jean-Romain-PointCloudViewer-6101481/DESCRIPTION’ ...
─  preparing ‘PointCloudViewer’:
✔  checking DESCRIPTION meta-information
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘PointCloudViewer_0.2.0.tar.gz’
   
* installing *source* package ‘PointCloudViewer’ ...
** using staged installation
** libs
x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I"/home/guslun/anaconda3/envs/renv/lib/R/include" -DNDEBUG  -I"/home/guslun/anaconda3/envs/renv/lib/R/library/Rcpp/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2  -I/home/guslun/anaconda3/envs/renv/include -Wl,-rpath-link,/home/guslun/anaconda3/envs/renv/lib  -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/guslun/anaconda3/envs/renv/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562872960081/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/home/guslun/anaconda3/envs/renv=/usr/local/src/conda-prefix  -c RcppExports.cpp -o RcppExports.o
x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I"/home/guslun/anaconda3/envs/renv/lib/R/include" -DNDEBUG  -I"/home/guslun/anaconda3/envs/renv/lib/R/library/Rcpp/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2  -I/home/guslun/anaconda3/envs/renv/include -Wl,-rpath-link,/home/guslun/anaconda3/envs/renv/lib  -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/guslun/anaconda3/envs/renv/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562872960081/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/home/guslun/anaconda3/envs/renv=/usr/local/src/conda-prefix  -c camera.cpp -o camera.o
In file included from camera.cpp:1:0:
camera.h:4:10: fatal error: SDL/SDL.h: No such file or directory
 #include <SDL/SDL.h>
          ^~~~~~~~~~~
compilation terminated.
make: *** [/home/guslun/anaconda3/envs/renv/lib/R/etc/Makeconf:175: camera.o] Error 1
ERROR: compilation failed for package ‘PointCloudViewer’
* removing ‘/home/guslun/anaconda3/envs/renv/lib/R/library/PointCloudViewer’
Error: Failed to install 'PointCloudViewer' from GitHub:
  (converted from warning) installation of package ‘/tmp/Rtmp8mfSL5/file67d87b71489e/PointCloudViewer_0.2.0.tar.gz’ had non-zero exit status

Both prereq libraries have been installed however, albeit with a warning for SDL that a newer verion is used as far as I understand the issue.

(renv) guslun@K2006559:~$ sudo apt-get install libsdl-dev freeglut3-dev
[sudo] password for guslun: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Note, selecting 'libsdl1.2-dev' instead of 'libsdl-dev'
freeglut3-dev is already the newest version (2.8.1-3).
libsdl1.2-dev is already the newest version (1.2.15+dfsg2-0.1ubuntu0.1).
0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.

(renv) guslun@K2006559:~$ locate SDL.h
/usr/include/SDL/SDL.h

Is there a way of getting the installation to find SDL.h so I can use the package properly?

installation on macOS

I successfully installed on macOS. But the package still doesn't work.

First I installed the dependencies:

brew install sdl
brew install freeglut

I changed some of the source files like so:

#if defined(__APPLE__)
#include <OpenGL/gl.h>
#include <OpenGL/glu.h>
#else
#include <GL/gl.h>
#include <GL/glu.h>
#endif

Then I deleted src/Makevars. Next, I created a configure file in the root folder:

#!/bin/bash
if [ $(uname) == "Linux" ]
then
  echo 'PKG_LIBS= -lGL -lGLU -lSDL -LSDmain' > ./src/Makevars
elif [ $(uname) == "Darwin" ]
then
  echo 'PKG_LIBS= -framework OpenGL -lSDL' > ./src/Makevars
fi

Now I can successfully install PointCloudViewer with:

R -e 'devtools::install(".")'

Finally, I tried an example to see if it worked:

#!/usr/bin/env Rscript

library(PointCloudViewer)

x   <- runif(1000, 0, 100)
y   <- runif(1000, 0, 100)
z   <- runif(1000, 0, 100)
col <- rainbow(10)
id  <- sample(1:10, length(x), replace = TRUE)
plot_xyzcol(x, y, z, col, id)

I can see the message Point cloud viewer must be closed before to run other R code, but I don't see any viewer.

Do you know what I might be missing?

Getting "file does not exist" error when reading '.las' file that works in RGL viewer

Can't install PointCloudViewer

Hi Jean,
It says the following warning. Warning in install.packages : package ‘PointCloudViewer’ is not available (for R version 3.6.3).

I exactly followed the steps advised in this link. Then it showed another issue after following the 2nd step for windows installation which is:

source("https://raw.githubusercontent.com/Jean-Romain/PointCloudViewer/master/sdl.R")
#> Downloading and installing SDL headers...
#> - SDL headers downloaded
#> - SDL headers uncompressed
#> Error in file.copy(includes, inc, recursive = TRUE) : more 'from' files than 'to' files
#> In addition: Warning message:
#> In dir.create(inc) : cannot create dir 'C:\PROGRA~1\R\R-36~1.3\include\SDL', reason 'Permission denied'
#> Called from: file.copy(includes, inc, recursive = TRUE)

Please let me know what could be the solution for installing this package.

Thanks and Regards,
Yogendra

install SDL on ubuntu22.04 for use with RStudio-Server

When I go to install libsdl-dev I get the error

Package libsdl-dev is a virtual package provided by:
libsdl1.2-dev 1.2.15+dfsg2-6
libsdl1.2-compat-dev 1.2.52-3
You should explicitly select one to install.

E: Package 'libsdl-dev' has no installation candidate

apt-get install libsdl2-2.0-0 appears to install fine, but when I execute, the following happens. Any ideas? thanks!

devtools::install_github("Jean-Romain/lidRviewer")
Downloading GitHub repo Jean-Romain/lidRviewer@HEAD
Skipping 1 packages ahead of CRAN: Rcpp
── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/tmp/RtmpantFq7/remotes22f58e3c5925be/Jean-Romain-lidRviewer-815fc53/DESCRIPTION’ (641ms)
─  preparing ‘lidRviewer’:
✔  checking DESCRIPTION meta-information
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
   Omitted ‘LazyData’ from DESCRIPTION
─  building ‘lidRviewer_0.2.0.tar.gz’
   Warning: invalid uid value replaced by that for user 'nobody'
   
Installing package into ‘/home/9nf/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
* installing *source* package ‘lidRviewer’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/9nf/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/9nf/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c camera.cpp -o camera.o
In file included from camera.cpp:1:
camera.h:4:10: fatal error: SDL/SDL.h: No such file or directory
    4 | #include <SDL/SDL.h>
      |          ^~~~~~~~~~~
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:178: camera.o] Error 1
ERROR: compilation failed for package ‘lidRviewer’
* removing ‘/home/9nf/R/x86_64-pc-linux-gnu-library/4.2/lidRviewer’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/RtmpantFq7/file22f58e57e6adb5/lidRviewer_0.2.0.tar.gz’ had non-zero exit status

Running RStudio-server on ubuntu22.04

how to run in Rstudio environment

Hello,
I am trying to render a LAS file using R studio (server). When I just try to plot following the command you provide I get a sort of error message and my R session hangs.
In your documentation I see that you say that the R viewer should be stopped...not sure how this can be done in R studio actually.

asUtr<-readLAS("/data2/utrechtCenter.las")  
plot(lasUtr,backend="pcv") 
#> Point cloud viewer must be closed before to run other R code
#> No protocol specified
#> No protocol specified
#> No protocol specified 
#> No protocol specified

Thanks for help in advance.

Failing to plot voxel values using the PCV

Dear Jean-Romain,

I've been using your R packages quite heavily lately, but now I'm running into issues I cannot quite fix. Thanks to your lidR plug-ins I've calculated voxels that represent LAD. Plotting these voxels with a correct color scheme did not work for me with the basic rgl viewer, that is why I tried the pcv instead. All the voxels appear with the same color (as can be seen in the picture below), while the LAD values should tell otherwise. FYI: for testing I took your Megaplot.laz, I'm using Windows 10 and there are 249690 voxels in the dataframe.

The calculation of the LAD voxels:

library(lidR)
library(lidRplugins)
library(PointCloudViewer)
LASfile <- system.file("extdata", "Megaplot.laz", package="lidR")
las = readLAS(LASfile)
voxelsLAD = grid_metrics3d(las, ~LAD(z=las@data$Z, dz = 1, k= 0.5, z0= 1), 5)
plot(voxelsLAD, color = "lad", colorPalette = heat.colors(5), bg = "black", legend = TRUE)

The plotting done with rgl:

plot(voxelsLAD, color = "lad", colorPalette = heat.colors(5), bg = "black", legend = TRUE)

The plotting done with pcv:

plot_xyzcol(voxelsLAD$X, voxelsLAD$Y, voxelsLAD$Z, col = heat.colors(10), id = cut(voxelsLAD$lad, 10, label = FALSE))

The cut(voxelsLAD$lad, 10, label = FALSE) results in a large integer looking like so: [1] 5 5 7 9 10 10 9 9 8 8 8 8 8 8 8 8 8 8 7 7 5 4 3 2 1 1 1 1 1 5 5 7 9 10 ...

The issue is that the colorramp is not applying itself to the LAD values. Any idea what is going wrong here? Thanks!

Missing file

Attempting to install the package. Apparently, a file is missing. See error:

In file included from camera.cpp:1:
./camera.h:4:10: fatal error: 'SDL/SDL.h' file not found
#include <SDL/SDL.h>
^~~~~~~~~~~
1 error generated.
make: *** [camera.o] Error 1
ERROR: compilation failed for package ‘lidRviewer’