Calling LAStools from R

[Bastien]

Hi all,

I would like to work with some LAStools's app within the R environment to also get access to the LidR package 'tools.

As LAStools is working with command lines I guess it's possible to call these command lines within R but I don't know exactly how to do it.

For example, I've got a list of .txt files that I want to convert to .las using txt2las within R environment.

The command line from LAStools is :     txt2las -i "C:\LAStools\data\tree1.txt" -parse xyz -odir "C:\LAStools\data" -o "tree1.las"

If someone has an exemple of R script that calls LAStools 's command lines I would be greatfull.

Cheers,

Bastien

[Luiz Carlos Estraviz Rodriguez]

Hi, Bastien.

   I have used the "call-from-inside-R approach" for a long time". It expands immensely the way you can handle the analysis, explore data, graph outcomes etc.

   One very flexible R script that implements the approach could be presented as follows (taking lasinfo as example, but would work with any lastools function):

----------

# Define the path for lastools executables

LAStoolsDir = "C:/LAStools/bin/"
# Define the R function that calls lastools executables

LAStool = function(tool, inputFile, ...){
        cmd = paste(paste(LAStoolsDir, tool, sep=''), '-i', inputFile , ...)
        cat(cmd)
        system(cmd)
        return(cmd)
}

# Define the directory for the ALS project

cloudPath  = "C:/ALS/PRJ_lidar/CLOUDS/"

# Define las/laz files to be processed

inFiles  = paste(cloudPath, '*.laz', sep='')

# Define output directory (and creates it ... if doesn't exist)

outDir = paste(cloudPath, 'info', sep='')

dir.create(outDir, showWarnings = F)
# Call the lastools function

#   (takes lasinfo as example ... any other lastool works fine too!)

cores = 3

LASrun = LAStool('lasinfo', inDir,
                 '-cores', cores,
                 '-cd',
                 '-histo gps_time 10',
                 '-histo intensity 20',
                 '-histo point_source 1',
                 '-histo z 10',
                 '-odir', outDir,
                 '-odix _info',
                 '-otxt -v')

# The rest of the code depends on what your want to do with the output in outDir

...

----------

    Add to it your own R expertise and it will work like "a charm".

    Have fun ...

 

Luiz C. E. Rodriguez

Department of Forest Sciences

Univeristy of Sao Paulo, Brazil

Chairman of Silvilaser 2019

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[Luiz Carlos Estraviz Rodriguez]

Oops ... sorry for one glitch:

replace

LASrun = LAStool('lasinfo', inDir,

with

LASrun = LAStool('lasinfo', inFiles,  

[Bastien]

Hi Luiz,

I just give it a try and it works pretty well!

Thank you very much, it will give me a good start for pushing my analysis further within R!

Cheers,

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[Tim Ritter]

Hi Bastien,
running LAStools from within R works quite easy using system() and
paste() commands, please find a short example below.
There is only one little trap that you have to avoid: Do not use
linebreaks within the paste() command, otherwise LAStools will not
work...

Best,
Tim

#### Begin: R Example###

# Rotate, reoffset, thin out and change to las
system(paste("C:/Users/tim/Documents/LAStools/bin/txt2las -i
D:/faro/original_txt/Abt30k.xyz -rotate_xy -8.25 0 0 -reoffset 0 0 0
-parse xyz -rescale 0.00001 0.00001 0.00001 -o
D:/faro/ALL_POINTS/temp_all/30k_rot.laz -olaz"))

# translate
system(paste("C:/Users/tim/Documents/LAStools/bin/las2las -i
D:/faro/ALL_POINTS/temp_all/30k_rot.laz -translate_xyz -3329.372
282345.7 0 -reoffset -3329.372 282345.7 0 -o
D:/faro/ALL_POINTS/30k_proj.laz -olaz"))

# lasindex for faster processing
system(paste("C:/Users/bokuadmin/Documents/LAStools/bin/lasindex -i
D:/faro/ALL_POINTS/30k_proj.laz"))

#### End: R Example###

--
Dr. Tim Ritter
Senior Scientist

Fon: +43-1-47654-91414
Fax: +43-1-47654-2991414

Universität für Bodenkultur
Institut für Waldwachstum
Peter-Jordan-Str. 82
1190 Wien
ÖSTERREICH

University of Natural Resources and Life Sciences
Institute of Forest Growth
Peter-Jordan-Str. 82
1190 Vienna
AUSTRIA

--
Download LAStools at
http://lastools.org
http://rapidlasso.com
Be social with LAStools at
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http://twitter.com/LAStools
http://linkedin.com/groups/LAStools-4408378
Manage your settings at
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[Michael Treglia]

I'll put out there a GitHub repository with some code for calling lastools from R from a few years back. It's not something I actively maintain, and it's not particularly elegant, but putting it out there in case it's useful for others. 

https://github.com/mltConsEcol/OK_LiDAR_Processing

Hope this helps!

Best regards,

Mike Treglia

Please pardon any typos, this message was sent from a mobile device.

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