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LAStools

LAStools is a collection of tools for LiDAR data processing.

Usage

Using LAStools

LAStools is included in following modules:

  • lastools: 2022 (more exactly 220613)

Load one of these modules, for example:

module load lastools

You can test LAStools loaded successfully with

lasinfo -h

LAStools commands

Puhti installation includes only the open source tools of LAStools.

  • las2las - extracts last returns, clips, subsamples, translates, etc ...
  • las2txt - turns LAS into human-readable and easy-to-parse ASCII
  • lasdiff - compares the data of two LAS/LAZ/ASCII files
  • lasindex - creates a spatial index LAX file for fast spatial queries
  • lasinfo - prints out a quick overview of the contents of a LAS file
  • lasmerge - merges several LAS or LAZ files into a single LAS or LAZ file
  • lasprecision - analyses the actual precision of the LIDAR points
  • laszip - compresses the LAS files in a completely lossless manner
  • txt2las - converts LIDAR data from ASCII text to binary LAS format

Using a licensed version

Not open source LasTools tools are available only as .exe files, so they have to be run with wine (Windows emulator). Only the command-line tools work, not the graphical interface. If you have a LAStools license, you can install the .exe files easily yourself for your project. Download and unzip LAStools to your projappl disk area.

cd /projappl/<your_project>
wget https://lastools.github.io/download/LAStools.zip
unzip LAStools.zip

Then just add your license file to the /bin folder and you can start running the .exe files with wine64

Notice you can only use the 64-bit versions of the tools with wine64

Here is an example of running lasinfo64.exe with wine64

module load wine
wine64 lasinfo64.exe -i <LAS file>

Finnish National Land Survey's lidar data in Puhti

The Finnish national lidar data is already stored in Puhti. You can find it from filepath: /appl/data/geo/mml/laserkeilaus. More info.

LAStools and array jobs

If you are processing large number of lidar files with LAStools, the best practice would be to use an batch array job

First create a text file with filepaths to the lidar files. This is one way of doing it

cd folder_with_laz_files
ls -d -1 "$PWD/"*.laz > lazfilepaths.txt

Create an batch array job script that takes this list as an argument. This example had 12 files

#!/bin/bash -l
#SBATCH --account=<YOUR_PROJECT>
#SBATCH --job-name las2las_test
#SBATCH --output array_job_out_%A_%a.txt
#SBATCH --error array_job_err_%A_%a.txt
#SBATCH --time 00:10:00
#SBATCH --ntasks 1
#SBATCH --mem-per-cpu=1000
#SBATCH --array=1-12
#SBATCH --partition small

### load geoconda that has the open source lastools commands
module load lastools

### read a filepath to the .laz file given in the list of files
inputfilepath=$(sed -n "$SLURM_ARRAY_TASK_ID"p $1)

### retrieve just the filename from the filepath and remove extension
outputfilename="${filepath##*/}"
outputfilename="${filename%.*}"

### extract the first returns only and save to a .las file in directory out/ (needs to exist)
las2las -i $inputfilepath -o out/$outputfilename.las -first_only

Now you can submit the job with

sbatch las2las_test.sh lazfilepaths.txt

License and acknowledgement

For information on the legal use and licensing of LAStools, please read the LAStools LICENSE.

Please acknowledge CSC and Geoportti in your publications, it is important for project continuation and funding reports. As an example, you can write "The authors wish to thank CSC - IT Center for Science, Finland (urn:nbn:fi:research-infras-2016072531) and the Open Geospatial Information Infrastructure for Research (Geoportti, urn:nbn:fi:research-infras-2016072513) for computational resources and support".

References