Work With Lidar-derived Rasters in R

May 14, 2015
NEON

This workshop will provide hands on experience with working lidar data in raster format in R. It will cover the basics of what lidar data are and commonly derived data products.

Objectives

After completing this workshop, you will be able to:

  • Explain what lidar data are and how they're used in science.
  • Describe the key lidar data products - digital surface model, digital terrain model and canopy height model.
  • Work with, analyze and export results of lidar derived rasters in R.

Things to Do Before the Workshop

To participant in this workshop, you will need a laptop with the most current version of R and, preferably, RStudio loaded on your computer. For details on setting up R & RStudio in Mac, PC, or Linux operating systems please see Additional Set up Resources below.

Install R Packages

You can chose to install each library individually if you already have some installed. Or you can download the script below and run it to install all libraries at once.

  • raster: install.packages("raster")
  • rgdal: install.packages("rgdal")
  • maptools: install.packages("maptools")
  • ggplot2: install.packages("ggplot2")
  • rgeos: install.packages("rgeos")
  • dplyr:install.packages("dplyr")

Download Script to Install Packages in R

Download The Data

Download NEON Teaching Data Subset: Field Site Spatial Data

These remote sensing data files provide information on the vegetation at the National Ecological Observatory Network's San Joaquin Experimental Range and Soaproot Saddle field sites. The entire dataset can be accessed by request from the NEON Data Portal.

Download NEON Teaching Data Subset: Sample LiDAR Point Cloud Data (.las)

This .las file contains sample LiDAR point cloud data collected by National Ecological Observatory Network's Airborne Observation Platform group. The .las file format is a commonly used file format to store LIDAR point cloud data.

Background Materials

Workshop Instructors

  • Natalie Robinson
  • Leah A. Wasser

Schedule

Time Topic
12:00 Working with Raster Data in R
12:45 Working With Image Formatted Rasters in R
1:15 The Basics of LiDAR - Light Detection and Ranging - Remote Sensing
1:20 Explore with Lidar Point Clouds in a free online viewer: plas.io
1:45 Create a Canopy Height Model from LiDAR-derived Rasters in R
2:30 Capstone - Create NDVI from GeoTIFFs in R
2:50 Wrap-up, Feedback, Questions

Optional resources

QGIS

QGIS is a cross-platform Open Source Geographic Information system.

Online LiDAR Data Viewer (las viewer)

Plas.io is an open source LiDAR data viewer developed by Martin Isenberg of Las Tools and several of his colleagues.


Additional Set Up Instructions


Additional Set Up Instructions

R & RStudio

Prior to the workshop you should have R and, preferably, RStudio installed on your computer.

Setting Up R & RStudio

Windows R/RStudio Setup

Once R and RStudio are installed, click to open RStudio. If you don't get any error messages you are set. If there is an error message, you will need to re-install the program.

Mac R/RStudio Setup

  • If your Mac is set up for UiO use, you can install R from Managed Software Center

  • Go to CRAN and click on Download R for (Mac) OS X

  • Select the .pkg file for the version of OS X that you have and the file will download.
  • Double click on the file that was downloaded and R will install
  • Go to the RStudio Download page
  • Under Installers select RStudio 0.98.1103 - Mac OS X 10.6+ (64-bit) to download it.
  • Once it's downloaded, double click the file to install it

Once R and RStudio are installed, click to open RStudio. If you don't get any error messages you are set. If there is an error message, you will need to re-install the program.

Linux R/RStudio Setup

  • R is available through most Linux package managers. You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo yum install R).
  • To install RStudi, go to the RStudio Download page
  • Under Installers select the version for your distribution.
  • Once it's downloaded, double click the file to install it

Once R and RStudio are installed, click to open RStudio. If you don't get any error messages you are set. If there is an error message, you will need to re-install the program.

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h2 id="set-wd">Set Working Directory to Downloaded Data

1) Download Data

After clicking on the Download Data button, the data will automatically download to the computer.

2) Locate .zip file

Second, find the downloaded .zip file. Many browsers save downloaded files to your computer’s Downloads directory. If you have previously specified a specific directory (folder) for downloaded files, the .zip file will download there.

3) Move to **data** directory

Third, move the downloaded file to a directory called data within the Documents directory on your computer. You can choose to place the data in other locations, however, you will need to remember to set your R Working Directory to that location and not as we demonstrate in the workshop.

4) Unzip/uncompress

Fourth, we need to unzip/uncompress the file so that the data files can be accessed. Use your favorite tool that can unpackage/open .zip files (e.g., winzip, Archive Utility, etc). The files will now be accessible in three directories:

These directories contain all of the subdirectories and files that we will use in this workshop.

5) Set working directory

Fifth, we need to set the working directory in R to this data directory that is parent to the directories containing the data we want. For complete directions, on how to do that check out the Set A Working Directory in R tutorial.

Install HDFView

The free HDFView application allows you to explore the contents of an HDF5 file.

To install HDFView:

  1. Click to go to the download page.

  2. From the section titled HDF-Java 2.1x Pre-Built Binary Distributions select the HDFView download option that matches the operating system and computer setup (32 bit vs 64 bit) that you have. The download will start automatically.

  3. Open the downloaded file.

    • Mac - You may want to add the HDFView application to your Applications directory.
    • Windows - Unzip the file, open the folder, run the .exe file, and follow directions to complete installation.
  4. Open HDFView to ensure that the program installed correctly.

Data Tip: The HDFView application requires Java to be up to date. If you are having issues opening HDFView, try to update Java first!

QGIS (Optional)

QGIS is a cross-platform Open Source Geographic Information system.

Online LiDAR Data/las Viewer (Optional)

Plas.io is a open source LiDAR data viewer developed by Martin Isenberg of Las Tools and several of his colleagues.

Tutorial: What is a CHM, DSM and DTM? About Gridded, Raster LiDAR Data

You can choose to do this optional data activity (opens in a new window), or continue to the next lesson plan.

Tutorial: Image Raster Data in R - An Intro

You can choose to do this optional data activity (opens in a new window), or continue to the next lesson plan.

Tutorial: The Basics of LiDAR - Light Detection and Ranging - Remote Sensing

You can choose to do this optional data activity (opens in a new window), or continue to the next lesson plan.

Tutorial: Plas.io: Free Online Data Viz to Explore LiDAR Data

You can choose to do this optional data activity (opens in a new window), or continue to the next lesson plan.

Tutorial: Create a Canopy Height Model from LiDAR-derived Rasters in R

You can choose to do this optional data activity (opens in a new window), or continue to the next lesson plan.

Tutorial: Spatial Data Tutorial Series Capstone Challenges

You can choose to do this optional data activity (opens in a new window), or continue to the next lesson plan.

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