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NEON EDUCATION

Devoted to open data and open source in science and education.

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R programming (50)
Hierarchical Data Formats (HDF5) (11)
Spatial Data & GIS (19)
LiDAR (5)
Remote Sensing (9)
Data Visualization (4)
Hyperspectral Remote Sensing (7)
Time Series (15)
Phenology (7)
Raster Data (8)
Vector Data (6)
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R Bloggers
Date(s): - Jun 25, 2015

This workshop will providing hands on experience with working with hyperspectral imagery in hierarchical data formats(HDF5) in R. It will also cover basic raster data analysis in R.

Goals/Objectives

After completing this workshop, you will be able to:

  • Explain what hyperspectral remote sensing data are.
  • Create and read from HDF5 files containing spatial data in R.
  • Describe the key attributes of raster data that you need to spatially locate raster data in R.

Things to do, before the workshop:

Data to Download

Download NEON Teaching Data Subset: Imaging Spectrometer Data - HDF5

These hyperspectral remote sensing data provide information on the National Ecological Observatory Network’s San Joaquin Experimental Range field site. The data were collected over the San Joaquin field site located in California (Domain 17) and processed at NEON headquarters. The entire dataset can be accessed from the NEON website.

R Libraries to Install

Please have these packages installed and updated prior to the start of the workshop.

  • rhdf5: source("http://bioconductor.org/biocLite.R"); biocLite("rhdf5")
  • raster: install.packages("raster")
  • rgdal: install.packages("rgdal")

Updating R Packages

In RStudio, you can go to Tools --> Check for package updates to update previously installed packages on your computer.

Or you can use update.packages() to update all packages that are installed in R automatically.

Background Materials to Read

An Introduction to Remote Sensing

Please watch this video on remote sensing prior to the workshop

SCHEDULE

Time Topic
12:00 Raster Data in R - the skinny
12:30 About Hyperspectral Remote Sensing Data
1:00 Intro to Working with Hyperspectral Remote Sensing Data in HDF5 Format in R
2:30 Create a Raster Stack from Hyperspectral Imagery in HDF5 Format in R

Setup

To participate in the workshop, you will need working copies of the software described below. Please make sure to install everything before the start of the workshop.

HDFView

Hierarchical Data Format 5 (HDF5) is a file format used to store, package, and simultaneously organize large quantities of related data. Although we will use R to analyze data stored in this format, HDFView is free-ware that allows for quick and easy viewing and editing of these files.

R

R is a programming language that specializes in statistical computing. It is a powerful tool for exploratory data analysis. To interact with R, we recommend, but do not require, RStudio, an interactive development environment (IDE).

Downloads

  1. The package installation script here,
  2. The gdal libraries, and
  3. The hdf5 libraries.

Optional resources

QGIS

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

Online LiDAR Data Viewer (las viewer)

http://plas.io is a Open Source LiDAR data viewer developed by Martin Isenberg of Las Tools and several of his colleagues.