Mapping the Invisible

About Hyperspectral Remote Sensing Data

The electromagnetic spectrum is composed of thousands of bands representing different types of light energy. Imaging spectrometers (instruments that collect hyperspectral data) break the electromagnetic spectrum into groups of bands that support classification of objects by their spectral properties on the earth's surface. Hyperspectral data consists of many bands -- up to hundreds of bands -- that cover the electromagnetic spectrum.

The NEON imaging spectrometer collects data within the 380nm to 2510nm portions of the electromagnetic spectrum within bands that are approximately 5nm in width. This results in a hyperspectral data cube that contains approximately 426 bands - which means big, big data.

Key Metadata for Hyperspectral Data

Bands and Wavelengths

A band represents a group of wavelengths. For example, the wavelength values between 695nm and 700nm might be one band as captured by an imaging spectrometer. The imaging spectrometer collects reflected light energy in a pixel for light in that band. Often when you work with a multi or hyperspectral dataset, the band information is reported as the center wavelength value. This value represents the center point value of the wavelengths represented in that band. Thus in a band spanning 695-700 nm, the center would be 697.5).

Spectral Resolution

The spectral resolution of a dataset that has more than one band, refers to the width of each band in the dataset. In the example above, a band was defined as spanning 695-700nm. The width or spatial resolution of the band is thus 5 nanometers. To see an example of this, check out the band widths for the Landsat sensors.

Full Width Half Max (FWHM)

The full width half max (FWHM) will also often be reported in a multi or hyperspectral dataset. This value represents the spread of the band around that center point.

In the illustration above, the band that covers 695-700nm has a FWHM of 5 nm. While a general spectral resolution of the sensor is often provided, not all sensors create bands of uniform widths. For instance bands 1-9 of Landsat 8 are listed below (Courtesy of USGS)

In this tutorial, we will show how to read and extract NEON reflectance data stored within an HDF5 file using R.

About Hyperspectral Remote Sensing Data

The electromagnetic spectrum is composed of thousands of bands representing different types of light energy. Imaging spectrometers (instruments that collect hyperspectral data) break the electromagnetic spectrum into groups of bands that support classification of objects by their spectral properties on the Earth's surface. Hyperspectral data consists of many bands - up to hundreds of bands - that span a portion of the electromagnetic spectrum, from the visible to the Short Wave Infrared (SWIR) regions.

The NEON imaging spectrometer (NIS) collects data within the 380 nm to 2510 nm portions of the electromagnetic spectrum within bands that are approximately 5 nm in width. This results in a hyperspectral data cube that contains approximately 426 bands - which means BIG DATA.

The HDF5 data model natively compresses data stored within it (makes it smaller) and supports data slicing (extracting only the portions of the data that you need to work with rather than reading the entire dataset into memory). These features make it ideal for working with large data cubes such as those generated by imaging spectrometers, in addition to supporting spatial data and associated metadata.

In this tutorial we will demonstrate how to read and extract spatial raster data stored within an HDF5 file using R.

Read HDF5 data into R

We will use the terra and rhdf5 packages to read in the HDF5 file that contains hyperspectral data for the NEON San Joaquin (SJER) field site. Let's start by calling the needed packages and reading in our NEON HDF5 file.

Please be sure that you have at least version 2.10 of rhdf5 installed. Use: packageVersion("rhdf5") to check the package version.

# Load `terra` and `rhdf5` packages to read NIS data into R

library(terra)

library(rhdf5)

library(neonUtilities)

Set the working directory to ensure R can find the file we are importing, and we know where the file is being saved. You can move the file that is downloaded afterward, but be sure to re-set the path to the file.

wd <- "~/data/" #This will depend on your local environment

setwd(wd)

We can use the neonUtilities function byTileAOP to download a single reflectance tile. You can run help(byTileAOP) to see more details on what the various inputs are. For this exercise, we'll specify the UTM Easting and Northing to be (257500, 4112500), which will download the tile with the lower left corner (257000,4112000). By default, the function will check the size total size of the download and ask you whether you wish to proceed (y/n). This file is ~672.7 MB, so make sure you have enough space on your local drive. You can set check.size=FALSE if you want to download without a prompt.

byTileAOP(dpID='DP3.30006.001',

          site='SJER',

          year='2021',

          easting=257500,

          northing=4112500,

          check.size=TRUE, # set to FALSE if you don't want to enter y/n

          savepath = wd)

This file will be downloaded into a nested subdirectory under the ~/data folder, inside a folder named DP3.30006.001 (the Data Product ID). The file should show up in this location: ~/data/DP3.30006.001/neon-aop-products/2021/FullSite/D17/2021_SJER_5/L3/Spectrometer/Reflectance/NEON_D17_SJER_DP3_257000_4112000_reflectance.h5.

# Define the h5 file name to be opened

h5_file <- paste0(wd,"DP3.30006.001/neon-aop-products/2021/FullSite/D17/2021_SJER_5/L3/Spectrometer/Reflectance/NEON_D17_SJER_DP3_257000_4112000_reflectance.h5")

You can use h5ls and/or View(h5ls(...)) to look at the contents of the hdf5 file, as follows:

# look at the HDF5 file structure 

View(h5ls(h5_file,all=T))

When you look at the structure of the data, take note of the "map info" dataset, the Coordinate_System group, and the wavelength and Reflectance datasets. The Coordinate_System folder contains the spatial attributes of the data including its EPSG Code, which is easily converted to a Coordinate Reference System (CRS). The CRS documents how the data are physically located on the Earth. The wavelength dataset contains the wavelength values for each band in the data. The Reflectance dataset contains the image data that we will use for both data processing and visualization.

More Information on raster metadata:

• Raster Data in R - The Basics - this tutorial explains more about how rasters work in R and their associated metadata.

• About Hyperspectral Remote Sensing Data -this tutorial explains more about metadata and important concepts associated with multi-band (multi and hyperspectral) rasters.

We can use the h5readAttributes() function to read and extract metadata from the HDF5 file. Let's start by learning about the wavelengths described within this file.

# get information about the wavelengths of this dataset

wavelengthInfo <- h5readAttributes(h5_file,"/SJER/Reflectance/Metadata/Spectral_Data/Wavelength")

wavelengthInfo

## $Description
## [1] "Central wavelength of the reflectance bands."
## 
## $Units
## [1] "nanometers"

Next, we can use the h5read function to read the data contained within the HDF5 file. Let's read in the wavelengths of the band centers:

# read in the wavelength information from the HDF5 file

wavelengths <- h5read(h5_file,"/SJER/Reflectance/Metadata/Spectral_Data/Wavelength")

head(wavelengths)

## [1] 381.6035 386.6132 391.6229 396.6327 401.6424 406.6522

tail(wavelengths)

## [1] 2485.693 2490.703 2495.713 2500.722 2505.732 2510.742

Which wavelength is band 21 associated with?

(Hint: look at the wavelengths vector that we just imported and check out the data located at index 21 - wavelengths[21]).

Band 21 has a associated wavelength center of 481.7982 nanometers (nm) which is in the blue portion (~380-500 nm) of the visible electromagnetic spectrum (~380-700 nm).

Bands and Wavelengths

A band represents a group of wavelengths. For example, the wavelength values between 695 nm and 700 nm might be one band captured by an imaging spectrometer. The imaging spectrometer collects reflected light energy in a pixel for light in that band. Often when you work with a multi- or hyperspectral dataset, the band information is reported as the center wavelength value. This value represents the mean value of the wavelengths represented in that band. Thus in a band spanning 695-700 nm, the center would be 697.5 nm). The full width half max (FWHM) will also be reported. This value can be thought of as the spread of the band around that center point. So, a band that covers 800-805 nm might have a FWHM of 5 nm and a wavelength value of 802.5 nm.

The HDF5 dataset that we are working with in this activity may contain more information than we need to work with. For example, we don't necessarily need to process all 426 bands available in a full NEON hyperspectral reflectance file - if we are interested in creating a product like NDVI which only uses bands in the Near InfraRed (NIR) and Red portions of the spectrum. Or we might only be interested in a spatial subset of the data - perhaps an area where we have collected corresponding ground data in the field.

The HDF5 format allows us to slice (or subset) the data - quickly extracting the subset that we need to process. Let's extract one of the green bands - band 34.

By the way - what is the center wavelength value associated with band 34?

Hint: wavelengths[34].

How do we know this band is a green band in the visible portion of the spectrum?

In order to effectively subset our data, let's first read the reflectance metadata stored as attributes in the "Reflectance_Data" dataset.

# First, we need to extract the reflectance metadata:

reflInfo <- h5readAttributes(h5_file, "/SJER/Reflectance/Reflectance_Data")

reflInfo

## $Cloud_conditions
## [1] "For cloud conditions information see Weather Quality Index dataset."
## 
## $Cloud_type
## [1] "Cloud type may have been selected from multiple flight trajectories."
## 
## $Data_Ignore_Value
## [1] -9999
## 
## $Description
## [1] "Atmospherically corrected reflectance."
## 
## $Dimension_Labels
## [1] "Line, Sample, Wavelength"
## 
## $Dimensions
## [1] 1000 1000  426
## 
## $Interleave
## [1] "BSQ"
## 
## $Scale_Factor
## [1] 10000
## 
## $Spatial_Extent_meters
## [1]  257000  258000 4112000 4113000
## 
## $Spatial_Resolution_X_Y
## [1] 1 1
## 
## $Units
## [1] "Unitless."
## 
## $Units_Valid_range
## [1]     0 10000

# Next, we read the different dimensions



nRows <- reflInfo$Dimensions[1]

nCols <- reflInfo$Dimensions[2]

nBands <- reflInfo$Dimensions[3]



nRows

## [1] 1000

nCols

## [1] 1000

nBands

## [1] 426

The HDF5 read function reads data in the order: Bands, Cols, Rows. This is different from how R reads data. We'll adjust for this later.

# Extract or "slice" data for band 34 from the HDF5 file

b34 <- h5read(h5_file,"/SJER/Reflectance/Reflectance_Data",index=list(34,1:nCols,1:nRows)) 



# what type of object is b34?

class(b34)

## [1] "array"

A Note About Data Slicing in HDF5

Data slicing allows us to extract and work with subsets of the data rather than reading in the entire dataset into memory. In this example, we will extract and plot the green band without reading in all 426 bands. The ability to slice large datasets makes HDF5 ideal for working with big data.

Next, let's convert our data from an array (more than 2 dimensions) to a matrix (just 2 dimensions). We need to have our data in a matrix format to plot it.

# convert from array to matrix by selecting only the first band

b34 <- b34[1,,]



# display the class of this re-defined variable

class(b34)

## [1] "matrix" "array"

Arrays vs. Matrices

Arrays are matrices with more than 2 dimensions. When we say dimension, we are talking about the "z" associated with the data (imagine a series of tabs in a spreadsheet). Put the other way: matrices are arrays with only 2 dimensions. Arrays can have any number of dimensions one, two, ten or more.

Here is a matrix that is 4 x 3 in size (4 rows and 3 columns):

Dimensions in Arrays

An array contains 1 or more dimensions in the "z" direction. For example, let's say that we collected the same set of species data for every day in a 30 day month. We might then have a matrix like the one above for each day for a total of 30 days making a 4 x 3 x 30 array (this dataset has more than 2 dimensions). More on R object types here (links to external site, DataCamp).

Next, let's look at the metadata for the reflectance data. When we do this, take note of 1) the scale factor and 2) the data ignore value. Then we can plot the band 34 data. Plotting spatial data as a visual "data check" is a good idea to make sure processing is being performed correctly and all is well with the image.

# look at the metadata for the reflectance dataset

h5readAttributes(h5_file,"/SJER/Reflectance/Reflectance_Data")

## $Cloud_conditions
## [1] "For cloud conditions information see Weather Quality Index dataset."
## 
## $Cloud_type
## [1] "Cloud type may have been selected from multiple flight trajectories."
## 
## $Data_Ignore_Value
## [1] -9999
## 
## $Description
## [1] "Atmospherically corrected reflectance."
## 
## $Dimension_Labels
## [1] "Line, Sample, Wavelength"
## 
## $Dimensions
## [1] 1000 1000  426
## 
## $Interleave
## [1] "BSQ"
## 
## $Scale_Factor
## [1] 10000
## 
## $Spatial_Extent_meters
## [1]  257000  258000 4112000 4113000
## 
## $Spatial_Resolution_X_Y
## [1] 1 1
## 
## $Units
## [1] "Unitless."
## 
## $Units_Valid_range
## [1]     0 10000

# plot the image

image(b34)

What do you notice about the first image? It's washed out and lacking any detail. What could be causing this? It got better when plotting the log of the values, but still not great.

# this is a little hard to visually interpret - what happens if we plot a log of the data?

image(log(b34))

Let's look at the distribution of reflectance values in our data to figure out what is going on.

# Plot range of reflectance values as a histogram to view range

# and distribution of values.

hist(b34,breaks=50,col="darkmagenta")

# View values between 0 and 5000

hist(b34,breaks=100,col="darkmagenta",xlim = c(0, 5000))

# View higher values

hist(b34, breaks=100,col="darkmagenta",xlim = c(5000, 15000),ylim = c(0, 750))

As you're examining the histograms above, keep in mind that reflectance values range between 0-1. The data scale factor in the metadata tells us to divide all reflectance values by 10,000. Thus, a value of 5,000 equates to a reflectance value of 0.50. Storing data as integers (without decimal places) compared to floating points (with decimal places) creates a smaller file. This type of scaling is commin in remote sensing datasets.

Notice in the data that there are some larger reflectance values (>5,000) that represent a smaller number of pixels. These pixels are skewing how the image renders.

Data Ignore Value

Image data in raster format will often contain a data ignore value and a scale factor. The data ignore value represents pixels where there are no data. Among other causes, no data values may be attributed to the sensor not collecting data in that area of the image or to processing results which yield null values.

Remember that the metadata for the Reflectance dataset designated -9999 as data ignore value. Thus, let's set all pixels with a value == -9999 to NA (no value). If we do this, R won't render these pixels.

# there is a no data value in our raster - let's define it

noDataValue <- as.numeric(reflInfo$Data_Ignore_Value)

noDataValue

## [1] -9999

# set all values equal to the no data value (-9999) to NA

b34[b34 == noDataValue] <- NA



# plot the image now

image(b34)

Reflectance Values and Image Stretch

Our image still looks dark because R is trying to render all reflectance values between 0 and 14999 as if they were distributed equally in the histogram. However we know they are not distributed equally. There are many more values between 0-5000 than there are values >5000.

Images contain a distribution of reflectance values. A typical image viewing program will render the values by distributing the entire range of reflectance values across a range of "shades" that the monitor can render - between 0 and 255. However, often the distribution of reflectance values is not linear. For example, in the case of our data, most of the reflectance values fall between 0 and 0.5. Yet there are a few values >0.8 that are heavily impacting the way the image is drawn on our monitor. Imaging processing programs like ENVI, QGIS and ArcGIS (and even Adobe Photoshop) allow you to adjust the stretch of the image. This is similar to adjusting the contrast and brightness in Photoshop.

The proper way to adjust our data would be to apply what's called an image stretch. We will learn how to stretch our image data later. For now, let's plot the values as the log function on the pixel reflectance values to factor out those larger values.

image(log(b34))

The log applied to our image increases the contrast making it look more like an image. However, look at the images below. The top one is an RGB image as the image should look. The bottom one is our log-adjusted image. Notice a difference?

Transpose Image

Notice that there are three data dimensions for this file: Bands x Rows x Columns. However, when R reads in the dataset, it reads them as: Columns x Bands x Rows. The data are flipped. We can quickly transpose the data to correct for this using the t or transpose command in R.

The orientation is rotated in our log adjusted image. This is because R reads in matrices starting from the upper left hand corner. While most rasters read pixels starting from the lower left hand corner. In the next section, we will deal with this issue by creating a proper georeferenced (spatially located) raster in R. The raster format will read in pixels following the same methods as other GIS and imaging processing software like QGIS and ENVI do.

# We need to transpose x and y values in order for our 

# final image to plot properly

b34 <- t(b34)

image(log(b34), main="Transposed Image")

Create a Georeferenced Raster

Next, we will create a proper raster using the b34 matrix. The raster format will allow us to define and manage:

• Image stretch
• Coordinate reference system & spatial reference
• Resolution
• and other raster attributes...

It will also account for the orientation issue discussed above.

To create a raster in R, we need a few pieces of information, including:

• The coordinate reference system (CRS)
• The spatial extent of the image

Define Raster CRS

First, we need to define the Coordinate reference system (CRS) of the raster. To do that, we can first grab the EPSG code from the HDF5 attributes, and covert the EPSG to a CRS string. Then we can assign that CRS to the raster object.

# Extract the EPSG from the h5 dataset

h5EPSG <- h5read(h5_file, "/SJER/Reflectance/Metadata/Coordinate_System/EPSG Code")



# convert the EPSG code to a CRS string

h5CRS <- crs(paste0("+init=epsg:",h5EPSG))



# define final raster with projection info 

# note that capitalization will throw errors on a MAC.

# if UTM is all caps it might cause an error!

b34r <- rast(b34, 
        crs=h5CRS)



# view the raster attributes

b34r

## class       : SpatRaster 
## dimensions  : 1000, 1000, 1  (nrow, ncol, nlyr)
## resolution  : 1, 1  (x, y)
## extent      : 0, 1000, 0, 1000  (xmin, xmax, ymin, ymax)
## coord. ref. : WGS 84 / UTM zone 11N 
## source(s)   : memory
## name        : lyr.1 
## min value   :    32 
## max value   : 13129

# let's have a look at our properly oriented raster. Take note of the 

# coordinates on the x and y axis.



image(log(b34r), 
      xlab = "UTM Easting", 
      ylab = "UTM Northing",
      main = "Properly Oriented Raster")

Next we define the extents of our raster. The extents will be used to calculate the raster's resolution. Fortunately, the spatial extent is provided in the HDF5 file "Reflectance_Data" group attributes that we saved before as reflInfo.

# Grab the UTM coordinates of the spatial extent

xMin <- reflInfo$Spatial_Extent_meters[1]

xMax <- reflInfo$Spatial_Extent_meters[2]

yMin <- reflInfo$Spatial_Extent_meters[3]

yMax <- reflInfo$Spatial_Extent_meters[4]



# define the extent (left, right, top, bottom)

rasExt <- ext(xMin,xMax,yMin,yMax)

rasExt

## SpatExtent : 257000, 258000, 4112000, 4113000 (xmin, xmax, ymin, ymax)

# assign the spatial extent to the raster

ext(b34r) <- rasExt



# look at raster attributes

b34r

## class       : SpatRaster 
## dimensions  : 1000, 1000, 1  (nrow, ncol, nlyr)
## resolution  : 1, 1  (x, y)
## extent      : 257000, 258000, 4112000, 4113000  (xmin, xmax, ymin, ymax)
## coord. ref. : WGS 84 / UTM zone 11N 
## source(s)   : memory
## name        : lyr.1 
## min value   :    32 
## max value   : 13129

Learn more about working with Raster data in R in the Data Carpentry workshop: Introduction to Geospatial Raster and Vector Data with R.

We can adjust the colors of our raster as well, if desired.

# let's change the colors of our raster and adjust the zlim 

col <- terrain.colors(25)



image(b34r,  
      xlab = "UTM Easting", 
      ylab = "UTM Northing",
      main= "Spatially Referenced Raster",
      col=col, 
      zlim=c(0,3000))

We've now created a raster from band 34 reflectance data. We can export the data as a raster, using the writeRaster command. Note that it's good practice to close the H5 connection before moving on!

# write out the raster as a geotiff

writeRaster(b34r,

            file=paste0(wd,"band34.tif"),

            overwrite=TRUE)



# close the H5 file

H5close()

In this tutorial, we will learn how to create multi (3) band images from hyperspectral data. We will also learn how to perform some basic raster calculations (known as raster math in the GIS world).

About Hyperspectral Data

We often want to generate a 3 band image from multi or hyperspectral data. The most commonly recognized band combination is RGB which stands for Red, Green and Blue. RGB images are just like an image that your camera takes. But other band combinations can be useful too. For example, near infrared images highlight healthy vegetation, which makes it easy to classify or identify where vegetation is located on the ground.

Create a Raster Stack in R

In the previous lesson, we exported a single band of the NEON Reflectance data from a HDF5 file. In this activity, we will create a full color image using 3 (red, green and blue - RGB) bands. We will follow many of the steps we followed in the Intro to Working with Hyperspectral Remote Sensing Data in HDF5 Format in R tutorial. These steps included loading required packages, downloading the data (optionally, you don't need to do this if you downloaded the data from the previous lesson), and reading in our file and viewing the hdf5 file structure.

First, let's load the required R packages, terra and rhdf5.

library(terra)

library(rhdf5)

library(neonUtilities)

Next set the working directory to ensure R can find the file we wish to import. Be sure to move the download into your working directory!

# set working directory (this will depend on your local environment)

wd <- "~/data/"

setwd(wd)

We can use the neonUtilities function byTileAOP to download a single reflectance tile. You can run help(byTileAOP) to see more details on what the various inputs are. For this exercise, we'll specify the UTM Easting and Northing to be (257500, 4112500), which will download the tile with the lower left corner (257000, 4112000).

byTileAOP(dpID = 'DP3.30006.001',

          site = 'SJER',

          year = '2021',

          easting = 257500,

          northing = 4112500,

          savepath = wd)

This file will be downloaded into a nested subdirectory under the ~/data folder, inside a folder named DP3.30006.001 (the Data Product ID). The file should show up in this location: ~/data/DP3.30006.001/neon-aop-products/2021/FullSite/D17/2021_SJER_5/L3/Spectrometer/Reflectance/NEON_D17_SJER_DP3_257000_4112000_reflectance.h5.

Now we can read in the file. You can move this file to a different location, but make sure to change the path accordingly.

# Define the h5 file name to be opened

h5_file <- paste0(wd,"DP3.30006.001/neon-aop-products/2021/FullSite/D17/2021_SJER_5/L3/Spectrometer/Reflectance/NEON_D17_SJER_DP3_257000_4112000_reflectance.h5")

As in the last lesson, let's use View(h5ls) to take a look inside this hdf5 dataset:

View(h5ls(h5_file,all=T))

To spatially locate our raster data, we need a few key attributes:

• The coordinate reference system
• The spatial extent of the raster

We'll begin by grabbing these key attributes from the H5 file.

# define coordinate reference system from the EPSG code provided in the HDF5 file

h5EPSG <- h5read(h5_file,"/SJER/Reflectance/Metadata/Coordinate_System/EPSG Code" )

h5CRS <- crs(paste0("+init=epsg:",h5EPSG))



# get the Reflectance_Data attributes

reflInfo <- h5readAttributes(h5_file,"/SJER/Reflectance/Reflectance_Data" )



# Grab the UTM coordinates of the spatial extent

xMin <- reflInfo$Spatial_Extent_meters[1]

xMax <- reflInfo$Spatial_Extent_meters[2]

yMin <- reflInfo$Spatial_Extent_meters[3]

yMax <- reflInfo$Spatial_Extent_meters[4]



# define the extent (left, right, top, bottom)

rastExt <- ext(xMin,xMax,yMin,yMax)



# view the extent to make sure that it looks right

rastExt

## SpatExtent : 257000, 258000, 4112000, 4113000 (xmin, xmax, ymin, ymax)

# Finally, define the no data value for later

h5NoDataValue <- as.integer(reflInfo$Data_Ignore_Value)

cat('No Data Value:',h5NoDataValue)

## No Data Value: -9999

Next, we'll write a function that will perform the processing that we did step by step in the Intro to Working with Hyperspectral Remote Sensing Data in HDF5 Format in R. This will allow us to process multiple bands in bulk.

The function band2Rast slices a band of data from the HDF5 file, and extracts the reflectance array for that band. It then converts the data into a matrix, converts it to a raster, and finally returns a spatially corrected raster for the specified band.

The function requires the following variables:

• file: the hdf5 reflectance file
• band: the band number we wish to extract
• noDataValue: the noDataValue for the raster
• extent: a terra spatial extent (SpatExtent) object .
• crs: the Coordinate Reference System for the raster

The function output is a spatially referenced, R terra object.

# file: the hdf5 file

# band: the band you want to process

# returns: a matrix containing the reflectance data for the specific band



band2Raster <- function(file, band, noDataValue, extent, CRS){
    # first, read in the raster
    out <- h5read(file,"/SJER/Reflectance/Reflectance_Data",index=list(band,NULL,NULL))
	  # Convert from array to matrix
	  out <- (out[1,,])
	  # transpose data to fix flipped row and column order 
    # depending upon how your data are formatted you might not have to perform this
    # step.
	  out <- t(out)
    # assign data ignore values to NA
    # note, you might chose to assign values of 15000 to NA
    out[out == noDataValue] <- NA
	  
    # turn the out object into a raster
    outr <- rast(out,crs=CRS)
   
    # assign the extents to the raster
    ext(outr) <- extent
   
    # return the terra raster object
    return(outr)
}

Now that the function is created, we can create our list of rasters. The list specifies which bands (or dimensions in our hyperspectral dataset) we want to include in our raster stack. Let's start with a typical RGB (red, green, blue) combination. We will use bands 14, 9, and 4 (bands 58, 34, and 19 in a full NEON hyperspectral dataset).

# create a list of the bands (R,G,B) we want to include in our stack

rgb <- list(58,34,19)



# lapply tells R to apply the function to each element in the list

rgb_rast <- lapply(rgb,FUN=band2Raster, file = h5_file,
                   noDataValue=h5NoDataValue, 
                   ext=rastExt,
                   CRS=h5CRS)

Check out the properties or rgb_rast:

rgb_rast

## [[1]]
## class       : SpatRaster 
## dimensions  : 1000, 1000, 1  (nrow, ncol, nlyr)
## resolution  : 1, 1  (x, y)
## extent      : 257000, 258000, 4112000, 4113000  (xmin, xmax, ymin, ymax)
## coord. ref. : WGS 84 / UTM zone 11N 
## source(s)   : memory
## name        : lyr.1 
## min value   :     0 
## max value   : 14950 
## 
## [[2]]
## class       : SpatRaster 
## dimensions  : 1000, 1000, 1  (nrow, ncol, nlyr)
## resolution  : 1, 1  (x, y)
## extent      : 257000, 258000, 4112000, 4113000  (xmin, xmax, ymin, ymax)
## coord. ref. : WGS 84 / UTM zone 11N 
## source(s)   : memory
## name        : lyr.1 
## min value   :    32 
## max value   : 13129 
## 
## [[3]]
## class       : SpatRaster 
## dimensions  : 1000, 1000, 1  (nrow, ncol, nlyr)
## resolution  : 1, 1  (x, y)
## extent      : 257000, 258000, 4112000, 4113000  (xmin, xmax, ymin, ymax)
## coord. ref. : WGS 84 / UTM zone 11N 
## source(s)   : memory
## name        : lyr.1 
## min value   :     9 
## max value   : 11802

Note that it displays properties of 3 rasters. Finally, we can create a raster stack from our list of rasters as follows:

rgbStack <- rast(rgb_rast)

In the code chunk above, we used the lapply() function, which is a powerful, flexible way to apply a function (in this case, our band2Raster() function) multiple times. You can learn more about lapply() here.

NOTE: We are using the raster stack object in R to store several rasters that are of the same CRS and extent. This is a popular and convenient way to organize co-incident rasters.

Next, add the names of the bands to the raster so we can easily keep track of the bands in the list.

# Create a list of band names

bandNames <- paste("Band_",unlist(rgb),sep="")



# set the rasterStack's names equal to the list of bandNames created above

names(rgbStack) <- bandNames



# check properties of the raster list - note the band names

rgbStack

## class       : SpatRaster 
## dimensions  : 1000, 1000, 3  (nrow, ncol, nlyr)
## resolution  : 1, 1  (x, y)
## extent      : 257000, 258000, 4112000, 4113000  (xmin, xmax, ymin, ymax)
## coord. ref. : WGS 84 / UTM zone 11N 
## source(s)   : memory
## names       : Band_58, Band_34, Band_19 
## min values  :       0,      32,       9 
## max values  :   14950,   13129,   11802


# scale the data as specified in the reflInfo$Scale Factor

rgbStack <- rgbStack/as.integer(reflInfo$Scale_Factor)



# plot one raster in the stack to make sure things look OK.

plot(rgbStack$Band_58, main="Band 58")

We can play with the color ramps too if we want:

# change the colors of our raster 

colors1 <- terrain.colors(25)

image(rgbStack$Band_58, main="Band 58", col=colors1)

# adjust the zlims or the stretch of the image

image(rgbStack$Band_58, main="Band 58", col=colors1, zlim = c(0,.5))

# try a different color palette

colors2 <- topo.colors(15, alpha = 1)

image(rgbStack$Band_58, main="Band 58", col=colors2, zlim=c(0,.5))

The plotRGB function allows you to combine three bands to create an true-color image.

# create a 3 band RGB image

plotRGB(rgbStack,
        r=1,g=2,b=3,
        stretch = "lin")

A note about image stretching: Notice that we use the argument stretch="lin" in this plotting function, which automatically stretches the brightness values for us to produce a natural-looking image.

Once you've created your raster, you can export it as a GeoTIFF using writeRaster. You can bring this GeoTIFF into any GIS software, such as QGIS or ArcGIS.

# Write out final raster	

# Note: if you set overwrite to TRUE, then you will overwrite (and lose) any older version of the tif file! 

writeRaster(rgbStack, file=paste0(wd,"NEON_hyperspectral_tutorial_example_RGB_image.tif"), overwrite=TRUE)

Raster Math - Creating NDVI and other Vegetation Indices in R

In this last part, we will calculate some vegetation indices using raster math in R! We will start by creating NDVI or Normalized Difference Vegetation Index.

About NDVI

NDVI is a ratio between the near infrared (NIR) portion of the electromagnetic spectrum and the red portion of the spectrum.

$$ NDVI = \frac{NIR-RED}{NIR+RED} $$

Please keep in mind that there are different ways to aggregate bands when using hyperspectral data. This example is using individual bands to perform the NDVI calculation. Using individual bands is not necessarily the best way to calculate NDVI from hyperspectral data.

# Calculate NDVI

# select bands to use in calculation (red, NIR)

ndviBands <- c(58,90)



# create raster list and then a stack using those two bands

ndviRast <- lapply(ndviBands,FUN=band2Raster, file = h5_file,
                   noDataValue=h5NoDataValue, 
                   ext=rastExt, CRS=h5CRS)

ndviStack <- rast(ndviRast)



# make the names pretty

bandNDVINames <- paste("Band_",unlist(ndviBands),sep="")

names(ndviStack) <- bandNDVINames



# view the properties of the new raster stack

ndviStack

## class       : SpatRaster 
## dimensions  : 1000, 1000, 2  (nrow, ncol, nlyr)
## resolution  : 1, 1  (x, y)
## extent      : 257000, 258000, 4112000, 4113000  (xmin, xmax, ymin, ymax)
## coord. ref. : WGS 84 / UTM zone 11N 
## source(s)   : memory
## names       : Band_58, Band_90 
## min values  :       0,      11 
## max values  :   14950,   14887

#calculate NDVI

NDVI <- function(x) {
	  (x[,2]-x[,1])/(x[,2]+x[,1])
}

ndviCalc <- app(ndviStack,NDVI)

plot(ndviCalc, main="NDVI for the NEON SJER Field Site")

# Now, play with breaks and colors to create a meaningful map

# add a color map with 4 colors

myCol <- rev(terrain.colors(4)) # use the 'rev()' function to put green as the highest NDVI value

# add breaks to the colormap, including lowest and highest values (4 breaks = 3 segments)

brk <- c(0, .25, .5, .75, 1)



# plot the image using breaks

plot(ndviCalc, main="NDVI for the NEON SJER Field Site", col=myCol, breaks=brk)

Everything on our planet reflects electromagnetic radiation from the Sun, and different types of land cover often have dramatically different reflectance properties across the spectrum. One of the most powerful aspects of the NEON Imaging Spectrometer (NIS, or hyperspectral sensor) is that it can accurately measure these reflectance properties at a very high spectral resolution. When you plot the reflectance values across the observed spectrum, you will see that different land cover types (vegetation, pavement, bare soils, etc.) have distinct patterns in their reflectance values, a property that we call the 'spectral signature' of a particular land cover class.

In this tutorial, we will extract the reflectance values for all bands of a single pixel to plot a spectral signature for that pixel. In order to do this, we need to pair the reflectance values for that pixel with the wavelength values of the bands that are represented in those measurements. We will also need to adjust the reflectance values by the scaling factor that is saved as an 'attribute' in the HDF5 file. First, let's start by defining the working directory and reading in the example dataset.

# Call required packages

library(rhdf5)

library(plyr)

library(ggplot2)

library(neonUtilities)



wd <- "~/data/" #This will depend on your local environment

setwd(wd)

If you haven't already downloaded the hyperspectral data tile (in one of the previous tutorials in this series), you can use the neonUtilities function byTileAOP to download a single reflectance tile. You can run help(byTileAOP) to see more details on what the various inputs are. For this exercise, we'll specify the UTM Easting and Northing to be (257500, 4112500), which will download the tile with the lower left corner (257000, 4112000).

byTileAOP(dpID = 'DP3.30006.001',

          site = 'SJER',

          year = '2021',

          easting = 257500,

          northing = 4112500,

          savepath = wd)

This file will be downloaded into a nested subdirectory under the ~/data folder (your working directory), inside a folder named DP3.30006.001 (the Data Product ID). The file should show up in this location: ~/data/DP3.30006.001/neon-aop-products/2021/FullSite/D17/2021_SJER_5/L3/Spectrometer/Reflectance/NEON_D17_SJER_DP3_257000_4112000_reflectance.h5.

Now we can read in the file and look at the contents using h5ls. You can move this file to a different location, but make sure to change the path accordingly.

# define the h5 file name (specify the full path)

h5_file <- paste0(wd,"DP3.30006.001/neon-aop-products/2021/FullSite/D17/2021_SJER_5/L3/Spectrometer/Reflectance/NEON_D17_SJER_DP3_257000_4112000_reflectance.h5")



# look at the HDF5 file structure 

h5ls(h5_file) #optionally specify all=True if you want to see all of the information

##                                           group                                 name       otype  dclass               dim
## 0                                             /                                 SJER   H5I_GROUP                          
## 1                                         /SJER                          Reflectance   H5I_GROUP                          
## 2                             /SJER/Reflectance                             Metadata   H5I_GROUP                          
## 3                    /SJER/Reflectance/Metadata                    Ancillary_Imagery   H5I_GROUP                          
## 4  /SJER/Reflectance/Metadata/Ancillary_Imagery                Aerosol_Optical_Depth H5I_DATASET INTEGER       1000 x 1000
## 5  /SJER/Reflectance/Metadata/Ancillary_Imagery                               Aspect H5I_DATASET   FLOAT       1000 x 1000
## 6  /SJER/Reflectance/Metadata/Ancillary_Imagery                          Cast_Shadow H5I_DATASET INTEGER       1000 x 1000
## 7  /SJER/Reflectance/Metadata/Ancillary_Imagery Dark_Dense_Vegetation_Classification H5I_DATASET INTEGER       1000 x 1000
## 8  /SJER/Reflectance/Metadata/Ancillary_Imagery                 Data_Selection_Index H5I_DATASET INTEGER       1000 x 1000
## 9  /SJER/Reflectance/Metadata/Ancillary_Imagery                 Haze_Cloud_Water_Map H5I_DATASET INTEGER       1000 x 1000
## 10 /SJER/Reflectance/Metadata/Ancillary_Imagery                  Illumination_Factor H5I_DATASET INTEGER       1000 x 1000
## 11 /SJER/Reflectance/Metadata/Ancillary_Imagery                          Path_Length H5I_DATASET   FLOAT       1000 x 1000
## 12 /SJER/Reflectance/Metadata/Ancillary_Imagery                      Sky_View_Factor H5I_DATASET INTEGER       1000 x 1000
## 13 /SJER/Reflectance/Metadata/Ancillary_Imagery                                Slope H5I_DATASET   FLOAT       1000 x 1000
## 14 /SJER/Reflectance/Metadata/Ancillary_Imagery             Smooth_Surface_Elevation H5I_DATASET   FLOAT       1000 x 1000
## 15 /SJER/Reflectance/Metadata/Ancillary_Imagery                 Visibility_Index_Map H5I_DATASET INTEGER       1000 x 1000
## 16 /SJER/Reflectance/Metadata/Ancillary_Imagery                   Water_Vapor_Column H5I_DATASET   FLOAT       1000 x 1000
## 17 /SJER/Reflectance/Metadata/Ancillary_Imagery            Weather_Quality_Indicator H5I_DATASET INTEGER   3 x 1000 x 1000
## 18                   /SJER/Reflectance/Metadata                    Coordinate_System   H5I_GROUP                          
## 19 /SJER/Reflectance/Metadata/Coordinate_System             Coordinate_System_String H5I_DATASET  STRING             ( 0 )
## 20 /SJER/Reflectance/Metadata/Coordinate_System                            EPSG Code H5I_DATASET  STRING             ( 0 )
## 21 /SJER/Reflectance/Metadata/Coordinate_System                             Map_Info H5I_DATASET  STRING             ( 0 )
## 22 /SJER/Reflectance/Metadata/Coordinate_System                                Proj4 H5I_DATASET  STRING             ( 0 )
## 23                   /SJER/Reflectance/Metadata                    Flight_Trajectory   H5I_GROUP                          
## 24                   /SJER/Reflectance/Metadata                                 Logs   H5I_GROUP                          
## 25              /SJER/Reflectance/Metadata/Logs                               195724   H5I_GROUP                          
## 26       /SJER/Reflectance/Metadata/Logs/195724                     ATCOR_Input_file H5I_DATASET  STRING             ( 0 )
## 27       /SJER/Reflectance/Metadata/Logs/195724                 ATCOR_Processing_Log H5I_DATASET  STRING             ( 0 )
## 28       /SJER/Reflectance/Metadata/Logs/195724                Shadow_Processing_Log H5I_DATASET  STRING             ( 0 )
## 29       /SJER/Reflectance/Metadata/Logs/195724               Skyview_Processing_Log H5I_DATASET  STRING             ( 0 )
## 30       /SJER/Reflectance/Metadata/Logs/195724                  Solar_Azimuth_Angle H5I_DATASET   FLOAT             ( 0 )
## 31       /SJER/Reflectance/Metadata/Logs/195724                   Solar_Zenith_Angle H5I_DATASET   FLOAT             ( 0 )
## 32              /SJER/Reflectance/Metadata/Logs                               200251   H5I_GROUP                          
## 33       /SJER/Reflectance/Metadata/Logs/200251                     ATCOR_Input_file H5I_DATASET  STRING             ( 0 )
## 34       /SJER/Reflectance/Metadata/Logs/200251                 ATCOR_Processing_Log H5I_DATASET  STRING             ( 0 )
## 35       /SJER/Reflectance/Metadata/Logs/200251                Shadow_Processing_Log H5I_DATASET  STRING             ( 0 )
## 36       /SJER/Reflectance/Metadata/Logs/200251               Skyview_Processing_Log H5I_DATASET  STRING             ( 0 )
## 37       /SJER/Reflectance/Metadata/Logs/200251                  Solar_Azimuth_Angle H5I_DATASET   FLOAT             ( 0 )
## 38       /SJER/Reflectance/Metadata/Logs/200251                   Solar_Zenith_Angle H5I_DATASET   FLOAT             ( 0 )
## 39              /SJER/Reflectance/Metadata/Logs                               200812   H5I_GROUP                          
## 40       /SJER/Reflectance/Metadata/Logs/200812                     ATCOR_Input_file H5I_DATASET  STRING             ( 0 )
## 41       /SJER/Reflectance/Metadata/Logs/200812                 ATCOR_Processing_Log H5I_DATASET  STRING             ( 0 )
## 42       /SJER/Reflectance/Metadata/Logs/200812                Shadow_Processing_Log H5I_DATASET  STRING             ( 0 )
## 43       /SJER/Reflectance/Metadata/Logs/200812               Skyview_Processing_Log H5I_DATASET  STRING             ( 0 )
## 44       /SJER/Reflectance/Metadata/Logs/200812                  Solar_Azimuth_Angle H5I_DATASET   FLOAT             ( 0 )
## 45       /SJER/Reflectance/Metadata/Logs/200812                   Solar_Zenith_Angle H5I_DATASET   FLOAT             ( 0 )
## 46              /SJER/Reflectance/Metadata/Logs                               201441   H5I_GROUP                          
## 47       /SJER/Reflectance/Metadata/Logs/201441                     ATCOR_Input_file H5I_DATASET  STRING             ( 0 )
## 48       /SJER/Reflectance/Metadata/Logs/201441                 ATCOR_Processing_Log H5I_DATASET  STRING             ( 0 )
## 49       /SJER/Reflectance/Metadata/Logs/201441                Shadow_Processing_Log H5I_DATASET  STRING             ( 0 )
## 50       /SJER/Reflectance/Metadata/Logs/201441               Skyview_Processing_Log H5I_DATASET  STRING             ( 0 )
## 51       /SJER/Reflectance/Metadata/Logs/201441                  Solar_Azimuth_Angle H5I_DATASET   FLOAT             ( 0 )
## 52       /SJER/Reflectance/Metadata/Logs/201441                   Solar_Zenith_Angle H5I_DATASET   FLOAT             ( 0 )
## 53                   /SJER/Reflectance/Metadata                        Spectral_Data   H5I_GROUP                          
## 54     /SJER/Reflectance/Metadata/Spectral_Data                                 FWHM H5I_DATASET   FLOAT               426
## 55     /SJER/Reflectance/Metadata/Spectral_Data                           Wavelength H5I_DATASET   FLOAT               426
## 56                   /SJER/Reflectance/Metadata              to-sensor_azimuth_angle H5I_DATASET   FLOAT       1000 x 1000
## 57                   /SJER/Reflectance/Metadata               to-sensor_zenith_angle H5I_DATASET   FLOAT       1000 x 1000
## 58                            /SJER/Reflectance                     Reflectance_Data H5I_DATASET INTEGER 426 x 1000 x 1000

Read Wavelength Values

Next, let's read in the wavelength center associated with each band in the HDF5 file. We will later match these with the reflectance values and show both in our final spectral signature plot.

# read in the wavelength information from the HDF5 file

wavelengths <- h5read(h5_file,"/SJER/Reflectance/Metadata/Spectral_Data/Wavelength")

Extract Z-dimension data slice

Next, we will extract all reflectance values for one pixel. This makes up the spectral signature or profile of the pixel. To do that, we'll use the h5read() function. Here we pick an arbitrary pixel at (100,35), and use the NULL value to select all bands from that location.

# extract all bands from a single pixel

aPixel <- h5read(h5_file,"/SJER/Reflectance/Reflectance_Data",index=list(NULL,100,35))



# The line above generates a vector of reflectance values.

# Next, we reshape the data and turn them into a dataframe

b <- adply(aPixel,c(1))



# create clean data frame

aPixeldf <- b[2]



# add wavelength data to matrix

aPixeldf$Wavelength <- wavelengths



head(aPixeldf)

##    V1 Wavelength
## 1 206   381.6035
## 2 266   386.6132
## 3 274   391.6229
## 4 297   396.6327
## 5 236   401.6424
## 6 236   406.6522

Scale Factor

Then, we can pull the spatial attributes that we'll need to adjust the reflectance values. Often, large raster data contain floating point (values with decimals) information. However, floating point data consume more space (yield a larger file size) compared to integer values. Thus, to keep the file sizes smaller, the data will be scaled by a factor of 10, 100, 10000, etc. This scale factor will be noted in the data attributes.

# grab scale factor from the Reflectance attributes

reflectanceAttr <- h5readAttributes(h5_file,"/SJER/Reflectance/Reflectance_Data" )



scaleFact <- reflectanceAttr$Scale_Factor



# add scaled data column to DF

aPixeldf$scaled <- (aPixeldf$V1/as.vector(scaleFact))



# make nice column names

names(aPixeldf) <- c('Reflectance','Wavelength','ScaledReflectance')

head(aPixeldf)

##   Reflectance Wavelength ScaledReflectance
## 1         206   381.6035            0.0206
## 2         266   386.6132            0.0266
## 3         274   391.6229            0.0274
## 4         297   396.6327            0.0297
## 5         236   401.6424            0.0236
## 6         236   406.6522            0.0236

Plot Spectral Signature

Now we're ready to plot our spectral signature!

ggplot(data=aPixeldf)+
   geom_line(aes(x=Wavelength, y=ScaledReflectance))+
   xlab("Wavelength (nm)")+
   ylab("Reflectance")

In this tutorial, we will learn how to plot spectral signatures of several different land cover types using an interactive click feature of the terra package.

Getting Started

First, we need to load our required packages and set the working directory.

# load required packages

library(rhdf5)

library(reshape2)

library(terra)

library(plyr)

library(ggplot2)

library(grDevices)



# set working directory, you can change this if desired

wd <- "~/data/" 

setwd(wd)

Download the reflectance tile, if you haven't already, using neonUtilities::byTileAOP:

byTileAOP(dpID = 'DP3.30006.001',

          site = 'SJER',

          year = '2021',

          easting = 257500,

          northing = 4112500,

          savepath = wd)

And then we can read in the hyperspectral hdf5 data. We will also collect a few other important pieces of information (band wavelengths and scaling factor) while we're at it.

# define filepath to the hyperspectral dataset

h5_file <- paste0(wd,"DP3.30006.001/neon-aop-products/2021/FullSite/D17/2021_SJER_5/L3/Spectrometer/Reflectance/NEON_D17_SJER_DP3_257000_4112000_reflectance.h5")



# read in the wavelength information from the HDF5 file

wavelengths <- h5read(h5_file,"/SJER/Reflectance/Metadata/Spectral_Data/Wavelength")



# grab scale factor from the Reflectance attributes

reflInfo <- h5readAttributes(h5_file,"/SJER/Reflectance/Reflectance_Data" )



scaleFact <- reflInfo$Scale_Factor

Now, we will read in the RGB image that we created in an earlier tutorial and plot it.

# read in RGB image as a 'stack' rather than a plain 'raster'

rgbStack <- rast(paste0(wd,"NEON_hyperspectral_tutorial_example_RGB_image.tif"))



# plot as RGB image, with a linear stretch

plotRGB(rgbStack,
        r=1,g=2,b=3, scale=300, 
        stretch = "lin")

Interactive click Function from the terra Package

Next, we use an interactive clicking function to identify the pixels that we want to extract spectral signatures for. To follow along with this tutorial, we suggest the following six cover types (exact locations shown in the image below).

1. Water
2. Tree canopy (avoid the shaded northwestern side of the tree)
3. Irrigated grass
4. Bare soil (baseball diamond infield)
5. Building roof (blue)
6. Road

As shown here:

For this next part, if you are following along in RStudio, you will need to enter these line below directly in the Console. dev.new(noRStudioGD = TRUE) will open up a separate window for plotting, which is where you will click the pixels to extract spectra, using the terra::click functionality.

dev.new(noRStudioGD = TRUE)

Now we can create our RGB plot, and start clicking on this in the pop-out Graphics window.

# change plotting parameters to better see the points and numbers generated from clicking

par(col="red", cex=2)



# use a histogram stretch in order to provide more contrast for selecting pixels

plotRGB(rgbStack, r=1, g=2, b=3, scale=300, stretch = "hist") 



# use the 'click' function

c <- click(rgbStack, n = 6, id=TRUE, xy=TRUE, cell=TRUE, type="p", pch=16, col="red", col.lab="red")

Once you have clicked your six points, the graphics window should close. If you want to choose new points, or if you accidentally clicked a point that you didn't intend to, run the previous 2 chunks of code again to re-start.

The click() function identifies the cell number that you clicked, but in order to extract spectral signatures, we need to convert that cell number into a row and column, as shown here:

# convert raster cell number into row and column (used to extract spectral signature below)

c$row <- c$cell%/%nrow(rgbStack)+1 # add 1 because R is 1-indexed

c$col <- c$cell%%ncol(rgbStack)

Extract Spectral Signatures from HDF5 file

Next, we will loop through each of the cells that and use the h5read() function to extract the reflectance values of all bands from the given pixel (row and column).

# create a new dataframe from the band wavelengths so that we can add the reflectance values for each cover type

pixel_df <- as.data.frame(wavelengths)

# loop through each of the cells that we selected

for(i in 1:length(c$cell)){
# extract spectral values from a single pixel
aPixel <- h5read(h5_file,"/SJER/Reflectance/Reflectance_Data",
                 index=list(NULL,c$col[i],c$row[i]))

# scale reflectance values from 0-1
aPixel <- aPixel/as.vector(scaleFact)

# reshape the data and turn into dataframe
b <- adply(aPixel,c(1))

# rename the column that we just created
names(b)[2] <- paste0("Point_",i)

# add reflectance values for this pixel to our combined data.frame called pixel_df
pixel_df <- cbind(pixel_df,b[2])
}

Plot Spectral signatures using ggplot2

Finally, we have everything that we need to plot the spectral signatures for each of the pixels that we clicked. In order to color our lines by the different land cover types, we will first reshape our data using the melt() function, then plot the spectral signatures.

# Use the melt() function to reshape the dataframe into a format that ggplot prefers

pixel.melt <- reshape2::melt(pixel_df, id.vars = "wavelengths", value.name = "Reflectance")

# Now, let's plot the spectral signatures!

ggplot()+
  geom_line(data = pixel.melt, mapping = aes(x=wavelengths, y=Reflectance, color=variable), lwd=1.5)+
  scale_colour_manual(values = c("blue3","green4","green2","tan4","grey50","black"),
                      labels = c("Water","Tree","Grass","Soil","Roof","Road"))+
  labs(color = "Cover Type")+
  ggtitle("Land cover spectral signatures")+
  theme(plot.title = element_text(hjust = 0.5, size=20))+
  xlab("Wavelength")

Nice! However, there seems to be something weird going on in the wavelengths near ~1400nm and ~1850 nm...

Atmospheric Absorption Bands

Those irregularities around 1400nm and 1850 nm are two major atmospheric absorption bands - regions where gasses in the atmosphere (primarily carbon dioxide and water vapor) absorb radiation, and therefore, obscure the reflected radiation that the imaging spectrometer measures. Fortunately, the lower and upper bound of each of those atmospheric absorption bands is specified in the HDF5 file. Let's read those bands and plot rectangles where the reflectance measurements are obscured by atmospheric absorption.

# grab reflectance metadata (which contains absorption band limits)

reflMetadata <- h5readAttributes(h5_file,"/SJER/Reflectance" )

ab1 <- reflMetadata$Band_Window_1_Nanometers

ab2 <- reflMetadata$Band_Window_2_Nanometers

# Plot spectral signatures again with grey rectangles highlighting the absorption bands

ggplot()+
  geom_line(data = pixel.melt, mapping = aes(x=wavelengths, y=Reflectance, color=variable), lwd=1.5)+
  geom_rect(mapping=aes(ymin=min(pixel.melt$Reflectance),ymax=max(pixel.melt$Reflectance), xmin=ab1[1], xmax=ab1[2]), color="black", fill="grey40", alpha=0.8)+
  geom_rect(mapping=aes(ymin=min(pixel.melt$Reflectance),ymax=max(pixel.melt$Reflectance), xmin=ab2[1], xmax=ab2[2]), color="black", fill="grey40", alpha=0.8)+
  scale_colour_manual(values = c("blue3","green4","green2","tan4","grey50","black"),
                      labels = c("Water","Tree","Grass","Soil","Roof","Road"))+
  labs(color = "Cover Type")+
  ggtitle("Land cover spectral signatures with\n atmospheric absorption bands greyed out")+
  theme(plot.title = element_text(hjust = 0.5, size=20))+
  xlab("Wavelength")

Now we can clearly see that the noisy sections of each spectral signature are within the atmospheric absorption bands. For our final step, let's take all reflectance values from within each absorption band and set them to NA to remove the noisiest sections from the plot.

# Duplicate the spectral signatures into a new data.frame

pixel.melt.masked <- pixel.melt

# Mask out all values within each of the two atmospheric absorption bands

pixel.melt.masked[pixel.melt.masked$wavelengths>ab1[1]&pixel.melt.masked$wavelengths<ab1[2],]$Reflectance <- NA

pixel.melt.masked[pixel.melt.masked$wavelengths>ab2[1]&pixel.melt.masked$wavelengths<ab2[2],]$Reflectance <- NA



# Plot the masked spectral signatures

ggplot()+
  geom_line(data = pixel.melt.masked, mapping = aes(x=wavelengths, y=Reflectance, color=variable), lwd=1.5)+
  scale_colour_manual(values = c("blue3","green4","green2","tan4","grey50","black"),
                      labels = c("Water","Tree","Grass","Soil","Roof","Road"))+
  labs(color = "Cover Type")+
  ggtitle("Land cover spectral signatures with\n atmospheric absorption bands removed")+
  theme(plot.title = element_text(hjust = 0.5, size=20))+
  xlab("Wavelength")

There you have it, spectral signatures for six different land cover types, with the regions from the atmospheric absorption bands removed.