Intro to Raster Data
Last updated on 2023-01-03 | Edit this page
WARNING
Warning in
download.file("http://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip", :
cannot open URL
'https://www.naturalearthdata.com/http/www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip':
HTTP status was '404 Not Found'ERROR
Error in download.file("http://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip", : cannot open URL 'http://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip'Overview
Questions
- What is a raster dataset?
- How do I work with and plot raster data in R?
- How can I handle missing or bad data values for a raster?
Objectives
- Describe the fundamental attributes of a raster dataset.
- Explore raster attributes and metadata using R.
- Import rasters into R using the
rasterpackage. - Plot a raster file in R using the
ggplot2package. - Describe the difference between single- and multi-band rasters.
Things You’ll Need To Complete This Episode
See the lesson homepage for detailed information about the software, data, and other prerequisites you will need to work through the examples in this episode.
In this episode, we will introduce the fundamental principles, packages and metadata/raster attributes that are needed to work with raster data in R. We will discuss some of the core metadata elements that we need to understand to work with rasters in R, including CRS and resolution. We will also explore missing and bad data values as stored in a raster and how R handles these elements.
We will continue to work with the dplyr and
ggplot2 packages that were introduced in the Introduction to R
for Geospatial Data lesson. We will use two additional packages in
this episode to work with raster data - the raster and
rgdal packages. Make sure that you have these packages
loaded.
R
library(raster)
library(rgdal)
library(ggplot2)
library(dplyr)
Introduce the Data
If not already discussed, introduce the datasets that will be used in this lesson. A brief introduction to the datasets can be found on the Geospatial workshop homepage.
For more detailed information about the datasets, check out the Geospatial workshop data page.
View Raster File Attributes
We will be working with a series of GeoTIFF files in this lesson. The
GeoTIFF format contains a set of embedded tags with metadata about the
raster data. We can use the function GDALinfo() to get
information about our raster data before we read that data into R. It is
ideal to do this before importing your data.
R
GDALinfo("data/NEON-DS-Airborne-Remote-Sensing/HARV/DSM/HARV_dsmCrop.tif")
WARNING
Warning: GDAL support is provided by the sf and terra packages among othersWARNING
Warning: GDAL support is provided by the sf and terra packages among othersWARNING
Warning: GDAL support is provided by the sf and terra packages among othersOUTPUT
rows 1367
columns 1697
bands 1
lower left origin.x 731453
lower left origin.y 4712471
res.x 1
res.y 1
ysign -1
oblique.x 0
oblique.y 0
driver GTiff
projection +proj=utm +zone=18 +datum=WGS84 +units=m +no_defs
file data/NEON-DS-Airborne-Remote-Sensing/HARV/DSM/HARV_dsmCrop.tif
apparent band summary:
GDType hasNoDataValue NoDataValue blockSize1 blockSize2
1 Float64 TRUE -9999 1 1697
apparent band statistics:
Bmin Bmax Bmean Bsd
1 305.07 416.07 359.8531 17.83169
Metadata:
AREA_OR_POINT=Area If you wish to store this information in R, you can do the following:
R
HARV_dsmCrop_info <- capture.output(
GDALinfo("data/NEON-DS-Airborne-Remote-Sensing/HARV/DSM/HARV_dsmCrop.tif")
)
WARNING
Warning: GDAL support is provided by the sf and terra packages among othersWARNING
Warning: GDAL support is provided by the sf and terra packages among othersWARNING
Warning: GDAL support is provided by the sf and terra packages among othersEach line of text that was printed to the console is now stored as an
element of the character vector HARV_dsmCrop_info. We will
be exploring this data throughout this episode. By the end of this
episode, you will be able to explain and understand the output
above.
Open a Raster in R
Now that we’ve previewed the metadata for our GeoTIFF, let’s import
this raster dataset into R and explore its metadata more closely. We can
use the raster() function to open a raster in R.
First we will load our raster file into R and view the data structure.
R
DSM_HARV <-
raster("data/NEON-DS-Airborne-Remote-Sensing/HARV/DSM/HARV_dsmCrop.tif")
DSM_HARV
OUTPUT
class : RasterLayer
dimensions : 1367, 1697, 2319799 (nrow, ncol, ncell)
resolution : 1, 1 (x, y)
extent : 731453, 733150, 4712471, 4713838 (xmin, xmax, ymin, ymax)
crs : +proj=utm +zone=18 +datum=WGS84 +units=m +no_defs
source : HARV_dsmCrop.tif
names : HARV_dsmCrop
values : 305.07, 416.07 (min, max)The information above includes a report of min and max values, but no other data range statistics. Similar to other R data structures like vectors and data frame columns, descriptive statistics for raster data can be retrieved like
R
summary(DSM_HARV)
WARNING
Warning in .local(object, ...): summary is an estimate based on a sample of 1e+05 cells (4.31% of all cells)OUTPUT
HARV_dsmCrop
Min. 305.5500
1st Qu. 345.6500
Median 359.6450
3rd Qu. 374.2825
Max. 413.9000
NA's 0.0000but note the warning - unless you force R to calculate these
statistics using every cell in the raster, it will take a random sample
of 100,000 cells and calculate from that instead. To force calculation
on more, or even all values, you can use the parameter
maxsamp:
R
summary(DSM_HARV, maxsamp = ncell(DSM_HARV))
OUTPUT
HARV_dsmCrop
Min. 305.07
1st Qu. 345.59
Median 359.67
3rd Qu. 374.28
Max. 416.07
NA's 0.00You may not see major differences in summary stats as
maxsamp increases, except with very large rasters.
To visualise this data in R using ggplot2, we need to
convert it to a dataframe. We learned about dataframes in an
earlier lesson. The raster package has an built-in
function for conversion to a plotable dataframe.
R
DSM_HARV_df <- as.data.frame(DSM_HARV, xy = TRUE)
Now when we view the structure of our data, we will see a standard dataframe format.
R
str(DSM_HARV_df)
OUTPUT
'data.frame': 2319799 obs. of 3 variables:
$ x : num 731454 731454 731456 731456 731458 ...
$ y : num 4713838 4713838 4713838 4713838 4713838 ...
$ HARV_dsmCrop: num 409 408 407 407 409 ...We can use ggplot() to plot this data. We will set the
color scale to scale_fill_viridis_c which is a
color-blindness friendly color scale. We will also use the
coord_quickmap() function to use an approximate Mercator
projection for our plots. This approximation is suitable for small areas
that are not too close to the poles. Other coordinate systems are
available in ggplot2 if needed, you can learn about them at their help
page ?coord_map.
R
ggplot() +
geom_raster(data = DSM_HARV_df , aes(x = x, y = y, fill = HARV_dsmCrop)) +
scale_fill_viridis_c() +
coord_quickmap()
Plotting Tip
More information about the Viridis palette used above at R Viridis package documentation.
This map shows the elevation of our study site in Harvard Forest. From the legend, we can see that the maximum elevation is ~400, but we can’t tell whether this is 400 feet or 400 meters because the legend doesn’t show us the units. We can look at the metadata of our object to see what the units are. Much of the metadata that we’re interested in is part of the CRS. We introduced the concept of a CRS in an earlier lesson.
Now we will see how features of the CRS appear in our data file and what meanings they have.
View Raster Coordinate Reference System (CRS) in R
We can view the CRS string associated with our R object using
thecrs() function.
R
crs(DSM_HARV)
OUTPUT
Coordinate Reference System:
Deprecated Proj.4 representation:
+proj=utm +zone=18 +datum=WGS84 +units=m +no_defs
WKT2 2019 representation:
PROJCRS["unknown",
BASEGEOGCRS["unknown",
DATUM["World Geodetic System 1984",
ELLIPSOID["WGS 84",6378137,298.257223563,
LENGTHUNIT["metre",1]],
ID["EPSG",6326]],
PRIMEM["Greenwich",0,
ANGLEUNIT["degree",0.0174532925199433],
ID["EPSG",8901]]],
CONVERSION["UTM zone 18N",
METHOD["Transverse Mercator",
ID["EPSG",9807]],
PARAMETER["Latitude of natural origin",0,
ANGLEUNIT["degree",0.0174532925199433],
ID["EPSG",8801]],
PARAMETER["Longitude of natural origin",-75,
ANGLEUNIT["degree",0.0174532925199433],
ID["EPSG",8802]],
PARAMETER["Scale factor at natural origin",0.9996,
SCALEUNIT["unity",1],
ID["EPSG",8805]],
PARAMETER["False easting",500000,
LENGTHUNIT["metre",1],
ID["EPSG",8806]],
PARAMETER["False northing",0,
LENGTHUNIT["metre",1],
ID["EPSG",8807]],
ID["EPSG",16018]],
CS[Cartesian,2],
AXIS["(E)",east,
ORDER[1],
LENGTHUNIT["metre",1,
ID["EPSG",9001]]],
AXIS["(N)",north,
ORDER[2],
LENGTHUNIT["metre",1,
ID["EPSG",9001]]]] +units=m tells us that our data is in meters.
Understanding CRS in Proj4 Format
The CRS for our data is given to us by R in proj4
format. Let’s break down the pieces of proj4 string. The
string contains all of the individual CRS elements that R or another GIS
might need. Each element is specified with a + sign,
similar to how a .csv file is delimited or broken up by a
,. After each + we see the CRS element being
defined. For example projection (proj=) and datum
(datum=).
UTM Proj4 String
Our projection string for DSM_HARV specifies the UTM
projection as follows:
+proj=utm +zone=18 +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0
- proj=utm: the projection is UTM, UTM has several zones.
- zone=18: the zone is 18
- datum=WGS84: the datum is WGS84 (the datum refers to the 0,0 reference for the coordinate system used in the projection)
- units=m: the units for the coordinates are in meters
- ellps=WGS84: the ellipsoid (how the earth’s roundness is calculated) for the data is WGS84
Note that the zone is unique to the UTM projection. Not all CRSs will have a zone. Image source: Chrismurf at English Wikipedia, via Wikimedia Commons (CC-BY).
Calculate Raster Min and Max Values
It is useful to know the minimum or maximum values of a raster dataset. In this case, given we are working with elevation data, these values represent the min/max elevation range at our site.
Raster statistics are often calculated and embedded in a GeoTIFF for us. We can view these values:
R
minValue(DSM_HARV)
OUTPUT
[1] 305.07R
maxValue(DSM_HARV)
OUTPUT
[1] 416.07We can see that the elevation at our site ranges from 305.0700073m to 416.0699768m.
Raster Bands
The Digital Surface Model object (DSM_HARV) that we’ve
been working with is a single band raster. This means that there is only
one dataset stored in the raster: surface elevation in meters for one
time period.
A raster dataset can contain one or more bands. We can use the
raster() function to import one single band from a single
or multi-band raster. We can view the number of bands in a raster using
the nlayers() function.
R
nlayers(DSM_HARV)
OUTPUT
[1] 1However, raster data can also be multi-band, meaning that one raster
file contains data for more than one variable or time period for each
cell. By default the raster() function only imports the
first band in a raster regardless of whether it has one or more bands.
Jump to a later episode in this series for information on working with
multi-band rasters: Work with
Multi-band Rasters in R.
Dealing with Missing Data
Raster data often has a NoDataValue associated with it.
This is a value assigned to pixels where data is missing or no data were
collected.
By default the shape of a raster is always rectangular. So if we have
a dataset that has a shape that isn’t rectangular, some pixels at the
edge of the raster will have NoDataValues. This often
happens when the data were collected by an airplane which only flew over
some part of a defined region.
In the image below, the pixels that are black have
NoDataValues. The camera did not collect data in these
areas.
In the next image, the black edges have been assigned
NoDataValue. R doesn’t render pixels that contain a
specified NoDataValue. R assigns missing data with the
NoDataValue as NA.
The difference here shows up as ragged edges on the plot, rather than black spaces where there is no data.
If your raster already has NA values set correctly but
you aren’t sure where they are, you can deliberately plot them in a
particular colour. This can be useful when checking a dataset’s
coverage. For instance, sometimes data can be missing where a sensor
could not ‘see’ its target data, and you may wish to locate that missing
data and fill it in.
To highlight NA values in ggplot, alter the
scale_fill_*() layer to contain a colour instruction for
NA values, like
scale_fill_viridis_c(na.value = 'deeppink')
The value that is conventionally used to take note of missing data
(the NoDataValue value) varies by the raster data type. For
floating-point rasters, the figure -3.4e+38 is a common
default, and for integers, -9999 is common. Some
disciplines have specific conventions that vary from these common
values.
In some cases, other NA values may be more appropriate.
An NA value should be a) outside the range of valid values,
and b) a value that fits the data type in use. For instance, if your
data ranges continuously from -20 to 100, 0 is not an acceptable
NA value! Or, for categories that number 1-15, 0 might be
fine for NA, but using -.000003 will force you to save the
GeoTIFF on disk as a floating point raster, resulting in a bigger
file.
If we are lucky, our GeoTIFF file has a tag that tells us what is the
NoDataValue. If we are less lucky, we can find that
information in the raster’s metadata. If a NoDataValue was
stored in the GeoTIFF tag, when R opens up the raster, it will assign
each instance of the value to NA. Values of NA
will be ignored by R as demonstrated above.
Challenge
Use the output from the GDALinfo() function to find out
what NoDataValue is used for our DSM_HARV
dataset.
R
GDALinfo("data/NEON-DS-Airborne-Remote-Sensing/HARV/DSM/HARV_dsmCrop.tif")
WARNING
Warning: GDAL support is provided by the sf and terra packages among othersWARNING
Warning: GDAL support is provided by the sf and terra packages among othersWARNING
Warning: GDAL support is provided by the sf and terra packages among othersOUTPUT
rows 1367
columns 1697
bands 1
lower left origin.x 731453
lower left origin.y 4712471
res.x 1
res.y 1
ysign -1
oblique.x 0
oblique.y 0
driver GTiff
projection +proj=utm +zone=18 +datum=WGS84 +units=m +no_defs
file data/NEON-DS-Airborne-Remote-Sensing/HARV/DSM/HARV_dsmCrop.tif
apparent band summary:
GDType hasNoDataValue NoDataValue blockSize1 blockSize2
1 Float64 TRUE -9999 1 1697
apparent band statistics:
Bmin Bmax Bmean Bsd
1 305.07 416.07 359.8531 17.83169
Metadata:
AREA_OR_POINT=Area NoDataValue are encoded as -9999.
Bad Data Values in Rasters
Bad data values are different from NoDataValues. Bad
data values are values that fall outside of the applicable range of a
dataset.
Examples of Bad Data Values:
- The normalized difference vegetation index (NDVI), which is a measure of greenness, has a valid range of -1 to 1. Any value outside of that range would be considered a “bad” or miscalculated value.
- Reflectance data in an image will often range from 0-1 or 0-10,000 depending upon how the data are scaled. Thus a value greater than 1 or greater than 10,000 is likely caused by an error in either data collection or processing.
Find Bad Data Values
Sometimes a raster’s metadata will tell us the range of expected values for a raster. Values outside of this range are suspect and we need to consider that when we analyze the data. Sometimes, we need to use some common sense and scientific insight as we examine the data - just as we would for field data to identify questionable values.
Plotting data with appropriate highlighting can help reveal patterns in bad values and may suggest a solution. Below, reclassification is used to highlight elevation values over 400m with a contrasting colour.
Create A Histogram of Raster Values
We can explore the distribution of values contained within our raster
using the geom_histogram() function which produces a
histogram. Histograms are often useful in identifying outliers and bad
data values in our raster data.
R
ggplot() +
geom_histogram(data = DSM_HARV_df, aes(HARV_dsmCrop))
OUTPUT
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Notice that a warning message is thrown when R creates the histogram.
stat_bin() using bins = 30. Pick better
value with binwidth.
This warning is caused by a default setting in
geom_histogram enforcing that there are 30 bins for the
data. We can define the number of bins we want in the histogram by using
the bins value in the geom_histogram()
function.
R
ggplot() +
geom_histogram(data = DSM_HARV_df, aes(HARV_dsmCrop), bins = 40)
Note that the shape of this histogram looks similar to the previous
one that was created using the default of 30 bins. The distribution of
elevation values for our Digital Surface Model (DSM) looks
reasonable. It is likely there are no bad data values in this particular
raster.
Challenge: Explore Raster Metadata
Use
GDALinfo()to determine the following about theNEON-DS-Airborne-Remote-Sensing/HARV/DSM/HARV_DSMhill.tiffile:
- Does this file have the same CRS as
DSM_HARV?- What is the
NoDataValue?- What is resolution of the raster data?
- How large would a 5x5 pixel area be on the Earth’s surface?
- Is the file a multi- or single-band raster?
Notice: this file is a hillshade. We will learn about hillshades in the Working with Multi-band Rasters in R episode.
Answers
GDALinfo(“data/NEON-DS-Airborne-Remote-Sensing/HARV/DSM/HARV_DSMhill.tif”)
1. If this file has the same CRS as DSM_HARV? Yes: UTM Zone 18, WGS84, meters.
2. What format `NoDataValues` take? -9999
3. The resolution of the raster data? 1x1
4. How large a 5x5 pixel area would be? 5mx5m How? We are given resolution of 1x1 and units in meters, therefore resolution of 5x5 means 5x5m.
5. Is the file a multi- or single-band raster? Single.