Using the stars package

Originally posted on 2021-03-29
Last updated 2021-07-02

This page is just a few examples and reminders about common tasks using the stars package.

library(tidyverse)
library(patchwork)
library(stars)
library(sf)

1 Load data

tif = system.file("tif/L7_ETMs.tif", package = "stars")
(x = read_stars(tif))

## stars object with 3 dimensions and 1 attribute
## attribute(s):
##   L7_ETMs.tif    
##  Min.   :  1.00  
##  1st Qu.: 54.00  
##  Median : 69.00  
##  Mean   : 68.91  
##  3rd Qu.: 86.00  
##  Max.   :255.00  
## dimension(s):
##      from  to  offset delta                       refsys point values x/y
## x       1 349  288776  28.5 UTM Zone 25, Southern Hem... FALSE   NULL [x]
## y       1 352 9120761 -28.5 UTM Zone 25, Southern Hem... FALSE   NULL [y]
## band    1   6      NA    NA                           NA    NA   NULL

1.1 Rename bands

x <- st_set_dimensions(x, "band", c("blue","green","red","nir","swir1","swir2"))
st_get_dimension_values(x, "band")

## [1] "blue"  "green" "red"   "nir"   "swir1" "swir2"

1.2 Rename attribute

x <- x %>% setNames("value")
names(x)

## [1] "value"

1.3 Plot bands

ggplot() + 
  geom_stars(data = x) + 
  coord_equal() + 
  theme_void() + 
  scale_fill_viridis_c() + 
  facet_wrap(~band, ncol = 6)

1.4 Plot RGB

ggplot() + 
  geom_stars(data = st_rgb(x[,,,c(3,2,1)])) + 
  coord_equal() + 
  scale_fill_identity() +
  theme_void() + 
  labs(title = "3,2,1")|
ggplot() + 
  geom_stars(data = st_rgb(x[,,,c(4,3,2)])) + 
  coord_equal() + 
  scale_fill_identity() +
  theme_void() + 
  labs(title = "4,3,2")|
ggplot() + 
  geom_stars(data = st_rgb(x[,,,c(6,4,2)])) + 
  coord_equal() + 
  scale_fill_identity() +
  theme_void() + 
  labs(title = "6,4,2")

2 Clip to sf

my_bbox <- x %>% st_bbox() %>% st_as_sfc() %>% st_as_sf()
my_centroid <- my_bbox %>% st_centroid()
my_aoi <- my_centroid %>% st_buffer(1000)

ggplot() + 
  geom_stars(data = x) +
  geom_sf(data = my_aoi, fill = NA, color = "red") + 
  theme_void()| 
ggplot() + 
  geom_stars(data = x[my_aoi]) +
  geom_sf(data = my_aoi, fill = NA, color = "red") + 
  theme_void()

3 Summarize stack

ggplot() + 
  geom_stars(data = st_apply(x, c("x", "y"), max)) + 
  coord_equal() + 
  theme_void() + 
  scale_fill_viridis_c() 

4 Stack calculations

calc_ndvi <- function(x) (x[4] - x[3])/(x[4] + x[3])
ndvi <-  st_apply(x, c("x", "y"), FUN = calc_ndvi)

ggplot() + 
  geom_stars(data = ndvi) + 
  coord_equal() +
  theme_void() +
  scale_fill_gradientn(colours = RColorBrewer::brewer.pal(n = 9, name = "RdYlGn"), 
                       limits = c(-1,1), 
                       guide = guide_colorbar(barheight = 10, 
                                              frame.colour = "black", 
                                              frame.linewidth = 1.5,
                                              ticks.colour = NA)) + 
  labs(fill = "NDVI")

5 stars to sf

ndvi$groups <- cut(ndvi$calc_ndvi, c(-Inf,-0.5,0,0.5,Inf), c(-0.75,-0.25,0.25,0.75))

ndvi_sf <- ndvi["groups"] %>% st_as_sf(merge = T)

ggplot() + 
  geom_sf(data = ndvi_sf, aes(fill = groups)) +
  labs(fill = "NDVI groups") + 
  theme_void()