Is there a faster way to mask multiple rasters using multiple polygons? - r

Question

Basically I have 12 multispectral images, and I want to mask them using 2 polygons (small waterbodies). The 2 polygons are in one shapefile, but I can break them up if it would make the process easier. With the help of some nice users on here, I tested this all out using the 12 images on one polygon and it works just fine, but I'll eventually need to do this for multiple polygons so I want to adapt my code.
The loop to crop all rasters using a single polygon:
#The single polygon
mask <- st_read(here::here("data", "mask.shp") %>%
st_as_sf()
#Creates list of input files and their paths
crop_in <- list.files(here::here("data", "s2_rasters"), pattern="tif$", full.names=TRUE)
#Creates list of output files and their directory.
crop_out <- gsub(here::here("data", "s2_rasters"), here::here("data", "s2_cropped"), crop_in)
for (i in seq_along(crop_in)) {
b <- brick(crop_in[i])
crop(b, mask, filename = crop_out[i])
}
Like I said this works just fine, but I want to mask instead of crop. Additionally, I need to mask using multiple polygons.
My working loop to do the same thing but for multiple (2) polygons:
masks_2 <- st_read(here::here("data", "multiple_masks.shp")) %>%
st_as_sf()
for (i in seq_along(crop_in)) {
b <- brick(crop_in[i])
mask(b, masks_2, filename = crop_out[i], overwrite = TRUE)
}
This took around 2 hours (which makes me suspicious) and I think it lost the polygon id somewhere along the way. When I tried plotting the results the plot was empty. My final output should be 24 rasterstacks, 12 for each polygon. I will need to do further image analysis so I will need to keep the names. I hope this makes sense and thank you!

Answer 1

Here is a minimal, self-contained, reproducible example using terra because it is much faster than raster (make sure you are using the current version)
Raster dataset with 12 layers
library(terra)
f <- system.file("ex/elev.tif", package="terra")
r <- rast(f)
r <- rep(r, 12) * 1:12
names(r) <- paste0("band", 1:12)
Two "lakes"
v <- vect(system.file("ex/lux.shp", package="terra"))
v <- v[c(1,12)]
Solution:
x <- mask(r, v)
And always try things for a single case before running the loop.
So if you have 12 files, you can do something like
inf <- list.files("data/s2_rasters", pattern="tif$", full.names=TRUE)
outf <- gsub(".tif$", "_masked.tif", inf)
for (for i in 1:length(inf)) {
r <- rast(inf[i])
m <- mask(r, v, filename=outf[i])
}
It might be a little faster to instead do this (only rasterize the polygons once)
msk <- rast(inf[1])
msk <- rasterize(v, msk)
for (for i in 1:length(inf)) {
r <- rast(inf[i])
m <- mask(r, msk, filename=outf[i])
}
Or make one object/file, if that is practical.
rr <- rast(inf)
mm <- mask(rr, v)