I have a folder that contains around 191 GeoTIFF files (each file is a different DEM (elevation) tile of a much larger area). I want to merge all the tiles into one raster file. I am using the terra package and was successfully able to load each raster and aggregate them from 2 metre resolution to 30 metre resolution. However, when running the mosaic function to merge them all, I run into an error (see error message below). I have been able to run the mosaic function on a smaller subset of just three tiles, but when I scale up to all the files, this becomes an issue.
By calling the summary of the rasters (see below), the aggregation does slightly change the extent - could this be the issue? resample might be an option, but each individual raster has a different extent and I'm not exactly sure how to implement this fix.
Not sure a sample data set would help since I know the functions work. I am running this code on a high-performance cluster so it's not very efficient to run small batches of code.
library(terra)
files <- as.list(list.files("./DEM_tiles", full.names = TRUE))
raster.list <- lapply(files, rast)
for(i in 1:length(raster.list)){
raster.list[[i]] <- aggregate(raster.list[[i]], fact = 15)
}
raster.mosaic <- do.call(mosaic, raster.list)
> Error: [mosaic] internal error: extents do not match ()
> Execution halted
Below is an example of what two of the tiles look like:
### Before Aggregation
[[1]]
class : SpatRaster
dimensions : 25000, 25000, 1 (nrow, ncol, nlyr)
resolution : 2, 2 (x, y)
extent : -1800000, -1750000, -6e+05, -550000 (xmin, xmax, ymin, ymax)
coord. ref. : +proj=stere +lat_0=90 +lat_ts=70 +lon_0=-45 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs
source : 35_23_1_1_2m_v3.0_reg_dem.tif
name : 35_23_1_1_2m_v3.0_reg_dem
[[2]]
class : SpatRaster
dimensions : 25000, 25000, 1 (nrow, ncol, nlyr)
resolution : 2, 2 (x, y)
extent : -1800000, -1750000, -550000, -5e+05 (xmin, xmax, ymin, ymax)
coord. ref. : +proj=stere +lat_0=90 +lat_ts=70 +lon_0=-45 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs
source : 35_23_1_2_2m_v3.0_reg_dem.tif
name : 35_23_1_2_2m_v3.0_reg_dem
### After Aggregation
[[1]]
class : SpatRaster
dimensions : 1667, 1667, 1 (nrow, ncol, nlyr)
resolution : 30, 30 (x, y)
extent : -1800000, -1749990, -600010, -550000 (xmin, xmax, ymin, ymax)
coord. ref. : +proj=stere +lat_0=90 +lat_ts=70 +lon_0=-45 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs
source : memory
name : 35_23_1_1_2m_v3.0_reg_dem
min value : -15.62178
max value : 233.6489
[[2]]
class : SpatRaster
dimensions : 1667, 1667, 1 (nrow, ncol, nlyr)
resolution : 30, 30 (x, y)
extent : -1800000, -1749990, -550010, -5e+05 (xmin, xmax, ymin, ymax)
coord. ref. : +proj=stere +lat_0=90 +lat_ts=70 +lon_0=-45 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs
source : memory
name : 35_23_1_2_2m_v3.0_reg_dem
min value : -15.27713
max value : 243.0772
The error was because the rasters were not aligned, and due to a bug. I now get
library(terra)
#terra version 1.2.1
crs <- "+proj=stere +lat_0=90 +lat_ts=70 +lon_0=-45 +x_0=0 +y_0=0 +datum=WGS84 +units=m"
r1 <- rast(nrow=1667, ncol=1667, ext=c(-1800000, -1749990, -600010, -550000), crs=crs)
r2 <- rast(nrow=1667, ncol=1667, ext=c(-1800000, -1749990, -550010, -5e+05), crs=crs)
values(r1) <- 1:ncell(r1)
values(r2) <- 1:ncell(r2)
m <- mosaic(r1, r2)
#Warning message:
#[mosaic] rasters did not align and were resampled
m
#class : SpatRaster
#dimensions : 3334, 1667, 1 (nrow, ncol, nlyr)
#resolution : 30, 30 (x, y)
#extent : -1800000, -1749990, -600010, -499990 (xmin, xmax, ymin, ymax)
#coord. ref. : +proj=stere +lat_0=90 +lat_ts=70 +lon_0=-45 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs
#source : memory
#name : lyr.1
#min value : 1
#max value : 2778889
Also
@Elia's suggestion is a good work-around:
r1 <- writeRaster(r1, "test1.tif", overwrite=TRUE)
r2 <- writeRaster(r2, "test2.tif", overwrite=TRUE)
v <- vrt(c("test1.tif", "test2.tif"), "test.vrt", overwrite=TRUE)
v
#class : SpatRaster
#dimensions : 3334, 1667, 1 (nrow, ncol, nlyr)
#resolution : 30, 30 (x, y)
#extent : -1800000, -1749990, -600020, -5e+05 (xmin, xmax, ymin, ymax)
#coord. ref. : +proj=stere +lat_0=90 +lat_ts=70 +lon_0=-45 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs
#source : test.vrt
#name : test
#min value : 1
#max value : 2778889