Error in mosaic of rasters from different extent using terra package in R?

Question

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

One way to go could be to built a vrt file with all the tiles and then write it as tif. — Elia

Robert Hijmans Robert Hijmans · Accepted Answer · 2021-04-20T16:08:21

I can reproduce the message like this

library(terra)
r1 <- rast(nrow=1667, ncol=1667, ext=c(-1800000, -1749990, -600010, -550000))
r2 <- rast(nrow=1667, ncol=1667, ext=c(-1800000, -1749990, -550010, -5e+05))
values(r1) <- 1:ncell(r1)
values(r2) <- 1:ncell(r2)
m <- mosaic(r1, r2)
#Error: [mosaic] internal error: extents do not match ()

And merge fails too. This is a bug that I will look into. It works in raster

library(raster)
x1 <- raster(r1)
x2 <- raster(r2)
m <- mosaic(x1, x2, fun=mean)
mm <- merge(x1, x2)

Later:

The error was because the rasters were not aligned. With terra 1.2-1 (currently the development version) 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

Error in mosaic of rasters from different extent using terra package in R?

1 Answers