Renaming and exporting a list of rasters using terra

Question

I've a list of hundreds of rasters that I've renamed, but when I export using writeRaster, the filenames have not changed.

For example:

library(terra)
library(tidyverse)
# all the of the packages I have loaded during actual work session... 
# if (!require("pacman")) install.packages("pacman"); library(pacman)
# p_load(here, tidyverse, sf,lubridate, raster, terra, janitor)

# read  list of files
(file_list <- list.files(here("test_set"), 
                         pattern="tif$", full.names = TRUE, recursive=FALSE))
# get names from list 
(file_names <- tools::file_path_sans_ext(list.files(here("test_set"), 
                                                    pattern="tif$", full.names = FALSE)) %>% 
    # remove everything after 1st underscore 
    str_extract("[^_]+"))
# read list of rasters
(r <- map(file_list, rast))

# rename the list 
(names(r) <- file_names)

map(r, function (i) 
  writeRaster(i, filename=paste0(here("test_set/new_names//"), names(i),".tif"), overwrite=TRUE))

I'd like to write the rasters to disk using the shortened names.

Answer 1

You are really over complicating this endeavor. This can easily be done with an iterator (for, lapply, ...) by simply operating on the vector of raster names.

library(terra)
library(stringr)
in.dir <- "C:/inrast"
out.dir <- "C:/outrast"

file_list <- list.files(in.dir, "tif$", full.names = TRUE)

lapply(file_list, function(i) { 
 writeRaster(rast(i), file.path(out.dir, 
   paste0(str_extract(basename(i), "[^_]+"), ".tif")))
  })  

So, in unpacking this code, lapply is acting as an iterator on the file_list vector of raster names. We are reading the raster on-the-fly using terra::rast within terra::writeRaster. The raster is being written to the out.dir (just to keep results separate). I am using the same syntax for stringr::str_extract and basename just extracts the end of the path name.

Here is a break down the nested function calls used in naming the new raster;

( x <- "C:/indir/file01_to_rename.tif" )
    # "C:/indir/file01_to_rename.tif"
( x <- basename(x) )
    # "file01_to_rename.tif"
( x <- str_extract(x, "[^_]+") ) 
    # "file01"
file.path("C:/outrast", paste0(x, ".tif"))
    # "C:/outrast/file01.tif"

Now put together, if the paths and names are included

file.path("C:/outrast", 
  paste0(str_extract(basename("C:/indir/file01_to_rename.tif"), 
    "[^_]+"), ".tif"))
      # "C:/outrast/file01.tif"

Answer 2

Why would you use writeRaster if your (apparent) goal it to just copy the files to a new path/name?

# get the input files (*not* a list!)
fin  <- list.files("test_set", pattern="tif$", full.names=TRUE))

# we do not have your files, so I use example names instead
fin <- c("test_set/rat1_1.tif", "test_set/rat2_2.tif", "test_set/rat3_3.tif")

# remove everything after first underscore
fout <- sapply(basename(fin), \(i) strsplit(i, "_")[[1]][1], USE.NAMES=FALSE)
# make output files
fout <- paste0("test_set/new_names/", fout, ".tif")
fout
#[1] "test_set/new_names/rat1.tif" "test_set/new_names/rat2.tif"
#[3] "test_set/new_names/rat3.tif"

# copy the files
file.copy(fin, fout)

But if you were changing the format or compression or something like that, you could do something like this

library(terra)
for (i in seq_along(fin)) {
   rast(fin[i]) |> writeRaster(fout[i])
}