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Parallelize spatial computation over multiple raster files

Source: R/scale_process.R
par_multirasters.Rd

Large raster files usually exceed the memory capacity in size. This function can be helpful to process heterogenous raster files with homogeneous summary functions. Heterogenous raster files refer to rasters with different spatial extents and resolutions. Cropping a large raster into a small subset even consumes a lot of memory and adds processing time. This function leverages terra SpatRaster to distribute computation jobs over multiple threads. It is assumed that users have multiple large raster files in their disk, then each file path is assigned to a thread. Each thread will directly read raster values from the disk using C++ pointers that operate in terra functions. For use, it is strongly recommended to use vector data with small and confined spatial extent for computation to avoid out-of-memory error. y argument in fun_dist will be used as-is. That means no preprocessing or subsetting will be applied. Please be aware of the spatial extent and size of the inputs.

Usage

par_multirasters(filenames, fun_dist, ..., .debug = FALSE)

Arguments

filenames

character. A vector or list of full file paths of raster files. n is the total number of raster files.

fun_dist

terra or chopin functions that accept SpatRaster object in an argument. In particular, x and y arguments should be present and x should be a SpatRaster.

...

Arguments passed to the argument fun_dist.

.debug

logical(1). Default is FALSE. If TRUE and a unit computation fails, the error message and the file path where the error occurred will be included in the output.

Value

a data.frame object with computation results. For entries of the results, consult the function used in fun_dist argument.

See also

future::multisession, future::multicore, future::cluster, future.mirai::mirai_multisession, future::plan, par_convert_f

Other Parallelization: par_cut_coords(), par_grid(), par_hierarchy(), par_make_grid(), par_merge_grid(), par_pad_balanced(), par_pad_grid(), par_split_list()

Author

Insang Song geoissong@gmail.com

Examples

library(terra)
library(sf)
library(future)
library(future.mirai)
sf::sf_use_s2(FALSE)
future::plan(future.mirai::mirai_multisession, workers = 2)

ncpath <- system.file("extdata/nc_hierarchy.gpkg", package = "chopin")
nccnty <- sf::st_read(ncpath, layer = "county")
#> Reading layer `county' from data source 
#>   `/home/runner/work/_temp/Library/chopin/extdata/nc_hierarchy.gpkg' 
#>   using driver `GPKG'
#> Simple feature collection with 100 features and 1 field
#> Geometry type: POLYGON
#> Dimension:     XY
#> Bounding box:  xmin: 1054155 ymin: 1341756 xmax: 1838923 ymax: 1690176
#> Projected CRS: NAD83 / Conus Albers
ncelev <-
  system.file("extdata/nc_srtm15_otm.tif", package = "chopin")
ncelevras <- terra::rast(ncelev)

tdir <- tempdir(check = TRUE)
terra::writeRaster(ncelevras, file.path(tdir, "test1.tif"), overwrite = TRUE)
terra::writeRaster(ncelevras, file.path(tdir, "test2.tif"), overwrite = TRUE)
testfiles <- list.files(tdir, pattern = "tif$", full.names = TRUE)

res <- par_multirasters(
  filenames = testfiles,
  fun_dist = extract_at,
  x = ncelev,
  y = nccnty,
  id = "GEOID",
  func = "mean"
)
#> ℹ Input is not a character.
#> Input is a character. Attempt to read it with terra::rast...
#> ℹ Your input function at /tmp/Rtmps5j76n/test1.tif is dispatched.
#> Input is a character. Attempt to read it with terra::rast...
#> ℹ Your input function at /tmp/Rtmps5j76n/test2.tif is dispatched.