Parallelize a SpatRaster function

The function splits a SpatRaster into virtual tiles and applies a user supplied function to each tile, and assembles the per-tile results back into a single SpatRaster. The work can be distributed over a cluster of worker processes.

Usage

tile_apply(x, fun, cores=1, cpkgs=NULL, tiles=NULL, buffer=0, ...,
  filename="", overwrite=FALSE, wopt=list(), overlap_fun=NULL)

Arguments

x

SpatRaster. Preferably backed by a file so that workers can re-open it cheaply; in-memory rasters are shipped to the workers via wrap

fun

function. Takes a SpatRaster as its first argument and must return a SpatRaster. It is called once per tile, with the windowed x as the first argument and any extra ... arguments appended

cores

one of: an integer (> 1 creates a PSOCK cluster of that size, torn down at the end of the call); a cluster object created with parallel::makeCluster; the string "future" (use future_lapply with the currently-active future::plan); or a future strategy object (e.g. future::multisession()), which is set as the plan for the duration of the call. The "future" and plan-object paths require the future and future.apply packages

cpkgs

character. Names of packages that must be loaded on each worker before fun is called (e.g. "randomForest")

tiles

specification of the tiles. If NULL (the default), the tile size is chosen automatically and a per-worker memory budget that depends on cores (see getTileExtents. Otherwise one of: a SpatExtent; a list of SpatExtents; a 4-column matrix of extents (xmin, xmax, ymin, ymax) as returned by getTileExtents; a SpatRaster or SpatVector that defines the tile geometry; or one or two integers specifying the number of rows and columns per tile (passed on to getTileExtents)

buffer

integer. Number of additional rows and columns (one number, or two for separate row/column buffers) of x to read on each side of every tile, so that fun can compute neighbourhood-dependent values (e.g. focal) without edge artefacts. The result of fun is then cropped back to the un-buffered tile extent before it is written, so the per-tile outputs are non-overlapping. Only used when tiles = NULL; ignored with a warning otherwise (when supplying tiles explicitly, build the overlap into the tiles yourself with getTileExtents(..., buffer=) and pick an overlap_fun)

...

additional arguments passed to fun. When cores > 1 these are serialized and shipped to each worker; SpatRaster, SpatVector and other terra objects in ... are automatically wrapped and unwrapped

filename

character. Output filename for the assembled result. When empty (the default) and overlap_fun = NULL, a virtual raster (VRT) is returned that references the per-tile files (see Details)

overwrite

logical. If TRUE, filename is overwritten if it exists

wopt

list. Writing options as in writeRaster

overlap_fun

character or NULL. The function name used by mosaic to combine overlapping cells (e.g. "mean", "min", "max", "sum", "first"). Use this when tiles was built with overlap (e.g. getTileExtents(..., buffer=)). When NULL (the default), tiles are assembled with vrt, which is correct for non-overlapping tiles (including the auto path with buffer, which crops away the overlap) and is essentially free

Details

Buffered tiles for focal-style operations. When tiles = NULL and buffer > 0, each tile is read on an expanded extent of (buffer cells on each side, clamped to x's extent), fun is applied, and the result is cropped back to the un-buffered tile extent before it is written. This avoids the edge effects that operations like focal would otherwise produce at tile boundaries.

The per-tile files are then assembled into the final SpatRaster:

• When overlap_fun = NULL (the default), the assembly is a virtual raster (vrt). This is fast and correct as long as the tiles do not overlap. If they do, the value of the last tile in the overlapping regions is used.

• When overlap_fun is set (e.g. "mean"), the assembly uses mosaic and applies the function to the values of overlapping cells.

If filename is empty and a VRT is returned, the tiled data files are kept for the rest of the R session, but they are lost after the session.

Extra arguments passed via ... must be named when cores > 1.

Value

A SpatRaster.

See also

getTileExtents, makeTiles, mosaic, vrt, window, wrap

Examples

# \donttest{
f <- system.file("ex/elev.tif", package="terra")
r <- rast(f)

# not parallel
# Returned object is a VRT backed by per-tile files in tempdir().
out1 <- tile_apply(r, function(x) x * 2)

# focal, use a buffer wide enough for the focal window
out3 <- tile_apply(r, function(x) focal(x, w=5, fun="mean", 
    na.rm=TRUE), buffer=2)

# parallel on 2 workers
if (FALSE) { # \dontrun{
out4 <- tile_apply(r, function(x) x * 2, cores=2)

# pass extra arguments by name; nested terra objects are auto-wrapped
out5 <- tile_apply(r, function(x, k) x * k, cores=2, tiles=50, k=10)

# use a future plan instead of a cluster
if (requireNamespace("future", quietly=TRUE) &&
    requireNamespace("future.apply", quietly=TRUE)) {
    future::plan(future::multisession, workers=2)
    out6 <- tile_apply(r, function(x) x * 2, cores="future")
    future::plan(future::sequential)
}
} # }
# }