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Split a raster into tiles that can be iterated over with dynamic branching

Source: R/tar_terra_tiles.R
tar_terra_tiles.Rd

Creates two targets, a list of extents defining tiles and a downstream pattern that maps over these extents to create a list of SpatRaster objects that can be used with dynamic branching.

Usage

tar_terra_tiles(
  name,
  raster,
  tile_fun,
  filetype = geotargets_option_get("gdal.raster.driver"),
  gdal = geotargets_option_get("gdal.raster.creation.options"),
  ...,
  packages = targets::tar_option_get("packages"),
  library = targets::tar_option_get("library"),
  repository = targets::tar_option_get("repository"),
  error = targets::tar_option_get("error"),
  memory = targets::tar_option_get("memory"),
  garbage_collection = targets::tar_option_get("garbage_collection"),
  deployment = targets::tar_option_get("deployment"),
  priority = targets::tar_option_get("priority"),
  resources = targets::tar_option_get("resources"),
  storage = targets::tar_option_get("storage"),
  retrieval = targets::tar_option_get("retrieval"),
  cue = targets::tar_option_get("cue"),
  description = targets::tar_option_get("description")
)

Arguments

name

Symbol, name of the target. A target name must be a valid name for a symbol in R, and it must not start with a dot. See targets::tar_target() for more information.

raster

a SpatRaster object to be split into tiles.

tile_fun

a helper function that returns a list of numeric vectors such as tile_grid(), tile_n() or tile_blocksize specified in one of the following ways:

  • A named function, e.g. tile_blocksize or "tile_blocksize".

  • An anonymous function, e.g. \(x) tile_grid(x, nrow = 2, ncol = 2).

filetype

character. File format expressed as GDAL driver names passed to terra::makeTiles().

gdal

character. GDAL driver specific datasource creation options passed to terra::makeTiles().

...

additional arguments not yet used.

packages

Character vector of packages to load right before the target runs or the output data is reloaded for downstream targets. Use tar_option_set() to set packages globally for all subsequent targets you define.

library

Character vector of library paths to try when loading packages.

repository

Character of length 1, remote repository for target storage. Choices:

Note: if repository is not "local" and format is "file" then the target should create a single output file. That output file is uploaded to the cloud and tracked for changes where it exists in the cloud. The local file is deleted after the target runs.

error

Character of length 1, what to do if the target stops and throws an error. Options:

  • "stop": the whole pipeline stops and throws an error.

  • "continue": the whole pipeline keeps going.

  • "null": The errored target continues and returns NULL. The data hash is deliberately wrong so the target is not up to date for the next run of the pipeline. In addition, as of version 1.8.0.9011, a value of NULL is given to upstream dependencies with error = "null" if loading fails.

  • "abridge": any currently running targets keep running, but no new targets launch after that.

  • "trim": all currently running targets stay running. A queued target is allowed to start if:

    1. It is not downstream of the error, and

    2. It is not a sibling branch from the same tar_target() call (if the error happened in a dynamic branch).

    The idea is to avoid starting any new work that the immediate error impacts. error = "trim" is just like error = "abridge", but it allows potentially healthy regions of the dependency graph to begin running. (Visit https://books.ropensci.org/targets/debugging.html to learn how to debug targets using saved workspaces.)

memory

Character of length 1, memory strategy. Possible values:

  • "auto": new in targets version 1.8.0.9011, memory = "auto" is equivalent to memory = "transient" for dynamic branching (a non-null pattern argument) and memory = "persistent" for targets that do not use dynamic branching.

  • "persistent": the target stays in memory until the end of the pipeline (unless storage is "worker", in which case targets unloads the value from memory right after storing it in order to avoid sending copious data over a network).

  • "transient": the target gets unloaded after every new target completes. Either way, the target gets automatically loaded into memory whenever another target needs the value.

For cloud-based dynamic files (e.g. format = "file" with repository = "aws"), the memory option applies to the temporary local copy of the file: "persistent" means it remains until the end of the pipeline and is then deleted, and "transient" means it gets deleted as soon as possible. The former conserves bandwidth, and the latter conserves local storage.

garbage_collection

Logical: TRUE to run base::gc() just before the target runs, FALSE to omit garbage collection. In the case of high-performance computing, gc() runs both locally and on the parallel worker. All this garbage collection is skipped if the actual target is skipped in the pipeline. Non-logical values of garbage_collection are converted to TRUE or FALSE using isTRUE(). In other words, non-logical values are converted FALSE. For example, garbage_collection = 2 is equivalent to garbage_collection = FALSE.

deployment

Character of length 1. If deployment is "main", then the target will run on the central controlling R process. Otherwise, if deployment is "worker" and you set up the pipeline with distributed/parallel computing, then the target runs on a parallel worker. For more on distributed/parallel computing in targets, please visit https://books.ropensci.org/targets/crew.html.

priority

Numeric of length 1 between 0 and 1. Controls which targets get deployed first when multiple competing targets are ready simultaneously. Targets with priorities closer to 1 get dispatched earlier (and polled earlier in tar_make_future()).

resources

Object returned by tar_resources() with optional settings for high-performance computing functionality, alternative data storage formats, and other optional capabilities of targets. See tar_resources() for details.

storage

Character string to control when the output of the target is saved to storage. Only relevant when using targets with parallel workers (https://books.ropensci.org/targets/crew.html). Must be one of the following values:

  • "main": the target's return value is sent back to the host machine and saved/uploaded locally.

  • "worker": the worker saves/uploads the value.

  • "none": targets makes no attempt to save the result of the target to storage in the location where targets expects it to be. Saving to storage is the responsibility of the user. Use with caution.

retrieval

Character string to control when the current target loads its dependencies into memory before running. (Here, a "dependency" is another target upstream that the current one depends on.) Only relevant when using targets with parallel workers (https://books.ropensci.org/targets/crew.html). Must be one of the following values:

  • "main": the target's dependencies are loaded on the host machine and sent to the worker before the target runs.

  • "worker": the worker loads the target's dependencies.

  • "none": targets makes no attempt to load its dependencies. With retrieval = "none", loading dependencies is the responsibility of the user. Use with caution.

cue

An optional object from tar_cue() to customize the rules that decide whether the target is up to date.

description

Character of length 1, a custom free-form human-readable text description of the target. Descriptions appear as target labels in functions like tar_manifest() and tar_visnetwork(), and they let you select subsets of targets for the names argument of functions like tar_make(). For example, tar_manifest(names = tar_described_as(starts_with("survival model"))) lists all the targets whose descriptions start with the character string "survival model".

Value

a list of two targets: an upstream target that creates a list of extents and a downstream pattern that maps over these extents to create a list of SpatRaster objects.

Details

When a raster is too large or too high resolution to work on in-memory, one possible solution is to iterate over tiles. Raster tiles can then be operated on one at a time, or possibly in parallel if resources are available, and then the results can be aggregated. A natural way to do this in the context of a targets pipeline is to split the raster into multiple raster targets with dynamic branching so that downstream targets can be applied to each branch of the upstream target with the pattern argument to tar_terra_rast() or tar_target(). tar_terra_tiles() facilitates creation of such a dynamically branched target. This workflow isn't appropriate for operations that aggregate spatially, only pixel-wise operations (possibly aggregating across multiple layers).

This target factory is useful when a raster is too large or too high resolution to work on in-memory. It can instead be split into tiles that can be iterated over using dynamic branching.

Note

The iteration argument is unavailable because it is hard-coded to "list", the only option that works currently.

When using the tile_blocksize() helper function, you may need to set memory = "transient" on the upstream target provided to the raster argument of tar_terra_tiles(). More details are in the help file for tile_blocksize().

See also

tile_n(), tile_grid(), tile_blocksize(), tar_terra_rast()

Author

Eric Scott

Examples

# For CRAN. Ensures these examples run under certain conditions.
# To run this locally, run the code inside this if statement
if (Sys.getenv("TAR_LONG_EXAMPLES") == "true") {
  targets::tar_dir({
    targets::tar_script({
        library(targets)
        library(geotargets)
        library(terra)
        list(
            tar_target(
                my_file,
                system.file("ex/elev.tif", package="terra"),
                format = "file"
            ),
            tar_terra_rast(
                my_map,
                terra::rast(my_file)
            ),
            tar_terra_tiles(
                name = rast_split,
                raster = my_map,
                tile_fun = \(x) tile_grid(x, ncol = 2, nrow = 2)
            )
        )
    })
    targets::tar_manifest()
  })
}