initGRASS: Initiate GRASS session

In rsbivand/rgrass7: Interface Between 'GRASS' Geographical Information System and 'R'

Initiate GRASS session

Description

Run GRASS interface in an R session not started within GRASS. In general, most users will use initGRASS in throwaway locations, to use GRASS modules on R objects without the need to define and populate a location. The function initializes environment variables used by GRASS, the .gisrc used by GRASS for further environment variables, and a temporary location.

On Windows, if OSGeo4W GRASS is being used, the R session must be started in the OSGeo4W shell. If not, the non-standard placing of files and of environment variables confuses the function. If toupper(gisBase) contains "OSGEO4W64/APPS/GRASS" or "OSGEO4W/APPS/GRASS" (and after converting "\" to "/"), but the environment variable OSGEO4W_ROOT is not defined, initGRASS() will exit with an error before confusion leads to further errors. For further details, see https://github.com/rsbivand/rgrass/issues/16 and https://github.com/rsbivand/rgrass/issues/16.

The same restriction applies to use of GRASS with QGIS Windows standalone installations, which may be used with initGRASS only if the R session is started from the OSGeo4W shell shipped as part of the standalone installer (see https://github.com/rsbivand/rgrass/issues/87). The function will exit with an error if R was not started from the QGIS OSGeo4W shell before confusion leads to further errors.

The locking functions are used internally, but are exposed for experienced R/GRASS scripters needing to use the GRASS module "g.mapset" through initGRASS in an existing GRASS location. In particular, "g.mapset" may leave a .gislock file in the current MAPSET, so it may be important to call unlink_.gislock to clean up before quitting the R session. remove_GISRC may be used to try to remove the file given in the "GISRC" environment variable if created by initGRASS with argument ⁠remove_GISRC=⁠ TRUE.

Usage

initGRASS(
  gisBase = NULL,
  home,
  SG,
  gisDbase,
  addon_base,
  location,
  mapset,
  override = FALSE,
  use_g.dirseps.exe = TRUE,
  pid,
  remove_GISRC = FALSE,
  ignore.stderr = get.ignore.stderrOption()
)

get.GIS_LOCK()

set.GIS_LOCK(pid)

unset.GIS_LOCK()

unlink_.gislock()

remove_GISRC()

Arguments

gisBase	The directory path to GRASS binaries and libraries, containing bin and lib subdirectories among others; if NULL, set from environment variable GRASS_INSTALLATION if found, if not found, system("grass --config path") is tried.
home	The directory in which to create the .gisrc file; defaults to ⁠$HOME⁠ on Unix systems and to USERPROFILE on Windows systems; can usually be set to tempdir().
SG	An optional SpatRaster or SpatialGrid object to define the DEFAULT_WIND of the temporary location.
gisDbase	if missing, tempdir() will be used; GRASS GISDBASE directory for the working session.
addon_base	if missing, assumed to be "$HOME/.grass7/addons" on Unix-like platforms, on MS Windows "\ and checked for existence.
location	if missing, basename(tempfile()) will be used; GRASS location directory for the working session.
mapset	if missing, basename(tempfile()) will be used; GRASS mapset directory for the working session.
override	default FALSE, set to TRUE if accidental trashing of GRASS .gisrc files and locations is not a problem.
use_g.dirseps.exe	default TRUE; when TRUE appears to work for WinGRASS Native binaries, when FALSE for QGIS GRASS binaries; ignored on other platforms.
pid	default as.integer(round(runif(1, 1, 1000))), integer used to identify GIS_LOCK; the value here is arbitrary, but probably should be set correctly.
remove_GISRC	default FALSE; if TRUE, attempt to unlink the temporary file named in the "GISRC" environment variable when the R session terminates or when this package is unloaded.
ignore.stderr	default taking the value set by set.ignore.stderrOption; can be set to TRUE to silence system() output to standard error; does not apply on Windows platforms.

Details

The function establishes an out-of-GRASS working environment providing GRASS commands with the environment variable support required, and may also provide a temporary location for use until the end of the running R session if the home argument is set to tempdir(), and the gisDbase argument is not given. Running gmeta shows where the location is, should it be desired to archive it before leaving R.

Value

The function runs gmeta6 before returning the current values of the running GRASS session that it provides.

Note

If any package command fails with a UTF-8 error from the XML package, try using setXMLencoding to work around the problem that GRASS modules declare –interface-description output as UTF-8 without ensuring that it is.

Author(s)

Roger S. Bivand, e-mail: [e-mail]

See Also

gmeta()

Examples

# Run only if GRASS installation is found and 'terra' package is installed
GRASS_INSTALLATION <- Sys.getenv("GRASS_INSTALLATION")
run <- nzchar(GRASS_INSTALLATION) &&
       file.exists(GRASS_INSTALLATION) &&
       file.info(GRASS_INSTALLATION)$isdir &&
       require(terra, quietly = TRUE)

if (run) {
  # Plot the terra example dataset
  f <- system.file("ex/elev.tif", package="terra")
  r <- rast(f)
  plot(r, col = terrain.colors(50))

  # Initialize a temporary GRASS project using the example data
  loc <- initGRASS(
    GRASS_INSTALLATION,
    home = tempdir(),
    SG = r,
    override = TRUE
  )

  # Write the example data to the GRASS database
  write_RAST(r, "elev", flags = "overwrite")
  execGRASS("r.info", map = "elev")

  # Calculate slope and aspect raster
  execGRASS(
    "r.slope.aspect",
    flags    = "overwrite",
    elevation = "elev",
    slope    = "slope",
    aspect   = "aspect"
  )

  # Read the results back into R and plot
  u1 <- read_RAST(c("elev", "slope", "aspect"), return_format = "terra")
  plot(u1[["elev"]], col = terrain.colors(50))
}

rsbivand/rgrass7 documentation built on Nov. 3, 2024, 6:06 a.m.