st_apply apply a function to array dimensions: aggregate over space, time, or something else

# S3 method for stars
st_apply(
  X,
  MARGIN,
  FUN,
  ...,
  CLUSTER = NULL,
  PROGRESS = FALSE,
  FUTURE = FALSE,
  rename = TRUE,
  .fname,
  single_arg = has_single_arg(FUN, list(...)) || can_single_arg(FUN),
  keep = FALSE
)

Arguments

X

object of class stars

MARGIN

see apply; index number(s) or name(s) of the dimensions over which FUN will be applied

FUN

see apply and see Details.

...

arguments passed on to FUN

CLUSTER

cluster to use for parallel apply; see makeCluster

PROGRESS

logical; if TRUE, use pbapply::pbapply to show progress bar

FUTURE

logical;if TRUE, use future.apply::future_apply

rename

logical; if TRUE and X has only one attribute and FUN is a simple function name, rename the attribute of the returned object to the function name

.fname

function name for the new attribute name (if one or more dimensions are reduced) or the new dimension (if a new dimension is created); if missing, the name of FUN is used

single_arg

logical; if TRUE, FUN takes a single argument (like fn_ndvi1 below), if FALSE FUN takes multiple arguments (like fn_ndvi2 below).

keep

logical; if TRUE, preserve dimension metadata (e.g. time stamps)

Value

object of class stars with accordingly reduced number of dimensions; in case FUN returns more than one value, a new dimension is created carrying the name of the function used; see the examples. Following the logic of apply, This new dimension is put before the other dimensions; use aperm to rearrange this, see last example.

Details

FUN is a function which either operates on a single object, which will be the data of each iteration step over dimensions MARGIN, or a function that has as many arguments as there are elements in such an object. See the NDVI examples below. The second form can be VERY much faster e.g. when a trivial function is not being called for every pixel, but only once (example).

The heuristics for the default of single_arg work often, but not always; try setting this to the right value when st_apply gives an error.

Examples

tif = system.file("tif/L7_ETMs.tif", package = "stars")
x = read_stars(tif)
st_apply(x, 1:2, mean) # mean band value for each pixel
#> stars object with 2 dimensions and 1 attribute
#> attribute(s):
#>       Min.  1st Qu.   Median     Mean 3rd Qu. Max.
#> mean  25.5 53.33333 68.33333 68.91242      82  255
#> dimension(s):
#>   from  to  offset delta                     refsys point values x/y
#> x    1 349  288776  28.5 SIRGAS 2000 / UTM zone 25S FALSE   NULL [x]
#> y    1 352 9120761 -28.5 SIRGAS 2000 / UTM zone 25S FALSE   NULL [y]
st_apply(x, c("x", "y"), mean) # equivalent to the above
#> stars object with 2 dimensions and 1 attribute
#> attribute(s):
#>       Min.  1st Qu.   Median     Mean 3rd Qu. Max.
#> mean  25.5 53.33333 68.33333 68.91242      82  255
#> dimension(s):
#>   from  to  offset delta                     refsys point values x/y
#> x    1 349  288776  28.5 SIRGAS 2000 / UTM zone 25S FALSE   NULL [x]
#> y    1 352 9120761 -28.5 SIRGAS 2000 / UTM zone 25S FALSE   NULL [y]
st_apply(x, 3, mean)   # mean of all pixels for each band
#> stars object with 1 dimensions and 1 attribute
#> attribute(s):
#>           Min.  1st Qu.   Median     Mean  3rd Qu.     Max.
#> mean  59.23541 61.07112 65.96675 68.91242 76.25445 83.18266
#> dimension(s):
#>      from to offset delta refsys point values
#> band    1  6     NA    NA     NA    NA   NULL
if (FALSE) {
 st_apply(x, "band", mean) # equivalent to the above
 st_apply(x, 1:2, range) # min and max band value for each pixel
 fn_ndvi1 = function(x) (x[4]-x[3])/(x[4]+x[3]) # ONE argument: will be called for each pixel
 fn_ndvi2 = function(red,nir) (nir-red)/(nir+red) # n arguments: will be called only once
 ndvi1 = st_apply(x, 1:2, fn_ndvi1)
   # note that we can select bands 3 and 4 in the first argument:
 ndvi2 = st_apply(x[,,,3:4], 1:2, fn_ndvi2) 
 all.equal(ndvi1, ndvi2)
 # compute the (spatial) variance of each band; https://github.com/r-spatial/stars/issues/430
 st_apply(x, 3, function(x) var(as.vector(x))) # as.vector is required!
 # to get a progress bar also in non-interactive mode, specify:
 if (require(pbapply)) { # install it, if FALSE
   pboptions(type = "timer")
 }
 st_apply(x, 1:2, range) # dimension "range" is first; rearrange by:
 st_apply(x, 1:2, range) %>% aperm(c(2,3,1))
}