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Run focal function on a multi-layer raster

3 messages · Loïc Dutrieux, Thiago V. dos Santos

Thiago V. dos Santos
# 
I have a multi-layer raster, in this case a rasterbrick, on which I would like to apply a focal function on each layer, and get another rasterbrick as a result.

I am trying to use calc, but apparently I am not assembling my function in the proper way:

require(raster)
r <- raster(ncol=50, nrow=50)
r[]=1:ncell(r)
b <- brick(r,r,r,r,r,r)
b <- b * 1:6

myfocalfun <- function(x){
b.f <- focal(x, w=matrix(1, 5, 5), mean)
return(b.f)
}

b1 <- calc(b, myfocalfun)

Error in .calcTest(x[1:5], fun, na.rm, forcefun, forceapply) : 
cannot use this function

What am I missing here?
 Greetings,
 -- Thiago V. dos Santos

PhD student
Land and Atmospheric Science
University of Minnesota
Loïc Dutrieux
# 
Hi Thiago,

calc is not aware of neighbouring pixels in the x,y dimensions, so 
functions like focal cannot work.

I found the function below in an old repos of mine. It still seems to 
work fine :)

#' Focal for RasterBrick or RasterStack
#'
#' @param x RasterBrick/Stack or character pointing to multilayer raster 
object written on disk
#' @param w See \code{\link{focal}}
#' @param ... Arguments to be passed to \code{\link{focal}}
#'
#' @import raster
#' @export
#'

multiFocal <- function(x, w=matrix(1, nr=3, nc=3), ...) {

   if(is.character(x)) {
     x <- brick(x)
   }
   # The function to be applied to each individual layer
   fun <- function(ind, x, w, ...){
     focal(x[[ind]], w=w, ...)
   }

   n <- seq(nlayers(x))
   list <- lapply(X=n, FUN=fun, x=x, w=w, ...)

   out <- stack(list)
   return(out)
}
On 05/21/2016 10:02 PM, Thiago V. dos Santos via R-sig-Geo wrote:
multiFocal(b, w=matrix(1, 5, 5), mean)

Cheers,
Lo?c
Thiago V. dos Santos
# 
Hi Lo?c,

Thanks for the hint - it worked like a charm!
 Greetings,
 -- Thiago V. dos Santos

PhD student
Land and Atmospheric Science
University of Minnesota
On Saturday, May 21, 2016 3:54 PM, Lo?c Dutrieux <loic.dutrieux at wur.nl> wrote:
Hi Thiago,

calc is not aware of neighbouring pixels in the x,y dimensions, so 
functions like focal cannot work.

I found the function below in an old repos of mine. It still seems to 
work fine :)

#' Focal for RasterBrick or RasterStack
#'
#' @param x RasterBrick/Stack or character pointing to multilayer raster 
object written on disk
#' @param w See \code{\link{focal}}
#' @param ... Arguments to be passed to \code{\link{focal}}
#'
#' @import raster
#' @export
#'

multiFocal <- function(x, w=matrix(1, nr=3, nc=3), ...) {

   if(is.character(x)) {
     x <- brick(x)
   }
   # The function to be applied to each individual layer
   fun <- function(ind, x, w, ...){
     focal(x[[ind]], w=w, ...)
   }

   n <- seq(nlayers(x))
   list <- lapply(X=n, FUN=fun, x=x, w=w, ...)

   out <- stack(list)
   return(out)
}
On 05/21/2016 10:02 PM, Thiago V. dos Santos via R-sig-Geo wrote:
multiFocal(b, w=matrix(1, 5, 5), mean)

Cheers,
Lo?c

            

      
      
      
    

        
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