focalCpp: Compute focal values with an iterating C++ function

In terra: Spatial Data Analysis

Compute focal values with an iterating C++ function

Description

Calculate focal values with a C++ function that iterates over cells to speed up computations by avoiding an R loop (with apply).

See focal for an easier to use method.

Usage

## S4 method for signature 'SpatRaster'
focalCpp(x, w=3, fun, ..., fillvalue=NA, 
		silent=TRUE, filename="", overwrite=FALSE, wopt=list())

Arguments

x	SpatRaster
w	window. The window can be defined as one (for a square) or two numbers (row, col); or with an odd-sized weights matrix. See the Details section in focal
fun	cppFunction that iterates over cells. For C++ functions that operate on a single focal window, or for R functions use focal instead. The function must have at least three arguments. The first argument can have any name, but it must be a Rcpp::NumericVector, Rcpp::IntegerVector or a std::vector<double>. This is the container that receives the focal values. The other two arguments ni and wi must be of type size_t. ni represents the number of cells and nw represents the size of (number of elements in) the window
...	additional arguments to fun
fillvalue	numeric. The value of the cells in the virtual rows and columns outside of the raster
silent	logical. If TRUE error messages are printed that may occur when trying fun to determine the length of the returned value. This can be useful in debugging a fun that does not work
filename	character. Output filename
overwrite	logical. If TRUE, filename is overwritten
wopt	additional arguments for writing files as in writeRaster

Value

SpatRaster

See Also

focal, focalValues

Examples

## Not run: 
library(Rcpp)
cppFunction( 
	'NumericVector sum_and_multiply(NumericVector x, double m, size_t ni, size_t nw) {
		NumericVector out(ni);
		// loop over cells
		size_t start = 0;
		for (size_t i=0; i<ni; i++) {
			size_t end = start + nw;
			// compute something for a window
			double v = 0;
			// loop over the values of a window
			for (size_t j=start; j<end; j++) {
				v += x[j];
			}
			out[i] = v * m;
			start = end;
		}
		return out;
	}'
)

nr <- nc <- 10
r <- rast(ncols=nc, nrows=nr, ext= c(0, nc, 0, nr))
values(r) <- 1:ncell(r)

raw <- focalCpp(r, w=3, fun=sum_and_multiply, fillvalue=0, m=10)

# same as
f1 <- focal(r, w=3, fun=sum, fillvalue=0) *10
all(values(f1) == values(raw))

# and as
ffun <- function(x, m) { sum(x) * m }
f2 <- focal(r, w=3, fun=ffun, fillvalue=0, m=10)


# You can also use an R function with focalCpp but this
# is not recommended 

R_sm_iter <- function(x, m, ni, nw) {
	out <- NULL
	for (i in 1:ni) {
		start <- (i-1) * nw + 1
		out[i] <- sum(x[start:(start+nw-1)]) * m
	}
	out
}

fr <- focalCpp(r, w=3, fun=R_sm_iter, fillvalue=0, m=10)


## End(Not run)

terra documentation built on Oct. 14, 2024, 5:07 p.m.