zeroasna

R/generics.R

@@ -5,9 +5,9 @@
 
 
 setMethod("patches", signature(x="SpatRaster"), 
-	function(x, directions=4, filename="", ...) {
+	function(x, directions=4, zeroAsNA=FALSE, filename="", ...) {
 		opt <- spatOptions(filename, ...)
-		x@ptr <- x@ptr$patches(directions[1], opt)
+		x@ptr <- x@ptr$patches(directions[1], zeroAsNA[1], opt)
 		messages(x, "patches")
 	}
 )

man/patches.Rd

@@ -6,16 +6,17 @@
 \title{Detect patches (clumps) of cells}
 
 \description{
-Detect patches (clumps). Patches are groups of cells that are surrounded by cells that are \code{NA}. To also ignore cells that are zero, first use \code{\link{classify)} (see examples below).
+Detect patches (clumps). Patches are groups of cells that are surrounded by cells that are \code{NA}. Set \code{zeroAsNA} to \code{TRUE} to also identify patches separated by cells with values of zero. 
 }
 
 \usage{
-\S4method{patches}{SpatRaster}(x, directions=4, filename="", ...)
+\S4method{patches}{SpatRaster}(x, directions=4, zeroAsNA=FALSE, filename="", ...)
 }
 
 \arguments{
 \item{x}{SpatRaster}
 \item{directions}{integer indicating which cells are considered adjacent. Should be 8 (Queen's case) or 4 (Rook's case)}
+  \item{zeroAsNA}{logical. If \code{TRUE} treat cells that are zero as if they were \code{NA}}
   \item{filename}{character. Output filename}
   \item{...}{options for writing files as in \code{\link{writeRaster}}}
 }
@@ -41,15 +42,16 @@ r[4, 4] <- 10
 r[5, 5:8] <- 12
 r[6, 6:9] <- 12
 
-# remove zeros if need be
-r <- classify(r, cbind(0, NA))
+# remove zeros if need be with zeroAsNA
 
-p4 <- patches(r)
-p8 <- patches(r, 8)
+p4 <- patches(r, zeroAsNA=TRUE)
+p8 <- patches(r, 8, zeroAsNA=TRUE)
 
 # patches for different values
+# remove zeros
+rr <- classify(r, cbind(0, NA))
 # first make layers for each value
-s <- separate(r, keep=TRUE, other=NA)
+s <- separate(rr, keep=TRUE, other=NA)
 p <- patches(s)
 
 }

src/clump.cpp

@@ -158,7 +158,7 @@ void broom_clumps(std::vector<double> &v, std::vector<double>& above, const size
 
 
 
-SpatRaster SpatRaster::clumps(int directions, SpatOptions &opt) {
+SpatRaster SpatRaster::clumps(int directions, bool zeroAsNA, SpatOptions &opt) {
 
 	SpatRaster out = geometry(1);
 	if (nlyr() > 1) {
@@ -168,7 +168,7 @@ SpatRaster SpatRaster::clumps(int directions, SpatOptions &opt) {
 		for (size_t i=0; i<nlyr(); i++) {
 			std::vector<unsigned> lyr = {(unsigned)i};
 			SpatRaster x = subset(lyr, ops);
-			x = x.clumps(directions, ops);
+			x = x.clumps(directions, zeroAsNA, ops);
 			out.addSource(x);
 		}
 		if (filename != "") {
@@ -212,13 +212,15 @@ SpatRaster SpatRaster::clumps(int directions, SpatOptions &opt) {
 	std::vector<std::vector<size_t>> rcl(2);
 	for (size_t i = 0; i < out.bs.n; i++) {
         v = readBlock(out.bs, i);
+		if (zeroAsNA) {
+			std::replace(v.begin(), v.end(), 0.0, NAN);
+		}
         broom_clumps(v, above, directions, ncps, out.bs.nrows[i], nc, rcl);
 		if (!out.writeValues(v, out.bs.row[i], out.bs.nrows[i], 0, nc)) return out;
 	}
 	out.writeStop();
 	readStop();
 
-
 	opt.set_filenames({filename});
 	if (rcl[0].size() > 0) {
 		//for (size_t i=0; i<rcl[0].size(); i++) {

src/spatRaster.h

@@ -499,7 +499,7 @@ class SpatRaster {
         SpatRaster disaggregate(std::vector<unsigned> fact, SpatOptions &opt);
 		SpatRaster distance(SpatOptions &opt);
 		SpatRaster distance(SpatVector p, SpatOptions &opt);
-		SpatRaster clumps(int directions, SpatOptions &opt);
+		SpatRaster clumps(int directions, bool zeroAsNA, SpatOptions &opt);
 
 		SpatRaster edges(bool classes, std::string type, unsigned directions, SpatOptions &opt);
 		SpatRaster extend(SpatExtent e, SpatOptions &opt);