address r-spatial/stars#484

* handle 0 and gaps in attribute and color tables

R/stars.R

@@ -43,22 +43,42 @@ gdal_write = function(x, ..., file, driver = "GTiff", options = character(0), ty
 		from = c(0, 0) # nocov end
 	} else {
 		mat = x[[1]]
+		dm = dim(mat)
+		if (is.factor(mat)) {
+			rgba = NULL
+			ex = attr(mat, "exclude")
+			if (is.null(ex))
+				lev = c("", levels(mat)) # add "" for value 0: R factors start at 1
+			else {
+				if (any(ex)) {
+					lev = vector("character", length(ex)) # fills with ""
+					lev[!ex] = levels(mat)
+					rgba = if (!is.null(co <- attr(mat, "rgba"))) {
+						n = length(ex)
+						coltab = cbind(rep(0., n), rep(0, n), rep(0, n), rep(255, n))
+						coltab[!ex,] = co
+						coltab 
+					}
+					values = which(!ex) - 1
+					mat = values[as.numeric(mat)]
+				} else
+					lev = levels(mat)
+			}
+			mat = structure(mat, class = NULL, levels = lev, dim = dm, rgba = rgba)
+		}
 		only_create = FALSE # write x too
 		if (! update) {
 			if (!all(from == 0))
 				stop("cannot write sub-rasters only")
-			if (!all(dims == dim(mat)))
+			if (!all(dims == dm))
 				stop("dimensions don't match")
 		}
-		dm = dim(mat)
 		dim(mat) = c(dm[1], prod(dm[-1])) # flatten to 2-D matrix
 	}
 	if (length(dims) == 2)
 		dims = c(dims, 1) # one band
-	else { # add band descriptions?
-		if (is.character(d[[3]]$values))
-			attr(mat, "descriptions") = d[[3]]$values
-	}
+	else if (is.character(d[[3]]$values)) # add band descriptions?
+		attr(mat, "descriptions") = d[[3]]$values
 
 	CPL_write_gdal(mat, file, driver, options, type, dims, from, geotransform,
 		st_crs(x)[[2]], as.double(NA_value), create = !update, only_create = only_create)

src/stars.cpp

@@ -589,13 +589,9 @@ void CPL_write_gdal(NumericMatrix x, CharacterVector fname, CharacterVector driv
 		// write factor levels to CategoryNames:
 		if (x.attr("levels") != R_NilValue) {
 			Rcpp::CharacterVector levels = x.attr("levels");
-			Rcpp::CharacterVector l(levels.size() + 1);
-			l[0] = ""; // levels start at 1, CategoryNames at 0.
-			for (int i = 0; i < levels.size(); i++)
-				l[i+1] = levels[i];
 			for (int band = 1; band <= dims(2); band++) {
 				GDALRasterBand *poBand = poDstDS->GetRasterBand( band );
-				if (poBand->SetCategoryNames(create_options(l).data()) != CE_None)
+				if (poBand->SetCategoryNames(create_options(levels).data()) != CE_None)
 					warning("error writing factor levels to raster band");
 			}
 		}
@@ -604,14 +600,12 @@ void CPL_write_gdal(NumericMatrix x, CharacterVector fname, CharacterVector driv
 			Rcpp::NumericMatrix co = x.attr("rgba"); // r g b alpha in columns; levels in rows
 			GDALColorTable ct = GDALColorTable(GPI_RGB);
 			GDALColorEntry ce;
-			ce.c1 = 0; ce.c2 = 0; ce.c3 = 0; ce.c4 = 0;
-			ct.SetColorEntry(0, &ce);
 			for (int i = 0; i < co.nrow(); i++) {
 				ce.c1 = co(i, 0);
 				ce.c2 = co(i, 1);
 				ce.c3 = co(i, 2);
 				ce.c4 = co(i, 3);
-				ct.SetColorEntry(i + 1, &ce);
+				ct.SetColorEntry(i, &ce);
 			}
 			GDALRasterBand *poBand = poDstDS->GetRasterBand( 1 ); // can only set CT for band 1
 			if (poBand->SetColorTable(&ct) != CE_None)