Hi, Thanks for updating the example - it is much easier. I'm still not sure of exactly what you are after, but my day is young and there is still coffee to be had.
One thing I suggest is that you modify your computation of cells. As you have it, you are computing a matrix of x and y locations. > cells<- xyFromCell(antscount, ants1) But I really think you want to compute the cell numbers (1,2,3,... left-to-right, top-to-bottom) from your original data locations (your geo.form). Also, if I have followed correctly, I think you are looking for a list of occupied cells regardless of how many ants in each cell. > cells <- unique(cellFromXY(antscount, geo.form)) Then I get a series of plots that "look" right to me with little squares across the plot. Cheers, Ben On Mon, Nov 9, 2020 at 7:48 PM ASANTOS <alexandresanto...@yahoo.com.br> wrote: > > Dear Ben, > > Sorry about of lot of mistakes, you are sure some part of code are > confusing and/or with errors. I'll try again with some corrections: > > First, I have the rasterization process of ants presence (0 is absence) > in a 10x10 units raster: > > #Packages > library(spatstat) > library(raster) > > #Selection of ants data set > data(ants) > geo.form<-cbind(x=ants$x,y=ants$y) > > #Definition of raster resolution - 10 units > ants.w<-as.owin(ants) > ext <- as(extent(c(ants.w$xrange,ants.w$yrange)), "SpatialPolygons") > ants.res<-rasterToPoints(raster(ext, resolution = 10), spatial = TRUE) > # coerce to SpatialPixelsDataFrame > gridded(ants.res) <- TRUE > > #Rasterize > antscount<- rasterize(geo.form, raster(ants.res), fun='count', background=0) > values(antscount)[values(antscount) > 0] = 1 > > #Vizualize > plot(antscount) > > Now, I'd like to create 1 pixels around each pixel of ant presence > (Total of 9 pixels in each ant presence in antscount raster): > > # For 1 pixel neighborhood > neigh1 <- matrix(1L, nrow=3, ncol=3); neigh1[2,2] <- 0L > ants1<-which(values(antscount)> 0) > cells<- xyFromCell(antscount, ants1) > e1<-adjacent(antscount, cells, directions=neigh1, pairs=FALSE) > ng_coords1 <- xyFromCell(antscount, e1) > points(ng_coords1, col="red") > > I need that's this new create pixels has 1 as value too. > > #Rasterize for 1 pixel neighborhood > antscount.9<- rasterize(ng_coords1 , raster(ants.res), fun='count', > background=0) > plot(antscount.9) > > The problem is my ng_coords1 coordinates is wrong and just only in the > top of the antscount raster, despite xyFromCell(antscount, ants1) > condition. My goal is a new ant presence raster with 8 pixels > surrounding the neigourhood of each pixel (ant) in the original > antscount raster. > > Any ideas? > > Thanks in advanced, > > Alexandre > > > -- > Alexandre dos Santos > Geotechnologies and Spatial Statistics applied to Forest Entomology > Instituto Federal de Mato Grosso (IFMT) - Campus Caceres > Caixa Postal 244 (PO Box) > Avenida dos Ramires, s/n - Vila Real > Caceres - MT - CEP 78201-380 (ZIP code) > Phone: (+55) 65 99686-6970 / (+55) 65 3221-2674 > Lattes CV: http://lattes.cnpq.br/1360403201088680 > OrcID: orcid.org/0000-0001-8232-6722 > ResearchGate: www.researchgate.net/profile/Alexandre_Santos10 > Publons: https://publons.com/researcher/3085587/alexandre-dos-santos/ > -- > > Em 09/11/2020 19:41, Ben Tupper escreveu: > > Hi, > > > > Your example isn't fully reproducible. Or maybe it just has some little > > errors. I can't get past this spot... > > > > ants.w<-as.owin(ants) > >> ext <- as(extent(c(ants.w$xrange,ants.w$yrange)), "SpatialPolygons") > >> ants.res<-rasterToPoints(raster(ext, resolution = 10), spatial = TRUE) > >> coordinates(ants.res) <- ~ x + y > >> > > You have requested that raster::rasterToPoints() return a spatial points > > object, so there shouldn't be a need for sp::coordinates() to cast to a > > spatial object. > > > > Also, I think you are invoking "antscounts" and "antscount" as the same > > variable. Maybe? It's not clear to me. > > > > Finally, when you call raster::adjacent() you haven't defined the value for > > the cells argument when computing e1 and e2. What do you want them to be? > > > > I wish I could be more helpful. > > > > Cheers, > > Ben > > > > On Mon, Nov 9, 2020 at 12:46 PM ASANTOS via R-sig-Geo < > > r-sig-geo@r-project.org> wrote: > > > >> Dear r-sig-geo Members, > >> > >> I'd like to find any way to create 1 (total 9 pixels) and 2 pixels > >> (total 25 pixels) surrounding the neighborhood of each pixel (ant) in my > >> plot image (antscount). > >> > >> In my example: > >> > >> #Packages > >> library(spatstat) > >> library(raster) > >> > >> #Selection of ants data set > >> data(ants) > >> geo.form<-cbind(x=ants$x,y=ants$y) > >> > >> #Definition of raster resolution - 10 units > >> ants.w<-as.owin(ants) > >> ext <- as(extent(c(ants.w$xrange,ants.w$yrange)), "SpatialPolygons") > >> ants.res<-rasterToPoints(raster(ext, resolution = 10), spatial = TRUE) > >> coordinates(ants.res) <- ~ x + y > >> # coerce to SpatialPixelsDataFrame > >> gridded(ants.res) <- TRUE > >> > >> #Rasterize > >> antscount<- rasterize(geo.form, raster(ants.res), fun='count', > >> background=0) > >> values(antscount)[values(antscount) > 0] = 1 > >> > >> #Vizualize > >> plot(antscounts) > >> > >> Now, the selection of neighborhood pixels sounds easy, something like: > >> > >> # For 1 pixel neighborhood > >> neigh1 <- matrix(1L, nrow=3, ncol=3) > >> e1<-adjacent(antscounts, cells , directions=neigh1, pairs=FALSE) > >> ng_coords1 <- xyFromCell(antscounts, e1) > >> > >> # For 2 pixel neighborhood > >> neigh2 <- matrix(1L, nrow=5, ncol=5) > >> e2<-adjacent(antscounts, cells , directions=neigh2, pairs=FALSE) > >> ng_coords5 <- xyFromCell(antscounts, e2) > >> > >> But for the combination of all the information (0 and 1 new pixel > >> values) and the new raster representation (antscounts) I don't have > >> success. Please, any ideas? > >> > >> Thanks in advanced, > >> > >> Alexandre > >> > >> -- > >> Alexandre dos Santos > >> Geotechnologies and Spatial Statistics applied to Forest Entomology > >> Instituto Federal de Mato Grosso (IFMT) - Campus Caceres > >> Caixa Postal 244 (PO Box) > >> Avenida dos Ramires, s/n - Vila Real > >> Caceres - MT - CEP 78201-380 (ZIP code) > >> Phone: (+55) 65 99686-6970 / (+55) 65 3221-2674 > >> Lattes CV: http://lattes.cnpq.br/1360403201088680 > >> OrcID: orcid.org/0000-0001-8232-6722 > >> ResearchGate: www.researchgate.net/profile/Alexandre_Santos10 > >> Publons: https://publons.com/researcher/3085587/alexandre-dos-santos/ > >> -- > >> > >> _______________________________________________ > >> R-sig-Geo mailing list > >> R-sig-Geo@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo > >> > > -- Ben Tupper Bigelow Laboratory for Ocean Science East Boothbay, Maine http://www.bigelow.org/ https://eco.bigelow.org _______________________________________________ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo