[R-sig-Geo] Create pixels neighborhood in a raster

[Ben Tupper]

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 <alexandresantosbr using 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 using 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 using 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