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

[ASANTOS]

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/
>> --
>>
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>