Thanks Ben,
Little things do matter, I changed cells<- xyFromCell(antscount, ants1)
by cells <- unique(cellFromXY(antscount, geo.form)) and works!!
Final solution:
#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)
# For 1 pixel neighborhood
neigh1 <- matrix(1L, nrow=3, ncol=3); neigh1[2,2] <- 0L
ants1<-which(values(antscount)> 0)
cells <- unique(cellFromXY(antscount, geo.form))
e1<-adjacent(antscount, cells, directions=neigh1, pairs=FALSE)
ng_coords1 <- xyFromCell(antscount, e1)
points(ng_coords1, col="red")
#Rasterize for 1 pixel neighborhood
ng_coords2<-rbind(ng_coords1,geo.form)
antscount.9<- rasterize(ng_coords2, raster(ants.res), fun='count',
background=0)
values(antscount.9)[values(antscount.9) > 0] = 1
plot(antscount.9)
--
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 10/11/2020 09:24, Ben Tupper escreveu:
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/
--
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