I am struggling with the task to set one point in each pixel (of a given raster) in a distance of 3km of my points.

I tried buffering in QGIS and R but cannot find a way to set exactly one point in each pixel. I think it will work with creating a matrix around the points but I couldn´t find a way doing this.

Data: 46 species presence points; Raster Stack with environmental Data Res: 100x100m

enter image description here

raster with presence points (zoomed in)

Crosses: pts; false buffers in purple

presence points: black crosses, buffers(false): purple, backgroundraster: allbands

enter image description here



# Points in Matrix around Presence Data 

# #---------------------------------------------------------------------
# Prework

# Packs 

# Data 

# Presence Points: 
pts <-readOGR("D://GIDEON_korrigiert_aktuell_repro_EPSG32648_forR.shp")

> pts
class       : SpatialPointsDataFrame 
features    : 46 
extent      : -507313, 812849.9, 761011.2, 2831574  (xmin, xmax, ymin, ymax)
crs         : +proj=utm +zone=48 +datum=WGS84 +units=m +no_defs 
variables   : 2
names       :    Lat,     Lon 
min values  : 10,230, 100,030 
max values  :  7,880,  99,950 

# Raster: 
allbands <- raster("D:/Database/AllReproCliped_for_DOWN/ForestFrek/Stack_8er_Prec_Wet_Temp_Land_Tree_Short_Bare_ForestFrek.tif")

> allbands
class      : RasterLayer 
band       : 1  (of  8  bands)
dimensions : 23913, 17032, 407286216  (nrow, ncol, ncell)
resolution : 106.8938, 106.8938  (x, y)
extent     : -835901.2, 984713.7, 624198, 3180349  (xmin, xmax, ymin, ymax)
crs        : +proj=utm +zone=48 +datum=WGS84 +units=m +no_defs 
source     : D:/Chris/Studium/BA/QGIS_Datein/Database/AllReproCliped_for_DOWN/ForestFrek/Stack_8er_Prec_Wet_Temp_Land_Tree_Short_Bare_ForestFrek.tif 
names      : Stack_8er_Prec_Wet_Temp_Land_Tree_Short_Bare_ForestFrek 
values     : -6.3375, 28.77083  (min, max)

# Plot 

plot(pts, add= TRUE)

enter image description here

# Buffer 

pres_st <- st_as_sf(pts, crs= "bogus")

d = 3000 
buf <- st_buffer(pres_st, dist=d)

gridpts <- st_as_sf(
    mask(allbands, buf),



enter image description here

plot(pts, add=TRUE)
plot(gridpts, add=TRUE)

enter image description here


  • 1
    I can't quite understand what your expected output is. Your input is 46 points and a raster. Is your output a set of points? 46 of them? Or do you want a point for every pixel in your raster? Across the whole of your raster, or only the non-missing area (land?)?
    – Spacedman
    Apr 27 '21 at 7:44
  • My expected output is a layer with spatial points around my existing presence points. Apr 27 '21 at 8:18
  • Try Raster Sampling in the Toolbox. It samples the raster at the vector locations.
    – wingnut
    Apr 27 '21 at 9:33
  • 1
    Please Edit the question in response to requests for clarification. Code in comments is barely legible to illegible, depending on the language.
    – Vince
    Apr 27 '21 at 13:29
  • 1
    That looks like it has not picked up the X and Y coordinates from the as.data.frame conversion of the raster. Try coords=c("x","y") instead of coords=1:2?
    – Spacedman
    Apr 30 '21 at 13:55

I have a dem and some points:

> plot(dem)
> plot(pts, add=TRUE)

enter image description here

I'll make a 1km buffer for my data:

> d = 1000
> buf = st_buffer(pts, dist=d)

Then I can get all the grid points in the buffer by masking the DEM to the buffer and taking all the coordinates of non-NA pixels and making an sf points data frame out of them:

> gridpts = st_as_sf(

which looks like this:

enter image description here

which is actually nearly 3000 points so close together you can't tell them apart.

  • This works perfectly. Thank you very much for that. Unfortunately it does not work with my data. I have updated the post so you can see the problem. When I plot the points by themselves, they are all in line with each other and not near my presence points.I have tried data conversion but could not find a solution. Apr 30 '21 at 8:41
  • If my answer doesnt work then why have you ticked it as an accepted answer? I still can't see the problem even after your edit. What points are "all in a line with each other"? I don't see points in a line on your question.
    – Spacedman
    Apr 30 '21 at 8:49
  • Thanks for noticing that! I have updated the post to make it clearer. Apr 30 '21 at 9:08
  • 1
    Its not clearer unless you include the code you used! From your edits I see you have a SpatialPointsDataFrame which will not work with my code because I'm using the sf package, and functions like st_buffer will not work with that. Show your working in your question alongside the summary outputs of your data objects.
    – Spacedman
    Apr 30 '21 at 9:45

Here is an approach with terra

Example data

#terra version 1.2.5
f <- system.file("ex/elev.tif", package="terra")
r <- rast(f)
pts <- spatSample(r, 2, xy=TRUE, values=FALSE, as.points=TRUE, na.rm=TRUE)


b <- buffer(pts, 5000)
cnrs <- cells(r, b)
xy <- xyFromCell(r, cnrs[,2])

lines(b, col="red", lwd=2)

enter image description here

  • I tried your solution with the exact same data but got the error: Error in .local(x, ...) : not used argument (values = FALSE, as.points = TRUE) when running pts <- .... // terra version: terra_1.1-17 Apr 28 '21 at 15:57
  • You need current terra (version 1.2-5) May 4 '21 at 5:00

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