I have a binary raster in R. It has only 55 cells with value 1 and all the others have value 0 or NA. Now I want to write 55 rasters. For each cell with value 1, I want to write one raster. In these final rasters I only want to have one cell with value 1. My Idea is to loop through all the cells of the input-raster and in case it finds a cell with value 1 write a new raster with only that cell beeing of value 1 and all others of value 0 or NA.

The input raster looks like this:

class      : RasterLayer 
dimensions : 1482, 1274, 1888068  (nrow, ncol, ncell)
resolution : 12.5, 12.5  (x, y)
extent     : 347279.6, 363204.6, 6255207, 6273732  (xmin, xmax, ymin, ymax)
crs        : +proj=utm +zone=19 +south +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0 
source     : memory
names      : raster
values     : 0, 1  (min, max)

My idea would lood kind of like this:

for (i in 1:length(raster){
    if (raster[i] == 1){
    name = paste0("rastercell_", i, ".tif")
    ras = raster(...)
    writeRaster(ras, name)

It's just that I don't know how to create the raster (ras = raster()) from scratch with only that single cell being of value 1 and all others 0 or NA.

  • 1
    Did you use the python tag by mistake or are you willing to use Python to accomplish this as well? Commented Mar 2, 2020 at 15:27
  • sorry the confusion. This was due to my mixed up head.. Commented Mar 2, 2020 at 15:33
  • 1
    This workflow is unique! Could you please describe what your ultimate goal is? Perhaps we can recommend a different approach.
    – Aaron
    Commented Mar 2, 2020 at 15:40
  • My goal is to run a module from SAGA GIS to model the runout length for debris flows. This model takes as input a raster with release cells. And I wanted a single result for each cell;) Don't know if this helped... Commented Mar 2, 2020 at 16:56

2 Answers 2


It seems like there might be a better solution to the basic issue, but without details on what that is, we can only solve the stated problem. So let us do that...
Let us start by reducing the length of the loop. There is absolutely no reason to iterate over all the 0-pixels, when you only want the 1s.

targetPixels <- which(values(inputRaster)==1)

From there, we go onto the loop:

for (i in targetPixels){
  if (inputRaster[i] == 1){
    name <- paste0("rastercell_", i, ".tif")
    ras <- inputRaster*0   # creating a raster that is entirely 0
    ras[i] <- 1            # putting in the single 1
    writeRaster(ras, name) # writing the raster
  • thank you very much!! Already helped a lot!! Commented Mar 2, 2020 at 15:34
  • @RobinKohrs - don't forget to upvote / accept answers that provide you with the requested information. :) Commented Mar 2, 2020 at 15:38
  • 1
    right right sorry about that. Completely forgot it... Commented Mar 2, 2020 at 15:39

Just for reference, here is another way to do this. Functionally, I create a vector of cell ids that have the desired value in the original raster. Then I replicate the raster into a stack and iterate through each raster in the stack, turning everything but the single index cell location to zeros.

First, create some example data

r <- raster(nrow=20,ncol=20)
  r[] <- rep(0,ncell(r))
    r[sample(1:ncell(r),5)] <- 1

Then, create a cell index and a stack of the replicated raster. The idx vector represents all of the cells in the raster and is used to assign zeros.

n = which(r[] == 1)
  idx <- 1:ncell(r)
    r <- stack(replicate(length(n), r))

for(i in 1:length(n)) { 
  r[[i]][idx[-n[i]]] <- 0


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