Remove clumps of pixels in R

Question

I would like to remove isolated pixels (or clumps of pixels <9) from my raster image.

library(raster)
# create some raster data
r <- raster(ncols=12, nrows=12)
set.seed(0)
r[] <- round(runif(ncell(r))*0.7 )
rc <- clump(r) 

Before removing clumps of pixels <9

After removing clumps of pixels <9 :

In Erdas, there is the Sieve tool to do this, but how to replace it in R?

Answer 1

Thanks to @gene and https://geoscripting-wur.github.io/AdvancedRasterAnalysis/ I can now answer my question (copied and modified):

library(raster)

# create some raster data
r <- raster(ncols=12, nrows=12)
set.seed(0)
r[] <- round(runif(ncell(r))*0.7 )
r[r==0]<-NA

# extend r with a number of rows and culomns (at each side)
# to isolate clumps adjacents to plot axes 
r2<-extend(r, c(1,1))
rc <- clump(r2, directions = 8) 

# get frequency table    
f<-freq(rc)
# save frequency table as data frame
f<-as.data.frame(f)

# which rows of the data.frame are only represented by clumps under 9pixels?
str(which(f$count <= 9))
# which values do these correspond to?
str(f$value[which(f$count <= 9)])
# put these into a vector of clump ID's to be removed
excludeID <- f$value[which(f$count <= 9)]

# make a new raster to be sieved
formaskSieve <- rc
# assign NA to all clumps whose IDs are found in excludeID
formaskSieve[rc %in% excludeID] <- NA

plot(formaskSieve)

and result wanted (with one row and one column of NA added on each side of raster).

Answer 2

#reproducible example
r <- raster(ncols=12, nrows=12)
set.seed(0)
r[] <- round(runif(ncell(r))*0.7 )
rc <- clump(r) 

#extract IDs of clumps according to some criteria
clump9 = data.frame(freq(rc))
clump9 = clump9[ ! clump9$count < 9, ] #remove clump observations with frequency smaller than 9
clump9 = as.vector(clump9$value) # record IDs from clumps which met the criteria in previous step

rc[rc != clump9[1] & rc != clump9[2]] = NA #replace cells with IDs which do not belong to the group of interest 

plot(rc,col="black",legend=FALSE)

Note that from the clump function, the clump ID "4" had 2 cells in the right side connecting with cells on the left.

head(rc)
    1  2  3  4  5  6  7  8  9 10 11 12
1  NA NA NA NA  2 NA  2  2 NA NA NA NA
2  NA NA NA  2 NA  2  2 NA  2  2 NA NA
3  NA NA NA NA NA  2 NA NA NA NA NA NA
4  NA  4 NA  2 NA  2 NA NA NA NA NA NA
5  NA  4 NA NA  2 NA NA NA NA NA NA NA
6  NA  4 NA NA NA NA NA NA NA NA NA NA
7   4 NA NA NA NA NA NA NA NA NA NA NA
8  NA  4 NA NA NA NA NA NA NA NA  4  4
9   4 NA NA NA NA NA NA NA NA NA NA NA
10 NA  4 NA NA NA NA NA NA NA NA NA NA

Answer 3

An additional answer for projected data. bfastSpatial::areaSieve() takes a threshold argument, such that clumps smaller than the threshold are removed.

https://www.rdocumentation.org/packages/bfastSpatial/versions/0.6.2/topics/areaSieve