Assign a unique ID number to each patch in a raster

I think Nelly points out that package raster lacks a more general

clumping tool (i.e., the equivalent to r.clump in grass) that I've

often missed too.

I'm not sure circumventing the way Ben suggest would work for large

raster layers, for which package raster was designed.

I have a note to myself regarding this

https://gist.github.com/johnbaums/6d155cfca28e02b05ad5

and

www.openforis.org/tools/geospatial-toolkit.html

but have not tried it.



Agus



On Fri, Jan 27, 2017 at 1:19 AM, Ben Tupper <btupper at bigelow.org> wrote:

Hi,

I think you are asking for connected component labeling. raster::clump()

expects your features to be like islands surrounded by NA or 0 background.
There might be more Raster* centric ways to do it, but you could use plain
old vanilla image processing using the very good imager package (
https://cran.r-project.org/web/packages/imager/ <
https://cran.r-project.org/web/packages/imager/> ).  The steps below show
in color your actual values with the connected component IDs labeled on
each cell.  I used the 8-connected labeling but 4-connected is also
available.

library(raster)

library(imager)

set.seed(10)

nc <- 8

nr <- 8

MIN <- 1

MAX <- 4

LUT <- c("orange", "green", "darkgoldenrod", "cornflowerblue")

r <- raster(ncols=nc, nrows=nr)

r[] <- round(runif(ncell(r),MIN, MAX),digits=0)

cc <- r

img <- imager::as.cimg(as.matrix(r))

labeled <- imager::label(img, high_connectivity = TRUE)

cc[] <- as.matrix(labeled)

plot(r, col = LUT)

txt <- cc[]

xy <- raster::xyFromCell(cc, 1:raster::ncell(cc))

text(xy[,1], xy[,2], txt )

Cheers,

Ben

On Jan 26, 2017, at 4:48 PM, Nelly Reduan <nell.redu at hotmail.fr> wrote:

Hello,

I would like to assign a unique ID number to each patch (a patch is

composed of a set of adjacent cells) as shown in this figure:

 <2328.png>

I tested the clump function (package raster) by applying an eight

adjacent cells rule but this function mixes all cell values into single
patch.

Here is a code example to create a raster. The raster contains values

ranged from 1 to 9.

r <- raster(ncols=12, nrows=12)

r[] <- round(runif(ncell(r),1,9),digits=0)

plot(r)

Is there a way to assign a unique ID number to grouping cells that form

a patch for each class (i.e., values 1, 2, 3, 4, 5, 6, 7, 8, 9) ?

Thanks a lot for your time

Nell

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