[R-sig-Geo] Assign a unique ID number to each patch in a raster

[John Baumgartner]

Yes, my gist mentioned by Agustin should do the trick. See the example in
the comment at https://gist.github.com/johnbaums/6d155cfca28e02b05ad5.

On Sun, 26 Feb 2017 at 21:42, Agustin Lobo <alobolistas at gmail.com> wrote:

> 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
>
> >>
>
> >>
>
> >> _______________________________________________
>
> >> R-sig-Geo mailing list
>
> >> R-sig-Geo at r-project.org <mailto:R-sig-Geo at r-project.org>
>
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo <
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo>
>
> > Ben Tupper
>
> > Bigelow Laboratory for Ocean Sciences
>
> > 60 Bigelow Drive, P.O. Box 380
>
> > East Boothbay, Maine 04544
>
> > http://www.bigelow.org
>
> >
>
> >
>
> >
>
> >
>
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>
> >
>
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>
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>
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>
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>
>
>
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