[R-sig-Geo] raster::clump not working?

[Michael Sumner]

Joao, this is what you are after I think.  It's important to use
sf/fasterize otherwise any holes filled by other patches won't be
identified (and it's faster). It won't scale well given rasterToPolygons,
but there might be other options using sf related tricks.

library(raster)
r <- raster(volcano) %/% 20
## p has six distinct values (multipolygons)
p <- rasterToPolygons(r, dissolve = TRUE)
## pp has ten distinct patches
pp <- disaggregate(p)
pp$patch <- seq_len(nrow(pp))

## back to raster
#rr <- rasterize(pp, r, field = pp$patch)
# or faster with sf/fasterize (also this gets the holes filled correctly)
rr <- fasterize::fasterize(sf::st_as_sf(pp), r, field = "patch")
unique(values(rr))

Cheers, Mike.


On Fri, 25 May 2018 at 21:15 João Carreiras <jmbcarreiras using gmail.com> wrote:

> Dear Ben,
>
> Thank you for your prompt reply.
>
> Now I see what clump does. I just thought clump would give the same
> result as ArcGIS "Region Group". I need some command to assign a
> different value to each patch. And by patch I mean contiguous pixels
> having the same value, so that in this (absurd) example I would get
> 648 patches.
>
> Take care
> Joao
>
> On 25 May 2018 at 11:35, Ben Tupper <btupper using bigelow.org> wrote:
> > Hi,
> >
> > I think it is actually correct - there is only one 'clump' of connected
> > cells.  In raster clumps are separated from other clumps by backgound (0
> or
> > NA).  In your example there is no background anywhere so there is just
> one
> > clump.
> >
> > You can see the difference if you divide x in to halves with a row of
> NAs.
> > Note that limited spatial extent so the clumping doesn't wrap around the
> > globe which it will for [-180, 180].
> >
> > r <- raster(ncols=36, nrows=18, xmn = 0, xmx = 36, ymn = 0, ymx = 18)
> > x <- init(r, fun='cell')
> >
> > x[9,1:36] <- NA
> > y <- clump(x)
> > y
> > # class       : RasterLayer
> > # dimensions  : 18, 36, 648  (nrow, ncol, ncell)
> > # resolution  : 1, 1  (x, y)
> > # extent      : 0, 36, 0, 18  (xmin, xmax, ymin, ymax)
> > # coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
> > # data source : in memory
> > # names       : clumps
> > # values      : 1, 2  (min, max)
> >
> > x[1:18, 18] <- NA
> > y
> > # class       : RasterLayer
> > # dimensions  : 18, 36, 648  (nrow, ncol, ncell)
> > # resolution  : 1, 1  (x, y)
> > # extent      : 0, 36, 0, 18  (xmin, xmax, ymin, ymax)
> > # coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
> > # data source : in memory
> > # names       : clumps
> > # values      : 1, 4  (min, max)
> >
> >
> > Cheers,
> > Ben
> >
> >
> > On May 25, 2018, at 6:00 AM, João Carreiras <jmbcarreiras using gmail.com>
> wrote:
> >
> > Hi!
> >
> > I've been trying to run the clump command but the output is consistently
> a
> > raster with values == 1. Please find below an example.
> >
> > I'm sure I'm doing something stupid. However, the command is really
> > straightforward and I can't seem to identify what the problem might be.
> >
> > Any help really appreciated.
> > Thanks
> > Joao
> >
> > r <- raster(ncols=36, nrows=18)
> > x <- init(r, fun='cell')
> > x
> > class       : RasterLayer
> > dimensions  : 18, 36, 648  (nrow, ncol, ncell)
> > resolution  : 10, 10  (x, y)
> > extent      : -180, 180, -90, 90  (xmin, xmax, ymin, ymax)
> > coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
> > data source : in memory
> > names       : layer
> > values      : 1, 648  (min, max)
> > a <- clump(x)
> > a
> > class       : RasterLayer
> > dimensions  : 18, 36, 648  (nrow, ncol, ncell)
> > resolution  : 10, 10  (x, y)
> > extent      : -180, 180, -90, 90  (xmin, xmax, ymin, ymax)
> > coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
> > data source : in memory
> > names       : clumps
> > values      : 1, 1  (min, max)
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > R-sig-Geo using r-project.org
> > 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
> >
> > Ecological Forecasting: https://eco.bigelow.org/
> >
> >
> >
> >
> >
>
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-- 
Dr. Michael Sumner
Software and Database Engineer
Australian Antarctic Division
203 Channel Highway
Kingston Tasmania 7050 Australia

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