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

[João Carreiras]

Dear Mike,

great and many thanks as this is exactly what I was after.

Cheers
Joao

On 25 May 2018 at 12:58, Michael Sumner <mdsumner using gmail.com> wrote:
> 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
>