[R-sig-Geo] How to reduce the buffering time with the function "buffer" (package raster)

[Michael Sumner]

I think we still haven't seen a print of the raster object?

It may be a tiled file on disk? Try readAll to pull into memory, if it is
tiled and read in on demand via gdal tools like extract will be very slow
since access is done line by line.

But just guessing, please give full details and ideally a reproducible
example.

Cheers, Mije

On Wed, 13 Apr 2016, 02:33 Nelly Reduan <nell.redu at hotmail.fr> wrote:

> Yes, I tested the functions "distance" and "buffer" by using a cropped
> raster with around 5 million cells. But my original raster has 48096864
> cells. Ideally, I would like to build the buffers from my original raster.
> Here are some characteristics of the original raster:
>
>
> class       : RasterLayer
>
> dimensions  : 4876, 9864, 48096864  (nrow, ncol, ncell)
>
> extent      : 188384.5, 484304.5, 4914481, 5060761  (xmin, xmax, ymin,
> ymax)
>
> coord. ref. : +proj=tmerc +lat_0=0 +lon_0=-73.5 +k=0.9999 +x_0=304800
> +y_0=0 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs
>
>
> Thanks a lot for your help.
>
> Have a nice day.
>
> Nell
>
>
>
> ________________________________
> De : Forrest Stevens <r-sig-geo at forreststevens.com>
> Envoyé : lundi 11 avril 2016 18:55
> À : Nelly Reduan; Forrest Stevens; r-sig-geo at r-project.org
> Objet : Re: [R-sig-Geo] How to reduce the buffering time with the function
> "buffer" (package raster)
>
> And this is for a raster with around 5 milliion cells? Your results
> surprise me a bit, especially if the bottleneck is at the call to
> buffer()/distance().  Your best bet is to wait for a response from Robert
> Hijmans or someone else working on the package, they might have some other
> tricks up their sleeves. In any case, I agree, 5+ hours is extremely
> excessive.
>
> Sincerely,
> Forrest
>
> On Mon, Apr 11, 2016 at 6:57 PM Nelly Reduan <nell.redu at hotmail.fr<mailto:
> nell.redu at hotmail.fr>> wrote:
>
> Thank you very much Forrest for your answer. I don't think I have memory
> problems (my computer has a 32 GB memory).
>
>
> Here is my code to draw the 100-m buffers with the function "buffer"
> (package raster):
>
> r1 <- r ## r is the original raster and has a resolution of 10m
> r1[(r1[]!=2 & r1[]!=5)]=NA
> plot(r1)
> r2 <- buffer(r1, 10)
>
>
> I also tested the function distance (package raster):
>
> r1 <- r ## r is the original raster and has a resolution of 10m
> r1[(r1[]!=2 & r1[]!=5)]=NA
> plot(r1)
> r3 <- distance(r1)
>
>
> In the two cases, I stopped the functions afer 5 hours as this was too
> long ! For the moment, I haven't find solutions.
>
>
> Thanks a lot for your time.
>
> Have a nice day.
>
> Nell
>
>
>
> ________________________________
> De : Forrest Stevens <r-sig-geo at forreststevens.com<mailto:
> r-sig-geo at forreststevens.com>>
> Envoyé : lundi 11 avril 2016 09:09
> À : Nelly Reduan; r-sig-geo at r-project.org<mailto:r-sig-geo at r-project.org>
> Objet : Re: [R-sig-Geo] How to reduce the buffering time with the function
> "buffer" (package raster)
>
> Five million cells isn't all that many, how slow is too slow? Buffering a
> raster of about 10 million cells on my laptop takes on the order of 20
> seconds or so for a binary raster. Is it possible that you're fighting
> memory problems?
>
> In the past when doing multiple ring buffers I've found it faster to
> calculate a distance-to raster first, and then apply multiple logical
> comparisons on the distance raster.  I don't know if this applies to your
> situation or not but it's one trick that might help.
>
> Sincerely,
> Forrest
>
> On Mon, Apr 11, 2016 at 10:58 AM Nelly Reduan <nell.redu at hotmail.fr
> <mailto:nell.redu at hotmail.fr>> wrote:
>
> Hello,
>
>
> I would like to build 100-m buffers (representing ecological corridors)
> around land cover attributes in a raster layer and to assign a given value
> (i.e., value of 13) to buffer cells.
>
>
> To do this, I'm using the function "buffer" (package raster) to draw the
> buffers around particular raster cells (i.e., cell values of 2 and 5). For
> example, in the image below, the buffers are represented in blue (cell
> values of 13) and the particular raster cells are represented in yellow
> (cell values of 2).
>
>
> The problem is that the time to run the function "buffer" is very low
> because I have a raster of 5000000 cells. Does anyone know how I can reduce
> the buffering time ?
>
>
> Thanks a lot for your time.
>
> Have a nice day.
>
> Nell
>
>
> [Capture.PNG]
>
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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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