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

Tue May 10 03:51:56 CEST 2016

I've attempted to use "OSGeo4W.bat" and the like, and have also seen such
error messages.

Shell functions like "OSGeo4W.bat" are transcriptions of Linux/UNIX shell
scripts and can't be expected to work in a Windows environment, and are a
very low priority in open source spatial software, which have many more
important problems.  (Google "OSGeo4W.bat" to see a variety of problem
reports.)  It's well worth the effort of assembling a Linux environment and
learning to use it, for any important problems to be solved with open
source tools, including GDAL.

>From https://translate.google.com,

Les fonctions "Shell" comme "OSGeo4W.bat" sont des transcriptions de Linux
/ UNIX ''shell scripts" -- ne peuvent pas être appelés à travailler dans un
environnement Windows, et sont une priorité très faible en logiciel open
source spatiale, qui ont des problèmes beaucoup plus importants. (Google
"OSGeo4W.bat" pour voir une variété de rapports de problèmes.) Il vaut bien
l'effort d'assemblage d'un environnement Linux et d'apprendre à l'utiliser,
pour tous les problèmes importants à résoudre avec des outils open source,
y compris GDAL.

Sorry, best I can do.  Good luck!

On Mon, May 9, 2016 at 1:36 PM, Nelly Reduan <nell.redu at hotmail.fr> wrote:

> I have tried the following code to compute distances from raster pixels of
> 5 via the function "gdal_proximity":
>
>
>     pypath <- Sys.which("C:\\OSGeo4W64\\bin\\gdal_proximity")
>     owd <- getwd()
>     on.exit(setwd(owd))
>     setwd(dirname(pypath))
>     rastpath <- "H:\\Project\\grassland.tif"
>     outpath <- "H:\\Project\\distance.shp"
>     maxDist <- 50
>     system2("C:\\OSGeo4W64\\OSGeo4W.bat",
> args=c(pypath,rastpath,outpath,maxDist))
>
>
> But I obtain the error message:
>
>     gdal_proximity.py srcfile dstfile [-srcband n] [-dstband n]
>                       [-of format] [-co name=value]*
>                       [-ot Byte/Int16/Int32/Float32/etc]
>                       [-values n,n,n] [-distunits PIXEL/GEO]
>                       [-maxdist n] [-nodata n] [-fixed-buf-val n] [-q]
>     Warning message:
>     running command '"C:\OSGeo4W64\OSGeo4W.bat"
> C:\OSGEO4~1\bin\GDAL_P~2.BAT H:\Project\grassland.tif
> H:\Project\distance.shp 50' had status 1
>
>
> Here are some details about the raster "grassland.tif"
>
>     > grassland
>     class       : RasterLayer
>     dimensions  : 9887, 30532, 301869884  (nrow, ncol, ncell)
>     resolution  : 10, 10  (x, y)
>     extent      : -515893.7, -210573.7, 110739.6, 209609.6  (xmin, xmax,
> ymin, ymax)
>     coord. ref. : +proj=lcc +lat_1=46 +lat_2=60 +lat_0=44 +lon_0=-68.5
> +x_0=0 +y_0=0 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs
>     values      : 5, 5  (min, max)
>
>
> Thanks a lot for your time.
> Have a nice day
> Nell
>
>
> ________________________________
> De : Nelly Reduan
> Envoyé : vendredi 6 mai 2016 12:00:36
> À : Forrest Stevens; Michael Sumner; r-sig-geo at r-project.org
> Objet : RE: [R-sig-Geo] How to reduce the buffering time with the function
> "buffer" (package raster)
>
>
> Thank you very much Forrest for your answer. How can I call the function
> "gdal_proximity" in R via system() ?
>
>
> Thanks a lot for your time.
>
> Nell
>
> ________________________________
> De : Forrest Stevens <r-sig-geo at forreststevens.com>
> Envoyé : mercredi 13 avril 2016 22:37:01
> À : Nelly Reduan; Michael Sumner; 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)
>
> So you're correct, the buffer() and distance() functions you're using will
> take a long period of time.  The code below illustrates the shortcut that
> I've used in the past when buffering only by the limit of one pixel, since
> it uses queens-case connectance and distance between cell-centers based on
> that connectance rule. This uses the gridDistance() function which is much
> faster than calculating straight line distances. You can see that the
> distance-based calculation takes under 40 seconds. But do notice that the
> buffer it creates by setting the threshold is around both classes and is
> indiscriminate of the nearest class:
>
> library(raster)
>
> clip_buff <- raster("clip_study_area_2010.tif")
>
> system.time(d <- gridDistance(clip_buff, c(2,3)))
> #   user  system elapsed
> #  37.36   11.00   48.41
>
> rf[(rf != 2 & rf != 3)] <- NA
>
> ## Set buffer to 10m just for fun and assign
> ## value of 4 to that buffered region:
> rf[ d > 0 & d <= 10 ] <- 4
> plot(rf)
>
> If you want to buffer by more than one pixel dimension then you'll
> probably want straight line distances and I'd suggest using GDAL and using
> the gdal_proximity utility via a system() call. Alternatively, you could
> look into other utilities that have better-optimized raster-based distance
> tools. Hopefully this gives you some ideas on how to proceed?
>
> Sincerely,
> Forrest
>
>
> On Wed, Apr 13, 2016 at 9:18 PM Nelly Reduan <nell.redu at hotmail.fr<mailto:
> nell.redu at hotmail.fr>> wrote:
>
> I put a cropped raster with 3581676 cells in the link below:
>
>
> https://www.dropbox.com/sh/ewaz4yncdqt7kxj/AAAEHyuWyHzBE7gSINA1oayTa?dl=0
>
>
> Here is my code to built the buffers:
>
> rf <- clip_buff
>
> rf [(rf != 2 & rf != 3)] <- NA
>
> plot(rf)
>
> system.time(corr <- buffer(rf, 10))
>
> system.time(dist_rf <- distance(rf))
>
>
> I stopped the code with the functions "buffer" and "distance" after two
> hours.
>
>
> Thanks a lot for your time.
>
> Have a nice day.
>
> Nell
>
>
>
> ________________________________
> De : Michael Sumner <mdsumner at gmail.com<mailto:mdsumner at gmail.com>>
> Envoyé : mardi 12 avril 2016 20:36
>
> À : Nelly Reduan; Forrest Stevens; 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)
>
> 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<mailto:
> 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<mailto:
> 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<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)
>
> 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><mailto: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><mailto: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
> ><mailto: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><mailto: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
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>
>
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