[R-sig-Geo] rasterize in parrallel

[Jérome Mathieu]

Dear All,

Thanks a lot for your brilliant replies. It does work (fast) now!

Jerome


2015-07-14 6:02 GMT+02:00 Robert J. Hijmans <r.hijmans at gmail.com>:

> Jerome,
>
> rasterize is indeed a bit slow, it is #1 on the list of functions that
> need a rewrite for speed. However, I think your assumption is wrong.
> You can rasterize all fields in one step, and it is pretty quick for
> the example data:
>
> library(raster)
> polyg <- shapefile("polyg.shp")
> grain <- 50
> nsc <- 4
> r <- raster(polyg, res=c(grain, grain))
>
> x <- rasterize(polyg, r)
> # perhaps followed by
> y <- deratify(x)
>
>
> So clustering is inefficient here, but I think the below shows how you
> would do athat, using much simplified code (whenever you think you
> need a construction like "eval(parse(text=paste(", you are wrong).
>
> library(raster)
> polyg <- shapefile("polyg.shp")
>
> library(doParallel)
> cl <- makeCluster(4)
> registerDoParallel(cl)
> grain <- 50
> nsc <- 4
> r <- raster(polyg, res=c(grain, grain), crs=crs(polyg))
>
> rr <- foreach(i= 1:nsc, .packages="raster", .combine=c) %dopar% {
>      rasterize(polyg, r, field=paste0("sc", i))
> }
>
> stopCluster(cl)
>
>
>
> Best, Robert
>
> On Mon, Jul 13, 2015 at 3:03 PM, Jérome Mathieu <jerome.mathieu at upmc.fr>
> wrote:
> > Dear all,
> >
> > I need to rasterize the same shapefile according to different fields
> stored
> > in the @data of the shapefile. So I need to loop trough the fields (named
> > sc1 to sc27) to rasterize upon each field. With a regular sequential loop
> > it takes a very long time (much longer than in ArcMap), so I would like
> to
> > parallelize it, but I didn't succeed so far.
> >
> > I tried :
> >
> > # read shapefile
> >  library(maptools)
> >  polyg<-readShapePoly("D:\\polyg.shp")
> >  polyg at proj4string <- CRS("+init=epsg:2154")
> >
> > library(doParallel)
> > cl <- makeCluster(4)
> > registerDoParallel(cl)
> >
> > grain<-50
> > nsc<-4
> >
> > foreach(idxsc = 1 : nsc , .packages="raster", polyg=polyg) %dopar% {
> >
> >
> eval(parse(text=paste("RRpolyg_",idxsc,"<-raster(polyg,res=c(grain,grain))",sep="")))
> > # create raster template
> > eval(parse(text=paste("projection(RRpolyg_",idxsc,") <-
> > proj4string(polyg)",sep="")))      # projection
> >
> eval(parse(text=paste("RRpolyg_",idxsc,"<-rasterize(polyg,RRpolyg_",idxsc,",field=polyg at data
> $sc",idxsc,")",sep="")))
> > # rasterization
> >
> > }
> >
> > stopCluster(cl)
> >
> > and I get the following error :
> >
> > Error in { :
> >   task 1 failed - "unable to find an inherited method for function
> 'raster'
> > for signature '"numeric"'"
> >
> >
> > the data are here
> >
> > http://we.tl/7qqegfLoBA
> >
> >
> > Any help would be greatly appreciated !
> >
> > Jerome
> >
> >
> >> sessionInfo()
> > R version 3.1.3 (2015-03-09)
> > Platform: x86_64-w64-mingw32/x64 (64-bit)
> > Running under: Windows 7 x64 (build 7601) Service Pack 1
> >
> > locale:
> > [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
> > LC_MONETARY=French_France.1252 LC_NUMERIC=C
> > LC_TIME=French_France.1252
> >
> > attached base packages:
> > [1] parallel  stats     graphics  grDevices utils     datasets  methods
> > base
> >
> > other attached packages:
> >  [1] rgeos_0.3-11     rgdal_0.9-2      maptools_0.8-36  lattice_0.20-31
> > foreign_0.8-63   raster_2.3-40    sp_1.1-0         doParallel_1.0.8
> > iterators_1.0.7  foreach_1.4.2
> >
> > loaded via a namespace (and not attached):
> > [1] codetools_0.2-11 compiler_3.1.3   grid_3.1.3       tools_3.1.3
> >
> >
> >
> >
> >
> >
> >
> > --
> > Jérôme Mathieu
> > Université Pierre & Marie Curie
> > Institute of Ecology and Environmental Science (Paris)
> >
> > Bât. A - 7ème Etage, porte 715
> > 7 quai St.-Bernard
> > F-75252 Paris Cedex 05
> >
> > tel: 01 44 27 34 22
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > R-sig-Geo at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>



-- 
Jérôme Mathieu
Université Pierre & Marie Curie
Institute of Ecology and Environmental Science (Paris)

Bât. A - 7ème Etage, porte 715
7 quai St.-Bernard
F-75252 Paris Cedex 05

tel: 01 44 27 34 22

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