[R-spatial-devel] [STATSGRASS] speed of GRASS/R interface
Carlos "Guâno" Grohmann
carlos.grohmann at gmail.com
Mon Oct 8 14:12:47 EDT 2007
It took about 6 seconds to read a raster with 2200x2500 cells, and
about 3 secs to build a truehist().
don't have any categorical map, though.
Carlos
On 10/8/07, Agustin Lobo <Agustin.Lobo at ija.csic.es> wrote:
> How long it takes computing the histogram of the 900*3600 raster in R?
> If you have a categorical map for the same region, could you check
> how long it takes computing the stratified statistics?
>
> Thanks!
>
> Agus
>
> Carlos "Guâno" Grohmann escribió:
> > Hi,
> >
> > I just downloaded/compiled/installed the current sourceforge CVS for
> > sp and spgrass6, and it's WAY faster than before.
> >
> > thanks, Roger!
> >
> > Carlos
> >
> >
> > On 10/6/07, Roger Bivand <Roger.Bivand at nhh.no> wrote:
> >> Hi,
> >>
> >> Modification also committed in sp on sourceforge, speedup from from ~ 12
> >> minutes to 6.5 seconds on a 900 by 3600 raster, and no memory explosion.
> >> I'm seeing similar speedups in rgdal. Still no idea why - a change in the
> >> methods package? When we release a fresh sp, the need for special fixes
> >> will go away, I hope.
> >>
> >> Could somebody try the current sourceforge CVS of sp and see if you see
> >> the same speedup? May need to wait for the anonymous CVS to synch.
> >>
> >> Best wishes,
> >>
> >> Roger
> >>
> >>
> >> On Sat, 6 Oct 2007, Roger Bivand wrote:
> >>
> >>> On Sat, 6 Oct 2007, jarekj at amu.edu.pl wrote:
> >>>
> >>>> Roger!
> >>>>
> >>>> I also notice that of Carlos wrote.
> >>>>
> >>>> That hangs not occured when spgrass6 was based on r.out.ascii instead of
> >>>> binary input-output and in fact it was realably faster. Maybe back to
> >>>> previouis solution be good temporal solution. I also exchange data
> >>>> between grass and R very often so that hang make me sometimes inpatient
> >>>>
> >>>> greetengs and regards
> >>>> Jarek
> >>> The problem is in new("SpatialGrid", SPix):
> >>>
> >>> library(sp)
> >>> sessionInfo()
> >>> cellcentre.offset <- c(-16.821667, 13.060307)
> >>> cellsize <- c(0.000833, 0.000833)
> >>> cells.dim <- c(3629.000000, 921.00000)
> >>> grd <- GridTopology(cellcentre.offset, cellsize, cells.dim)
> >>> pts <- sp:::boguspoints(grd)
> >>> pts at bbox[,1] = pts at bbox[,1] - 0.5 * grd at cellsize
> >>> pts at bbox[,2] = pts at bbox[,2] + 0.5 * grd at cellsize
> >>> proj4string(pts) = CRS(paste("+proj=longlat +a=6378137 +rf=298.257223563",
> >>> "+no_defs +towgs84=0.000,0.000,0.000"))
> >>> SPix <- new("SpatialPixels", pts, grid = grd, grid.index = integer(0))
> >>> SG <- new("SpatialGrid", SPix)
> >>>
> >>> with rapidly increasing memory use. I have no idea why. My system:
> >>>
> >>>> sessionInfo()
> >>> R version 2.6.0 (2007-10-03)
> >>> i686-pc-linux-gnu
> >>>
> >>> locale:
> >>> LC_CTYPE=en_GB;LC_NUMERIC=C;LC_TIME=en_GB;LC_COLLATE=en_GB;LC_MONETARY=en_GB;LC_MESSAGES=en_GB;LC_PAPER=en_GB;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB;LC_IDENTIFICATION=C
> >>>
> >>> attached base packages:
> >>> [1] stats graphics grDevices utils datasets methods base
> >>>
> >>> other attached packages:
> >>> [1] sp_0.9-14
> >>>
> >>> loaded via a namespace (and not attached):
> >>> [1] grid_2.6.0 lattice_0.16-5 rcompgen_0.1-15
> >>>
> >>> and the message after Ctrl-C:
> >>>
> >>> Error in coordinates(coords) :
> >>> error in evaluating the argument 'obj' in selecting a method for function
> >>> 'coordinates'
> >>> Error in bbox(object) :
> >>> error in evaluating the argument 'obj' in selecting a method for function
> >>> 'bbox'
> >>>
> >>> which makes me suspect that the new() is (now?) going to completely senseless
> >>> places. This has the same effect:
> >>>
> >>> sG <- new("SpatialGrid", bbox=pts at bbox, proj4string=pts at proj4string,
> >>> coords=pts at coords, grid=grd, grid.index=integer(0))
> >>>
> >>> unfortunately. It also impacts the rgdal route, because its call to make the
> >>> output SGDF is the same.
> >>>
> >>> However, replacing the call to new("SpatialGrid", ...) to one of building an
> >>> empty object with just new(), and stuffing the slots manually with slot() <-
> >>> reduces import from over 12 minutes to 6 seconds (!). Perhaps the problem is
> >>> that S4 classes have got "cleverer" and dislike the definition of SpatialGrid
> >>> as only having a "SpatialPixels" representation?
> >>>
> >>> I have committed the very draft readRAST6() to CVS on sourceforge, but the
> >>> real solution needs doing in sp itself (end of the SpatialGrid() function in
> >>> SpatialGrid-methods.R).
> >>>
> >>> I'll carry on playing ...
> >>>
> >>> Roger
> >>>
> >>>
> >>>>
> >>>> 6/10/2007, "Roger Bivand" <Roger.Bivand at nhh.no> napisa?/a:
> >>>>
> >>>>> On Tue, 2 Oct 2007, Carlos "Guâno" Grohmann wrote:
> >>>>>
> >>>>>> I've been thinking about the time it takes to import a raster from
> >>>>>> GRASS to
> >>>>>> R. I have some rasters with about 2000 rows and 2500 columns.
> >>>>>> importing
> >>>>>> starts fine, creates the header, then goes to 100%, and it hangs there
> >>>>>> for
> >>>>>> about 10 minutes, before get ready for the next command.
> >>>>>> Any way of decrease this waiting time?
> >>>>> I'm looking into this, as far as I can see as of now it is somewhere in
> >>>>> the new("SpatialGridDataFrame", ...) call in
> >>>>> res <- SpatialGridDataFrame(...) in readBinGrid(). Confusingly, the
> >>>>> Rprof() output points at unlist() taking 90% of the total run time. I'll
> >>>>> let you know where I get.
> >>>>>
> >>>>> Roger
> >>>>>
> >>>>>> cheers
> >>>>>>
> >>>>>> Carlos
> >>>>>>
> >>>>>>
> >>>>> --
> >>>>> Roger Bivand
> >>>>> Economic Geography Section, Department of Economics, Norwegian School of
> >>>>> Economics and Business Administration, Helleveien 30, N-5045 Bergen,
> >>>>> Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
> >>>>> e-mail: Roger.Bivand at nhh.no
> >>>
> >> --
> >> Roger Bivand
> >> Economic Geography Section, Department of Economics, Norwegian School of
> >> Economics and Business Administration, Helleveien 30, N-5045 Bergen,
> >> Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
> >> e-mail: Roger.Bivand at nhh.no
> >>
> >
> >
>
> --
> Dr. Agustin Lobo
> Institut de Ciencies de la Terra "Jaume Almera" (CSIC)
> LLuis Sole Sabaris s/n
> 08028 Barcelona
> Spain
> Tel. 34 934095410
> Fax. 34 934110012
> email: Agustin.Lobo at ija.csic.es
> http://www.ija.csic.es/gt/obster
>
--
+-----------------------------------------------------------+
Carlos Henrique Grohmann - Guano
Visiting Researcher at Kingston University London - UK
Geologist M.Sc - Doctorate Student at IGc-USP - Brazil
Linux User #89721 - carlos dot grohmann at gmail dot com
+-----------------------------------------------------------+
_________________
"Good morning, doctors. I have taken the liberty of removing Windows
95 from my hard drive."
--The winning entry in a "What were HAL's first words" contest judged
by 2001: A SPACE ODYSSEY creator Arthur C. Clarke
Can't stop the signal.
More information about the grass-stats
mailing list