[R-sig-Geo] Array indices for very large multi-band images

[Robert J. Hijmans]

Guido,

Perhaps the function getValuesBlock in 'raster' makes this easier to do:

library(raster)
b <- brick(system.file("external/Rlogo.grd", package="raster"))
getValuesBlock(b, row=1, nrows=3, col=1, ncols=3)

Robert

On Fri, Apr 9, 2010 at 3:05 AM,  <guido.lemoine at jrc.ec.europa.eu> wrote:
> Dears,
>
> I just joined the list, so please bear with me if my problem
> has been dealt with already. I did an extensive google search,
> making sure r-gis-geo was included, so am sort of sure my
> problem is relevant.
>
> I have a (very) large 3 band ENVI file (32431 x 47262, 4.5 Gb,
> i.e. too big for normal GeoTIFF). I would like to generate
> statistics for 200 by 200 sized cells (including cross-correlation
> between bands).
> I am using the rgdal package, trying to use the array indexing
> syntax of R, running into trouble when trying to subset all
> 3 bands at the same time.
>
> Using array index syntax is useful, because it produces a
> SpatialGridDataFrame, which makes further processing easier.
>
> Here's my trial script:
>
> require(rgdal)
> x<-GDAL.open("verylarge3channelENVIimage")
> r <- getRasterData(x, offset = c(14000, 14000), region.dim = c(200, 200))
> str(r)
> # This works, but produces a simple integer array
> int [1:200, 1:200, 1:3] 0 0 0 0 0 0 0 0 0 0 ...
> # I'd rather do this
> sub0 <- x[14000:14199, 14000:14199,]  # ... but doesn't work
> Error in x[14000:14199, 14000:14199, ] :
>  argument is missing, with no default
> # this then?
> sub1 <- x[14000:14199, 14000:14199,1:3] # no, running into memory trouble
> Error: cannot allocate vector of size 2.3 Gb
> # per band works:
> sub2 <- x[14000:14199, 14000:14199,1]  # produces a nice spatial object.
> summary(sub2)
> Object of class SpatialGridDataFrame
> ...
>
> Is there a way to get all 3 bands with array index syntax, preferably
> as a SpatialGridDataFrame with band1, band2, band3.
>
> Any help greatly appreciated,
>
> GL
>
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