[R-sig-Geo] Subsetting RasterBrick very slow
reeves at nceas.ucsb.edu
Fri Jul 1 18:20:28 CEST 2011
Yes indeed, my experience is that Raster package operations on very
large datasets take a long time,
on either Linux or Windows desktops.
As an alternative to the Raster package, I have had good experience
using the GDAL raster image utilities,
embedded within shell or Python scripts to perform first-order raster
subsampling and subimage generation.
Check out the gdalinfo, gdal_translate, and gdalwarp utilities. I have
been using these to work with 100 gigabyte-class
raster DEM images, with great success and relatively low execution times
(considering the size of the data sets).
On 7/1/2011 7:02 AM, Christian Kamenik wrote:
> Dear all,
> The package 'raster' provides excellent tools to work on geographic
> data. Subsetting a RasterBrick object, however, takes ages.
> I have the following RasterBrick object:
> class: RasterBrick
> dimensions: 43, 99, 1200 (nrow, ncol, nlayers)
> ncell: 4257
> projection: +proj=longlat +ellps=WGS84
> min values: -14.8 -22.1 -15.0 -8.6 -3.8 4.7 8.7
> 6.0 1.6 -2.4 ...
> max values: 2.1 -3.9 -2.1 1.8 6.6 15.7 18.0 14.8 10.7 7.7
> extent: 15, 31.5, 64, 71.16667 (xmin, xmax, ymin,
> resolution: 0.1666667, 0.1666667 (x, y)
> These are temperature readings from northern Fennoscandia, and each
> layer represents a month, thus each grid cell has monthly readings
> over the last 100 years.
> Now I want to extract the readings for only July:
> Months <- rep(month.abb,nlayers(Temp.CRU.cropped)/12)
> Temp.CRU.J <- subset(Temp.CRU.cropped,which(Months=='Jul'))
> But as I said, this takes ages. It is much faster to do the subsetting
> on an array:
> CRU.values <- getValues(Temp.CRU.cropped)
> Temp.CRU.J <- CRU.values[,which(Months=='Jul')]
> Temp.CRU.J <-
> Temp.CRU.J <- brick(Temp.CRU.J)
> Temp.CRU.J <- setExtent(Temp.CRU.J,extent(Temp.CRU.cropped))
> projection(Temp.CRU.J) <- projection(Temp.CRU.cropped)
> It is strange that several lines of code run much faster than the
> 'subset' command, and I was wondering why 'subset' takes at least a
> 1000 times longer.
> I would be interested in your opinion.
> Many thanks, Christian
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