RES: Import Part of a GeoTiff using readGDAL{rgdal}

If you want a multi-layer object you can create a RasterBrick in stead
of a RasterLayer. I.e. 'brick()' in stead of ?'raster()'

library(raster)
etopo1 <- brick("Etopo1.tif") # change here
e <- extent(-90, -32, -60, 15)
r <- crop(etopo1, e)


Alternatively, you could create three RasterLayer objects
etopo1 <- brick("Etopo1.tif", band=1)
etopo2 <- brick("Etopo1.tif", band=2)
etopo3 <- brick("Etopo1.tif", band=3)


Robert

On Fri, Jul 23, 2010 at 7:54 AM, Michael Sumner <mdsumner at gmail.com> wrote:

I know this is rather simplistic, and has bugs that I just don't have
the impetus to track down at the moment, but it should work for your
problem. I didn't realize that raster doesn't support (AFAICS)
multiband rasters, such as 3-band images.

Please use with caution - there are bugs! and very bad practices . . .

readpartGDAL <- function(x, xlim = NULL, ylim = NULL, ...) {
? ? ? ?require(rgdal)
? ? ? ?info <- GDALinfo(x)
? ? ? ?offs <- info[c("ll.x", "ll.y")]
? ? ? ?scl <- info[c("res.x", "res.y")]
? ? ? ?dimn <- info[c("columns", "rows")]
? ? ? ?## brain dead, but easy
? ? ? ?xs <- seq(offs[1], by = scl[1], length = dimn[1]) + scl[1]/2
? ? ? ?ys <- seq(offs[2], by = scl[2], length = dimn[2]) + scl[2]/2

? ? ? ?if (!is.null(xlim)) {
? ? ? ? ? ? ? ?if (!is.numeric(xlim)) stop("xlim must be numeric")
? ? ? ? ? ? ? ?if (!length(xlim) == 2) stop("xlim must be of length 2")
? ? ? ? ? ? ? ?if (!diff(xlim) > 0) stop("xlim[1] must be less than xlim[2]")
? ? ? ? ? ? ? ?xind <- which(xs >= xlim[1] & xs <= xlim[2])
? ? ? ?}

? ? ? ?if (!is.null(ylim)) {
? ? ? ? ? ? ? ?if (!is.numeric(ylim)) stop("ylim must be numeric")
? ? ? ? ? ? ? ?if (!length(ylim) == 2) stop("ylim must be of length 2")
? ? ? ? ? ? ? ?if (!diff(ylim) > 0) stop("ylim[1] must be less than ylim[2]")
? ? ? ? ? ? ? ?yind <- which(ys >= ylim[1] & ys <= ylim[2])
? ? ? ?}
? ? ? ?## probably need a sign check for info["ysign"]
? ? ? ?## reverse for y/x order in readGDAL
? ? ? ?rgdal.offset <- rev(c(min(xind), dimn[2] - max(yind)))
? ? ? ?rgdal.dim <- rev(c(length(xind), length(yind)))
? ? ? ?readGDAL(x, offset = rgdal.offset, region.dim = rgdal.dim, ...)
}

f <- "Etopo1.tif"

d <- readpartGDAL(f, xlim = c(-90, -32), ylim = c(-60, 15))

## assuming you have 3-bands describing RGB
## (see ?SGDF2PCT
cols <- SGDF2PCT(d)
d$idx <- cols$idx
image(d, "idx", col = cols$ct)



On Sat, Jul 24, 2010 at 12:09 AM, Rodrigo Aluizio <r.aluizio at gmail.com> wrote:

Well Etopo1 have the colored image as well (ftp://ftp.ngdc.noaa.gov/mgg/global/relief/ETOPO1/image/color_etopo1_ice_full.tif.gz). I'm not able to import it using readGDAL (because of the vector size), but normally when I do so with georeferenced images, the object created have, in the data slot, the three band (RGB) color codes as columns. Using raster{raster} and then as(x,'SpatialGridDataFrame') these data seems to get truncated and unrecognizable to image{sp}.

Regards.

Rodrigo

-----Mensagem original-----
De: Michael Sumner [mailto:mdsumner at gmail.com]
Enviada em: sexta-feira, 23 de julho de 2010 10:53
Para: Rodrigo Aluizio
Cc: R Help
Assunto: Re: [R-sig-Geo] RES: Import Part of a GeoTiff using readGDAL{rgdal}

I don't know what you mean by "band data structure" and "original colors". I just have the generic (ice/cell registered) Etopo1 which is elevation values as 16-bit integers. Perhaps you could describe the actual file you have more, where you got it, and how you have used it before.

Cheers, Mike.

On Fri, Jul 23, 2010 at 8:43 PM, Rodrigo Aluizio <r.aluizio at gmail.com> wrote:

Excellent suggestion, but I'm facing another little problem. When importing through raster{raster}, I lost the band data structure (but the data seems to still be there) which turns impossible to reproduce the original colors. Is there a way to bypass this?

Thanks.

Rodrigo.

-----Mensagem original-----
De: Michael Sumner [mailto:mdsumner at gmail.com] Enviada em:
quinta-feira, 22 de julho de 2010 12:50
Para: Rodrigo Aluizio
Cc: R Help
Assunto: Re: [R-sig-Geo] Import Part of a GeoTiff using
readGDAL{rgdal}

With readGDAL you must figure out the impled coordinates, referenced from the top left - it's confusing, but with some experimenting you will get it.

But, far easier is to use the raster package, which will let you deal with the entire Etopo1 if you want by accessing the file as needed, and there are simpler methods to crop the big raster - and coerce to SpatialGridDataFrame if need be.

E.g.
## all this works pretty fast as raster takes care of the memory
library(raster)
etopo1 <- raster("Etopo1.tif")
?e <- extent(-90, -32, -60, 15)
r <- crop(etopo1, e)
plot(r)

## if we want to enforce the full memory use as an sp object x <-
as(r, "SpatialGridDataFrame")
image(x)
summary(x)
Object of class SpatialGridDataFrame
Coordinates:
? min max
s1 -90 -32
s2 -60 ?15
Is projected: FALSE
proj4string :
[+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +towgs84=0,0,0] Number of points: 2 Grid attributes:
? cellcentre.offset ? cellsize cells.dim
s1 ? ? ? ? -89.99167 0.01666667 ? ? ?3480
s2 ? ? ? ? -59.99167 0.01666667 ? ? ?4500 Data attributes:
? Min. 1st Qu. ?Median ? ?Mean 3rd Qu. ? ?Max.
?-8086 ? -4188 ? -2583 ? -2025 ? ? 148 ? ?6494



sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-pc-mingw32

locale:
[1] LC_COLLATE=English_Australia.1252 ?LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C [5]
LC_TIME=English_Australia.1252

attached base packages:
[1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base

other attached packages:
[1] rgdal_0.6-27 raster_1.2-6 sp_0.9-65

loaded via a namespace (and not attached):
[1] grid_2.11.1 ? ?lattice_0.18-8 tools_2.11.1

On Fri, Jul 23, 2010 at 1:14 AM, Rodrigo Aluizio <r.aluizio at gmail.com> wrote:

Hi List.

I?m trying to import only a part of interest from a raster image map
(let say, ETOPO 1 Global Relief GeoTiff). I realize that, PROBABLY,
the readGDAL function can deal with my issue through the arguments:



offset - Number of rows and columns from the origin (usually the
upper left
corner) to begin reading from; presently ordered (y,x) - this may
change

region.dim - The number of rows and columns to read from the dataset;
presently ordered (y,x) - this may change



But, I don?t know exactly how to specify that I want the rows (and
columns?) which show only South America, I do know the SA coordinate
limits, but not the corresponding rows.

The real problem is that I don?t know how to use the function
resources properly. I?m trying to limit the region during import to
avoid memory limit issues, once importing the ETOPO 1 Geotiff tries to generate a huge vector.

Really Sorry About It, Thanks for Your Patience and Attention.



-------------------------------------------------------------

MSc. ?<mailto:r.aluizio at gmail.com> Rodrigo Aluizio

Centro de Estudos do Mar/UFPR
Laborat?rio de Micropaleontologia
Avenida Beira Mar s/n - CEP 83255-000 Pontal do Paran? - PR - Brasil




? ? ? ?[[alternative HTML version deleted]]

--
Michael Sumner
Institute for Marine and Antarctic Studies, University of Tasmania Hobart, Australia
e-mail: mdsumner at gmail.com

--
Michael Sumner
Institute for Marine and Antarctic Studies, University of Tasmania
Hobart, Australia
e-mail: mdsumner at gmail.com

--
Michael Sumner
Institute for Marine and Antarctic Studies, University of Tasmania
Hobart, Australia
e-mail: mdsumner at gmail.com