[R-sig-Geo] stars::RasterIO using extent info?

Michael Sumner md@umner @ending from gm@il@com
Wed Nov 14 23:55:29 CET 2018


FWIW I have a raster-delivering-front-end for RasterIO in this dev package:

https://github.com/hypertidy/lazyraster

It uses the more obvious extent() idioms and will even use an open plot if
nothing else is specified.

(It uses an independent binding to GDAL in the vapour package).

That might help, or not. It's on my list to find a sensible way for stars
to leverage this obvious ease-of-use.  rgdal::readGDAL always had an
interface to RasterIO, but only raster ever made use of that, and it's
indirect - raster doesn't allow a mix of extent and resolution in its
approach.

Cheers, Mike.

On Thu, 15 Nov 2018 at 02:27 Howard, Tim G (DEC) via R-sig-Geo <
r-sig-geo using r-project.org> wrote:

> Ok, fair enough that there's no magic involved. I've worked through the
> details with the small example as follows. The result is only a couple of
> cells different in each direction.
>
> library(stars)
> tif <- system.file("tif/L7_ETMs.tif", package = "stars")
> x <- read_stars(tif)
> x <- x[,,,1]
> # calculate a circular polygon at the center of the raster
> pol <- x %>% st_bbox() %>% st_as_sfc() %>% st_centroid() %>% st_buffer(500)
>
> bb_pol <- st_bbox(pol)
>
> xoff <- st_dimensions(x)$x$offset
> xdelt <- st_dimensions(x)$x$delta
> yoff <- st_dimensions(x)$y$offset
> ydelt <- st_dimensions(x)$y$delta
> cropXoff <- (bb_pol$xmin - xoff + xdelt)/xdelt
> cropXsize <- (bb_pol$xmax - bb_pol$xmin)/xdelt
> cropYoff <- (bb_pol$ymin - yoff + ydelt)/ydelt
> cropYsize <- (bb_pol$ymax - bb_pol$ymin)/ydelt
>
> # if ydelt is negative, get abs of ysize and move yoffset to the top
> if(cropYsize < 0){
>   cropYsize <- abs(cropYsize)
>   cropYoff <- cropYoff - cropYsize
> }
>
> rasterio <- list(nXOff = cropXoff, nYOff = cropYoff, nXSize = cropXsize,
> nYSize = cropYsize, bands = c(1))
> (z = read_stars(tif, RasterIO = rasterio))
> plot(z)
>
> # crop it if desired
> plot(z[pol])
>
> ## compare to proxy method
>
> x <- read_stars(tif, proxy = TRUE)
> x <- x[,,,1]
> y <- st_as_stars(x[pol])
> plot(y)
>
> # only a couple of cells off!
> z
> y
>
>
>
>
> ------------------------------
> Date: Tue, 13 Nov 2018 17:26:16 +0100
> From: Edzer Pebesma <edzer.pebesma using uni-muenster.de>
> To: r-sig-geo using r-project.org
> Subject: Re: [R-sig-Geo] stars::RasterIO using extent info?
> Message-ID: <9d037da7-dc9c-9886-d6fc-5864cf8b4a17 using uni-muenster.de>
> Content-Type: text/plain; charset="utf-8"
>
>
>
> On 11/13/18 4:10 PM, Howard, Tim G (DEC) via R-sig-Geo wrote:
> > Dear list,
> >
> > I am exploring the different options for reading parts of large imagery
> object in stars, as discussed here:
> >
> > https://r-spatial.github.io/stars/articles/proxy.html
> >
> > My ultimate goal is to read into RAM only a clipped portion of a large
> raster (well, actually a raster stack, but taking baby steps here).
> >
> > My immediate question: the `RasterIO` option of read_stars defines cell
> offsets and cell counts (*Size). Is there a straightforward way to
> calculate these values given extent information?
> >
> > Reproducible example (mostly taken from here:
> https://www.r-spatial.org/r/2018/03/22/stars2.html):
> >
> > library(stars)
> > tif <- system.file("tif/L7_ETMs.tif", package = "stars")
> > x <- read_stars(tif) # read entire tif into ram
> > x <- x[,,,1] #get just one layer for now
> > # calculate a circular polygon at the center of the raster
> > pol <- x %>% st_bbox() %>% st_as_sfc() %>% st_centroid() %>%
> st_buffer(500)
> > plot(x)
> > # interestingly, I don't think the circle is in the right place when
> plotted
> > plot(st_geometry(pol), add = TRUE, border = "red")
> > # this is what I'd like to be able to restrict to what is read in memory:
> > plot(x[pol])
> >
> > ## read only portion of tif using proxy object
> > x <- read_stars(tif, proxy = TRUE)
> > x <- x[,,,1]
> > y <- st_as_stars(x[pol])
> > plot(y) # this is cropped to the extent (but not the circle - let's not
> worry about that right now)
> >
> > Question: can I do the equivalent with the RasterIO options in stars?
> Said another way, instead of setting up the proxy, can I map my extent
> object (or bounding box) directly to the cell count values needed for
> RasterIO?
>
> stars can do the math, and so can you; it is explained here:
>
> https://r-spatial.github.io/stars/articles/data_model.html
>
> stars uses some functions directly from GDAL which it doesn't expose to
> the user, but there is no magic going on here.
>
> >
> >
> > Thanks in advance for any tips.
> > Tim
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > R-sig-Geo using r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >
>
> --
> Edzer Pebesma
> Institute for Geoinformatics
> Heisenbergstrasse 2, 48151 Muenster, Germany
> Phone: +49 251 8333081 <+49%20251%208333081>
>
> _______________________________________________
> R-sig-Geo mailing list
> R-sig-Geo using r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
-- 
Dr. Michael Sumner
Software and Database Engineer
Australian Antarctic Division
203 Channel Highway
Kingston Tasmania 7050 Australia

	[[alternative HTML version deleted]]



More information about the R-sig-Geo mailing list