Re: [R-sig-Geo] stars::RasterIO using extent info?
Mike, Thanks for the feedback - I'll check it out. Best, Tim From: Michael Sumner [mailto:mdsum...@gmail.com] Sent: Wednesday, November 14, 2018 5:55 PM To: Howard, Tim G (DEC) Cc: r-sig-geo@r-project.org Subject: Re: [R-sig-Geo] stars::RasterIO using extent info? 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 <mailto:r-sig-geo@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 <mailto:edzer.pebe...@uni-muenster.de> To: mailto:r-sig-geo@r-project.org Subject: Re: [R-sig-Geo] stars::RasterIO using extent info? Message-ID: <mailto:9d037da7-dc9c-9886-d6fc-5864cf8b4...@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 > > _
Re: [R-sig-Geo] stars::RasterIO using extent info?
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@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 > To: r-sig-geo@r-project.org > Subject: Re: [R-sig-Geo] stars::RasterIO using extent info? > Message-ID: <9d037da7-dc9c-9886-d6fc-5864cf8b4...@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
Re: [R-sig-Geo] stars::RasterIO using extent info?
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 To: r-sig-geo@r-project.org Subject: Re: [R-sig-Geo] stars::RasterIO using extent info? Message-ID: <9d037da7-dc9c-9886-d6fc-5864cf8b4...@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@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 ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Re: [R-sig-Geo] stars::RasterIO using extent info?
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@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 pEpkey.asc Description: application/pgp-keys ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
[R-sig-Geo] stars::RasterIO using extent info?
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? Thanks in advance for any tips. Tim ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo