Hi, I'm trying to use HDF5 files with this structure:
---<--------------------cut here---------------start------------------->--- $ gdalinfo conc_200901011200.hdf Driver: HDF5/Hierarchical Data Format Release 5 Files: conc_200901011200.hdf Size is 512, 512 Coordinate System is `' Subdatasets: SUBDATASET_0_NAME=HDF5:"conc_200901011200.hdf"://Data/data[00] SUBDATASET_0_DESC=[760x1120] //Data/data[00] (32-bit floating-point) Corner Coordinates: Upper Left ( 0.0, 0.0) Lower Left ( 0.0, 512.0) Upper Right ( 512.0, 0.0) Lower Right ( 512.0, 512.0) Center ( 256.0, 256.0) ---<--------------------cut here---------------end--------------------->--- The file (467 kb placed in http://members.shaw.ca/sluque/conc_200901011200.hdf) is a grid of a single variable (ice concentration) in a well defined polar stereographic projection, that loads ok in R, via rgdal's readGDAL(): ---<--------------------cut here---------------start------------------->--- R> p4s <- "+proj=stere +a=6378273 +b=6356889.44891 +lat_0=90 +lat_ts=70 +lon_0=-45" R> ice <- readGDAL("HDF5:\"conc_200901011200.hdf\"://Data/data[00]", p4s=p4s) HDF5:"conc_200901011200.hdf"://Data/data[00] has GDAL driver HDF5Image and has 760 rows and 1120 columns R> summary(ice) Object of class SpatialGridDataFrame Coordinates: min max x 0 1120 y 0 760 Is projected: TRUE proj4string : [+proj=stere +a=6378273 +b=6356889.44891 +lat_0=90 +lat_ts=70 +lon_0=-45] Number of points: 2 Grid attributes: cellcentre.offset cellsize cells.dim x 0.5 1 1120 y 0.5 1 760 Data attributes: Min. 1st Qu. Median Mean 3rd Qu. Max. -32800 -99 -99 -117 0 100 R> ## We are concerned only with the 0-100 range; other values are codes with R> ## various meanings, so we remove them R> i...@data[ice@data[[1]] < 0 | i...@data[[1]] > 100, ] <- NA R> summary(ice) Object of class SpatialGridDataFrame Coordinates: min max x 0 1120 y 0 760 Is projected: TRUE proj4string : [+proj=stere +a=6378273 +b=6356889.44891 +lat_0=90 +lat_ts=70 +lon_0=-45] Number of points: 2 Grid attributes: cellcentre.offset cellsize cells.dim x 0.5 1 1120 y 0.5 1 760 Data attributes: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 0.0 0.0 0.0 23.3 36.7 100.0 478521.0 ## but something is wrong with visualizing these data pdf("~/tmp/ice.pdf") spplot(ice) dev.off() R> sessionInfo() R version 2.8.1 (2008-12-22) x86_64-pc-linux-gnu locale: LC_CTYPE=en_CA.UTF-8;LC_NUMERIC=C;LC_TIME=en_CA.UTF-8;LC_COLLATE=en_CA.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_CA.UTF-8;LC_PAPER=en_CA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_CA.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rgdal_0.5-35 sp_0.9-29 slmisc_0.7.0 lattice_0.17-20 loaded via a namespace (and not attached): [1] grid_2.8.1 ---<--------------------cut here---------------end--------------------->--- I'm not attaching the resulting file because it's too large. However, the plot should look like http://members.shaw.ca/sluque/full.ps I'd appreciate any feedback on what the problem might be. Thanks. Cheers, -- Seb _______________________________________________ R-sig-Geo mailing list R-sig-Geo@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-geo
