see if gdal understands the coordinate arrays already, you can just churn it through the warper, otherwise construct a vrt that specifies them, which is a bit obscure how you do it admittedly - but this is a gdal not an R topic.
Best On Mon, 15 Nov 2021, 00:22 Edzer Pebesma, <edzer.pebe...@uni-muenster.de> wrote: > > On 14/11/2021 13:59, Edzer Pebesma wrote: > > Gabriel shared the data with me (off-list, 1Gb) and it contains two hdf5 > > datasets, one containing the raster of the longitude and latitude, the > > other rasters with the attributres (LST) but no coordinates. I could get > > a (rough: factor 50 downsampling) plot with stars using: > > > > library(stars) > > lat = > > > read_stars("HDF5:ECOSTRESS_L1B_GEO_11712_012_20200730T061029_0601_01.h5://Geolocation/latitude") > > > > > lon = > > > read_stars("HDF5:ECOSTRESS_L1B_GEO_11712_012_20200730T061029_0601_01.h5://Geolocation/longitude") > > > > > > > var = > > "HDF5:ECOSTRESS_L2_LSTE_11712_012_20200730T061029_0601_01.h5://SDS/LST" > > lst = read_stars(var, curvilinear = list(x = lon, y = lat)) > > plot(lst, downsample = 50, axes = TRUE, reset = FALSE) > > > > library(rnaturalearth) > > ne = ne_countries(returnclass = "sf") > > plot(st_geometry(ne), add = TRUE, border = 'yellow') > > # california border seems to make sense > > > > > > but I'm not sure how to make a regular raster (in some CRS) out of this > > for exporting to GeoTIFF. > > This might be useful: https://github.com/r-spatial/stars/issues/386 > but converting to polygons will be incredibly slow and memory hungry. > > > > > > On 14/11/2021 11:00, Edzer Pebesma wrote: > >> This might be because the grid is not regular but possibly > >> curvilinear, having two raster layers with the lon & lat values for > >> each pixel. Can you share a sample data set? > >> > >> On 14/11/2021 10:47, Gabriel Cotlier wrote: > >>> Dear Michael, > >>> > >>> Following your advice I have tired : > >>> > >>> library(terra) > >>> library(raster) > >>> library(dplyr) > >>> > >>> r = terra::rast(file.choose()) > >>> plot(r$LST) > >>> r_lst = r$LST > >>> r_lst %>% raster() > >>> plot(r_lst) > >>> > >>> Then I effectively get a raster layer format from the raster package > >>> as I > >>> wanted, but looking at the plot and the raster layer information--see > >>> bellow-- the scene appears to need both latitude and longitude for > >>> correct > >>> geolocation, how can I do this procedure? > >>> > >>>> r_lst %>% raster() > >>> class : RasterLayer > >>> dimensions : 5632, 5400, 30412800 (nrow, ncol, ncell) > >>> resolution : 1, 1 (x, y) > >>> extent : 0, 5400, 0, 5632 (xmin, xmax, ymin, ymax) > >>> crs : NA > >>> source : LST > >>> names : LST > >>> values : 0, 65535 (min, max) > >>> > >>> The extent and the resolution are not the correct ones. > >>> Maybe in the same .h5 is all the data for georeferencing it although I > >>> could not see how to get to it and apply it to the layer. > >>> There is also another file with complementary data related to > >>> geolocation > >>> but how can I query it, and get the data for geolocation and apply it > to > >>> the raster layer?. > >>> The objective is to save it as a GeoTIFF file to be opened in QGIS with > >>> correct geolocation. > >>> > >>> What do you suggest for converting the .h5 file to a georeferenced > >>> Raster > >>> Layer in GeoTIFF format ? > >>> > >>> Thanks a lot. > >>> Kind regards, > >>> Gabriel > >>> > >>> On Sat, Nov 13, 2021 at 12:22 PM Gabriel Cotlier <gabikl...@gmail.com> > >>> wrote: > >>> > >>>> Dear Michael Summer, > >>>> Thanks a lot for your swift reply. > >>>> I will give a try to the procedure you mentioned. > >>>> Kind regards, > >>>> Gabriel > >>>> > >>>> > >>>> On Sat, Nov 13, 2021 at 12:14 PM Michael Sumner <mdsum...@gmail.com> > >>>> wrote: > >>>> > >>>>> try terra::rast() or stars::read_stars() on the file, both use gdal > to > >>>>> interrogate and read. What you get depends on the structure of the > >>>>> files, > >>>>> variables interpreted as subdatasets. stars is more general but sees > >>>>> variables as 2D arrays with bands, terra calls these bands layers. > >>>>> > >>>>> Alternatively try raster::raster() or RNetCDF or tidync which might > be > >>>>> more straightforward than rhdf5 but all are quite different to each > >>>>> other > >>>>> and to the gdal view. > >>>>> > >>>>> hth > >>>>> > >>>>> On Sat, 13 Nov 2021, 18:56 Gabriel Cotlier, <gabikl...@gmail.com> > >>>>> wrote: > >>>>> > >>>>>> Hello, > >>>>>> > >>>>>> I would like to be able to visualize / plot a specific data layer > >>>>>> within > >>>>>> the structure a hierarchical data file format .h5 in R. I could > >>>>>> observe > >>>>>> the structure as follows : > >>>>>> > >>>>>> library(rhdf5) > >>>>>> r= h5ls(file.choose()) > >>>>>> r > >>>>>> > >>>>>> and also in this way identify the Group and Name of the data to be > >>>>>> plotted, > >>>>>> however I've tried I could not access the data itself, nor plot it > >>>>>> as a > >>>>>> raster layer with its corresponding geographic coordinates. > >>>>>> I would like to be able to select such data, plot it as a raster > >>>>>> layer > >>>>>> and > >>>>>> if possible save it as GeoTIFF file format to be further processed > >>>>>> with > >>>>>> the > >>>>>> raster package as a common raster layer. > >>>>>> > >>>>>> If any small guidance example, reprex, of this procedure is possible > >>>>>> it would be appreciated. > >>>>>> > >>>>>> Thanks a lot in advance > >>>>>> Kind regards, > >>>>>> Gabriel Cotlier > >>>>>> -- > >>>>>> Gabriel Cotlier, PhD > >>>>>> Haifa Research Center for Theoretical Physics and Astrophysics > >>>>>> (HCTPA) > >>>>>> University of Haifa > >>>>>> Israel > >>>>>> > >>>>>> [[alternative HTML version deleted]] > >>>>>> > >>>>>> _______________________________________________ > >>>>>> R-sig-Geo mailing list > >>>>>> R-sig-Geo@r-project.org > >>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo > >>>>>> > >>>>> > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> _______________________________________________ > >>> 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 > [[alternative HTML version deleted]] _______________________________________________ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo