[R-sig-Geo] Question on hierarchical data format 5 .h5 file format

Sun Nov 14 14:11:26 CET 2021

Hello Edzer,
Thanks a lot.
The scaling factor to convert to LST is 0.02
Regards,
Gabriel

On Sun, Nov 14, 2021 at 2:59 PM Edzer Pebesma <edzer.pebesma using uni-muenster.de>
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.
>
> 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 <gabiklm01 using 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 <mdsumner using 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, <gabiklm01 using 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]]
> >>>>>
> >>>>> _______________________________________________
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> >>>>> R-sig-Geo using r-project.org
> >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >>>>>
> >>>>
> >>
> >>     [[alternative HTML version deleted]]
> >>
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> >>
> >
>
> --
> Edzer Pebesma
> Institute for Geoinformatics
> Heisenbergstrasse 2, 48151 Muenster, Germany
> Phone: +49 251 8333081
>
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