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

[Edzer Pebesma]

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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>>>>> 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