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

[Edzer Pebesma]

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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>>>
> 
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-- 
Edzer Pebesma
Institute for Geoinformatics
Heisenbergstrasse 2, 48151 Muenster, Germany
Phone: +49 251 8333081