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

[Gabriel Cotlier]

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
>>>
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>>>
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>>> R-sig-Geo using r-project.org
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>>

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