Question on hierarchical data format 5 .h5 file format

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 at 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 at 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 at 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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