Let's assume a netCDF4 (.nc) file downloaded from https://s5phub.copernicus.eu/dhus/odata/v1/Products('e6e91b26-ca43-43d4-9c08-c9c14dd6737e')/$value . This is sulphur dioxide measurement dataset over Vietnam, China and Filippines, given in the linked image.
I wish to transform this into a GeoTIFF file for further processing so that I can process the values in
(lon, lat, value) manner. I start by the following command line
gdal_translate -ot float32 -unscale -CO COMPRESS=deflate HDF5:"S5P_NRTI_L2__SO2____20181030T054006_20181030T054506_05418_01_010102_20181030T062719.nc"://PRODUCT/sulfurdioxide_total_vertical_column so2.tif.
When I open the resulting GeoTIFF file, it's almost pitch black with some little grey dots. Using Panoply to plot a diagram produces the following
I also see in the metadata there reads
float sulfurdioxide_total_vertical_column(time=1, scanline=278, ground_pixel=450); :_FillValue = 9.96921E36f; // float :units = "mol m-2"; :standard_name = "atmosphere_mole_content_of_sulfur_dioxide"; :long_name = "total vertical column of sulfur dioxide for the polluted scenario derived from the total slant column"; :coordinates = "/PRODUCT/longitude /PRODUCT/latitude"; :multiplication_factor_to_convert_to_DU = 2241.15f; // float :multiplication_factor_to_convert_to_molecules_percm2 = 6.02214E19f; // float :_ChunkSizes = 1U, 278U, 450U; // uint
Do I make this right so that the data values are correct if I intend to use them later as (lon, lat, value) (with WGS84 projection, read from metadata) in various calculations?
E.g. that I don't accidentally corrupt the coordinates or the data values (by accidentally scaling, say). Put otherway, I'm a n00b and asking if this method of using the tooling is OK before banging my head further. I'm still in process of learning the other parts of data processing and checking the correctness of those steps would be easier if I were sure about this step.
<edit 1: Looking at the tiff metadata, it doesn't appear the data is georeferenced. However
gdalwarp so2.tif so2georef.tif -t_srs "+proj=longlat +ellps=WGS84" fails with
ERROR 1: The transformation is already "north up" or a transformation between pixel/line and georeferenced coordinates cannot be computed for so2georef.tif. There is no affine transformation and no GCPs. Specify transformation option SRC_METH OD=NO_GEOTRANSFORM to bypass this check.
It think this is further confirmed by
gdal_translate -of XYZ so2.tif so2.xyz that shows values beginning with
0.5 0.5 9.96920996838686905e+36 1.5 0.5 9.96920996838686905e+36 2.5 0.5 -2.67918767349328846e-06 3.5 0.5 0.000152658714796416461 4.5 0.5 -0.000818965549115091562 5.5 0.5 0.000193428524653427303 6.5 0.5 0.00010718178964452818 7.5 0.5 -0.00120470335241407156 8.5 0.5 0.000939452263992279768
So either something is wrong with the initial command or the original
.nc file data needs to be augmented. I'm currently too rookie to understand all the metadata but I do see the portal has shapefiles etc.
<edit 2: It appears the glitch was about environment variables and doing a bit of fiddling with that, a new command line I tried is
gdal_translate -ot float32 -unscale -CO COMPRESS=deflate -of GTiff -a_srs EPSG:4326 HDF5:"S5P_NRTI_L2__SO2____20181030T054006_20181030T054506_05418_01_010102_20181030T062719.nc"://PRODUCT/sulfurdioxide_total_vertical_column so2.tif
So I added
-of GTiff -a_srs EPSG:4326 and it appears the values I get to the
xyz file are still the same. It appears the metadata now tells the coordinates are georeferenced, but they aren't really transformed as should, just the metadata added without real transformation. In the metadata I have spotted
geolocation_grid_from_band=3 geospatial_lat_max=25.532017 geospatial_lat_min=2.1418159 geospatial_lon_max=99.929924 geospatial_lon_min=128.72141
This is probably data that can be explicitly used. If so, might be nice to know if
gdal_translate could automatically use it, perhaps with an explicit switch.
<edit 3: There's S-P instruction manual at http://www.tropomi.eu/sites/default/files/files/S5P-KNMI-L2-0009-SD-S5P_level_2_Input_Output_Data_Definition-9.0.0-20170614.pdf, from there the following explanation. Then judging from https://www.gdal.org/gdal_translate.html maybe
-a_srs EPSG:4326 -a_ullr 2.1418159 128.72141 25.532017 99.929924 could be added (or in some other order) to the original command line.