GDAL/Python : converting Zarr to TIFF

Question

I have a Zarr file stored on a S3 custom storage (not AWS), that I want to save as a TIFF file locally. I'm trying to use GDAL for the first time here so I don't fully understand the methods. So far, I've been able to open the source file (Water Bodies from Copernicus land), but the 2 variables and all the dimensions (lat, lon, time) are opened each as a separate sub dataset :

ds.GetSubDatasets()

[('ZARR:"/vsis3/###/copernicus-land/water-bodies.zarr":/lat',
  'Array /lat'),
 ('ZARR:"/vsis3/###/copernicus-land/water-bodies.zarr":/lon',
  'Array /lon'),
 ('ZARR:"/vsis3/###/copernicus-land/water-bodies.zarr":/time',
  'Array /time'),
 ('ZARR:"/vsis3/###/copernicus-land/water-bodies.zarr":/QUAL',
  'Array /QUAL'),
 ('ZARR:"/vsis3/###/copernicus-land/water-bodies.zarr":/WB',
  'Array /WB'),
 ('ZARR:"/vsis3/###/copernicus-land/water-bodies.zarr":/crs',
  'Array /crs')]

So when I try to use gdal.Translate i get :

g = gdal.Translate("output.tif", ds, format="GTiff")

> RuntimeError: output.tif: Unable to export GeoTIFF files with zero bands.

And opening a subdataset :

sub_name = ds.GetSubDatasets()[4][0]
sub = gdal.Open(sub_name)

> RuntimeError: Indices of extra dimensions must be specified

I guess my problem is understanding the Dataset object, I don't get the transformation from dimensions to sub datasets.

Answer 1

I think you can output a slice of a subset, you can try and read the time data and in geospatial zarrs it is usually a one dimentional raster with the size (n x 1). where n is the available time slices.

time_ds = gdal.Open('ZARR:"/vsis3/###/copernicus-land/water-bodies.zarr":/time')

#this should give you the number of the time slices
available_time_slices = time_ds.RasterXSize

for example try and open the water bodies band slice one :

ds = gdal.Open('ZARR:"/vsis3/###/copernicus-land/water-bodies.zarr":/WB:0')

this dataset shoud be translatable into tiff ( sometimes the size is too much though). You could also consider using gdal.MultiDimTranslate function. I think you will also have to translate only a 2D slice of the data if you want a tiff output.