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I have NetCDF files containing subdatasets with 4 dimensions: time, height, latitude, longitude.

Here is an example of the output of GDAL GetSubDatasets():

('NETCDF:"Martinique_ALT22.nc":height', '[30x30x30] height (32-bit floating-point)'), 
('NETCDF:"Martinique_ALT22.nc":latitude', '[30x30] latitude (32-bit floating-point)'), 
('NETCDF:"Martinique_ALT22.nc":longitude', '[30x30] longitude (32-bit floating-point)'), 
('NETCDF:"Martinique_ALT22.nc":Water_Vapor_Concentration', '[2x30x30x30] Water_Vapor_Concentration (32-bit floating-point)')

When opening these subdatasets in Python with gdal.Open() and ReadAsArray(), the first two dimensions are overlapped and I get a 3 dimensions numpy array.

>>> band = gdal.Open(dataset.GetSubDatasets()[-1][0])
>>> array=band.ReadAsArray()
>>> print(array.shape)
(60, 30, 30)

I read somewhere that this is due to the GDAL raster format accepting only 3 dimensions: bands, rows, columns.

Is there a way to keep the first two dimensions separated and extract these subdatasets in 4-dimension numpy arrays?

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  • Cant really check if this works without the actual file, hence just a comment: I think you can just do a reshape to get 4 dimensions again, i.e.: array = band.ReadAsArray().reshape((2, 30, 30, 30), order = 'C') you might have to change the order from C to either F or A (docs.scipy.org/doc/numpy/reference/generated/numpy.reshape.html), not sure about that. Otherwise, I would definitely consider using the netCDF4 package (unidata.github.io/netcdf4-python), which can easily handle many dimensions. Commented Mar 15, 2019 at 13:42
  • I think xarray is going to handle this case much better. Commented Mar 15, 2019 at 14:01
  • @BertCoerver The reshape() method worked for me. Strangely enough, the order option had no impact on the output. I had not worked with NetCDF files in a while and forgot about the netCDF4 library: thanks for the reminder, I am totally getting back to this library. If you want to repost your comment as an answer I would gladly accept it. Commented Mar 15, 2019 at 15:45

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By applying a reshape to the "array" variable you can get back the original dimensions:

array = band.ReadAsArray().reshape((2, 30, 30, 30))

Just a side note, it might be interesting to look into the netcdf4 package (https://unidata.github.io/netcdf4-python/) or the xarray package (http://xarray.pydata.org/en/stable/). These can easily handle variables with many dimensions.

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