Decompressing a netCDF file

Question

I have a compressed netCDF file called in.nc with a (_DeflateLevel=4). I want to decompress the file.

I've already tried using the following command but it doesn't change anything:

nccopy -d 0 in.nc out.nc

Here are the in.nc specifications:

time_counter = UNLIMITED ; // (12 currently)
    y = 552 ;
    x = 552 ;
variables:
    float Q16c(time_counter, y, x) ;
        Q16c:long_name = "Deep Sediment Particulate organic Matter" ;
        Q16c:units = "mg C/m2" ;
        Q16c:online_operation = "average" ;
        Q16c:interval_operation = "900 s" ;
        Q16c:interval_write = "1 month" ;
        Q16c:cell_methods = "time: mean (interval: 900 s)" ;
        Q16c:_FillValue = 1.e+20f ;
        Q16c:missing_value = 1.e+20f ;
        Q16c:coordinates = "time_centered nav_lat nav_lon" ;
        Q16c:_Storage = "chunked" ;
        Q16c:_ChunkSizes = 1, 552, 552 ;
        Q16c:_DeflateLevel = 4 ;
        Q16c:_Endianness = "little" ;

Is the size of `in.nc` and `out.nc` the same? – msi_gerva Feb 20 '23 at 12:24 — msi_gerva, Feb 20 '23 at 12:24
Yes, both files have the same size! – Amr Talaat Feb 20 '23 at 13:17 — Amr Talaat, Feb 20 '23 at 13:17

Charlie Zender · Answer 1 · 2023-02-20T21:10:29.957

2

The way to decompress a compressed file with NCO is straightforward:

ncks -L 0 in.nc out.nc

p.s.: this method should work for the most common codecs, including DEFLATE, Zstandard, and Bzip2.

edited Feb 20 '23 at 21:10

answered Feb 20 '23 at 20:20

Charlie Zender

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Great, thank you so much Charlie, your command has solved the problem. – Amr Talaat Feb 21 '23 at 10:34

score 1 · Answer 2 · answered Apr 14 '23 at 07:20

I think the way to decompress files in cdo is

cdo -z zip_0 copy in.nc out.nc

If they are compressed using 2 byte shorts with an add_offset and scale_factor (e.g. ERA5 etc) then you can decompress those by converting to float like this

cdo unpack in.nc out.nc

or alternatively

cdo -b f32 copy in.nc out.nc

Decompressing a netCDF file

2 Answers2