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not understanding why ncwa output is all fill values

Developers
Christine Smit
2017-01-20
2017-01-23

  • Christine Smit

    Christine Smit - 2017-01-20

    I have a netcdf file with a variable that has no fill values and a mask variable that is also free from fill values, but the output averaged file ends up with all fill values. What am I missing? Why is the output of the average a fill value?

    The command I ran was:

    ncwa -O -o areaavg.nc -a "lat,lon" -m "shape_mask" -v AIRX3STM_006_TotCO_A concat_with_mask.nc

    my input file, concat_with_mask.nc, is:

    netcdf concat_with_mask {
    dimensions:
    time = UNLIMITED ; // (3 currently)
    lat = 4 ;
    lon = 6 ;
    latv = 2 ;
    lonv = 2 ;
    nv = 2 ;
    variables:
    float AIRX3STM_006_TotCO_A(time, lat, lon) ;
    AIRX3STM_006_TotCO_A:_FillValue = -9999.f ;
    AIRX3STM_006_TotCO_A:standard_name = "atmosphere_mass_content_of_carbon_monoxide" ;
    AIRX3STM_006_TotCO_A:quantity_type = "CO" ;
    AIRX3STM_006_TotCO_A:product_short_name = "AIRX3STM" ;
    AIRX3STM_006_TotCO_A:product_version = "006" ;
    AIRX3STM_006_TotCO_A:long_name = "Carbon Monoxide Total Column (Daytime/Ascending)" ;
    AIRX3STM_006_TotCO_A:coordinates = "time lat lon" ;
    AIRX3STM_006_TotCO_A:units = "mol/cm2" ;
    int datamonth(time) ;
    datamonth:long_name = "Standardized Date Label" ;
    double lat(lat) ;
    lat:units = "degrees_north" ;
    lat:format = "F5.1" ;
    lat:missing_value = -9999.f ;
    lat:standard_name = "latitude" ;
    lat:bounds = "lat_bnds" ;
    double lat_bnds(lat, latv) ;
    lat_bnds:units = "degrees_north" ;
    double lon(lon) ;
    lon:units = "degrees_east" ;
    lon:format = "F6.1" ;
    lon:missing_value = -9999.f ;
    lon:standard_name = "longitude" ;
    lon:bounds = "lon_bnds" ;
    double lon_bnds(lon, lonv) ;
    lon_bnds:units = "degrees_east" ;
    int time(time) ;
    time:long_name = "time" ;
    time:standard_name = "time" ;
    time:units = "seconds since 1970-01-01 00:00:00" ;
    time:bounds = "time_bnds" ;
    int time_bnds(time, nv) ;
    time_bnds:units = "seconds since 1970-01-01 00:00:00" ;
    double shape_mask(lat, lon) ;
    shape_mask:cell_methods = "contrib: mean" ;
    shape_mask:units = "degrees_north" ;

    // global attributes:
    :Conventions = "CF-1.4" ;
    :start_time = "2003-12-01T00:00:00Z" ;
    :end_time = "2003-12-31T23:59:59Z" ;
    :temporal_resolution = "monthly" ;
    :NCO = "\"4.5.3\"" ;
    :nco_openmp_thread_number = 1 ;
    :history = "Thu Jan 19 17:54:50 2017: ncks -O -o concat.nc -d lat,37.4,40.6 -d lon,-79.6,-74.4 concat.nc\n",
    "Thu Jan 19 17:31:49 2017: ncrcat -o concat.nc scrubbed.AIRX3STM_006_TotCO_A.20031201.nc scrubbed.AIRX3STM_006_TotCO_A.20040101.nc scrubbed.AIRX3STM_006_TotCO_A.20040201.nc" ;
    data:

    AIRX3STM_006_TotCO_A =
    2.016065e+18, 2.112892e+18, 2.184668e+18, 2.182557e+18, 2.172987e+18,
    2.197053e+18,
    1.895452e+18, 2.038864e+18, 2.173691e+18, 2.212675e+18, 2.212112e+18,
    2.212956e+18,
    1.98088e+18, 2.058849e+18, 2.155676e+18, 2.202823e+18, 2.21366e+18,
    2.229986e+18,
    2.039568e+18, 2.02085e+18, 2.131329e+18, 2.162854e+18, 2.176365e+18,
    2.213238e+18,
    2.273896e+18, 2.359042e+18, 2.381278e+18, 2.390004e+18, 2.384656e+18,
    2.383812e+18,
    2.084604e+18, 2.267422e+18, 2.384656e+18, 2.397885e+18, 2.386626e+18,
    2.394226e+18,
    2.119647e+18, 2.237445e+18, 2.325828e+18, 2.362982e+18, 2.371145e+18,
    2.391411e+18,
    2.200149e+18, 2.181431e+18, 2.231252e+18, 2.299369e+18, 2.317383e+18,
    2.367205e+18,
    2.350035e+18, 2.466284e+18, 2.533556e+18, 2.514134e+18, 2.475291e+18,
    2.468817e+18,
    2.220838e+18, 2.396759e+18, 2.527645e+18, 2.519764e+18, 2.52849e+18,
    2.470224e+18,
    2.282903e+18, 2.359042e+18, 2.47895e+18, 2.513572e+18, 2.537497e+18,
    2.501468e+18,
    2.393945e+18, 2.323294e+18, 2.421811e+18, 2.469098e+18, 2.491616e+18,
    2.528208e+18 ;

    datamonth = 200312, 200401, 200402 ;

    lat = 37.5, 38.5, 39.5, 40.5 ;

    lat_bnds =
    37, 38,
    38, 39,
    39, 40,
    40, 41 ;

    lon = -79.5, -78.5, -77.5, -76.5, -75.5, -74.5 ;

    lon_bnds =
    -80, -79,
    -79, -78,
    -78, -77,
    -77, -76,
    -76, -75,
    -75, -74 ;

    time = 1070236800, 1072915200, 1075593600 ;

    time_bnds =
    1070236800, 1072915199,
    1072915200, 1075593599,
    1075593600, 1078099199 ;

    shape_mask =
    0, 0, 0, 0.0991691675364044, 0.0991691675364044, 0,
    0, 0, 0.293478058819655, 0.782608156852414, 0.58695611763931,
    0.0489130098032759,
    0.241132682308662, 0.241132682308662, 0.530491901079058, 0.57871843754079,
    0.19290614584693, 0,
    0, 0, 0, 0, 0, 0 ;
    }

    The output file I get has all fill values for the AIRX3STM_006_TotCO_A variable:

    netcdf areaavg {
    dimensions:
    time = UNLIMITED ; // (3 currently)
    latv = 2 ;
    lonv = 2 ;
    nv = 2 ;
    variables:
    float AIRX3STM_006_TotCO_A(time) ;
    AIRX3STM_006_TotCO_A:_FillValue = -9999.f ;
    AIRX3STM_006_TotCO_A:standard_name = "atmosphere_mass_content_of_carbon_monoxide" ;
    AIRX3STM_006_TotCO_A:quantity_type = "CO" ;
    AIRX3STM_006_TotCO_A:product_short_name = "AIRX3STM" ;
    AIRX3STM_006_TotCO_A:product_version = "006" ;
    AIRX3STM_006_TotCO_A:long_name = "Carbon Monoxide Total Column (Daytime/Ascending)" ;
    AIRX3STM_006_TotCO_A:coordinates = "time " ;
    AIRX3STM_006_TotCO_A:units = "mol/cm2" ;
    AIRX3STM_006_TotCO_A:cell_methods = "lat, lon: mean" ;
    double lat ;
    lat:units = "degrees_north" ;
    lat:format = "F5.1" ;
    lat:missing_value = -9999.f ;
    lat:standard_name = "latitude" ;
    lat:bounds = "lat_bnds" ;
    lat:_FillValue = 9.96920996838687e+36 ;
    lat:cell_methods = "lat: mean" ;
    double lat_bnds(latv) ;
    lat_bnds:units = "degrees_north" ;
    lat_bnds:_FillValue = 9.96920996838687e+36 ;
    lat_bnds:cell_methods = "lat: mean" ;
    double lon ;
    lon:units = "degrees_east" ;
    lon:format = "F6.1" ;
    lon:missing_value = -9999.f ;
    lon:standard_name = "longitude" ;
    lon:bounds = "lon_bnds" ;
    lon:_FillValue = 9.96920996838687e+36 ;
    lon:cell_methods = "lon: mean" ;
    double lon_bnds(lonv) ;
    lon_bnds:units = "degrees_east" ;
    lon_bnds:_FillValue = 9.96920996838687e+36 ;
    lon_bnds:cell_methods = "lon: mean" ;
    int time(time) ;
    time:long_name = "time" ;
    time:standard_name = "time" ;
    time:units = "seconds since 1970-01-01 00:00:00" ;
    time:bounds = "time_bnds" ;
    int time_bnds(time, nv) ;
    time_bnds:units = "seconds since 1970-01-01 00:00:00" ;

    // global attributes:
    :Conventions = "CF-1.4" ;
    :start_time = "2003-12-01T00:00:00Z" ;
    :end_time = "2003-12-31T23:59:59Z" ;
    :temporal_resolution = "monthly" ;
    :NCO = "\"4.5.3\"" ;
    :nco_openmp_thread_number = 1 ;
    :history = "Fri Jan 20 19:22:22 2017: ncwa -O -o areaavg.nc -a lat,lon -m shape_mask -v AIRX3STM_006_TotCO_A concat_with_mask.nc\n",
    "Thu Jan 19 17:54:50 2017: ncks -O -o concat.nc -d lat,37.4,40.6 -d lon,-79.6,-74.4 concat.nc\n",
    "Thu Jan 19 17:31:49 2017: ncrcat -o concat.nc scrubbed.AIRX3STM_006_TotCO_A.20031201.nc scrubbed.AIRX3STM_006_TotCO_A.20040101.nc scrubbed.AIRX3STM_006_TotCO_A.20040201.nc" ;
    data:

    AIRX3STM_006_TotCO_A = , , _ ;

    lat = 39 ;

    lat_bnds = 38.5, 39.5 ;

    lon = -77 ;

    lon_bnds = -77.5, -76.5 ;

    time = 1070236800, 1072915200, 1075593600 ;

    time_bnds =
    1070236800, 1072915199,
    1072915200, 1075593599,
    1075593600, 1078099199 ;
    }

     

  • Charlie Zender

    Charlie Zender - 2017-01-21

    Please read the docs on the difference between a mask and a weight. A mask requires a mask_condition, e.g., --msk_cnd "ORO < 1" whereas a weight is just a multiplier. The default mask condition may lead to all missing values in your case.
    cz

     

  • Christine Smit

    Christine Smit - 2017-01-23

    Whoops. Yeah. I wanted -w for weights, not -m.

     

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