Hyperslab of a 4D netcdf variable using ncks

风流意气都作罢 提交于 2019-12-25 01:03:10

问题


I have a large large netcdf file, of which I only need certain data. Therefore, I want to create a subdivision of this netcdf file using ncks. The netcdf file is as following:

Source:
           F:\LECOB\Model\20091208_195356.nc
Format:
           64bit
Global Attributes:
           Model = 's26.bobshelf.20141113'
           Title = 'S-NWM_BiP'
Dimensions:
           ni_t = 682
           nj_t = 712
           nk_t = 29
           time = 1     (UNLIMITED)
           ni_w = 682
           nj_w = 712
           nk_w = 30
           ni_u = 681
           nj_u = 712
           nk_u = 29
           ni_v = 682
           nj_v = 711
           nk_v = 29
           ni_f = 681
           nj_f = 711
           nk_f = 29
Variables:
    time 
           Size:       1x1
           Dimensions: time
           Datatype:   double
           Attributes:
                       units         = 'seconds from 2009-dec-08 17:00:14'
                       long_name     = 'time'
                       standard_name = 'time'
                       time_origin   = '2009-dec-08 17:00:14'
                       calendar      = 'gregorian'
                       content       = 'T'
                       axis          = 'T'
                       associate     = 'undefined'
    ni_t 
           Size:       682x1
           Dimensions: ni_t
           Datatype:   single
           Attributes:
                       long_name     = 'x_grid_index'
                       standard_name = 'x_grid_index'
                       content       = 'X'
                       axis          = 'X'
    nj_t 
           Size:       712x1
           Dimensions: nj_t
           Datatype:   single
           Attributes:
                       long_name     = 'y_grid_index'
                       standard_name = 'y_grid_index'
                       content       = 'Y'
                       axis          = 'Y'
    nk_t 
           Size:       29x1
           Dimensions: nk_t
           Datatype:   single
           Attributes:
                       long_name     = 'z_grid_index'
                       standard_name = 'z_grid_index'
                       content       = 'Z'
                       axis          = 'Z'
                       positive      = 'up'
    ni_w 
           Size:       682x1
           Dimensions: ni_w
           Datatype:   single
           Attributes:
                       long_name     = 'x_grid_index_at_w_location'
                       standard_name = 'x_grid_index_at_w_location'
                       content       = 'X'
                       axis          = 'X'
    nj_w 
           Size:       712x1
           Dimensions: nj_w
           Datatype:   single
           Attributes:
                       long_name     = 'y_grid_index_at_w_location'
                       standard_name = 'y_grid_index_at_w_location'
                       content       = 'Y'
                       axis          = 'Y'
    nk_w 
           Size:       30x1
           Dimensions: nk_w
           Datatype:   single
           Attributes:
                       long_name     = 'z_grid_index_at_w_location'
                       standard_name = 'z_grid_index_at_w_location'
                       content       = 'Z'
                       axis          = 'Z'
                       positive      = 'up'
    ni_u 
           Size:       681x1
           Dimensions: ni_u
           Datatype:   single
           Attributes:
                       long_name     = 'x_grid_index_at_u_location'
                       standard_name = 'x_grid_index_at_u_location'
                       content       = 'X'
                       axis          = 'X'
    nj_u 
           Size:       712x1
           Dimensions: nj_u
           Datatype:   single
           Attributes:
                       long_name     = 'y_grid_index_at_u_location'
                       standard_name = 'y_grid_index_at_u_location'
                       content       = 'Y'
                       axis          = 'Y'
    nk_u 
           Size:       29x1
           Dimensions: nk_u
           Datatype:   single
           Attributes:
                       long_name     = 'z_grid_index_at_u_location'
                       standard_name = 'z_grid_index_at_u_location'
                       content       = 'Z'
                       axis          = 'Z'
                       positive      = 'up'
    ni_v 
           Size:       682x1
           Dimensions: ni_v
           Datatype:   single
           Attributes:
                       long_name     = 'x_grid_index_at_v_location'
                       standard_name = 'x_grid_index_at_v_location'
                       content       = 'X'
                       axis          = 'X'
    nj_v 
           Size:       711x1
           Dimensions: nj_v
           Datatype:   single
           Attributes:
                       long_name     = 'y_grid_index_at_v_location'
                       standard_name = 'y_grid_index_at_v_location'
                       content       = 'Y'
                       axis          = 'Y'
    nk_v 
           Size:       29x1
           Dimensions: nk_v
           Datatype:   single
           Attributes:
                       long_name     = 'z_grid_index_at_v_location'
                       standard_name = 'z_grid_index_at_v_location'
                       content       = 'Z'
                       axis          = 'Z'
                       positive      = 'up'
    ssh  
           Size:       682x712x1
           Dimensions: ni_t,nj_t,time
           Datatype:   single
           Attributes:
                       units         = 'm'
                       long_name     = 'sea surface height above geoid'
                       standard_name = 'sea_surface_height_above_geoid'
                       content       = 'TYX'
                       associate     = 'time latitude_t longitude_t'
                       coordinates   = 'time latitude_t longitude_t'
                       _FillValue    = -9999
    CFL2D
           Size:       682x712x1
           Dimensions: ni_t,nj_t,time
           Datatype:   single
           Attributes:
                       units         = 's'
                       long_name     = 'CFL2D'
                       standard_name = 'CFL2D'
                       content       = 'TYX'
                       associate     = 'time latitude_t longitude_t'
                       coordinates   = 'time latitude_t longitude_t'
                       _FillValue    = -9999
    tem  
           Size:       682x712x29x1
           Dimensions: ni_t,nj_t,nk_t,time
           Datatype:   single
           Attributes:
                       units         = 'degrees_Celsius'
                       long_name     = 'sea_water_potential_temperature'
                       standard_name = 'sea_water_potential_temperature'
                       content       = 'TZYX'
                       associate     = 'time depth_t latitude_t longitude_t'
                       coordinates   = 'time depth_t latitude_t longitude_t'
                       _FillValue    = -9999
                       positive      = 'up'
    sal  
           Size:       682x712x29x1
           Dimensions: ni_t,nj_t,nk_t,time
           Datatype:   single
           Attributes:
                       units         = '1e-3'
                       long_name     = 'sea water salinity'
                       standard_name = 'sea_water_salinity'
                       content       = 'TZYX'
                       associate     = 'time depth_t latitude_t longitude_t'
                       coordinates   = 'time depth_t latitude_t longitude_t'
                       _FillValue    = -9999
                       positive      = 'up'
    vel_u
           Size:       681x712x29x1
           Dimensions: ni_u,nj_u,nk_u,time
           Datatype:   single
           Attributes:
                       units         = 'm s-1'
                       long_name     = 'sea_water_x_velocity_at_u_location'
                       standard_name = 'sea_water_x_velocity_at_u_location'
                       content       = 'TZYX'
                       associate     = 'time depth_u latitude_u longitude_u'
                       coordinates   = 'time depth_u latitude_u longitude_u'
                       _FillValue    = -9999
                       positive      = 'up'
    vel_v
           Size:       682x711x29x1
           Dimensions: ni_v,nj_v,nk_v,time
           Datatype:   single
           Attributes:
                       units         = 'm s-1'
                       long_name     = 'sea_water_y_velocity_at_v_location'
                       standard_name = 'sea_water_y_velocity_at_v_location'
                       content       = 'TZYX'
                       associate     = 'time depth_v latitude_v longitude_v'
                       coordinates   = 'time depth_v latitude_v longitude_v'
                       _FillValue    = -9999
                       positive      = 'up'
    kh   
           Size:       682x712x30x1
           Dimensions: ni_w,nj_w,nk_w,time
           Datatype:   single
           Attributes:
                       units         = 'm2/s'
                       long_name     = 'kh'
                       standard_name = 'kh'
                       content       = 'TZYX'
                       associate     = 'time depth_w latitude_t longitude_t'
                       coordinates   = 'time depth_w latitude_t longitude_t'
                       _FillValue    = -9999
                       positive      = 'up'
    tken 
           Size:       682x712x30x1
           Dimensions: ni_w,nj_w,nk_w,time
           Datatype:   single
           Attributes:
                       units         = '(m/s)2'
                       long_name     = 'tken'
                       standard_name = 'tken'
                       content       = 'TZYX'
                       associate     = 'time depth_w latitude_t longitude_t'
                       coordinates   = 'time depth_w latitude_t longitude_t'
                       _FillValue    = -9999
                       positive      = 'up'
    w    
           Size:       682x712x30x1
           Dimensions: ni_w,nj_w,nk_w,time
           Datatype:   single
           Attributes:
                       units         = 'm s-1'
                       long_name     = 'vertical_sea_water_velocity_at_w_location'
                       standard_name = 'vertical_sea_water_velocity_at_w_location'
                       content       = 'TZYX'
                       associate     = 'time depth_w latitude_t longitude_t'
                       coordinates   = 'time depth_w latitude_t longitude_t'
                       _FillValue    = -9999
                       positive      = 'up'

Now I'm interested in the 4D variable vel_u (ni_u,nj_u,nk_u,time). I want to extract ni_u 151 to 152, nj_u 234 to 235 , nk_u everything and time everything. This question helped me along NCO: Extract a variable from NetCDF file using NCO ncks and so did the following link http://nco.sourceforge.net/nco.html#crd Using those, I tried the following code on my linux computer:

ncks -C -F -d vel_u,151,152,1 20091208_195356.nc test.nc

This gives me two problems:

  1. It copies all the variables and not just vel_u even though I used -C as suggested in question NCO: Extract a variable from NetCDF file using NCO ncks
  2. I have no idea how to specify to only use 234 to 235 of dimension nj_u

So how do I put those parts (ni_u 151 to 152, nj_u 234 to 235 ) of the vel_u variable in my test.nc file?

Any answer is deeply appreciated!


回答1:


I think I found the answer: -d is for dimensions and -v is for variables, making the answer to my question the following:

ncks -C -F -d nj_u,234,235,1 -d ni_u,151,152,1 -v vel_u 20091208_195356.nc test.nc

-C to make sure you only copy the variable vel_u

-F because caunting should start at 1 and not 0

-d NameDimension,Min,Max,Step

-v NameVariable

input.nc

output.nc

This seems to be giving me exactly what I want.



来源:https://stackoverflow.com/questions/54367298/hyperslab-of-a-4d-netcdf-variable-using-ncks

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