I want to use nco to extract variables and dimensions from a very large netcdf file. I know that I have to use ncks, but the structure of my original file is so complicated and huge that I will need some advices. I want to start with a file with multiple variables/dimensions to create a file with only 7 variables 4 dimensions and 2 global attributes. Below, the 2 descriptions of my files (i'm on linux). I don't know how to use ncks to extract more than 1 variable or if it's possible to do it in one step. Thank you for your help :-)
1/ My starting file
File champs_meno_BE201704.nc (NC_FORMAT_NETCDF4_CLASSIC):
21 variables (excluding dimension variables):
double latitude[ni,nj]
long_name: latitude
standard_name: latitude
units: degrees_north
_FillValue: 1.7e+38
valid_min: -90
valid_max: 90
double longitude[ni,nj]
long_name: longitude
standard_name: longitude
units: degrees_east
_FillValue: 1.7e+38
valid_min: -180
valid_max: 180
short longitude_u[ni_u,nj_u]
long_name: longitude at u location
standard_name: longitude_at_u_location
units: degrees_east
scale_factor: 0.000247199011200289
add_offset: 7.99996999999985
valid_min: -32767
valid_max: 32767
_FillValue: -32768
short longitude_v[ni_v,nj_v]
long_name: longitude at v location
standard_name: longitude_at_v_location
units: degrees_east
scale_factor: 0.000247199011200289
add_offset: 7.99996999999985
valid_min: -32767
valid_max: 32767
_FillValue: -32768
short latitude_u[ni_u,nj_u]
long_name: latitude at u location
standard_name: latitude_at_u_location
units: degrees_north
scale_factor: 7.93480483413422e-05
add_offset: 41.9999975000008
valid_min: -32767
valid_max: 32767
_FillValue: -32768
short latitude_v[ni_v,nj_v]
long_name: latitude at v location
standard_name: latitude_at_v_location
units: degrees_north
scale_factor: 7.93480483413422e-05
add_offset: 41.9999975000008
valid_min: -32767
valid_max: 32767
_FillValue: -32768
float SIG[level]
long_name: sigma variable
standard_name: ocean_s_variable
units:
valid_min: -1
valid_max: 0
_FillValue: 999
float Csu_sig[level]
long_name: C(s) law at mid layer
standard_name: ocean_s_coordinate_function_at_midlayer
units:
valid_min: -2
valid_max: 2
_FillValue: 999
formula_definition: C(k) = (1-b)*sinh(a*s(k))/sinh(a) + b*[tanh(a*(s(k)+0.5))-tanh(0.5*a)]/(2*tanh(0.5*a))
short hc[ni,nj]
long_name: depth over which the resolution is increased
standard_name: ocean_s_coordinate_thick_of_surface_resolution
units: m
coordinates: latitude longitude
scale_factor: 0.0079348124563694
add_offset: 240
valid_min: -32767
valid_max: 32767
_FillValue: -32768
float b[]
long_name: bottom control parameter
standard_name: ocean_s_coordinate_bottom_control
units:
valid_min: 0
valid_max: 1
_FillValue: 999
float theta[]
long_name: surface control parameter
standard_name: ocean_s_coordinate_surface_control
units:
valid_min: 0
valid_max: 20
_FillValue: 999
short H0[ni,nj]
long_name: bathymetry relative to the mean level
standard_name: model_sea_floor_depth_below_geoid
units: m
coordinates: latitude longitude
scale_factor: 0.15335550904274
add_offset: 4975
valid_min: -32767
valid_max: 32767
_FillValue: -32768
short HX[ni_u,nj_u]
long_name: bathymetry at u-location relative to the mean level
standard_name: model_sea_floor_depth_below_geoid_at_u_location
units: m
coordinates: latitude_u longitude_u
scale_factor: 0.15335550904274
add_offset: 4975
valid_min: -32767
valid_max: 32767
_FillValue: -32768
short HY[ni_v,nj_v]
long_name: bathymetry at v-location relative to the mean level
standard_name: model_sea_floor_depth_below_geoid_at_v_location
units: m
coordinates: latitude_v longitude_v
scale_factor: 0.15335550904274
add_offset: 4975
valid_min: -32767
valid_max: 32767
_FillValue: -32768
short XE[ni,nj,time]
long_name: sea surface height
standard_name: sea_surface_height_above_geoid
units: m
coordinates: latitude longitude
scale_factor: 0.00152592547237873
add_offset: 0
valid_min: -32767
valid_max: 32767
_FillValue: -32768
short UZ[ni_u,nj_u,level,time]
long_name: 3d zonal velocity
standard_name: sea_water_x_velocity_at_u_location
units: m s-1
coordinates: latitude_u longitude_u
scale_factor: 0.000610370188951492
add_offset: 0
valid_min: -32767
valid_max: 32767
_FillValue: -32768
short VZ[ni_v,nj_v,level,time]
long_name: 3d meridional velocity
standard_name: sea_water_y_velocity_at_v_location
units: m s-1
coordinates: latitude_v longitude_v
scale_factor: 0.000610370188951492
add_offset: 0
valid_min: -32767
valid_max: 32767
_FillValue: -32768
short SAL[ni,nj,level,time]
long_name: salinity
standard_name: sea_water_salinity
units: 1e-3
coordinates: latitude longitude
scale_factor: 0.000839259009808302
add_offset: 22.5
valid_min: -32767
valid_max: 32767
_FillValue: -32768
short TEMP[ni,nj,level,time]
long_name: temperature
standard_name: sea_water_potential_temperature
units: degrees_Celsius
coordinates: latitude longitude
scale_factor: 0.000839259009808302
add_offset: 22.5
valid_min: -32767
valid_max: 32767
_FillValue: -32768
short TAUX[ni_u,nj_u,time]
long_name: U-component of Surface Wind Stress
standard_name: surface_downward_x_stress_at_u_location
units: N m-2
coordinates: latitude_u longitude_u
scale_factor: 0.00152592547237873
add_offset: 0
valid_min: -32767
valid_max: 32767
_FillValue: -32768
short TAUY[ni_v,nj_v,time]
long_name: V-component of Surface Wind Stress
standard_name: surface_downward_y_stress_at_v_location
units: N m-2
coordinates: latitude_v longitude_v
scale_factor: 0.00152592547237873
add_offset: 0
valid_min: -32767
valid_max: 32767
_FillValue: -32768
10 dimensions:
ni Size:1101
long_name: x-dimension of the grid
standard_name: x_grid_index
c_grid_axis_shift: 0
axis: X
c_grid_dynamic_range: 4:1088
nj Size:463
long_name: y-dimension of the grid
standard_name: y_grid_index
axis: Y
c_grid_axis_shift: 0
c_grid_dynamic_range: 3:456
ni_u Size:1101
long_name: x-dimension of the grid at u location
standard_name: x_grid_index_at_u_location
c_grid_axis_shift: 0.5
axis: X
c_grid_dynamic_range: 4:1087
nj_u Size:463
long_name: y-dimension of the grid at u location
standard_name: y_grid_index_at_u_location
axis: Y
c_grid_axis_shift: 0
c_grid_dynamic_range: 3:456
ni_v Size:1101
long_name: x-dimension of the grid at v location
standard_name: x_grid_index_at_v_location
c_grid_axis_shift: 0
axis: X
c_grid_dynamic_range: 4:1088
nj_v Size:463
long_name: y-dimension of the grid at v location
standard_name: y_grid_index_at_v_location
axis: Y
c_grid_axis_shift: 0.5
c_grid_dynamic_range: 2:455
ni_f Size:1101
long_name: x-dimension of the grid at f location
standard_name: x_grid_index_at_f_location
c_grid_axis_shift: 0.5
axis: X
c_grid_dynamic_range: 4:1087
nj_f Size:463
long_name: y-dimension of the grid at f location
standard_name: y_grid_index_at_f_location
axis: Y
c_grid_axis_shift: 0.5
c_grid_dynamic_range: 2:455
time Size:240 *** is unlimited ***
long_name: time in seconds (UT)
standard_name: time
units: seconds since 1900-01-01T00:00:00Z
axis: T
time_origin: 01-JAN-1900 00:00:00
conventions: relative number of seconds with no decimal part
level Size:60
long_name: sigma level
axis: Z
c_grid_axis_shift: 0
positive: up
valid_min: -1
valid_max: 0
standard_name: ocean_s_coordinate
formula_terms: s: level eta: XE depth: H0 a: theta b: b depth_c: hc
formula_definition: z(n,k,j,i) = eta(n,j,i)*(1+s(k)) + depth_c*s(k) + (depth(j,i)-depth_c)*C(k)
57 global attributes:
limi: 0
lima: 1100
pasi: 1
ljmi: 0
ljma: 462
pasj: 1
lkmi: 1
lkma: 60
pask: 1
global_imin: 0
global_imax: 1100
global_jmin: 0
global_jmax: 462
data_type: OCO oriented grid
format_version: 1.3.1
Conventions: CF-1.6 OCO-1.3.1 COMODO-1.0
netcdf_version: 4.1.2
product_version: 1.0
references: http://www.previmer.org/
easting: longitude
northing: latitude
grid_projection: n/a
distribution_statement: Data restrictions: for registered users only
institution: IFREMER
institution_references: http://www.ifremer.fr/
data_centre: IFREMER OCO DATA CENTER
data_centre_references: http://www.previmer.org/
title: PREVIMER MENOR 1200 forecast
creation_date: 2017-04-04T21:09:49Z
run_time: 2017-04-04T21:09:49Z
history: ...(too long)
2017-04-04T21:09:49Z: creation
model_name: MARS
arakawa_grid_type: C1
source: MARS3D V10.10
area: North Western Mediterranean Sea
southernmost_latitude: 39.5000
northernmost_latitude: 44.5000
latitude_resolution: 1.082250000000000E-002
westernmost_longitude: 0.0000
easternmost_longitude: 15.9999
longitude_resolution: 1.454540000000000E-002
minimum_depth: 5.000000
maximum_depth: 3500.000
depth_resolution: n/a
forecast_range: 4-days forecast
forecast_type: forecast
operational_status: experimental
NCO: "4.6.4"
start_date: 2017-04-01T00:00:00Z
stop_date: 2017-04-01T00:00:00Z
software_version: PREVIMER forecasting system v2
product_name: PREVIMER_F2-MARS3D-MENOR1200_20170401T0000Z.nc
field_type: 3-hourly
comment: Use of Meteo-France ARPEGEHR meteorological data
contact: [email protected]
quality_index: 0
nco_openmp_thread_number: 1
2/ The structure (variables, dimensions and global attributes) I want for my output file below (of course this is not the same file, but another MARS3D file with the structure I need).
File mars-iroise.nc (NC_FORMAT_CLASSIC):
7 variables (excluding dimension variables):
float h0[longitude,latitude]
float temp[longitude,latitude,level,time]
float u[longitude,latitude,time]
float uz[longitude,latitude,level,time]
float v[longitude,latitude,time]
float vz[longitude,latitude,level,time]
float xe[longitude,latitude,time]
4 dimensions:
latitude Size:50
longitude Size:40
level Size:15
time Size:13 *** is unlimited ***
2 global attributes:
history: Mon Jan 22 17:01:24 2018: ncks --mk_rec_dmn time mars-iroise.nc mars-iroise.nc
NCO: "4.5.4"
