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mnc

A tool for Oceanographers and Meteorologists to easily create their NetCDF files using Matlab

https://github.com/humbertolvarona/mnc

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Repository

A tool for Oceanographers and Meteorologists to easily create their NetCDF files using Matlab

Basic Info
  • Host: GitHub
  • Owner: humbertolvarona
  • License: mit
  • Language: MATLAB
  • Default Branch: main
  • Size: 87.9 KB
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Created over 4 years ago · Last pushed almost 3 years ago
Metadata Files
Readme License Citation

README.md

mNC

A tool for Oceanographers and Meteorologists to easily create their NetCDF files using Matlab

DOI

DOI

Creates mytest.nc file from one-dimensional arrays of longitude and latitude

lon = [-38.5, -38, -37.5, -37, -36.5, -36, -35.5];

lat = [-1.5, -1, -0.5, 0, 0.5, 1, 1.5];

matlab:

create_NC('mytest.nc', [-38.5:0.5:-35.5], [-1.5:0.5:1.5]);

bash:

ncdump -v lon,lat mytest.nc

Result:

netcdf mytest {

dimensions:

lon = 7 ;

lat = 7 ;

variables:

double lon(lon) ;

    lon:standard_name = "logitude" ;

    lon:long_name = "logitude" ;

    lon:units = "degrees_east" ;

    lon:axis = "X" ;

double lat(lat) ;

    lat:standard_name = "latitude" ;

    lat:long_name = "latitude" ;

    lat:units = "degrees_north" ;

    lat:axis = "Y" ;

// global attributes:

    :creation_date = "13-Oct-2021 11:34:03" ;

    :Producer = "null text" ;

            :dataType = "2D Grid" ;

    :Comment = "no comments" ;

data:

lon = -38.5, -38, -37.5, -37, -36.5, -36, -35.5 ;

lat = -1.5, -1, -0.5, 0, 0.5, 1, 1.5 ;

}

Creates mytest_2.nc file from two-dimensional arrays of longitude and latitude

matlab:

lons = [-38.5, -38, -37.5, -37, -36.5, -36, -35.5];

lats = [-1.5, -1, -0.5, 0, 0.5];

[LATS, LONS] = meshgrid(lats, lons);

createNC2DCoordinates('mytest_2.nc', LONS, LATS);

bash:

ncdump -v lon,lat mytest.nc

Result:

netcdf mytest_2 {

dimensions:

lon = 7 ;

lat = 5 ;

variables:

double lon(lat, lon) ;

    lon:standard_name = "longitude" ;

    lon:long_name = "longitude" ;

    lon:units = "degrees_east" ;

    lon:axis = "X" ;

double lat(lat, lon) ;

    lat:standard_name = "latitude" ;

    lat:long_name = "latitude" ;

    lat:units = "degrees_north" ;

    lat:axis = "Y" ;

// global attributes:

    :creation_date = "13-Oct-2021 11:45:59" ;

    :Producer = "null text" ;

    :dataType = "2D Grid" ;

    :Comment = "no comments" ;

data:

lon = -38.5, -38, -37.5, -37, -36.5, -36, -35.5, -38.5, -38, -37.5, -37, -36.5, -36, -35.5, -38.5, -38, -37.5, -37, -36.5, -36, -35.5, -38.5, -38, -37.5, -37, -36.5, -36, -35.5, -38.5, -38, -37.5, -37, -36.5, -36, -35.5 ;

lat = -1.5, -1.5, -1.5, -1.5, -1.5, -1.5, -1.5, -1, -1, -1, -1, -1, -1, -1, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, 0, 0, 0, 0, 0, 0, 0, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5 ;

}

Inserts a 2D variable in the file mytest_2.nc

Example: a bathymetry where the depth ranges between -100 and -1 m

matlab:

[nLon, nLat] = size(LONS);

BathymetryRange = [-100:-1];

Bath = rand(nLon,nLat) * range(BathymetryRange) + BathymetryRange(1);

insertvariable2DNC('mytest2.nc', Bath, 'z', 'Bathymetry', 'Shallow water bathymetry', 'm')

bash:

ncdump -v lon,lat mytest_2.nc

Result:

netcdf mytest_2 {

dimensions:

lon = 7 ;

lat = 5 ;

variables:

double lon(lat, lon) ;

    lon:standard_name = "longitude" ;

    lon:long_name = "longitude" ;

    lon:units = "degrees_east" ;

    lon:axis = "X" ;

double lat(lat, lon) ;

    lat:standard_name = "latitude" ;

    lat:long_name = "latitude" ;

    lat:units = "degrees_north" ;

    lat:axis = "Y" ;

double z(lat, lon) ;

    z:standard_name = "Bathymetry" ;

    z:long_name = "Shallow water bathymetry" ;

    z:units = "m" ;

    z:missing_value = NaN ;

    z:FillValue = NaN ;

// global attributes:

    :creation_date = "13-Oct-2021 11:45:59" ;

    :Producer = "null text" ;

    :dataType = "2D Grid" ;

    :Comment = "no comments" ;

data:

z = -18.477674995598, -31.2119663253941, -68.6071514739748, -5.92801716500286, -96.589838030212, -56.5643083940166, -62.2257127477922, -24.2138379732488, -21.2752097874307, -81.4996121491165, -51.5133248169651, -55.886966129621, -36.0150119989848, -29.7728817450508, -25.2860184837463, -72.6735173771407, -32.7094349914862, -35.1452976065898, -83.9014382157316, -88.2192295257207, -50.6619588537678, -4.98534810690798, -66.3018130600528, -42.058492653002, -77.8426179903774, -25.6245611287404, -74.7455835695324, -49.9102518851509, -30.7914044569881, -11.8005779989559, -5.03014890466102, -45.8256625335835, -86.2761801599608, -85.2198934496533, -74.5066828417501 ;

}

Insert a three-dimensional static variable that is depth-dependent

BathymetryRange = [0, 10, 20, 30, 40, 50];

matlab:

BathymetryRange = [0:10:50];

TemperatureRange = [27:0.02:28];

[nLon, nLat] = size(LONS);

nDepth = length(BathymetryRange);

Temp = rand(nLon, nLat, nDepth) * range(TemperatureRange) + TemperatureRange(1);

% The depth values are inserted

insertdepthNC('mytest2.nc', BathymetryRange)

insertstaticvariable3DNC('mytest2.nc', Temp, 'pottemp', 'potential_temperature', 'Potential Temperature', '°C', 999.99)

bash:

ncdump -v depth,pottemp mytest_2.nc

Result:

netcdf mytest_2 {

dimensions:

lon = 7 ;

lat = 5 ;

depth = 6 ;

variables:

double lon(lat, lon) ;

    lon:standard_name = "longitude" ;

    lon:long_name = "longitude" ;

    lon:units = "degrees_east" ;

    lon:axis = "X" ;

double lat(lat, lon) ;

    lat:standard_name = "latitude" ;

    lat:long_name = "latitude" ;

    lat:units = "degrees_north" ;

    lat:axis = "Y" ;

double z(lat, lon) ;

    z:standard_name = "Bathymetry" ;

    z:long_name = "Shallow water bathymetry" ;

    z:units = "m" ;

    z:missing_value = NaN ;

    z:FillValue = NaN ;

double depth(depth) ;

    depth:standard_name = "Depth" ;

    depth:long_name = "Vertical axis" ;

    depth:units = "m" ;

    depth:axis = "Z" ;

double pottemp(depth, lat, lon) ;

    pottemp:standard_name = "potential_temperature" ;

    pottemp:long_name = "Potential Temperature" ;

    pottemp:units = "°C" ;

    pottemp:missing_value = 999.99 ;

    pottemp:FillValue = 999.99 ;

// global attributes:

    :creation_date = "13-Oct-2021 11:45:59" ;

    :Producer = "null text" ;

    :dataType = "2D Grid" ;

    :Comment = "no comments" ;

data:

depth = 0, 10, 20, 30, 40, 50 ;

pottemp = 27.8407172559837, 27.2542821789715, 27.8142848260688, 27.243524968725, 27.9292636231872, 27.3499837659848, 27.1965952504312, 27.251083857976, 27.6160446761466, 27.4732888489027, 27.351659507063,

...

...

...

27.3341630527375, 27.6987458323348, 27.1978098266859 ;

}

Insert a three-dimensional dynamic variable that is time-dependent

Time range = Daily data from '2001-05-03' to '1900-01-01'

(The '-' as a field separator in the date is mandatory)

Base time = '1900-01-01'

matlab:

% Daily mean

% Base time '1900-01-01'

timeRange = [datenum('2001-05-03'):datenum('2001-05-21')] - datenum('1900-01-01');

TemperatureRange = [27:0.02:28];

[nLon, nLat] = size(LONS);

nTime = length(timeRange);

Temp = rand(nLon, nLat, nTime) * range(TemperatureRange) + TemperatureRange(1);

inserttimeNC('mytest2.nc', timeRange, 'days since 1900-01-01');

insertdynamicvariable3DNC('mytest2.nc', Temp, 'temp', 'temperature', 'SST', '°C', 999.99)

bash:

ncdump -v temp,time -t mytest_2.nc

Result:

netcdf mytest_2 {

dimensions:

lon = 7 ;

lat = 5 ;

depth = 6 ;

time = UNLIMITED ; // (19 currently)

variables:

double lon(lat, lon) ;

    lon:standard_name = "longitude" ;

    lon:long_name = "longitude" ;

    lon:units = "degrees_east" ;

    lon:axis = "X" ;

double lat(lat, lon) ;

    lat:standard_name = "latitude" ;

    lat:long_name = "latitude" ;

    lat:units = "degrees_north" ;

    lat:axis = "Y" ;

double z(lat, lon) ;

    z:standard_name = "Bathymetry" ;

    z:long_name = "Shallow water bathymetry" ;

    z:units = "m" ;

    z:missing_value = NaN ;

    z:FillValue = NaN ;

double depth(depth) ;

    depth:standard_name = "Depth" ;

    depth:long_name = "Vertical axis" ;

    depth:units = "m" ;

    depth:axis = "Z" ;

double pottemp(depth, lat, lon) ;

    pottemp:standard_name = "potential_temperature" ;

    pottemp:long_name = "Potential Temperature" ;

    pottemp:units = "°C" ;

    pottemp:missing_value = 999.99 ;

    pottemp:FillValue = 999.99 ;

double time(time) ;

    time:standard_name = "time" ;

    time:long_name = "time" ;

    time:units = "days since 1900-01-01" ;

    time:calendar = "standard" ;

    time:axis = "T" ;

double temp(time, lat, lon) ;

    temp:standard_name = "temperature" ;

    temp:long_name = "SST" ;

    temp:units = "°C" ;

    temp:missing_value = 999.99 ;

    temp:FillValue = 999.99 ;

// global attributes:

    :creation_date = "13-Oct-2021 13:46:11" ;

    :Producer = "null text" ;

    :dataType = "2D Grid" ;

    :Comment = "no comments" ;

data:

time = "2001-05-03", "2001-05-04", "2001-05-05", "2001-05-06", "2001-05-07", "2001-05-08", "2001-05-09", "2001-05-10", "2001-05-11", "2001-05-12", "2001-05-13", "2001-05-14", "2001-05-15", "2001-05-16", "2001-05-17", "2001-05-18", "2001-05-19", "2001-05-20", "2001-05-21" ;

temp = 27.3130274882277, 27.0764394578121, 27.7914151469637, 27.3653839792903, 27.5850993892254, 27.1833367061834, 27.076918942246, 27.1536627665307, 27.826875990171, 27.3009567426333, 27.3838844900057,

...

...

...

27.3341630527375, 27.6987458323348, 27.1978098266859 ;

}

Inserting a depth and time dependent variable.

Functions insertdepthNC and inserttimeNC must be used previously.

matlab:

depthRange = [0:10:50];

timeRange = [datenum('2001-05-03'):datenum('2001-05-21')] - datenum('1900-01-01');

SaltRange = [35.5:0.1:36.5];

[nLon, nLat] = size(LONS);

nDepth = length(depthRange);

nTime = length(timeRange);

Salt = rand(nLon, nLat, nDepth, nTime) * range(SaltRange) + SaltRange(1);

insertdynamicvariable4DNC('mytest2.nc', Salt, 'salt', 'SSS', 'Sea Surface Salinity', 'psu', -999.0)

bash:

ncdump -v salt mytest_2.nc

Result:

netcdf mytest_2 {

dimensions:

lon = 7 ;

lat = 5 ;

depth = 6 ;

time = UNLIMITED ; // (19 currently)

variables:

...

...

...

double depth(depth) ;

    depth:standard_name = "Depth" ;

    depth:long_name = "Vertical axis" ;

    depth:units = "m" ;

    depth:axis = "Z" ;

double pottemp(depth, lat, lon) ;

    pottemp:standard_name = "potential_temperature" ;

    pottemp:long_name = "Potential Temperature" ;

    pottemp:units = "°C" ;

    pottemp:missing_value = 999.99 ;

    pottemp:FillValue = 999.99 ;

double time(time) ;

    time:standard_name = "time" ;

    time:long_name = "time" ;

    time:units = "days since 1900-01-01" ;

    time:calendar = "standard" ;

    time:axis = "T" ;

double temp(time, lat, lon) ;

    temp:standard_name = "temperature" ;

    temp:long_name = "SST" ;

    temp:units = "°C" ;

    temp:missing_value = 999.99 ;

    temp:FillValue = 999.99 ;

double salt(time, depth, lat, lon) ;

    salt:standard_name = "SSS" ;

    salt:long_name = "Sea Surface Salinity" ;

    salt:units = "psu" ;

    salt:missing_value = -999. ;

    salt:FillValue = -999. ;

// global attributes:

            :creation_date = "13-Oct-2021 15:01:43" ;

    :Producer = "null text" ;

    :dataType = "2D Grid" ;

    :Comment = "no comments" ;

}

Insert a time series

To insert a time series the functions inserttime_NC has to be used previously

matlab:

LHF_Range = [-150:10:-80];

timeRange = [datenum('2001-05-03'):datenum('2001-05-21')] - datenum('1900-01-01');

nTime = length(timeRange);

LHF = rand(1, nTime) * range(LHFRange) + LHFRange(1);

inserttimeserieNC('mytest2.nc', LHF, 'lhf', 'LHF', 'Latent Heat Flux', 'W/m^2', 1.e+20)

bash:

ncdump -v lhf mytest_2.nc

Result:

netcdf mytest_2 {

dimensions:

lon = 7 ;

lat = 5 ;

depth = 6 ;

time = UNLIMITED ; // (19 currently)

variables:

double lon(lat, lon) ;

    lon:standard_name = "longitude" ;

    lon:long_name = "longitude" ;

    lon:units = "degrees_east" ;

    lon:axis = "X" ;

double lat(lat, lon) ;

    lat:standard_name = "latitude" ;

    lat:long_name = "latitude" ;

    lat:units = "degrees_north" ;

    lat:axis = "Y" ;

double z(lat, lon) ;

    z:standard_name = "Bathymetry" ;

    z:long_name = "Shallow water bathymetry" ;

    z:units = "m" ;

    z:missing_value = NaN ;

    z:FillValue = NaN ;

double depth(depth) ;

    depth:standard_name = "Depth" ;

    depth:long_name = "Vertical axis" ;

    depth:units = "m" ;

    depth:axis = "Z" ;

double pottemp(depth, lat, lon) ;

    pottemp:standard_name = "potential_temperature" ;

    pottemp:long_name = "Potential Temperature" ;

    pottemp:units = "°C" ;

    pottemp:missing_value = 999.99 ;

    pottemp:FillValue = 999.99 ;

double time(time) ;

    time:standard_name = "time" ;

    time:long_name = "time" ;

    time:units = "days since 1900-01-01" ;

    time:calendar = "standard" ;

    time:axis = "T" ;

double temp(time, lat, lon) ;

    temp:standard_name = "temperature" ;

    temp:long_name = "SST" ;

    temp:units = "°C" ;

    temp:missing_value = 999.99 ;

    temp:FillValue = 999.99 ;

double salt(time, depth, lat, lon) ;

    salt:standard_name = "SSS" ;

    salt:long_name = "Sea Surface Salinity" ;

    salt:units = "psu" ;

    salt:missing_value = -999. ;

    salt:FillValue = -999. ;

double lhf(time) ;

    lhf:standard_name = "LHF" ;

    lhf:long_name = "Latent Heat Flux" ;

    lhf:units = "W/m^2" ;

    lhf:missing_value = 1.e+20 ;

    lhf:FillValue = 1.e+20 ;

// global attributes:

    :creation_date = "13-Oct-2021 15:01:43" ;

    :Producer = "null text" ;

    :dataType = "2D Grid" ;

    :Comment = "no comments" ;

data:

lhf = -125.379955123903, -123.719684788329, -129.544507133169, -126.458305049462, -91.5692549892492, -84.8326305071334, -103.772336089214, -93.9690344680875, -129.713354851269, -81.3917310092116, -84.5737397899491, -132.297764636527, -100.859013831388, -134.095709492856, -100.818057038615, -123.932837199952, -96.494980684739, -109.482836080872, -125.736495459038 ;

}

Create a NetCDF file with time series only

matlab:

timeRange = [datenum('2001-05-03'):datenum('2001-05-21')] - datenum('1900-01-01');

createtimeserieNC('mytest3.nc', timeRange, '1900-01-01')

SWR_Range = [180:10:250];

LWR_Range = [-100:10:-50];

nTime = length(timeRange);

SWR = rand(1, nTime) * range(SWRRange) + SWRRange(1);

LWR = rand(1, nTime) * range(LWRRange) + LWRRange(1);

inserttimeserieNC('mytest3.nc', SWR, 'swr', 'SWR', 'Short Wave Radiation', 'W/m^2', 1.e+20)

inserttimeserieNC('mytest3.nc', LWR, 'lwr', 'LWR', 'Long Wave Radiation', 'W/m^2', 1.e+20)

bash:

ncdump -v lwr,swr,time -t mytest_3.nc

Result:

netcdf mytest_3 {

dimensions:

time = UNLIMITED ; // (19 currently)

variables:

double time(time) ;

    time:standard_name = "time" ;

    time:long_name = "time" ;

    time:units = "days since 1900-01-01" ;

    time:calendar = "standard" ;

    time:axis = "T" ;

double swr(time) ;

    swr:standard_name = "SWR" ;

    swr:long_name = "Short Wave Radiation" ;

    swr:units = "W/m^2" ;

    swr:missing_value = 1.e+20 ;

    swr:FillValue = 1.e+20 ;

double lwr(time) ;

    lwr:standard_name = "LWR" ;

    lwr:long_name = "Long Wave Radiation" ;

    lwr:units = "W/m^2" ;

    lwr:missing_value = 1.e+20 ;

    lwr:FillValue = 1.e+20 ;

// global attributes:

    :creation_date = "13-Oct-2021 15:59:17" ;

    :Producer = "null text" ;

    :dataType = "Time series only" ;

    :Comment = "no comments" ;

data:

time = "2001-05-03", "2001-05-04", "2001-05-05", "2001-05-06", "2001-05-07", "2001-05-08", "2001-05-09", "2001-05-10", "2001-05-11", "2001-05-12", "2001-05-13", "2001-05-14", "2001-05-15", "2001-05-16", "2001-05-17", "2001-05-18", "2001-05-19", "2001-05-20", "2001-05-21" ;

swr = 209.679376465332, 249.097068762438, 210.909769744377, 235.104545828219, 218.205895421282, 240.182234958772, 243.346623294593, 235.004205938925, 241.68268679656, 186.877429186821, 195.80290627705, 225.488124656128, 213.019894526324, 229.115843377746, 190.362983352515, 194.062437958129, 206.378626897567, 203.281329439278, 204.329633483502 ;

lwr = -69.3865225685708, -74.6937604966374, -87.2313991934547, -50.3519323423257, -73.3152709634012, -84.355922245511, -79.7881506368443, -60.5495796817233, -98.9336126754137, -94.0063895900241, -85.5835296256372, -54.8947746739663, -74.6499192070357, -54.4607958681041, -86.5101360896428, -58.297106644226, -68.9318597650484, -70.7001552939819, -68.9116708557565 ;

}

Note

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

The function insertlevelNC is equivalent to insertdepthNC, the function insertstaticvariable3DAtmosphereNC is equivalent to insertstaticvariable3DNC and the function insertdynamicvariable4DAtmosphereNC is equivalent to insertdynamicvariable4DNC, with the only difference that they write the "level" parameter instead of the "depth" parameter.

Owner

  • Name: Humberto L. Varona
  • Login: humbertolvarona
  • Kind: user
  • Location: Brazil

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Varona"
  given-names: "Humberto L."
  orcid: "https://orcid.org/0000-0001-7405-4827"
title: "mNC: A tool for Oceanographers and Meteorologists to easily create their NetCDF files using Matlab"
version: 1.0
doi: 10.5281/zenodo.5572749
date-released: 2021-10-15
url: "https://doi.org/10.5281/zenodo.5572749"

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