Contents
- Create netCDF-CF of orthogonal lat-lon grid
- Define meta-info: global
- Define dimensions/coordinates: lat,lon sticks
- Define variable (define some data)
- 1.a Create netCDF file
- 1.b Add overall meta info
- 2 Create matrix span dimensions
- 3.a Create coordinate vector: longitude
- 3.b Create coordinate vector: latitude
- 3.c Create coordinate variables: coordinate system: WGS84 default
- 4 Create dependent variable
- 5.a Create all variables with attributes
- 5.b Fill all variables
- 6 Check file summary
- 7.a Load the data: using the variable names from nc_dump
- 7.b Load the data: using standard_names and coordinate attribute
- 7.c Load the data: using a dedicated function developed for grids
Create netCDF-CF of orthogonal lat-lon grid
example of how to make a netCDF file with CF conventions of a variable that is defined on a grid that is orthogonal in a lat-lon coordinate system. In this special case the dimensions coincide with the coordinate axes.
This case is described in: http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.4/cf-conventions.html#id2984551 as "Independent Latitude, Longitude Axes".
^ latitude (degrees_north) | | ncols | +------+ | | +--------+ | |05 10 15| + | | | | | |04 09 14| | | | | | | |03 08 xx| | nrows | | | | | |02 07 12| | | | | | | |01 06 11| + | +--------+ | +--------------------------> longitude (degrees_east)
%See also: SNCTOOLS, NC_CF_GRID, NC_CF_GRID_WRITE, % NC_CF_GRID_WRITE_LAT_LON_CURVILINEAR_TUTORIAL, % NC_CF_GRID_WRITE_X_Y_ORTHOGONAL_TUTORIAL, % NC_CF_GRID_WRITE_X_Y_CURVILINEAR_TUTORIAL, % NC_CF_STATIONTIMESERIES % This tool is part of <a href="http://www.OpenEarth.eu">OpenEarthTools</a> under the <a href="http://www.gnu.org/licenses/gpl.html">GPL</a> license.
Define meta-info: global
OPT.title = ''; OPT.institution = ''; OPT.source = ''; OPT.history = ['tranformation to netCDF: $HeadURL: https://repos.deltares.nl/repos/OpenEarthTools/trunk/matlab/io/netcdf/nctools/nc_cf_grid_write_lat_lon_orthogonal_tutorial.m $']; OPT.references = ''; OPT.email = ''; OPT.comment = ''; OPT.version = ''; OPT.acknowledge =['These data can be used freely for research purposes provided that the following source is acknowledged: ',OPT.institution]; OPT.disclaimer = 'This data is made available in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.';
Define dimensions/coordinates: lat,lon sticks
OPT.lat_type = 'single'; % 'single', 'double' for high-resolution data (eps 1m) OPT.lon_type = 'single'; % 'single', 'double' for high-resolution data (eps 1m) OPT.lon = [2 4 6]; OPT.lat = [50 51 52 53 54]; OPT.ncols = length(OPT.lon); OPT.nrows = length(OPT.lat); OPT.wgs84.code = 4326; % % epsg code of global grid: http://www.epsg-registry.org/ OPT.wgs84.name = 'WGS 84'; OPT.wgs84.semi_major_axis = 6378137.0; OPT.wgs84.semi_minor_axis = 6356752.314247833; OPT.wgs84.inv_flattening = 298.2572236;
Define variable (define some data)
OPT.val = [1 2 3 4 5;6 7 8 9 10;11 12 nan 14 15]; % use ncols as 1st array dimension to get correct plot in ncBrowse (snctools swaps for us) OPT.varname = 'depth'; % free to choose: will appear in netCDF tree OPT.units = 'm'; % from UDunits package: http://www.unidata.ucar.edu/software/udunits/ OPT.long_name = 'bottom depth';% free to choose: will appear in plots OPT.standard_name = 'sea_floor_depth_below_geoid'; % or 'altitude' OPT.val_type = 'single'; % 'single' or 'double' OPT.fillvalue = nan;
1.a Create netCDF file
ncfile = fullfile(fileparts(mfilename('fullpath')),[mfilename,'.nc']); nc_create_empty (ncfile)
1.b Add overall meta info
http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.4/cf-conventions.html#description-of-file-contents
nc_attput(ncfile, nc_global, 'title' , OPT.title); nc_attput(ncfile, nc_global, 'institution' , OPT.institution); nc_attput(ncfile, nc_global, 'source' , OPT.source); nc_attput(ncfile, nc_global, 'history' , OPT.history); nc_attput(ncfile, nc_global, 'references' , OPT.references); nc_attput(ncfile, nc_global, 'email' , OPT.email); nc_attput(ncfile, nc_global, 'comment' , OPT.comment); nc_attput(ncfile, nc_global, 'version' , OPT.version); nc_attput(ncfile, nc_global, 'Conventions' , 'CF-1.4'); nc_attput(ncfile, nc_global, 'CF:featureType', 'Grid'); % https://cf-pcmdi.llnl.gov/trac/wiki/PointObservationConventions nc_attput(ncfile, nc_global, 'terms_for_use' , OPT.acknowledge); nc_attput(ncfile, nc_global, 'disclaimer' , OPT.disclaimer);
2 Create matrix span dimensions
http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.4/cf-conventions.html#dimensions
nc_add_dimension(ncfile, 'lon', OPT.ncols); % !!! use this as 1st array dimension to get correct plot in ncBrowse (snctools swaps for us) nc_add_dimension(ncfile, 'lat', OPT.nrows); % !!! use this as 2nd array dimension to get correct plot in ncBrowse (snctools swaps for us) % You might insert a vector 'col' that runs [OPT.ncols:-1:1] to have % the arcGIS ASCII file approach of having upper-left corner of % the data matrix at index (1,1) rather than the default of having the % lower-left corner of the data matrix at index (1,1). % nc_add_dimension(ncfile, 'time', 1); % if you would like to include more instances of the same grid, % you can optionally use 'time' as a 3rd dimension. see % nc_cf_stationTimeSeries_write_tutorial for info on time.
3.a Create coordinate vector: longitude
http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.4/cf-conventions.html#longitude-coordinate
clear nc;ifld = 1; nc(ifld).Name = 'lon'; % dimension 'lon' is here filled with variable 'lon' nc(ifld).Nctype = nc_type(OPT.lon_type); nc(ifld).Dimension = {'lon'}; % !!! nc(ifld).Attribute( 1) = struct('Name', 'long_name' ,'Value', 'longitude'); nc(ifld).Attribute(end+1) = struct('Name', 'units' ,'Value', 'degrees_east'); nc(ifld).Attribute(end+1) = struct('Name', 'standard_name' ,'Value', 'longitude'); nc(ifld).Attribute(end+1) = struct('Name', 'actual_range' ,'Value', [min(OPT.lon(:)) max(OPT.lon(:))]); nc(ifld).Attribute(end+1) = struct('Name', 'grid_mapping' ,'Value', 'wgs84');
3.b Create coordinate vector: latitude
http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.4/cf-conventions.html#latitude-coordinate
ifld = ifld + 1; nc(ifld).Name = 'lat'; % dimension 'lat' is here filled with variable 'lat' nc(ifld).Nctype = nc_type(OPT.lat_type); nc(ifld).Dimension = {'lat'}; % !!! nc(ifld).Attribute( 1) = struct('Name', 'long_name' ,'Value', 'latitude'); nc(ifld).Attribute(end+1) = struct('Name', 'units' ,'Value', 'degrees_north'); nc(ifld).Attribute(end+1) = struct('Name', 'standard_name' ,'Value', 'latitude'); nc(ifld).Attribute(end+1) = struct('Name', 'actual_range' ,'Value', [min(OPT.lat(:)) max(OPT.lat(:))]); nc(ifld).Attribute(end+1) = struct('Name', 'grid_mapping' ,'Value', 'wgs84');
3.c Create coordinate variables: coordinate system: WGS84 default
global ellispes: WGS 84, ED 50, INT 1924, ETRS 89 and the upcoming ETRS update etc. http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.4/cf-conventions.html#grid-mappings-and-projections http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.4/cf-conventions.html#appendix-grid-mappings
ifld = ifld + 1; nc(ifld).Name = 'wgs84'; % preferred nc(ifld).Nctype = nc_int; nc(ifld).Dimension = {}; nc(ifld).Attribute = nc_cf_grid_mapping(OPT.wgs84.code); % is same as nc(ifld).Attribute = struct('Name', ... {'name',... 'epsg',... 'grid_mapping_name',... 'semi_major_axis', ... 'semi_minor_axis', ... 'inverse_flattening', ... 'comment'}, ... 'Value', ... {OPT.wgs84.name,... OPT.wgs84.code,... 'latitude_longitude',... OPT.wgs84.semi_major_axis, ... OPT.wgs84.semi_minor_axis, ... OPT.wgs84.inv_flattening, ... 'value is equal to EPSG code'});
4 Create dependent variable
http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.4/cf-conventions.html#variables Parameters with standard names: http://cf-pcmdi.llnl.gov/documents/cf-standard-names/standard-name-table/current/
ifld = ifld + 1; nc(ifld).Name = OPT.varname; nc(ifld).Nctype = nc_type(OPT.val_type); nc(ifld).Dimension = {'lon','lat'}; % {'time','lon','lat'} nc(ifld).Attribute( 1) = struct('Name', 'long_name' ,'Value', OPT.long_name ); nc(ifld).Attribute(end+1) = struct('Name', 'units' ,'Value', OPT.units ); nc(ifld).Attribute(end+1) = struct('Name', '_FillValue' ,'Value', OPT.fillvalue ); nc(ifld).Attribute(end+1) = struct('Name', 'actual_range' ,'Value', [min(OPT.val(:)) max(OPT.val(:))]); nc(ifld).Attribute(end+1) = struct('Name', 'coordinates' ,'Value', 'lat lon'); nc(ifld).Attribute(end+1) = struct('Name', 'grid_mapping' ,'Value', 'epsg'); if ~isempty(OPT.standard_name) nc(ifld).Attribute(end+1) = struct('Name', 'standard_name' ,'Value', OPT.standard_name); end
5.a Create all variables with attributes
for ifld=1:length(nc) nc_addvar(ncfile, nc(ifld)); end
5.b Fill all variables
nc_varput(ncfile, 'lon' , OPT.lon ); nc_varput(ncfile, 'lat' , OPT.lat ); nc_varput(ncfile, 'wgs84' , OPT.wgs84.code); nc_varput(ncfile, OPT.varname , OPT.val );
6 Check file summary
nc_dump(ncfile); fid = fopen(fullfile(fileparts(mfilename('fullpath')),[mfilename,'.cdl']),'w'); nc_dump(ncfile,fid); fclose(fid)
netCDF F:\checkouts\OpenEarthTools\matlab\io\netcdf\nctools\nc_cf_grid_write_lat_lon_orthogonal_tutorial.nc { dimensions: lon = 3 ; lat = 5 ; variables: // Preference 'PRESERVE_FVD': false, // dimensions consistent with ncBrowse, not with native MATLAB netcdf package. single lon(lon), shape = [3] lon:long_name = "longitude" lon:units = "degrees_east" lon:standard_name = "longitude" lon:actual_range = 2 6 lon:grid_mapping = "wgs84" single lat(lat), shape = [5] lat:long_name = "latitude" lat:units = "degrees_north" lat:standard_name = "latitude" lat:actual_range = 50 54 lat:grid_mapping = "wgs84" int32 wgs84([]), shape = [1] wgs84:name = "WGS 84" wgs84:epsg = 4326 wgs84:grid_mapping_name = "latitude_longitude" wgs84:semi_major_axis = 6.37814e+006 wgs84:semi_minor_axis = 6.35675e+006 wgs84:inverse_flattening = 298.257 wgs84:comment = "value is equal to EPSG code" single depth(lon,lat), shape = [3 5] depth:long_name = "bottom depth" depth:units = "m" depth:_FillValue = NaN depth:actual_range = 1 15 depth:coordinates = "lat lon" depth:grid_mapping = "epsg" depth:standard_name = "sea_floor_depth_below_geoid" //global attributes: :title = "" :institution = "" :source = "" :history = "tranformation to netCDF: $HeadURL: https://repos.deltares.nl/repos/OpenEarthTools/trunk/matlab/io/netcdf/nctools/nc_cf_grid_write_lat_lon_orthogonal_tutorial.m $" :references = "" :email = "" :comment = "" :version = "" :Conventions = "CF-1.4" :CF:featureType = "Grid" :terms_for_use = "These data can be used freely for research purposes provided that the following source is acknowledged: " :disclaimer = "This data is made available in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." } ans = 0
7.a Load the data: using the variable names from nc_dump
Da.dep = nc_varget(ncfile,'depth'); Da.lat = nc_varget(ncfile,'lon'); Da.lon = nc_varget(ncfile,'lat')
Da = dep: [3x5 double] lat: [3x1 single] lon: [5x1 single] datenum: [6x1 double] var: [1 2 3 NaN 5 6]
7.b Load the data: using standard_names and coordinate attribute
depname = nc_varfind(ncfile,'attributename', 'standard_name', 'attributevalue', 'sea_floor_depth_below_geoid') Db.z = nc_varget(ncfile,depname); coords = nc_attget(ncfile,depname,'coordinates'); [ax1,coords] = strtok(coords); ax2 = strtok(coords); if strcmpi(nc_attget(ncfile,ax1,'standard_name'),'latitude') Db.lat = nc_varget(ncfile,ax1); Db.lon = nc_varget(ncfile,ax2) else Db.lat = nc_varget(ncfile,ax2); Db.lon = nc_varget(ncfile,ax1) end
depname = depth Db = z: [3x5 double] lat: [5x1 single] lon: [3x1 single] datenum: [6x1 double] var: [1 2 3 NaN 5 6]
7.c Load the data: using a dedicated function developed for grids
[Dc,Mc] = nc_cf_grid(ncfile,OPT.varname)
Dc = lon: [2 4 6] lat: [50 51 52 53 54] depth: [3x5 double] Mc = lon: [1x1 struct] lat: [1x1 struct] depth: [1x1 struct]