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nc_extract.m
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nc_extract.m
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%==========================================================================
% nc_ks --- nc_toolbox
% Extract parts of NetCDF files (similar to the linux 'ncks')
%
% input :
% fin --- input NetCDF file path and name
% fout --- output NetCDF file path and name
% Variable --- name list of variables to be extracted (string)
% Dimension --- information list of dimensions to be changed (string)
% Overwrite --- overwrite flag
%
% output :
% \
%
% Example:
% nc_ks(fin, fout, 'Variable', ["XLONG" "ZNU"], ...
% 'Dimension', ["Time,2,3" "bottom_top,1"]);
%
% Siqi Li, SMAST
% 2023-03-15
%
% Updates:
%
%==========================================================================
function nc_extract(fin, fout, varargin)
varargin = read_varargin(varargin, {'Variable'}, {[]});
varargin = read_varargin(varargin, {'Dimension'}, {[]});
varargin = read_varargin2(varargin, {'Overwrite'});
if isempty(Variable) && isempty(Dimension)
error('Neither variable nor dimension settings are set.')
end
% clc
% clear
% fin = '/hosts/hydra.smast.umassd.edu/data3/siqili/case/wrf_2017_merged_windfarm03/wrfout/input/wrfout_d03_20171231';
% fout = './test.nc';
% Dimension = ["Time,2,3" "bottom_top,1"];
% Variable = ["XLONG" "XLAT" "ZNU"];
% Overwrite = 'Overwrite';
if ~isempty(Overwrite)
if exist(fout, 'file') == 2
delete(fout);
end
else
if exist(fout, 'file') == 2
error('The output exists. Change another fout or use Overwrite.')
end
end
info = ncinfo(fin);
dimensions = info.Dimensions;
variables = info.Variables;
ndim = length(Dimension);
nvar = length(Variable);
for i = 1 : ndim
tmp = split(Dimension{i}, ',');
j = find(ismember({dimensions.Name},tmp{1}));
if isempty(j)
error(['Unknown dimension name: ' tmp{1}])
end
dim(i).name = tmp{1};
dim(i).start = str2num(tmp{2});
dim(i).end = dim(i).start;
dim(i).stride = 1;
if length(tmp) > 2
dim(i(i)).end = str2num(tmp{3});
if length(tmp) > 3
dim(i(i)).stride = str2num(tmp{4});
end
end
end
for i = 1 : nvar
j = find(ismember({variables.Name},Variable{i}));
if isempty(j)
error(['Unknown dimension name: ' Variable{i}])
end
end
if isempty(Variable)
Variable = convertCharsToStrings({variables.Name});
end
% Copy global attributes
nc_copy_att(fin, [], fout, []);
% Define dimensions.
for i = 1 : length(dimensions)
name = dimensions(i).Name;
if dimensions(i).Unlimited
nc_def_dim(fout, name, 0);
else
j = find(ismember({dim.name}, name));
if isempty(j)
nc_def_dim(fout, name, dimensions(i).Length);
else
nc_def_dim(fout, name, length(dim(j).start:dim(j).stride:dim(j).end));
end
end
end
for i = 1 : length(Variable)
iv = find(ismember({variables.Name},Variable{i}));
name = variables(iv).Name;
disp(['----' name])
% Define variables
if ~isempty(variables(iv).Dimensions)
vardims = {variables(iv).Dimensions.Name};
d = '';
for j = 1 : length(vardims)
k = find(ismember({dim.name}, vardims{j}));
if isempty(k)
d = [d ':'];
else
d = [d num2str(dim(k).start) ':' num2str(dim(k).stride) ':' num2str(dim(k).end)];
end
if j < length(vardims)
d = [d ','];
end
end
d = ['(' d ')'];
else
vardims = [];
d = '';
end
nc_def_var(fout, name, variables(iv).Datatype, vardims);
% Copy attributes
nc_copy_att(fin, name, fout, name);
% Read the data
data = nc_get_var(fin, name);
eval(['data = data' d ';']);
% Write the data
nc_put_var(fout, name, data);
end