[106] | 1 | % 'struct2nc': create a netcdf file from a Matlab structure |
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| 2 | %--------------------------------------------------------------------- |
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| 3 | % errormsg=struct2nc(flname,Data) |
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| 4 | % |
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[811] | 5 | % OUTPUT: |
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[106] | 6 | % errormsg=error message, =[]: default, no error |
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| 7 | % |
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| 8 | % INPUT: |
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| 9 | % flname: name of the netcdf file to create (must end with the extension '.nc') |
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| 10 | % Data: structure containing all the information of the netcdf file (or netcdf object) |
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| 11 | % with fields: |
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| 12 | % (optional) .ListGlobalAttribute: list (cell array of character strings) of the names of the global attributes Att_1, Att_2... |
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| 13 | % .Att_1,Att_2...: values of the global attributes |
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| 14 | % (requested) .ListVarName: list of the variable names Var_1, Var_2....(cell array of character strings). |
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| 15 | % (requested) .VarDimName: list of dimension names for each element of .ListVarName (cell array of string cells) |
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| 16 | % (optional) .VarAttribute: cell array of structures of the form .VarAttribute{ivar}.key=value, defining an attribute key name and value for the variable #ivar |
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| 17 | % (requested) .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName |
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| 18 | |
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[809] | 19 | %======================================================================= |
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[924] | 20 | % Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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[809] | 21 | % http://www.legi.grenoble-inp.fr |
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| 22 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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| 23 | % |
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[106] | 24 | % This file is part of the toolbox UVMAT. |
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[809] | 25 | % |
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[106] | 26 | % UVMAT is free software; you can redistribute it and/or modify |
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[809] | 27 | % it under the terms of the GNU General Public License as published |
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| 28 | % by the Free Software Foundation; either version 2 of the license, |
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| 29 | % or (at your option) any later version. |
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| 30 | % |
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[106] | 31 | % UVMAT is distributed in the hope that it will be useful, |
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| 32 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 33 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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[809] | 34 | % GNU General Public License (see LICENSE.txt) for more details. |
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| 35 | %======================================================================= |
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[106] | 36 | |
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[930] | 37 | function [errormsg,nc]=struct2nc(flname,Data,action) |
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| 38 | nc=[]; |
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| 39 | % if ~ischar(flname) |
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| 40 | % errormsg='invalid input for the netcf file name'; |
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| 41 | % return |
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| 42 | % end |
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[106] | 43 | if ~exist('Data','var') |
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| 44 | errormsg='no data input for the netcdf file'; |
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| 45 | return |
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| 46 | end |
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[930] | 47 | if ~exist('action','var') |
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| 48 | action='one_input'; %fill the file with data and close it |
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[404] | 49 | end |
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[919] | 50 | |
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[930] | 51 | |
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[919] | 52 | %% check the validity of the input field structure |
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[404] | 53 | [errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(Data); |
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| 54 | if ~isempty(errormsg) |
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| 55 | errormsg=['error in struct2nc:invalid input structure_' errormsg]; |
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| 56 | return |
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| 57 | end |
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| 58 | ListVarName=Data.ListVarName; |
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[919] | 59 | |
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| 60 | %% create the netcdf file with name flname in format NETCDF4 |
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[930] | 61 | if ischar(flname) |
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| 62 | FilePath=fileparts(flname); |
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| 63 | if ~strcmp(FilePath,'') && ~exist(FilePath,'dir') |
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| 64 | errormsg=['directory ' FilePath ' needs to be created']; |
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| 65 | return |
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| 66 | end |
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| 67 | cmode = netcdf.getConstant('NETCDF4'); |
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| 68 | cmode = bitor(cmode, netcdf.getConstant('CLASSIC_MODEL')); |
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| 69 | cmode = bitor(cmode, netcdf.getConstant('CLOBBER')); |
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| 70 | nc = netcdf.create(flname, cmode); |
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| 71 | else |
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| 72 | nc=flname; |
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| 73 | end |
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[913] | 74 | |
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[919] | 75 | %% write global constants |
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[404] | 76 | if isfield(Data,'ListGlobalAttribute') |
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| 77 | keys=Data.ListGlobalAttribute; |
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| 78 | for iattr=1:length(keys) |
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| 79 | if isfield(Data,keys{iattr}) |
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| 80 | testvar=0; |
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| 81 | for ivar=1:length(ListVarName)% eliminate possible global attributes with the same name as a variable |
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| 82 | if isequal(ListVarName{ivar}, keys{iattr}) |
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| 83 | testvar=1; |
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| 84 | break |
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[106] | 85 | end |
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[404] | 86 | end |
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| 87 | if ~testvar |
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| 88 | eval(['cte=Data.' keys{iattr} ';']) |
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| 89 | if (ischar(cte) ||isnumeric(cte)) && ~isempty(cte)%&& ~isequal(cte,'') |
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| 90 | %write constant only if it is numeric or char string, and not empty |
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| 91 | netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),keys{iattr},cte) |
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[106] | 92 | end |
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| 93 | end |
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| 94 | end |
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| 95 | end |
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[404] | 96 | end |
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[919] | 97 | |
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| 98 | %% create the dimensions |
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[404] | 99 | dimid=zeros(1,length(ListDimName)); |
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| 100 | for idim=1:length(ListDimName) |
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| 101 | dimid(idim) = netcdf.defDim(nc,ListDimName{idim},DimValue(idim)); |
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| 102 | end |
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| 103 | VarAttribute={}; %default |
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| 104 | testattr=0; |
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| 105 | if isfield(Data,'VarAttribute') |
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| 106 | VarAttribute=Data.VarAttribute; |
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| 107 | testattr=1; |
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| 108 | end |
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[919] | 109 | |
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| 110 | |
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| 111 | %% create the variables |
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| 112 | varid=nan(1,length(Data.ListVarName)); |
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[404] | 113 | for ivar=1:length(ListVarName) |
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[919] | 114 | if isfield(Data,ListVarName{ivar}) |
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| 115 | VarClass=class(Data.(ListVarName{ivar})); |
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| 116 | VarType=''; |
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| 117 | switch VarClass |
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| 118 | case {'single','double'} |
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| 119 | VarType='nc_float'; % store all floating reals as single |
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| 120 | case {'uint8','int16','uint16','int32','uint32','int64','uint64'} |
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| 121 | VarType='nc_int'; |
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| 122 | case 'logical' |
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| 123 | VarType='nc_byte'; |
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| 124 | end |
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| 125 | if ~isempty(VarType) |
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| 126 | varid(ivar)=netcdf.defVar(nc,ListVarName{ivar},VarType,dimid(VarDimIndex{ivar}));%define variable |
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| 127 | end |
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| 128 | end |
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[404] | 129 | end |
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[919] | 130 | |
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| 131 | %% write variable attributes |
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[404] | 132 | if testattr |
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| 133 | for ivar=1:min(numel(VarAttribute),numel(ListVarName)) |
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[919] | 134 | if isstruct(VarAttribute{ivar}) && ~isnan(varid(ivar)) |
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[404] | 135 | attr_names=fields(VarAttribute{ivar}); |
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| 136 | for iattr=1:length(attr_names) |
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[526] | 137 | attr_val=VarAttribute{ivar}.(attr_names{iattr}); |
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| 138 | if ~isempty(attr_names{iattr})&& ~isempty(attr_val)&&~iscell(attr_val) |
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[404] | 139 | netcdf.putAtt(nc,varid(ivar),attr_names{iattr},attr_val); |
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[106] | 140 | end |
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| 141 | end |
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| 142 | end |
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| 143 | end |
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[404] | 144 | end |
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| 145 | netcdf.endDef(nc); %put in data mode |
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[919] | 146 | |
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| 147 | %% fill the variables with input data |
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[404] | 148 | for ivar=1:length(ListVarName) |
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[919] | 149 | if ~isnan(varid(ivar)) |
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[404] | 150 | VarVal=Data.(ListVarName{ivar}); |
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| 151 | %varval=values of the current variable |
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| 152 | VarDimName=Data.VarDimName{ivar}; |
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| 153 | if ischar(VarDimName) |
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| 154 | VarDimName={VarDimName}; |
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| 155 | end |
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| 156 | siz=size(VarVal); |
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| 157 | testrange=(numel(VarDimName)==1 && strcmp(VarDimName{1},ListVarName{ivar}) && numel(VarVal)==2);% case of a coordinate defined on a regular mesh by the first and last values. |
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| 158 | testline=isequal(length(siz),2) && isequal(siz(1),1)&& isequal(siz(2), DimValue(VarDimIndex{ivar}));%matlab vector |
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[919] | 159 | %testcolumn=isequal(length(siz),2) && isequal(siz(1), DimValue(VarDimIndex{ivar}))&& isequal(siz(2),1);%matlab column vector |
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[404] | 160 | if testline || testrange |
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| 161 | if testrange |
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| 162 | VarVal=linspace(VarVal(1),VarVal(2),DimValue(VarDimIndex{ivar}));% restitute the whole array of coordinate values |
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| 163 | end |
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| 164 | netcdf.putVar(nc,varid(ivar), double(VarVal')); |
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| 165 | else |
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| 166 | netcdf.putVar(nc,varid(ivar), double(VarVal)); |
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| 167 | end |
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[106] | 168 | end |
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| 169 | end |
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[930] | 170 | if strcmp(action,'one_input') |
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[404] | 171 | netcdf.close(nc) |
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[930] | 172 | end |
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[106] | 173 | |
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[530] | 174 | %'check_field_structure': check the validity of the field struture representation consistant with the netcdf format |
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| 175 | %------------------------------------------------------------------------ |
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[674] | 176 | % [errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(Data) |
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[530] | 177 | % |
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| 178 | % OUTPUT: |
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| 179 | % errormsg: error message which is not empty when the input structure does not have the right form |
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[674] | 180 | % ListDimName: list of dimension names (cell array of cahr strings) |
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| 181 | % DimValue: list of dimension values (numerical array with the same dimension as ListDimName) |
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| 182 | % VarDimIndex: cell array of dimension index (in the list ListDimName) for each element of Data.ListVarName |
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[530] | 183 | % |
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| 184 | % INPUT: |
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| 185 | % Data: structure containing |
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| 186 | % (optional) .ListGlobalAttribute: cell listing the names of the global attributes |
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| 187 | % .Att_1,Att_2... : values of the global attributes |
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| 188 | % (requested) .ListVarName: list of variable names to select (cell array of char strings {'VarName1', 'VarName2',...} ) |
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| 189 | % (requested) .VarDimName: list of dimension names for each element of .ListVarName (cell array of string cells) |
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| 190 | % (requested) .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName |
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| 191 | |
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| 192 | |
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| 193 | function [errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(Data) |
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| 194 | errormsg=''; |
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| 195 | ListDimName={}; |
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| 196 | DimValue=[]; %default |
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| 197 | VarDimIndex={}; |
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| 198 | if ~isstruct(Data) |
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| 199 | errormsg='input field is not a structure'; |
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| 200 | return |
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| 201 | end |
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| 202 | if isfield(Data,'ListVarName') && iscell(Data.ListVarName) |
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| 203 | nbfield=numel(Data.ListVarName); |
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| 204 | else |
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| 205 | errormsg='input field does not contain the cell array of variable names .ListVarName'; |
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| 206 | return |
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| 207 | end |
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| 208 | %check dimension names |
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| 209 | if (isfield(Data,'VarDimName') && iscell(Data.VarDimName)) |
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| 210 | if numel(Data.VarDimName)~=nbfield |
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| 211 | errormsg=' .ListVarName and .VarDimName have different lengths'; |
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| 212 | return |
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| 213 | end |
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| 214 | else |
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| 215 | errormsg='input field does not contain the cell array of dimension names .VarDimName'; |
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| 216 | return |
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| 217 | end |
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| 218 | nbdim=0; |
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| 219 | ListDimName={}; |
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| 220 | |
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| 221 | %% main loop on the list of variables |
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[674] | 222 | VarDimIndex=cell(1,nbfield); |
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[530] | 223 | for ivar=1:nbfield |
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| 224 | VarName=Data.ListVarName{ivar}; |
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| 225 | if ~isfield(Data,VarName) |
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| 226 | errormsg=['the listed variable ' VarName ' is not found']; |
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| 227 | return |
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| 228 | end |
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| 229 | sizvar=size(Data.(VarName));% sizvar = dimension of variable |
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| 230 | DimCell=Data.VarDimName{ivar}; |
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| 231 | if ischar(DimCell) |
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| 232 | DimCell={DimCell};%case of a single dimension name, defined by a string |
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| 233 | elseif ~iscell(DimCell) |
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| 234 | errormsg=['wrong format for .VarDimName{' num2str(ivar) ' (must be the cell of dimension names of the variable ' VarName]; |
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[674] | 235 | return |
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[530] | 236 | end |
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| 237 | nbcoord=numel(sizvar);%nbre of coordinates for variable named VarName |
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| 238 | testrange=0; |
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| 239 | if numel(DimCell)==0 |
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| 240 | errormsg=['empty declared dimension .VarDimName{' num2str(ivar) '} for ' VarName]; |
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| 241 | return |
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| 242 | elseif numel(DimCell)==1% one dimension declared |
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| 243 | if nbcoord==2 |
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| 244 | if sizvar(1)==1 |
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| 245 | sizvar(1)=sizvar(2); |
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| 246 | elseif sizvar(2)==1 |
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| 247 | else |
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| 248 | errormsg=['1 dimension declared in .VarDimName{' num2str(ivar) '} inconsistent with the nbre of dimensions =2 of the variable ' VarName]; |
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| 249 | return |
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| 250 | end |
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| 251 | if sizvar(1)==2 && isequal(VarName,DimCell{1}) |
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| 252 | testrange=1;% test for a dimension variable representing a range |
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| 253 | end |
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| 254 | else |
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| 255 | errormsg=['1 dimension declared in .VarDimName{' num2str(ivar) '} inconsistent with the nbre of dimensions =' num2str(nbcoord) ' of the variable ' VarName]; |
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| 256 | return |
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| 257 | end |
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| 258 | else |
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| 259 | if numel(DimCell)>nbcoord |
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| 260 | sizvar(nbcoord+1:numel(DimCell))=1;% case of singleton dimensions (not seen by the function size) |
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| 261 | elseif nbcoord > numel(DimCell) |
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| 262 | errormsg=['nbre of declared dimensions in .VarDimName{' num2str(ivar) '} smaller than the nbre of dimensions =' num2str(nbcoord) ' of the variable ' VarName]; |
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| 263 | return |
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| 264 | end |
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| 265 | end |
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| 266 | DimIndex=[]; |
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| 267 | for idim=1:numel(DimCell) %loop on the coordinates of variable #ivar |
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| 268 | DimName=DimCell{idim}; |
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| 269 | iprev=find(strcmp(DimName,ListDimName),1);%look for dimension name DimName in the current list |
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| 270 | if isempty(iprev)% append the dimension name to the current list |
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| 271 | nbdim=nbdim+1; |
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| 272 | RangeTest(nbdim)=0; %default |
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| 273 | if sizvar(idim)==2 && strcmp(DimName,VarName)%case of a coordinate defined by the two end values (regular spacing) |
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| 274 | RangeTest(nbdim)=1; %to be updated for a later variable |
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| 275 | end |
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| 276 | DimValue(nbdim)=sizvar(idim); |
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| 277 | ListDimName{nbdim}=DimName; |
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| 278 | DimIndex=[DimIndex nbdim]; |
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| 279 | else % DimName is detected in the current list of dimension names |
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| 280 | if ~isequal(DimValue(iprev),sizvar(idim)) |
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| 281 | if isequal(DimValue(iprev),2)&& RangeTest(iprev) % the dimension has been already detected as a range [min max] |
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| 282 | DimValue(iprev)=sizvar(idim); %update with actual value |
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| 283 | elseif ~testrange |
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| 284 | errormsg=['dimension declaration inconsistent with the size =[' num2str(sizvar) '] for ' VarName]; |
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| 285 | return |
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| 286 | end |
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| 287 | end |
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| 288 | DimIndex=[DimIndex iprev]; |
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| 289 | end |
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| 290 | end |
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| 291 | VarDimIndex{ivar}=DimIndex; |
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[801] | 292 | end |
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