[1001] | 1 |
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[816] | 2 | %'nc2struct': transform a NetCDF file in a corresponding matlab structure
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[8] | 3 | % it reads all the global attributes and all variables, or a selected list.
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| 4 | % The corresponding dimensions and variable attributes are then extracted
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| 5 | %----------------------------------------------------------------------
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[755] | 6 | % function [Data,var_detect,ichoice,errormsg]=nc2struct(nc,varargin)
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[8] | 7 | %
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| 8 | % OUTPUT:
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[816] | 9 | % Data: structure containing all the information of the NetCDF file (or NetCDF object)
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[140] | 10 | % with (optional)fields:
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| 11 | % .ListGlobalAttribute: cell listing the names of the global attributes
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[55] | 12 | % .Att_1,Att_2... : values of the global attributes
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[816] | 13 | % .ListVarName: list of variable names to select (cell array of char strings {'VarName1', 'VarName2',...} )
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| 14 | % .VarDimName: list of dimension names for each element of .ListVarName (cell array of string cells)
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[55] | 15 | % .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName
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[693] | 16 | % .ListDimName=list of dimension (added information, not requested for field description)
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| 17 | % .DimValue= vlalues of dimensions (added information, not requested for field description)
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[816] | 18 | % .VarType= integers giving the type of variable as coded by netcdf =2 for char, =4 for single,=( for double
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[140] | 19 | % var_detect: vector with same length as the cell array ListVarName, = 1 for each detected variable and 0 else.
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[816] | 20 | % var_detect=[] in the absence of input cell array
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| 21 | % ichoice: index of the selected line in the case of multiple choice
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| 22 | % (cell array of varible names with multiple lines) , =[] by default
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| 23 | %
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| 24 | % INPUT:
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| 25 | % nc: name of a NetCDF file (char string) or NetCDF object
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[140] | 26 | % additional arguments:
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[816] | 27 | % -no additional arguments: all the variables of the NetCDF file are read.
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| 28 | % -a cell array, ListVarName, made of char strings {'VarName1', 'VarName2',...} )
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[648] | 29 | % if ListVarName=[] or {}, no variable value is read (only global attributes and list of variables and dimensions)
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[816] | 30 | % if ListVarName is absent, or = '*', ALL the variables of the NetCDF file are read.
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[747] | 31 | % if ListVarName is a cell array with n lines, the set of variables will be sought by order of priority in the list,
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| 32 | % while output names will be set by the first line
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| 33 | % - the string 'ListGlobalAttribute' followed by a list of attribute names: reads only these attributes (fast reading)
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[816] | 34 | % - the string 'TimeVarName', a string (the name of the variable considered as time), an integer or vector with integer values
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[771] | 35 | % representing time indices to select for each variable, the cell of other input variable names.
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[816] | 36 | % - the string 'TimeDimName', a string (the name of the dimension considered as time), an integer or vector with integer values
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[771] | 37 | % representing time indices to select for each variable, the cell of other input variable names.
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[648] | 38 |
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[809] | 39 | %=======================================================================
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[1061] | 40 | % Copyright 2008-2019, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
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[809] | 41 | % http://www.legi.grenoble-inp.fr
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| 42 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
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| 43 | %
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[8] | 44 | % This file is part of the toolbox UVMAT.
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[809] | 45 | %
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[8] | 46 | % UVMAT is free software; you can redistribute it and/or modify
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[809] | 47 | % it under the terms of the GNU General Public License as published
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| 48 | % by the Free Software Foundation; either version 2 of the license,
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| 49 | % or (at your option) any later version.
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| 50 | %
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[8] | 51 | % UVMAT is distributed in the hope that it will be useful,
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| 52 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 53 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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[809] | 54 | % GNU General Public License (see LICENSE.txt) for more details.
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| 55 | %=======================================================================
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[816] | 56 |
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[747] | 57 | function [Data,var_detect,ichoice,errormsg]=nc2struct(nc,varargin)
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| 58 | errormsg='';%default error message
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[55] | 59 | if isempty(varargin)
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[56] | 60 | varargin{1}='*';
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[8] | 61 | end
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[816] | 62 | hhh=which('netcdf.open');% look for built-in matlab NetCDF library
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[8] | 63 |
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| 64 | if ~isequal(hhh,'')
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[140] | 65 | %% default output
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| 66 | Data=[];%default
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| 67 | var_detect=[];%default
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[8] | 68 | ichoice=[];%default
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[816] | 69 |
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| 70 | %% open the NetCDF file for reading
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[747] | 71 | if ischar(nc)
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[8] | 72 | if exist(nc,'file')
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[150] | 73 | try
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[747] | 74 | nc=netcdf.open(nc,'NC_NOWRITE');
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| 75 | testfile=1;
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[227] | 76 | catch ME
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[747] | 77 | errormsg=['ERROR opening ' nc ': ' ME.message];
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| 78 | return
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[150] | 79 | end
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[8] | 80 | else
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[1022] | 81 | if regexp(nc,'^http://')
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| 82 | nc=netcdf.open(nc,'NC_NOWRITE');
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| 83 | testfile=1;
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| 84 | else
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[747] | 85 | errormsg=['ERROR:file ' nc ' does not exist'];
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| 86 | return
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[1022] | 87 | end
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[8] | 88 | end
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| 89 | else
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| 90 | testfile=0;
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| 91 | end
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[816] | 92 |
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[227] | 93 | %% short reading option for global attributes only, if the first argument is 'ListGlobalAttribute'
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[56] | 94 | if isequal(varargin{1},'ListGlobalAttribute')
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| 95 | for ilist=2:numel(varargin)
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[227] | 96 | valuestr=[];%default
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[45] | 97 | try
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[747] | 98 | valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),varargin{ilist});
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[227] | 99 | catch ME
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[45] | 100 | end
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[56] | 101 | eval(['Data.' varargin{ilist} '=valuestr;'])
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[8] | 102 | end
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| 103 | netcdf.close(nc)
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[747] | 104 | return
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[8] | 105 | end
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[816] | 106 |
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[648] | 107 | %% time variable or dimension
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| 108 | input_index=1;
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[747] | 109 | CheckTimeVar=0;
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| 110 | TimeVarName='';
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[648] | 111 | if isequal(varargin{1},'TimeVarName')
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| 112 | TimeVarName=varargin{2};
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[747] | 113 | CheckTimeVar=1;
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| 114 | TimeIndex=varargin{3};
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| 115 | input_index=4;% list of varibles to read is at fourth argument
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[648] | 116 | elseif isequal(varargin{1},'TimeDimName')
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| 117 | TimeDimName=varargin{2};
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[747] | 118 | TimeIndex=varargin{3};
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[648] | 119 | input_index=4;
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| 120 | end
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[816] | 121 |
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[140] | 122 | %% full reading: get the nbre of dimensions, variables, global attributes
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[747] | 123 | ListVarName=varargin{input_index};
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[816] | 124 | [ndims,nvars,ngatts]=netcdf.inq(nc);%nbre of dimensions, variables, global attributes, in the NetCDF file
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| 125 |
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[140] | 126 | %% -------- read all global attributes (constants)-----------
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[8] | 127 | Data.ListGlobalAttribute={};%default
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[527] | 128 | att_key=cell(1,ngatts);%default
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[8] | 129 | for iatt=1:ngatts
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| 130 | keystr= netcdf.inqAttName(nc,netcdf.getConstant('NC_GLOBAL'),iatt-1);
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[227] | 131 | valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),keystr);
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| 132 | keystr=regexprep(keystr,{'\','/','\.','-',' '},{'','','','',''});%remove '\','.' or '-' if exists
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| 133 | if strcmp(keystr(1),'_')
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| 134 | keystr(1)=[];
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| 135 | end
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| 136 | try
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[236] | 137 | if ischar(valuestr) %& length(valuestr)<200 & double(valuestr)<=122 & double(valuestr)>=48 %usual characters
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[227] | 138 | eval(['Data.' keystr '=''' valuestr ''';'])
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[8] | 139 | elseif isnumeric(valuestr)
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| 140 | eval(['Data.' keystr '=valuestr;'])
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[227] | 141 | else
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[747] | 142 | eval(['Data.' keystr '='';'])
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[8] | 143 | end
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[227] | 144 | att_key{iatt}=keystr;
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| 145 | catch ME
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| 146 | att_key{iatt}=['attr_' num2str(iatt)];
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[527] | 147 | Data.(att_key{iatt})=[];
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[8] | 148 | end
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| 149 | end
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| 150 | Data.ListGlobalAttribute=att_key;
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[816] | 151 |
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[140] | 152 | %% -------- read dimension names-----------
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[527] | 153 | ListDimNameNetcdf=cell(1,ndims);
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| 154 | dim_value=zeros(1,ndims);
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[816] | 155 | for idim=1:ndims %loop on the dimensions of the NetCDF file
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[140] | 156 | [ListDimNameNetcdf{idim},dim_value(idim)] = netcdf.inqDim(nc,idim-1);%get name and value of each dimension
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[8] | 157 | end
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[747] | 158 | if ~isempty(ListDimNameNetcdf)
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[140] | 159 | flag_used=zeros(1,ndims);%initialize the flag indicating the selected dimensions in the list (0=unused)
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[8] | 160 | end
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[648] | 161 | if isequal(varargin{1},'TimeDimName')% time dimension introduced
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[747] | 162 | TimeDimIndex=find(strcmp(TimeDimName,ListDimNameNetcdf));
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[648] | 163 | if isempty(TimeDimIndex)
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[747] | 164 | errormsg=['requested time dimension ' varargin{2} ' not found'];
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[648] | 165 | return
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| 166 | end
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| 167 | if dim_value(TimeDimIndex)<varargin{3}
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[747] | 168 | errormsg=['requested time index ' num2str(varargin{3}) ' exceeds matrix dimension'];
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[648] | 169 | return
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| 170 | end
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[816] | 171 | end
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| 172 |
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[140] | 173 | %% -------- read names of variables -----------
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[527] | 174 | ListVarNameNetcdf=cell(1,nvars); %default
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| 175 | dimids=cell(1,nvars);
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| 176 | nbatt=zeros(1,nvars);
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[816] | 177 | for ncvar=1:nvars %loop on the variables of the NetCDF file
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[747] | 178 | %get name, type, dimensions and attribute numbers of each variable
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[693] | 179 | [ListVarNameNetcdf{ncvar},xtype(ncvar),dimids{ncvar},nbatt(ncvar)] = netcdf.inqVar(nc,ncvar-1);
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[747] | 180 | end
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| 181 | % testmulti=0;
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[140] | 182 | if isequal(ListVarName,'*')||isempty(ListVarName)
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[816] | 183 | var_index=1:nvars; %all the variables are selected in the NetCDF file
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[140] | 184 | Data.ListVarName=ListVarNameNetcdf;
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| 185 | else %select input variables, if requested by the input ListVarName
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[527] | 186 | check_keep=ones(1,size(ListVarName,2));
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| 187 | for ivar=1:size(ListVarName,2) % check redondancy of variable names
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| 188 | if ~isempty(find(strcmp(ListVarName{1,ivar},ListVarName(1:ivar-1)), 1))
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| 189 | check_keep(ivar)=0;% the variable #ivar is already in the list
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[517] | 190 | end
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| 191 | end
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[747] | 192 | ListVarName=ListVarName(:,logical(check_keep));
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[748] | 193 | if size(ListVarName,1)>1 %multiple choice of variable ranked by order of priority
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| 194 | for iline=1:size(ListVarName,1)
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[816] | 195 | search_index=find(strcmp(ListVarName{iline,1},ListVarNameNetcdf),1);%look for the first variable name in the list of NetCDF variables
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[140] | 196 | if ~isempty(search_index)
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| 197 | break % go to the next line
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[8] | 198 | end
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| 199 | end
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[140] | 200 | ichoice=iline-1;%selected line number in the list of input names of variables
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| 201 | else
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| 202 | iline=1;
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[8] | 203 | end
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[747] | 204 | %ListVarName=ListVarName(iline,:);% select the appropriate option for input variable (lin ein the input name matrix)
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| 205 | if CheckTimeVar
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| 206 | TimeVarIndex=find(strcmp(TimeVarName,ListVarNameNetcdf),1); %look for the index of the time variable in the netcdf list
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| 207 | if isempty(TimeVarIndex)
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| 208 | errormsg='requested variable for time is missing';
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| 209 | return
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| 210 | end
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| 211 | TimeDimIndex=dimids{TimeVarIndex}(1)+1;
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| 212 | ListVarName=[ListVarName {TimeVarName}];
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| 213 | end
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[748] | 214 | var_index=zeros(1,size(ListVarName,2));%default list of variable indices
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[747] | 215 | for ivar=1:size(ListVarName,2)
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[816] | 216 | search_index=find(strcmp(ListVarName{iline,ivar},ListVarNameNetcdf),1);%look for the variable name in the list of NetCDF file
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[140] | 217 | if ~isempty(search_index)
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| 218 | var_index(ivar)=search_index;%index of the netcdf list corresponding to the input list index ivar
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[8] | 219 | end
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| 220 | end
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[747] | 221 | var_detect=(var_index~=0);%=1 for detected variables
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[140] | 222 | list_index=find(var_index);% indices in the input list corresponding to a detected variable
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[816] | 223 | var_index=var_index(list_index);% NetCDF variable indices corresponding to the output list of read variable
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[140] | 224 | Data.ListVarName=ListVarName(1,list_index);%the first line of ListVarName sets the output names of the variables
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[8] | 225 | end
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[816] | 226 |
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[747] | 227 | %% get the dimensions and attributes associated to variables
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| 228 | var_dim=cell(size(var_index));% initiate list of dimensions for variables
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[140] | 229 | for ivar=1:length(var_index)
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| 230 | var_dim{ivar}=dimids{var_index(ivar)}+1; %netcdf dimension indices used by the variable #ivar
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| 231 | Data.VarDimName{ivar}=ListDimNameNetcdf(var_dim{ivar});
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| 232 | flag_used(var_dim{ivar})=ones(size(var_dim{ivar}));%flag_used =1 for the indices of used dimensions
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[8] | 233 | for iatt=1:nbatt(var_index(ivar))
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| 234 | attname = netcdf.inqAttName(nc,var_index(ivar)-1,iatt-1);
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| 235 | valuestr= netcdf.getAtt(nc,var_index(ivar)-1,attname);
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[227] | 236 | attname=regexprep(attname,{'\','/','\.','-',' '},{'','','','',''});%remove '\','.' or '-' if exists
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| 237 | if strcmp(attname(1),'_')
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| 238 | attname(1)=[];
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| 239 | end
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| 240 | try
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[871] | 241 | if ~isempty(valuestr)
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[747] | 242 | Data.VarAttribute{ivar}.(attname)=valuestr;
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| 243 | end
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[227] | 244 | catch ME
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| 245 | display(attname)
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| 246 | display(valuestr)
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[747] | 247 | display(ME.message)
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[693] | 248 | Data.VarAttribute{ivar}.(['atrr_' num2str(iatt)])='not read';
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[227] | 249 | end
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[8] | 250 | end
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| 251 | end
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[816] | 252 |
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[140] | 253 | %% select the dimensions used for the set of input variables
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[747] | 254 | if ~isempty(var_index)
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| 255 | dim_index=find(flag_used);%list of netcdf dimensions indices corresponding to used dimensions
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| 256 | Data.ListDimName=ListDimNameNetcdf(dim_index);
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[421] | 257 | Data.DimValue=dim_value(dim_index);
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[747] | 258 | if input_index==4% if a dimension is selected as time
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| 259 | Data.DimValue(TimeDimIndex)=numel(TimeIndex);
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| 260 | end
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[8] | 261 | end
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[816] | 262 |
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[140] | 263 | %% get the values of the input variables
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[8] | 264 | if ~isempty(ListVarName)
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[140] | 265 | for ivar=1:length(var_index)
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[8] | 266 | VarName=Data.ListVarName{ivar};
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[816] | 267 | VarName=regexprep(VarName,'-','_'); %suppress '-' if it exists in the NetCDF variable name (leads to errors in matlab)
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[747] | 268 | % CheckSub=0;
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[648] | 269 | if input_index==4% if a dimension is selected as time
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[747] | 270 | ind_vec=zeros(1,numel(var_dim{ivar}));% vector with zeros corresponding to al the dimensions of the variable VarName
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[756] | 271 | ind_size=dim_value(var_dim{ivar});% vector giving the size (for each dimension) of the variable VarName
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[747] | 272 | index_time=find(var_dim{ivar}==TimeDimIndex);
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| 273 | if ~isempty(index_time)
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[756] | 274 | if ind_size(index_time)<max(TimeIndex)
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| 275 | errormsg=['requested index ' num2str(TimeIndex) ' exceeds matrix dimension'];
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| 276 | return
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| 277 | end
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[747] | 278 | ind_vec(index_time)=TimeIndex-1;% selected index(or indices) to read
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| 279 | ind_size(index_time)=numel(TimeIndex);%length of the selected set of time indices
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| 280 | if numel(TimeIndex)==1 && ~strcmp(VarName,TimeVarName)
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[816] | 281 | Data.VarDimName{ivar}(index_time)=[];% for a single selected time remove the time in the list of dimensions (except for tTime itself)
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[747] | 282 | end
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[816] | 283 | end
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[943] | 284 | Data.(VarName)=netcdf.getVar(nc,var_index(ivar)-1,ind_vec,ind_size); %read the variable data
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[747] | 285 | Data.(VarName)=squeeze(Data.(VarName));%remove singeton dimension
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| 286 | else
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| 287 | Data.(VarName)=netcdf.getVar(nc,var_index(ivar)-1); %read the whole variable data
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[648] | 288 | end
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[747] | 289 | if xtype(var_index(ivar))==5
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[693] | 290 | Data.(VarName)=double(Data.(VarName)); %transform to double for single pecision
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[648] | 291 | end
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[8] | 292 | end
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| 293 | end
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[693] | 294 | Data.VarType=xtype(var_index);
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[816] | 295 |
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[140] | 296 | %% -------- close fle-----------
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[8] | 297 | if testfile==1
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[747] | 298 | netcdf.close(nc)
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[8] | 299 | end
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[816] | 300 |
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| 301 | %% old NetCDF library
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[8] | 302 | else
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| 303 | [Data,var_detect,ichoice]=nc2struct_toolbox(nc,varargin);
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[801] | 304 | end
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