[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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[977] | 40 | % Copyright 2008-2017, 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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[747] | 81 | errormsg=['ERROR:file ' nc ' does not exist'];
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| 82 | return
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[8] | 83 | end
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| 84 | else
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| 85 | testfile=0;
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| 86 | end
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[816] | 87 |
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[227] | 88 | %% short reading option for global attributes only, if the first argument is 'ListGlobalAttribute'
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[56] | 89 | if isequal(varargin{1},'ListGlobalAttribute')
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| 90 | for ilist=2:numel(varargin)
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[227] | 91 | valuestr=[];%default
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[45] | 92 | try
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[747] | 93 | valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),varargin{ilist});
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[227] | 94 | catch ME
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[45] | 95 | end
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[56] | 96 | eval(['Data.' varargin{ilist} '=valuestr;'])
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[8] | 97 | end
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| 98 | netcdf.close(nc)
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[747] | 99 | return
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[8] | 100 | end
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[816] | 101 |
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[648] | 102 | %% time variable or dimension
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| 103 | input_index=1;
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[747] | 104 | CheckTimeVar=0;
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| 105 | TimeVarName='';
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[648] | 106 | if isequal(varargin{1},'TimeVarName')
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| 107 | TimeVarName=varargin{2};
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[747] | 108 | CheckTimeVar=1;
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| 109 | TimeIndex=varargin{3};
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| 110 | input_index=4;% list of varibles to read is at fourth argument
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[648] | 111 | elseif isequal(varargin{1},'TimeDimName')
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| 112 | TimeDimName=varargin{2};
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[747] | 113 | TimeIndex=varargin{3};
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[648] | 114 | input_index=4;
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| 115 | end
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[816] | 116 |
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[140] | 117 | %% full reading: get the nbre of dimensions, variables, global attributes
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[747] | 118 | ListVarName=varargin{input_index};
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[816] | 119 | [ndims,nvars,ngatts]=netcdf.inq(nc);%nbre of dimensions, variables, global attributes, in the NetCDF file
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| 120 |
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[140] | 121 | %% -------- read all global attributes (constants)-----------
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[8] | 122 | Data.ListGlobalAttribute={};%default
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[527] | 123 | att_key=cell(1,ngatts);%default
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[8] | 124 | for iatt=1:ngatts
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| 125 | keystr= netcdf.inqAttName(nc,netcdf.getConstant('NC_GLOBAL'),iatt-1);
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[227] | 126 | valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),keystr);
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| 127 | keystr=regexprep(keystr,{'\','/','\.','-',' '},{'','','','',''});%remove '\','.' or '-' if exists
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| 128 | if strcmp(keystr(1),'_')
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| 129 | keystr(1)=[];
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| 130 | end
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| 131 | try
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[236] | 132 | if ischar(valuestr) %& length(valuestr)<200 & double(valuestr)<=122 & double(valuestr)>=48 %usual characters
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[227] | 133 | eval(['Data.' keystr '=''' valuestr ''';'])
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[8] | 134 | elseif isnumeric(valuestr)
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| 135 | eval(['Data.' keystr '=valuestr;'])
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[227] | 136 | else
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[747] | 137 | eval(['Data.' keystr '='';'])
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[8] | 138 | end
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[227] | 139 | att_key{iatt}=keystr;
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| 140 | catch ME
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| 141 | att_key{iatt}=['attr_' num2str(iatt)];
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[527] | 142 | Data.(att_key{iatt})=[];
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[8] | 143 | end
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| 144 | end
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| 145 | Data.ListGlobalAttribute=att_key;
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[816] | 146 |
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[140] | 147 | %% -------- read dimension names-----------
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[527] | 148 | ListDimNameNetcdf=cell(1,ndims);
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| 149 | dim_value=zeros(1,ndims);
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[816] | 150 | for idim=1:ndims %loop on the dimensions of the NetCDF file
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[140] | 151 | [ListDimNameNetcdf{idim},dim_value(idim)] = netcdf.inqDim(nc,idim-1);%get name and value of each dimension
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[8] | 152 | end
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[747] | 153 | if ~isempty(ListDimNameNetcdf)
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[140] | 154 | flag_used=zeros(1,ndims);%initialize the flag indicating the selected dimensions in the list (0=unused)
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[8] | 155 | end
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[648] | 156 | if isequal(varargin{1},'TimeDimName')% time dimension introduced
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[747] | 157 | TimeDimIndex=find(strcmp(TimeDimName,ListDimNameNetcdf));
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[648] | 158 | if isempty(TimeDimIndex)
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[747] | 159 | errormsg=['requested time dimension ' varargin{2} ' not found'];
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[648] | 160 | return
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| 161 | end
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| 162 | if dim_value(TimeDimIndex)<varargin{3}
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[747] | 163 | errormsg=['requested time index ' num2str(varargin{3}) ' exceeds matrix dimension'];
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[648] | 164 | return
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| 165 | end
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[816] | 166 | end
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| 167 |
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[140] | 168 | %% -------- read names of variables -----------
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[527] | 169 | ListVarNameNetcdf=cell(1,nvars); %default
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| 170 | dimids=cell(1,nvars);
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| 171 | nbatt=zeros(1,nvars);
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[816] | 172 | for ncvar=1:nvars %loop on the variables of the NetCDF file
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[747] | 173 | %get name, type, dimensions and attribute numbers of each variable
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[693] | 174 | [ListVarNameNetcdf{ncvar},xtype(ncvar),dimids{ncvar},nbatt(ncvar)] = netcdf.inqVar(nc,ncvar-1);
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[747] | 175 | end
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| 176 | % testmulti=0;
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[140] | 177 | if isequal(ListVarName,'*')||isempty(ListVarName)
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[816] | 178 | var_index=1:nvars; %all the variables are selected in the NetCDF file
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[140] | 179 | Data.ListVarName=ListVarNameNetcdf;
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| 180 | else %select input variables, if requested by the input ListVarName
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[527] | 181 | check_keep=ones(1,size(ListVarName,2));
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| 182 | for ivar=1:size(ListVarName,2) % check redondancy of variable names
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| 183 | if ~isempty(find(strcmp(ListVarName{1,ivar},ListVarName(1:ivar-1)), 1))
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| 184 | check_keep(ivar)=0;% the variable #ivar is already in the list
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[517] | 185 | end
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| 186 | end
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[747] | 187 | ListVarName=ListVarName(:,logical(check_keep));
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[748] | 188 | if size(ListVarName,1)>1 %multiple choice of variable ranked by order of priority
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| 189 | for iline=1:size(ListVarName,1)
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[816] | 190 | 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] | 191 | if ~isempty(search_index)
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| 192 | break % go to the next line
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[8] | 193 | end
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| 194 | end
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[140] | 195 | ichoice=iline-1;%selected line number in the list of input names of variables
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| 196 | else
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| 197 | iline=1;
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[8] | 198 | end
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[747] | 199 | %ListVarName=ListVarName(iline,:);% select the appropriate option for input variable (lin ein the input name matrix)
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| 200 | if CheckTimeVar
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| 201 | TimeVarIndex=find(strcmp(TimeVarName,ListVarNameNetcdf),1); %look for the index of the time variable in the netcdf list
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| 202 | if isempty(TimeVarIndex)
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| 203 | errormsg='requested variable for time is missing';
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| 204 | return
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| 205 | end
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| 206 | TimeDimIndex=dimids{TimeVarIndex}(1)+1;
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| 207 | ListVarName=[ListVarName {TimeVarName}];
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| 208 | end
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[748] | 209 | var_index=zeros(1,size(ListVarName,2));%default list of variable indices
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[747] | 210 | for ivar=1:size(ListVarName,2)
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[816] | 211 | 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] | 212 | if ~isempty(search_index)
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| 213 | var_index(ivar)=search_index;%index of the netcdf list corresponding to the input list index ivar
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[8] | 214 | end
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| 215 | end
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[747] | 216 | var_detect=(var_index~=0);%=1 for detected variables
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[140] | 217 | list_index=find(var_index);% indices in the input list corresponding to a detected variable
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[816] | 218 | var_index=var_index(list_index);% NetCDF variable indices corresponding to the output list of read variable
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[140] | 219 | Data.ListVarName=ListVarName(1,list_index);%the first line of ListVarName sets the output names of the variables
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[8] | 220 | end
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[816] | 221 |
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[747] | 222 | %% get the dimensions and attributes associated to variables
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| 223 | var_dim=cell(size(var_index));% initiate list of dimensions for variables
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[140] | 224 | for ivar=1:length(var_index)
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| 225 | var_dim{ivar}=dimids{var_index(ivar)}+1; %netcdf dimension indices used by the variable #ivar
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| 226 | Data.VarDimName{ivar}=ListDimNameNetcdf(var_dim{ivar});
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| 227 | flag_used(var_dim{ivar})=ones(size(var_dim{ivar}));%flag_used =1 for the indices of used dimensions
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[8] | 228 | for iatt=1:nbatt(var_index(ivar))
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| 229 | attname = netcdf.inqAttName(nc,var_index(ivar)-1,iatt-1);
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| 230 | valuestr= netcdf.getAtt(nc,var_index(ivar)-1,attname);
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[227] | 231 | attname=regexprep(attname,{'\','/','\.','-',' '},{'','','','',''});%remove '\','.' or '-' if exists
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| 232 | if strcmp(attname(1),'_')
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| 233 | attname(1)=[];
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| 234 | end
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| 235 | try
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[871] | 236 | if ~isempty(valuestr)
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[747] | 237 | Data.VarAttribute{ivar}.(attname)=valuestr;
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| 238 | end
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[227] | 239 | catch ME
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| 240 | display(attname)
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| 241 | display(valuestr)
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[747] | 242 | display(ME.message)
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[693] | 243 | Data.VarAttribute{ivar}.(['atrr_' num2str(iatt)])='not read';
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[227] | 244 | end
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[8] | 245 | end
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| 246 | end
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[816] | 247 |
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[140] | 248 | %% select the dimensions used for the set of input variables
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[747] | 249 | if ~isempty(var_index)
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| 250 | dim_index=find(flag_used);%list of netcdf dimensions indices corresponding to used dimensions
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| 251 | Data.ListDimName=ListDimNameNetcdf(dim_index);
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[421] | 252 | Data.DimValue=dim_value(dim_index);
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[747] | 253 | if input_index==4% if a dimension is selected as time
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| 254 | Data.DimValue(TimeDimIndex)=numel(TimeIndex);
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| 255 | end
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[8] | 256 | end
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[816] | 257 |
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[140] | 258 | %% get the values of the input variables
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[8] | 259 | if ~isempty(ListVarName)
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[140] | 260 | for ivar=1:length(var_index)
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[8] | 261 | VarName=Data.ListVarName{ivar};
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[816] | 262 | VarName=regexprep(VarName,'-','_'); %suppress '-' if it exists in the NetCDF variable name (leads to errors in matlab)
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[747] | 263 | % CheckSub=0;
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[648] | 264 | if input_index==4% if a dimension is selected as time
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[747] | 265 | 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] | 266 | ind_size=dim_value(var_dim{ivar});% vector giving the size (for each dimension) of the variable VarName
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[747] | 267 | index_time=find(var_dim{ivar}==TimeDimIndex);
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| 268 | if ~isempty(index_time)
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[756] | 269 | if ind_size(index_time)<max(TimeIndex)
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| 270 | errormsg=['requested index ' num2str(TimeIndex) ' exceeds matrix dimension'];
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| 271 | return
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| 272 | end
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[747] | 273 | ind_vec(index_time)=TimeIndex-1;% selected index(or indices) to read
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| 274 | ind_size(index_time)=numel(TimeIndex);%length of the selected set of time indices
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| 275 | if numel(TimeIndex)==1 && ~strcmp(VarName,TimeVarName)
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[816] | 276 | 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] | 277 | end
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[816] | 278 | end
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[943] | 279 | Data.(VarName)=netcdf.getVar(nc,var_index(ivar)-1,ind_vec,ind_size); %read the variable data
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[747] | 280 | Data.(VarName)=squeeze(Data.(VarName));%remove singeton dimension
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| 281 | else
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| 282 | Data.(VarName)=netcdf.getVar(nc,var_index(ivar)-1); %read the whole variable data
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[648] | 283 | end
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[747] | 284 | if xtype(var_index(ivar))==5
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[693] | 285 | Data.(VarName)=double(Data.(VarName)); %transform to double for single pecision
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[648] | 286 | end
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[8] | 287 | end
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| 288 | end
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[693] | 289 | Data.VarType=xtype(var_index);
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[816] | 290 |
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[140] | 291 | %% -------- close fle-----------
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[8] | 292 | if testfile==1
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[747] | 293 | netcdf.close(nc)
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[8] | 294 | end
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[816] | 295 |
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| 296 | %% old NetCDF library
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[8] | 297 | else
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| 298 | [Data,var_detect,ichoice]=nc2struct_toolbox(nc,varargin);
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[801] | 299 | end
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