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