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 | %%%%%% TODO: add the possibility to read only attributes, see nc2struct_toolbox %%%
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5 | %----------------------------------------------------------------------
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6 | % function [Data,var_detect,ichoice]=nc2struct(nc,ListVarName)
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7 | %
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8 | % OUTPUT:
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9 | % Data: structure containing all the information of the netcdf file (or netcdf object)
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10 | % with fields:
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11 | % .ListGlobalAttribute: cell listing the names of the global attributes
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12 | % .Att_1,Att_2... : values of the global attributes
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13 | % .ListDimName: cell listing the names of the array dimensions
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14 | % .DimValue: array dimension values (Matlab vector with the same length as .ListDimName
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15 | % .ListVarName: cell listing the names of the variables
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16 | % .VarDimIndex: cell containing the set of dimension indices (in list .ListDimName) for each variable of .ListVarName
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17 | % .VarDimName: cell containing a cell of dimension names (in list .ListDimName) for each variable of .ListVarName
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18 | % .VarAttribute: cell of structures s containing names and values of variable attributes (s.name=value) for each variable of .ListVarName
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19 | % .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName
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20 | % var_detect: vector with same length as ListVarName, with 1 for each detected variable and 0 else.
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21 | % ichoice: = line
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22 | %
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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 | % ListVarName: optional list of variable names to select (cell array of char strings {'VarName1', 'VarName2',...} )
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26 | % if ListVarName=[] or {}, no variables is read (only global attributes and lists of dimensions, variables and attriburtes)
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27 | % if ListVarName is absent, or = '*', ALL the variables are read.
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28 | % if ListVarName is a cell array with n lines, the set of variables
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29 | % will be sought by order of priority in the list, while output names will be set by the first line
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30 | %
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31 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
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32 | % Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
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33 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
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34 | % This file is part of the toolbox UVMAT.
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35 | %
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36 | % UVMAT is free software; you can redistribute it and/or modify
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37 | % it under the terms of the GNU General Public License as published by
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38 | % the Free Software Foundation; either version 2 of the License, or
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39 | % (at your option) any later version.
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40 | %
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41 | % UVMAT is distributed in the hope that it will be useful,
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42 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
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43 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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44 | % GNU General Public License (file UVMAT/COPYING.txt) for more details.
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45 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
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46 |
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47 | function [Data,var_detect,ichoice]=nc2struct(nc,varargin)
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48 | List=varargin;
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49 | if nargin==0
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50 | List{1}='*';
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51 | end
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52 | % if ~exist('ListVarName','var')
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53 | % ListVarName='*';
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54 | % end
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55 | hhh=which('netcdf.open');% look for built-in matlab netcdf library
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56 |
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57 | if ~isequal(hhh,'')
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58 | %default output
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59 | Data=[];
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60 | var_detect=[];
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61 | ichoice=[];%default
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62 | %open the netcdf file for reading
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63 | if ischar(nc)
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64 | if exist(nc,'file')
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65 | nc=netcdf.open(nc,'NC_NOWRITE');
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66 | testfile=1;
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67 | else
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68 | Data.Txt=['ERROR:file ' nc ' does not exist'];
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69 | return
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70 | end
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71 | else
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72 | testfile=0;
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73 | end
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74 | % short reading of global attributes
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75 | if isequal(List{1},'ListGlobalAttribute')
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76 | for ilist=2:numel(List)
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77 | try
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78 | valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),List{ilist});
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79 | catch
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80 | valuestr=[];
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81 | end
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82 | eval(['Data.' List{ilist} '=valuestr;'])
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83 | end
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84 | netcdf.close(nc)
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85 | return
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86 | end
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87 |
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88 | % reading of variables, including attributes
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89 | ListVarName=List{1};
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90 | [ndims,nvars,ngatts]=netcdf.inq(nc);%nbre of dimensions, variables, attributes
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91 |
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92 | % -------- read global attributes (constants)-----------
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93 | att_key={};%default
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94 | iatt_g=0;
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95 | Data.ListGlobalAttribute={};%default
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96 | for iatt=1:ngatts
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97 | keystr= netcdf.inqAttName(nc,netcdf.getConstant('NC_GLOBAL'),iatt-1);
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98 | indstr1=regexp(keystr,'\\');%detect '\\'
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99 | indstr2=regexp(keystr,'\.');%detect '\.'
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100 | if isempty(indstr1) && isempty(indstr2)
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101 | valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),keystr);
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102 | if ischar(valuestr) && length(valuestr)<200
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103 | iatt_g=iatt_g+1;
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104 | indstr1=regexp(keystr,'\\');%detect '\\'
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105 | indstr2=regexp(keystr,'\.');%detect '\.'
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106 | if isempty(indstr1) && isempty(indstr2)
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107 | eval(['Data.' keystr '=''' valuestr ''';'])
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108 | att_key{iatt_g}=keystr;
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109 | end
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110 | elseif isempty(valuestr)
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111 | iatt_g=iatt_g+1;
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112 | eval(['Data.' keystr '=[];'])
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113 | att_key{iatt_g}=keystr;
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114 | elseif isnumeric(valuestr)
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115 | iatt_g=iatt_g+1;
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116 | eval(['Data.' keystr '=valuestr;'])
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117 | att_key{iatt_g}=keystr;
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118 | end
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119 | end
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120 | end
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121 | Data.ListGlobalAttribute=att_key;
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122 |
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123 | % -------- read dimensions -----------
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124 | dim_name={};
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125 | dim_value=[];
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126 | for idim=1:ndims%length(dim_read);
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127 | [dim_name{idim},dim_value(idim)] = netcdf.inqDim(nc,idim-1);
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128 | end
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129 | if ~isempty(dim_name) && ~isempty(dim_value)
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130 | Data.ListDimName=dim_name;
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131 | Data.DimValue=dim_value;
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132 | % DimIndices=[1:ndims]; %index of the dimension in the netcdf file
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133 | dim_used=zeros(1,ndims);%initialize test of used dimensions
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134 | end
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135 |
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136 | % -------- read variables -----------
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137 | var_read={}; %default
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138 | dimids={};
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139 | nbatt=[];
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140 | for ivar=1:nvars
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141 | [var_read{ivar},xtype,dimids{ivar},nbatt(ivar)] = netcdf.inqVar(nc,ivar-1);
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142 | end
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143 | var_index=1:nvars; %default set of variable indices in the netcdf file
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144 | testmulti=0;
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145 | OutputList=[];
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146 | %select input variables, if requested by the input ListVarName
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147 | if ~(isequal(ListVarName,'*')||isempty(ListVarName))
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148 | sizvar=size(ListVarName);
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149 | testmulti=(sizvar(1)>1);
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150 | var_index=zeros(1,sizvar(2));%default
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151 | if testmulti
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152 | OutputList=ListVarName(1,:);
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153 | testend=0;
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154 | for iline=1:sizvar(1)
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155 | if testend
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156 | break
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157 | end
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158 | % var_index=zeros(size(ListVarName));%default
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159 | for ivar=1:sizvar(2)
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160 | if ~isempty(ListVarName{iline,ivar})
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161 | for ilist=1:nvars
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162 | if isequal(var_read{ilist},ListVarName{iline,ivar})
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163 | var_index(ivar)=ilist;
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164 | % var_detect(ivar)=1;
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165 | break
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166 | end
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167 | end
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168 | if ivar==1
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169 | if var_index(ivar)==0
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170 | break%go to next line if the first nc variable is not found
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171 | else
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172 | testend=1; %this line will be read
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173 | ichoice=iline-1; %selectedline number in the list of input names of variables
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174 | end
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175 | end
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176 | end
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177 | end
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178 | end
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179 | else %single list of input variables
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180 | for ivar=1:sizvar(2)
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181 | for ilist=1:nvars
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182 | if isequal(var_read{ilist},ListVarName{ivar})
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183 | var_index(ivar)=ilist;
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184 | var_detect(ivar)=1;
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185 | break
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186 | end
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187 | end
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188 | end
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189 | end
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190 | list_index=find(var_index);
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191 | if ~isempty(list_index)
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192 | if testmulti
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193 | OutputList=OutputList(list_index);
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194 | end
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195 | var_index=var_index(list_index);
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196 | var_detect=(var_index~=0);
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197 | var_read=var_read(var_index);
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198 | end
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199 | end
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200 |
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201 |
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202 | %select variable attributes and associate dimensions
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203 | % var_dim_index=[]; %default
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204 | Data.ListVarName={};%default
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205 | VarDimIndex={};%default
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206 | for ivar=1:length(var_read)
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207 | if testmulti
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208 | Data.ListVarName{ivar}=OutputList{ivar};%new name given by ListVarName(1,:)
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209 | else
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210 | Data.ListVarName{ivar}=var_read{ivar};%name of the variable
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211 | end
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212 | var_dim=dimids{var_index(ivar)}+1; %dimension indices used by the variable
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213 | dim_used(var_dim)=ones(size(var_dim));
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214 | VarDimIndex{ivar}=var_dim;
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215 |
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216 | %variable attributes
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217 | if ivar==1
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218 | Data.VarAttribute={};%initialisation of the list of variable attributes
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219 | end
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220 | %variable attributes
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221 | for iatt=1:nbatt(var_index(ivar))
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222 | attname = netcdf.inqAttName(nc,var_index(ivar)-1,iatt-1);
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223 | valuestr= netcdf.getAtt(nc,var_index(ivar)-1,attname);
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224 | if ischar(valuestr)
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225 | eval(['Data.VarAttribute{ivar}.' attname '=''' valuestr ''';'])
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226 | elseif isempty(valuestr)
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227 | eval(['Data.VarAttribute{ivar}.' attname '=[];'])
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228 | elseif isnumeric(valuestr)
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229 | eval(['Data.VarAttribute{ivar}.' attname '=valuestr;'])
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230 | end
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231 | end
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232 | end
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233 |
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234 | %select the used dimensions
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235 | if isempty(var_read)
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236 | if isfield(Data,'ListDimName') && isfield(Data,'DimValue')
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237 | Data=rmfield(Data,'ListDimName');
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238 | Data=rmfield(Data,'DimValue');
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239 | end
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240 | else
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241 | % list_dim=1:ndims;
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242 | dim_index=find(dim_used);
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243 | % list_dim=list_dim(dim_index);
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244 | old2new=cumsum(dim_used);
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245 | Data.ListDimName=Data.ListDimName(dim_index);
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246 | Data.DimValue=Data.DimValue(dim_index);
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247 | end
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248 | for ivar=1:length(var_read)
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249 | Data.VarDimIndex{ivar}=old2new(VarDimIndex{ivar});% ENLEVER Data.VarDimIndex ulterieurement
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250 | Data.VarDimName{ivar}=Data.ListDimName(Data.VarDimIndex{ivar});
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251 | end
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252 | %variable values
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253 | if ~isempty(ListVarName)
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254 | for ivar=1:length(Data.ListVarName)
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255 | VarName=Data.ListVarName{ivar};
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256 | indstr=regexp(VarName,'-');%detect '-'
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257 | if ~isempty(indstr)
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258 | VarName(indstr)=[];
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259 | end
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260 | eval(['Data.' VarName '=netcdf.getVar(nc,var_index(ivar)-1);'])%read the variable data
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261 | eval(['siz=size(Data.' VarName ');'])
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262 | if numel(siz)<=2
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263 | eval(['Data.' VarName '=Data.' VarName ''';'])%read the variable data
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264 | end
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265 | end
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266 | end
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267 | % -------- close fle-----------
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268 | if testfile==1
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269 | netcdf.close(nc)
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270 | end
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271 | else
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272 | [Data,var_detect,ichoice]=nc2struct_toolbox(nc,varargin);
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273 | end |
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