1 | %'nc2struct_toolbox': transform a netcdf file in a corresponding matlab structure, USE OLD NETCDF LIBRARY |
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2 | %---------------------------------------------------------------------- |
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3 | % function [Data,var_detect,ichoice]=nc2struct_toolbox(nc,ListField) |
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4 | % |
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5 | % OUTPUT: |
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6 | % Data: structure containing all the information of the netcdf file (or netcdf object) |
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7 | % with fields: |
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8 | % .ListGlobalAttribute: cell listing the names of the global attributes |
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9 | % .Att_1,Att_2... : values of the global attributes |
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10 | % .ListDimName: cell listing the names of the array dimensions |
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11 | % .DimValue: array dimension values (Matlab vector with the same length as .ListDimName |
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12 | % .ListVarName: cell listing the names of the variables |
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13 | % .VarDimIndex: cell containing the set of dimension indices (in list .ListDimName) for each variable of .ListVarName |
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14 | % .VarDimName: cell containing a cell of dimension names (in list .ListDimName) for each variable of .ListVarName |
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15 | % .VarAttribute: cell of structures s containing names and values of variable attributes (s.name=value) for each variable of .ListVarName |
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16 | % .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName |
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17 | % var_detect: vector with same length as ListVarName, with 1 for each detected variable and 0 else. |
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18 | % ichoice: = line |
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19 | % |
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20 | %INPUT: |
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21 | % nc: name of a netcdf file (char string) or netcdf object |
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22 | % ListField: optional list of variable names to select (cell array of char strings {'VarName1', 'VarName2',...} ) |
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23 | % if ListField is absent or ='*', ALL the attributes and variables are read. % |
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24 | % if ListField='ListGlobalAttribute', followed by the arguments 'name1', name2'..., only thes global attributes will be read (short option) |
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25 | % if ListField=[] or{}, no variables is read (only global attributes and lists of vdimensions, variables and attriburtes) |
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26 | % if ListField is a cell array with n lines, the set of variables |
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27 | % will be sought by order of priority in the list, while output names will be set by the first line |
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28 | % |
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29 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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30 | % Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. |
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31 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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32 | % This file is part of the toolbox UVMAT. |
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33 | % |
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34 | % UVMAT is free software; you can redistribute it and/or modify |
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35 | % it under the terms of the GNU General Public License as published by |
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36 | % the Free Software Foundation; either version 2 of the License, or |
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37 | % (at your option) any later version. |
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38 | % |
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39 | % UVMAT is distributed in the hope that it will be useful, |
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40 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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41 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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42 | % GNU General Public License (file UVMAT/COPYING.txt) for more details. |
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43 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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44 | |
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45 | function [Data,var_detect,ichoice]=nc2struct_toolbox(nc,varargin) |
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46 | |
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47 | List=varargin{1}; |
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48 | %default output |
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49 | Data=[]; |
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50 | var_detect=[]; |
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51 | ichoice=[];%default |
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52 | |
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53 | %open the netcdf file for reading |
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54 | if ischar(nc) |
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55 | if exist(nc,'file') % rmq: time for exist search = 0.5 ms CPU |
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56 | nc=netcdf(nc,'nowrite'); % rmq: time needed for opening = 2 ms CPU |
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57 | testfile=1; |
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58 | else |
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59 | Data.Txt=['ERROR:file ' nc ' does not exist']; |
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60 | return |
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61 | end |
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62 | else |
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63 | testfile=0; |
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64 | end |
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65 | |
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66 | % short reading of global attributes |
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67 | if ~isempty(List) && isequal(List{1},'ListGlobalAttribute') |
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68 | for ilist=2:numel(List) |
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69 | att_str=List{ilist}; |
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70 | eval(['Data.' att_str '=nc.' att_str '(:);']) |
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71 | end |
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72 | close(nc) |
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73 | %total time from beginning : 15 ms for a single attribute |
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74 | return |
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75 | end |
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76 | |
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77 | % reading of variables, including attributes |
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78 | if isempty(List) |
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79 | ListVarName='*'; |
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80 | else |
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81 | % if isempty(List{1}) |
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82 | % ListVarName='*'; |
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83 | % else |
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84 | ListVarName=List{1}; |
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85 | % end |
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86 | end |
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87 | % -------- read global attributes ----------- |
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88 | att_read=att(nc);%cell of 'global attributes' (nc objects), CPU time 30 ms |
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89 | att_key={};%default |
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90 | iatt_g=0; |
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91 | for iatt=1:length(att_read) |
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92 | aa=att_read{iatt}; |
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93 | keystr=name(aa); |
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94 | indstr1=regexp(keystr,'\\');%replace dots' |
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95 | indstr2=regexp(keystr,'\.');%replace dots' |
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96 | if ~isequal(keystr,'title') % PROBLEM WITH civx files do not read 'title' |
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97 | if isempty(indstr1) && isempty(indstr2) % |
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98 | eval(['valuestr=nc.' keystr '(:);']) |
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99 | if ischar(valuestr) && length(valuestr)<200 |
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100 | iatt_g=iatt_g+1; |
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101 | indstr1=regexp(keystr,'\\');%replace dots' |
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102 | indstr2=regexp(keystr,'\.');%replace dots' |
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103 | if isempty(indstr1) && isempty(indstr2) |
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104 | eval(['Data.' keystr '=''' valuestr ''';']) |
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105 | att_key{iatt_g}=keystr; |
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106 | end |
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107 | elseif isempty(valuestr) |
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108 | iatt_g=iatt_g+1; |
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109 | eval(['Data.' keystr '=[];']) |
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110 | att_key{iatt_g}=keystr; |
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111 | elseif isnumeric(valuestr) |
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112 | iatt_g=iatt_g+1; |
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113 | eval(['Data.' keystr '=valuestr;']) |
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114 | att_key{iatt_g}=keystr; |
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115 | end |
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116 | end |
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117 | end |
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118 | end |
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119 | Data.ListGlobalAttribute=att_key; |
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120 | nbattr=length(att_key); |
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121 | neworder=[nbattr+1 (1:nbattr)]; |
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122 | Data=orderfields(Data,neworder); |
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123 | |
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124 | % -------- read dimensions ----------- |
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125 | dim_read=dim(nc);%cell of variable dimension names (nc objects): CPU time 0.0013 |
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126 | dim_name={}; |
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127 | dim_value=[]; |
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128 | for idim=1:length(dim_read); |
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129 | aa=dim_read{idim}; |
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130 | if ~isempty(aa) |
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131 | dim_name{idim}=name(aa); |
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132 | dim_value(idim)=length(aa); |
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133 | end |
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134 | end |
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135 | if ~isempty(dim_name) && ~isempty(dim_value) |
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136 | Data.ListDimName=dim_name; |
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137 | Data.DimValue=dim_value; |
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138 | used=zeros(1,length(dim_value));%initialize test of used dimensions |
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139 | end |
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140 | |
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141 | % -------- read variables ----------- |
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142 | var_read={}; %default |
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143 | testmulti=0; |
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144 | OutputList=[]; |
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145 | if isequal(ListVarName,'*')%|| isempty(ListVarName) |
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146 | var_read=var(nc);%cell of all variables |
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147 | elseif ~isempty(ListVarName) |
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148 | sizvar=size(ListVarName); |
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149 | testmulti=(sizvar(1)>1); |
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150 | if testmulti |
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151 | OutputList=ListVarName(1,:); |
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152 | testend=0; |
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153 | for iline=1:sizvar(1) |
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154 | if testend |
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155 | break |
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156 | end |
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157 | for ivar=1:sizvar(2) |
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158 | var_read{ivar}=[];%default |
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159 | var_detect(ivar)=0;%default |
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160 | VarName=ListVarName{iline,ivar}; |
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161 | if ~isempty(VarName) |
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162 | var_read{ivar}=nc{VarName};%select the input variable names |
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163 | if ivar==1 |
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164 | if isempty (var_read{ivar}) |
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165 | break%go to next line if the first nc variable is not found |
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166 | else |
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167 | testend=1; %this line will be read |
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168 | ichoice=iline-1; %selectedline number in the list of input names of variables |
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169 | var_detect(ivar)=1; |
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170 | end |
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171 | else |
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172 | var_detect(ivar)=~isempty (var_read{ivar}); |
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173 | end |
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174 | end |
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175 | end |
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176 | end |
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177 | if ~isempty(find(var_detect,1)) |
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178 | OutputList=OutputList(find(var_detect)); |
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179 | end |
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180 | else %single list of input variables |
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181 | var_detect=ones(size(ListVarName)); |
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182 | for ivar=1:sizvar(2) |
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183 | var_read{ivar}=nc{ListVarName{ivar}};%select the input variable names |
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184 | var_detect(ivar)=~isempty(var_read{ivar}); |
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185 | end |
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186 | end |
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187 | var_read=var_read(find(var_detect)); |
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188 | end |
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189 | |
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190 | % var_dim_index=[]; %default |
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191 | Data.ListVarName={};%default |
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192 | for ivar=1:length(var_read) |
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193 | vv=var_read{ivar}; |
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194 | Data.ListVarName{ivar}=name(vv);%name of the variable |
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195 | if testmulti |
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196 | Data.ListVarName{ivar}=OutputList{ivar}; |
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197 | else |
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198 | Data.ListVarName{ivar}=name(vv);%name of the variable |
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199 | end |
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200 | var_dim=dim(vv);%dimension netcdf object of the variable |
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201 | for ivardim=1:length(var_dim) |
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202 | var_dim_name=name(var_dim{ivardim});%name of the dimension |
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203 | for idim=1:length(dim_name)% find the index of the current dimension in the list of dimensions |
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204 | if isequal(dim_name{idim},var_dim_name) |
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205 | Data.VarDimIndex{ivar}(ivardim)=idim; |
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206 | used(idim)=1; |
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207 | break |
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208 | end |
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209 | end |
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210 | end |
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211 | Data.VarDimName{ivar}={}; |
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212 | %variable attributes |
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213 | Data.VarAttribute{ivar}=[];%initialisation of the list of variable attributes |
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214 | %variable attributes |
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215 | att_read=att(vv); |
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216 | for iatt=1:length(att_read) |
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217 | aa=att_read{iatt}; |
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218 | eval(['valuestr=vv.' name(aa) '(:);']) |
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219 | if ischar(valuestr) |
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220 | eval(['Data.VarAttribute{ivar}.' name(aa) '=''' valuestr ''';']) |
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221 | elseif isempty(valuestr) |
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222 | eval(['Data.VarAttribute{ivar}.' name(aa) '=[];']) |
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223 | elseif isnumeric(valuestr) |
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224 | eval(['Data.VarAttribute{ivar}.' name(aa) '=valuestr;']) |
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225 | end |
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226 | end |
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227 | end |
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228 | |
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229 | %select the used dimensions |
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230 | if isempty(var_read) |
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231 | if isfield(Data,'ListDimName') && isfield(Data,'DimValue') |
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232 | Data=rmfield(Data,'ListDimName'); |
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233 | Data=rmfield(Data,'DimValue'); |
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234 | end |
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235 | else |
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236 | old_dim_index=find(used); %dimension indices which are used by the selected variables |
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237 | old2new=cumsum(used); |
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238 | Data.ListDimName=Data.ListDimName(old_dim_index); |
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239 | Data.DimValue=Data.DimValue(old_dim_index); |
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240 | end |
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241 | for ivar=1:length(var_read) |
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242 | Data.VarDimIndex{ivar}=(old2new(Data.VarDimIndex{ivar})); |
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243 | Data.VarDimName{ivar}=(Data.ListDimName(Data.VarDimIndex{ivar})); |
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244 | end |
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245 | %variable values |
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246 | |
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247 | if ~isempty(ListVarName) |
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248 | for ivar=1:length(Data.ListVarName) |
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249 | vv=var_read{ivar}; |
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250 | vdata=vv(:);%data array of the field variable |
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251 | eval(['Data.' Data.ListVarName{ivar} '=vdata;'])%read the variable data |
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252 | end |
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253 | end |
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254 | % -------- close fle----------- |
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255 | if testfile==1 |
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256 | close(nc) |
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257 | end |
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258 | |
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259 | %total time from beginning : 150 ms for a full civ2 field, 65 ms for four fields |
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260 | |
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