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15<div><a href="../index.html">Home</a> &gt;  <a href="index.html">.</a> &gt; nc2struct.m</div>
16
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19
20<h1>nc2struct
21</h1>
22
23<h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
24<div class="box"><strong>'nc2struct': transform a netcdf file in a corresponding matlab structure</strong></div>
25
26<h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
27<div class="box"><strong>function [Data,var_detect,ichoice]=nc2struct(nc,ListVarName) </strong></div>
28
29<h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
30<div class="fragment"><pre class="comment">'nc2struct': transform a netcdf file in a corresponding matlab structure
31----------------------------------------------------------------------
32 function [Data,var_detect,ichoice]=nc2struct(nc,ListVarName)
33
34 OUTPUT:
35  Data: structure containing all the information of the netcdf file (or netcdf object)
36           with fields:
37    .ListGlobalAttribute: cell listing the names of the global attributes
38        .Att_1,Att_2... : values of the global attributes
39            .ListDimName: cell listing the names of the array dimensions
40               .DimValue: array dimension values (Matlab vector with the same length as .ListDimName
41            .ListVarName: cell listing the names of the variables
42            .VarDimIndex: cell containing the set of dimension indices (in list .ListDimName) for each variable of .ListVarName
43            .VarDimName: cell containing a cell of dimension names (in list .ListDimName) for each variable of .ListVarName
44           .VarAttribute: cell of structures s containing names and values of variable attributes (s.name=value) for each variable of .ListVarName
45        .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName
46  var_detect: vector with same length as ListVarName, with 1 for each detected variable and 0 else.
47  ichoice: = line
48
49INPUT:
50     nc:      name of a netcdf file (char string) or netcdf object   
51 ListVarName: optional list of variable names to select (cell array of  char strings {'VarName1', 'VarName2',...} )
52         if ListVarName=[] or {}, no variables is read (only global attributes and lists of vdimensions, variables and attriburtes)
53         if ListVarName is absent, or = '*', ALL the variables are read.
54        if ListVarName is a cell array with n lines, the set of variables
55                        will be sought by order of priority in the list, while output names will be set by the first line
56 
57AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
58  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
59AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
60     This file is part of the toolbox UVMAT.
61 
62     UVMAT is free software; you can redistribute it and/or modify
63     it under the terms of the GNU General Public License as published by
64     the Free Software Foundation; either version 2 of the License, or
65     (at your option) any later version.
66 
67     UVMAT is distributed in the hope that it will be useful,
68     but WITHOUT ANY WARRANTY; without even the implied warranty of
69     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
70     GNU General Public License (file UVMAT/COPYING.txt) for more details.
71AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA</pre></div>
72
73<!-- crossreference -->
74<h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
75This function calls:
76<ul style="list-style-image:url(../matlabicon.gif)">
77<li><a href="nc2struct_toolbox.html" class="code" title="function [Data,var_detect,ichoice]=nc2struct_toolbox(nc,ListVarName)">nc2struct_toolbox</a>    'nc2struct_toolbox': transform a netcdf file in a corresponding matlab structure, USE OLD NETCDF LIBRARY</li></ul>
78This function is called by:
79<ul style="list-style-image:url(../matlabicon.gif)">
80<li><a href="civ.html" class="code" title="function varargout = civ(varargin)">civ</a>  'civ': function associated with the interface 'civ.fig' for PIV, spline interpolation and stereo PIV (patch)</li><li><a href="civ_3D.html" class="code" title="function varargout = civ_3D(varargin)">civ_3D</a>        'civ_3D': function associated with the interface 'civ_3D.fig' for PIV in volume</li><li><a href="get_field.html" class="code" title="function varargout = get_field(varargin)">get_field</a>    'get_field': display variables and attributes from a Netcdf file, and plot selected fields</li><li><a href="read_civxdata.html" class="code" title="function [Field,VelTypeOut]=read_civxdata(filename,FieldNames,VelType)">read_civxdata</a>   'read_civxdata': reads civx data from netcdf files</li><li><a href="read_get_field.html" class="code" title="function [SubField,errormsg]=read_get_field(hget_field)">read_get_field</a>        'read_get_field': read the list of selected variables from the GUI get_field (SAME AS THE FIRST</li><li><a href="read_get_field_old.html" class="code" title="function [SubField,errormsg]=read_get_field(hget_field)">read_get_field_old</a>   'read_get_field': read the list of selected variables from the GUI get_field (SAME AS THE FIRST</li><li><a href="series.html" class="code" title="function varargout = series(varargin)">series</a>     'series': master function associated to the GUI series.m for analysis field series</li><li><a href="uvmat.html" class="code" title="function varargout = uvmat(varargin)">uvmat</a>     'uvmat': function associated with the GUI 'uvmat.fig' for images and data field visualization</li></ul>
81<!-- crossreference -->
82
83
84<h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
85<div class="fragment"><pre>0001 <span class="comment">%'nc2struct': transform a netcdf file in a corresponding matlab structure</span>
860002 <span class="comment">%----------------------------------------------------------------------</span>
870003 <span class="comment">% function [Data,var_detect,ichoice]=nc2struct(nc,ListVarName)</span>
880004 <span class="comment">%</span>
890005 <span class="comment">% OUTPUT:</span>
900006 <span class="comment">%  Data: structure containing all the information of the netcdf file (or netcdf object)</span>
910007 <span class="comment">%           with fields:</span>
920008 <span class="comment">%    .ListGlobalAttribute: cell listing the names of the global attributes</span>
930009 <span class="comment">%        .Att_1,Att_2... : values of the global attributes</span>
940010 <span class="comment">%            .ListDimName: cell listing the names of the array dimensions</span>
950011 <span class="comment">%               .DimValue: array dimension values (Matlab vector with the same length as .ListDimName</span>
960012 <span class="comment">%            .ListVarName: cell listing the names of the variables</span>
970013 <span class="comment">%            .VarDimIndex: cell containing the set of dimension indices (in list .ListDimName) for each variable of .ListVarName</span>
980014 <span class="comment">%            .VarDimName: cell containing a cell of dimension names (in list .ListDimName) for each variable of .ListVarName</span>
990015 <span class="comment">%           .VarAttribute: cell of structures s containing names and values of variable attributes (s.name=value) for each variable of .ListVarName</span>
1000016 <span class="comment">%        .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName</span>
1010017 <span class="comment">%  var_detect: vector with same length as ListVarName, with 1 for each detected variable and 0 else.</span>
1020018 <span class="comment">%  ichoice: = line</span>
1030019 <span class="comment">%</span>
1040020 <span class="comment">%INPUT:</span>
1050021 <span class="comment">%     nc:      name of a netcdf file (char string) or netcdf object</span>
1060022 <span class="comment">% ListVarName: optional list of variable names to select (cell array of  char strings {'VarName1', 'VarName2',...} )</span>
1070023 <span class="comment">%         if ListVarName=[] or {}, no variables is read (only global attributes and lists of vdimensions, variables and attriburtes)</span>
1080024 <span class="comment">%         if ListVarName is absent, or = '*', ALL the variables are read.</span>
1090025 <span class="comment">%        if ListVarName is a cell array with n lines, the set of variables</span>
1100026 <span class="comment">%                        will be sought by order of priority in the list, while output names will be set by the first line</span>
1110027 <span class="comment">%</span>
1120028 <span class="comment">%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA</span>
1130029 <span class="comment">%  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.</span>
1140030 <span class="comment">%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA</span>
1150031 <span class="comment">%     This file is part of the toolbox UVMAT.</span>
1160032 <span class="comment">%</span>
1170033 <span class="comment">%     UVMAT is free software; you can redistribute it and/or modify</span>
1180034 <span class="comment">%     it under the terms of the GNU General Public License as published by</span>
1190035 <span class="comment">%     the Free Software Foundation; either version 2 of the License, or</span>
1200036 <span class="comment">%     (at your option) any later version.</span>
1210037 <span class="comment">%</span>
1220038 <span class="comment">%     UVMAT is distributed in the hope that it will be useful,</span>
1230039 <span class="comment">%     but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
1240040 <span class="comment">%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
1250041 <span class="comment">%     GNU General Public License (file UVMAT/COPYING.txt) for more details.</span>
1260042 <span class="comment">%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA</span>
1270043   
1280044 <a name="_sub0" href="#_subfunctions" class="code">function [Data,var_detect,ichoice]=nc2struct(nc,ListVarName)</a>
1290045
1300046 <span class="keyword">if</span> ~exist(<span class="string">'ListVarName'</span>,<span class="string">'var'</span>)
1310047     ListVarName=<span class="string">'*'</span>;
1320048 <span class="keyword">end</span>
1330049 hhh=which(<span class="string">'netcdf.open'</span>);<span class="comment">% look for built-in matlab netcdf library</span>
1340050
1350051 <span class="keyword">if</span> ~isequal(hhh,<span class="string">''</span>)
1360052     <span class="comment">%default output</span>
1370053     Data=[];
1380054 <span class="comment">%     ListIndex=[];</span>
1390055     var_detect=[];
1400056     ichoice=[];<span class="comment">%default</span>
1410057     <span class="comment">%open the netcdf file for reading</span>
1420058     <span class="keyword">if</span> ischar(nc)
1430059         <span class="keyword">if</span> exist(nc,<span class="string">'file'</span>)
1440060             nc=netcdf.open(nc,<span class="string">'NC_NOWRITE'</span>);
1450061             testfile=1;
1460062         <span class="keyword">else</span>
1470063            Data.Txt=[<span class="string">'ERROR:file '</span> nc <span class="string">' does not exist'</span>];
1480064            <span class="keyword">return</span>
1490065         <span class="keyword">end</span>
1500066     <span class="keyword">else</span>
1510067         testfile=0;
1520068     <span class="keyword">end</span>
1530069     [ndims,nvars,ngatts] = netcdf.inq(nc);<span class="comment">%nbre of dimensions, variables, attributes</span>
1540070     
1550071     <span class="comment">%  -------- read global attributes (constants)-----------</span>
1560072     att_key={};<span class="comment">%default</span>
1570073     iatt_g=0;
1580074     Data.ListGlobalAttribute={};<span class="comment">%default</span>
1590075     <span class="keyword">for</span> iatt=1:ngatts
1600076         keystr= netcdf.inqAttName(nc,netcdf.getConstant(<span class="string">'NC_GLOBAL'</span>),iatt-1);
1610077         indstr1=regexp(keystr,<span class="string">'\\'</span>);<span class="comment">%replace dots'</span>
1620078         indstr2=regexp(keystr,<span class="string">'\.'</span>);<span class="comment">%replace dots'</span>
1630079         <span class="keyword">if</span> isempty(indstr1) &amp;&amp; isempty(indstr2)
1640080            valuestr = netcdf.getAtt(nc,netcdf.getConstant(<span class="string">'NC_GLOBAL'</span>),keystr);
1650081            <span class="keyword">if</span> ischar(valuestr) &amp;&amp; length(valuestr)&lt;200
1660082                 iatt_g=iatt_g+1;
1670083                 indstr1=regexp(keystr,<span class="string">'\\'</span>);<span class="comment">%replace dots'</span>
1680084                 indstr2=regexp(keystr,<span class="string">'\.'</span>);<span class="comment">%replace dots'</span>
1690085                 <span class="keyword">if</span> isempty(indstr1) &amp;&amp; isempty(indstr2)
1700086                     eval([<span class="string">'Data.'</span> keystr <span class="string">'='''</span> valuestr <span class="string">''';'</span>])
1710087                     att_key{iatt_g}=keystr;
1720088                 <span class="keyword">end</span>
1730089             <span class="keyword">elseif</span> isempty(valuestr)
1740090                 iatt_g=iatt_g+1;
1750091                 eval([<span class="string">'Data.'</span> keystr <span class="string">'=[];'</span>])
1760092                 att_key{iatt_g}=keystr;
1770093             <span class="keyword">elseif</span> isnumeric(valuestr)
1780094                 iatt_g=iatt_g+1;
1790095                 eval([<span class="string">'Data.'</span> keystr <span class="string">'=valuestr;'</span>])
1800096                 att_key{iatt_g}=keystr;
1810097             <span class="keyword">end</span>
1820098         <span class="keyword">end</span>
1830099     <span class="keyword">end</span>
1840100     Data.ListGlobalAttribute=att_key;
1850101
1860102     <span class="comment">%  -------- read dimensions -----------</span>
1870103     dim_name={};
1880104     dim_value=[];
1890105     <span class="keyword">for</span> idim=1:ndims<span class="comment">%length(dim_read);</span>
1900106         [dim_name{idim},dim_value(idim)] = netcdf.inqDim(nc,idim-1);
1910107     <span class="keyword">end</span>
1920108     <span class="keyword">if</span> ~isempty(dim_name) &amp;&amp; ~isempty(dim_value)
1930109         Data.ListDimName=dim_name;
1940110         Data.DimValue=dim_value;
1950111 <span class="comment">%         DimIndices=[1:ndims]; %index of the dimension in the netcdf file</span>
1960112         dim_used=zeros(1,ndims);<span class="comment">%initialize test of used dimensions</span>
1970113     <span class="keyword">end</span>
1980114 
1990115     <span class="comment">%  -------- read variables -----------</span>
2000116     var_read={}; <span class="comment">%default</span>
2010117     dimids={};
2020118     nbatt=[];
2030119     <span class="keyword">for</span> ivar=1:nvars
2040120         [var_read{ivar},xtype,dimids{ivar},nbatt(ivar)] = netcdf.inqVar(nc,ivar-1);
2050121     <span class="keyword">end</span> 
2060122     var_index=1:nvars; <span class="comment">%default set of variable indices in the netcdf file</span>
2070123     testmulti=0;
2080124     OutputList=[];
2090125     
2100126     <span class="comment">%select input variables, if requested by the input ListVarName</span>
2110127     <span class="keyword">if</span> isequal(ListVarName,<span class="string">'*'</span>)||isemptyl(ListVarName)
2120128         sizvar=size(ListVarName);
2130129         testmulti=(sizvar(1)&gt;1);
2140130         var_index=zeros(1,sizvar(2));<span class="comment">%default</span>
2150131         <span class="keyword">if</span> testmulti
2160132             OutputList=ListVarName(1,:);
2170133             testend=0;
2180134             <span class="keyword">for</span> iline=1:sizvar(1)
2190135                 <span class="keyword">if</span> testend
2200136                     <span class="keyword">break</span>
2210137                 <span class="keyword">end</span>
2220138           <span class="comment">%      var_index=zeros(size(ListVarName));%default</span>
2230139                 <span class="keyword">for</span> ivar=1:sizvar(2)
2240140                     <span class="keyword">if</span> ~isempty(ListVarName{iline,ivar})
2250141                          <span class="keyword">for</span> ilist=1:nvars
2260142                             <span class="keyword">if</span> isequal(var_read{ilist},ListVarName{iline,ivar})
2270143                                 var_index(ivar)=ilist;
2280144      <span class="comment">%                          var_detect(ivar)=1;</span>
2290145                             <span class="keyword">break</span>
2300146                             <span class="keyword">end</span>
2310147                          <span class="keyword">end</span>
2320148                          <span class="keyword">if</span> ivar==1
2330149                             <span class="keyword">if</span> var_index(ivar)==0
2340150                                 <span class="keyword">break</span><span class="comment">%go to next line if the first nc variable is not found</span>
2350151                             <span class="keyword">else</span>
2360152                                 testend=1; <span class="comment">%this line will be read</span>
2370153                                 ichoice=iline-1; <span class="comment">%selectedline number in the list of input names of variables</span>
2380154                             <span class="keyword">end</span>
2390155                          <span class="keyword">end</span>
2400156                     <span class="keyword">end</span>
2410157                 <span class="keyword">end</span>
2420158             <span class="keyword">end</span>
2430159         <span class="keyword">else</span>   <span class="comment">%single list of input variables</span>
2440160             <span class="keyword">for</span> ivar=1:sizvar(2)
2450161                 <span class="keyword">for</span> ilist=1:nvars
2460162                     <span class="keyword">if</span> isequal(var_read{ilist},ListVarName{ivar})
2470163                         var_index(ivar)=ilist;
2480164                         var_detect(ivar)=1;
2490165                         <span class="keyword">break</span>
2500166                     <span class="keyword">end</span>
2510167                 <span class="keyword">end</span>
2520168             <span class="keyword">end</span>
2530169         <span class="keyword">end</span>
2540170         list_index=find(var_index);
2550171         <span class="keyword">if</span> ~isempty(list_index)
2560172             <span class="keyword">if</span> testmulti
2570173                 OutputList=OutputList(list_index);
2580174             <span class="keyword">end</span>
2590175             var_index=var_index(list_index);
2600176             var_detect=(var_index~=0);
2610177             var_read=var_read(var_index);         
2620178         <span class="keyword">end</span>
2630179     <span class="keyword">end</span>
2640180     
2650181     
2660182     <span class="comment">%select variable attributes and associate dimensions</span>
2670183 <span class="comment">%     var_dim_index=[]; %default</span>
2680184     Data.ListVarName={};<span class="comment">%default</span>
2690185     VarDimIndex={};<span class="comment">%default</span>
2700186     <span class="keyword">for</span> ivar=1:length(var_read)
2710187         <span class="keyword">if</span> testmulti
2720188             Data.ListVarName{ivar}=OutputList{ivar};<span class="comment">%new name given by ListVarName(1,:)</span>
2730189         <span class="keyword">else</span>
2740190             Data.ListVarName{ivar}=var_read{ivar};<span class="comment">%name of the variable</span>
2750191         <span class="keyword">end</span>
2760192         var_dim=dimids{var_index(ivar)}+1; <span class="comment">%dimension indices used by the variable</span>
2770193         dim_used(var_dim)=ones(size(var_dim));
2780194         VarDimIndex{ivar}=var_dim;
2790195
2800196         <span class="comment">%variable attributes</span>
2810197         <span class="keyword">if</span> ivar==1
2820198             Data.VarAttribute={};<span class="comment">%initialisation of the list of variable attributes</span>
2830199         <span class="keyword">end</span>
2840200         <span class="comment">%variable attributes</span>
2850201         <span class="keyword">for</span> iatt=1:nbatt(var_index(ivar))
2860202             attname = netcdf.inqAttName(nc,var_index(ivar)-1,iatt-1);
2870203             valuestr= netcdf.getAtt(nc,var_index(ivar)-1,attname);
2880204             <span class="keyword">if</span> ischar(valuestr)
2890205                 eval([<span class="string">'Data.VarAttribute{ivar}.'</span> attname <span class="string">'='''</span> valuestr <span class="string">''';'</span>])
2900206             <span class="keyword">elseif</span> isempty(valuestr)
2910207                 eval([<span class="string">'Data.VarAttribute{ivar}.'</span> attname <span class="string">'=[];'</span>])
2920208             <span class="keyword">elseif</span> isnumeric(valuestr)
2930209                 eval([<span class="string">'Data.VarAttribute{ivar}.'</span> attname <span class="string">'=valuestr;'</span>])
2940210             <span class="keyword">end</span>
2950211         <span class="keyword">end</span>
2960212     <span class="keyword">end</span>
2970213
2980214     <span class="comment">%select the used dimensions</span>
2990215     <span class="keyword">if</span> isempty(var_read)
3000216         <span class="keyword">if</span> isfield(Data,<span class="string">'ListDimName'</span>) &amp;&amp; isfield(Data,<span class="string">'DimValue'</span>)
3010217         Data=rmfield(Data,<span class="string">'ListDimName'</span>);
3020218         Data=rmfield(Data,<span class="string">'DimValue'</span>);
3030219         <span class="keyword">end</span>
3040220     <span class="keyword">else</span>
3050221 <span class="comment">%         list_dim=1:ndims;</span>
3060222         dim_index=find(dim_used);
3070223 <span class="comment">%         list_dim=list_dim(dim_index);</span>
3080224         old2new=cumsum(dim_used);
3090225         Data.ListDimName=Data.ListDimName(dim_index);
3100226         Data.DimValue=Data.DimValue(dim_index);
3110227     <span class="keyword">end</span>
3120228     <span class="keyword">for</span> ivar=1:length(var_read)
3130229         Data.VarDimIndex{ivar}=old2new(VarDimIndex{ivar});<span class="comment">% ENLEVER Data.VarDimIndex ulterieurement</span>
3140230         Data.VarDimName{ivar}=Data.ListDimName(Data.VarDimIndex{ivar});
3150231     <span class="keyword">end</span>
3160232     <span class="comment">%variable values</span>
3170233     <span class="keyword">if</span>  ~isempty(ListVarName)
3180234         <span class="keyword">for</span> ivar=1:length(Data.ListVarName)
3190235             eval([<span class="string">'Data.'</span> Data.ListVarName{ivar} <span class="string">'=netcdf.getVar(nc,var_index(ivar)-1);'</span>])<span class="comment">%read the variable data</span>
3200236             eval([<span class="string">'Data.'</span> Data.ListVarName{ivar} <span class="string">'=Data.'</span> Data.ListVarName{ivar} <span class="string">''';'</span>])<span class="comment">%read the variable data</span>
3210237         <span class="keyword">end</span>
3220238     <span class="keyword">end</span>
3230239     <span class="comment">%  -------- close fle-----------</span>
3240240     <span class="keyword">if</span> testfile==1
3250241         netcdf.close(nc)
3260242     <span class="keyword">end</span>
3270243 <span class="keyword">else</span>
3280244     [Data,var_detect,ichoice]=<a href="nc2struct_toolbox.html" class="code" title="function [Data,var_detect,ichoice]=nc2struct_toolbox(nc,ListVarName)">nc2struct_toolbox</a>(nc,ListVarName);
3290245 <span class="keyword">end</span></pre></div>
330<hr><address>Generated on Fri 13-Nov-2009 11:17:03 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/">m2html</a></strong> &copy; 2003</address>
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