source: trunk/src/nc2struct.m @ 527

Last change on this file since 527 was 527, checked in by sommeria, 9 years ago

various bugs corrected

File size: 11.1 KB
Line 
1%'nc2struct': transform a netcdf file in a corresponding matlab structure
2% it reads all the global attributes and all variables, or a selected list.
3% The corresponding dimensions and variable attributes are then extracted
4%----------------------------------------------------------------------
5% function [Data,var_detect,ichoice]=nc2struct(nc,varargin)
6%
7% OUTPUT:
8%  Data: structure containing all the information of the netcdf file (or netcdf object)
9%           with (optional)fields:
10%                    .ListGlobalAttribute: cell listing the names of the global attributes
11%                    .Att_1,Att_2... : values of the global attributes
12%                    .ListVarName: list of variable names to select (cell array of  char strings {'VarName1', 'VarName2',...} )
13%                    .VarDimName: list of dimension names for each element of .ListVarName (cell array of string cells)                         
14%                    .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName
15%                  ListDimName=list of dimension (added information, not requested for field description)
16%                  DimValue= vlalues of dimensions (added information, not requested for field description)
17%  var_detect: vector with same length as the cell array ListVarName, = 1 for each detected variable and 0 else.
18%            var_detect=[] in the absence of input cell array
19%  ichoice: index of the selected line in the case of multiple choice
20%        (cell array of varible names with multiple lines) , =[] by default
21%INPUT:
22%  nc:  name of a netcdf file (char string) or netcdf object   
23%  additional arguments:
24%       -no additional arguments: all the variables of the netcdf fiel are read.
25%       -a cell array, ListVarName, made of  char strings {'VarName1', 'VarName2',...} )
26%         if ListVarName=[] or {}, no variables is read (only global attributes)
27%         if ListVarName is absent, or = '*', ALL the variables of the netcdf file are read.
28%         if ListVarName is a cell array with n lines, the set of variables will be sought by order of priority
29%                  in the list, while output names will be set by the first line
30%        - the string 'ListGlobalAttribute' followed by a list of attribute  names: reads only these attributes (fast reading)
31%
32%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
33%  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
34%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
35%     This file is part of the toolbox UVMAT.
36%
37%     UVMAT is free software; you can redistribute it and/or modify
38%     it under the terms of the GNU General Public License as published by
39%     the Free Software Foundation; either version 2 of the License, or
40%     (at your option) any later version.
41%
42%     UVMAT is distributed in the hope that it will be useful,
43%     but WITHOUT ANY WARRANTY; without even the implied warranty of
44%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
45%     GNU General Public License (file UVMAT/COPYING.txt) for more details.
46%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
47   
48function [Data,var_detect,ichoice]=nc2struct(nc,varargin)
49
50if isempty(varargin)
51    varargin{1}='*';
52end
53hhh=which('netcdf.open');% look for built-in matlab netcdf library
54
55if ~isequal(hhh,'')
56    %% default output
57    Data=[];%default
58    var_detect=[];%default
59    ichoice=[];%default
60   
61    %% open the netcdf file for reading
62    if ischar(nc)
63        if exist(nc,'file')
64            try
65            nc=netcdf.open(nc,'NC_NOWRITE');
66            testfile=1;
67            catch ME
68              Data.Txt=['ERROR opening ' nc ': ' ME.message];
69              return
70            end
71        else
72           Data.Txt=['ERROR:file ' nc ' does not exist'];
73           return
74        end
75    else
76        testfile=0;
77    end
78   
79    %% short reading option for global attributes only, if the first argument is 'ListGlobalAttribute'
80    if isequal(varargin{1},'ListGlobalAttribute')
81        for ilist=2:numel(varargin)
82            valuestr=[];%default
83            try
84            valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),varargin{ilist});
85            catch ME
86            end
87            eval(['Data.' varargin{ilist} '=valuestr;'])
88        end
89        netcdf.close(nc)
90       return
91    end
92
93    %% full reading: get the nbre of dimensions, variables, global attributes
94    ListVarName=varargin{1};
95    [ndims,nvars,ngatts]=netcdf.inq(nc);%nbre of dimensions, variables, global attributes, in the netcdf file
96   
97    %%  -------- read all global attributes (constants)-----------
98    Data.ListGlobalAttribute={};%default
99    att_key=cell(1,ngatts);%default
100    for iatt=1:ngatts
101        keystr= netcdf.inqAttName(nc,netcdf.getConstant('NC_GLOBAL'),iatt-1);
102        valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),keystr);
103        keystr=regexprep(keystr,{'\','/','\.','-',' '},{'','','','',''});%remove  '\','.' or '-' if exists
104        if strcmp(keystr(1),'_')
105            keystr(1)=[];
106        end
107        try
108            if ischar(valuestr) %& length(valuestr)<200 & double(valuestr)<=122 & double(valuestr)>=48 %usual characters
109                eval(['Data.' keystr '=''' valuestr ''';'])
110            elseif isnumeric(valuestr)
111                eval(['Data.' keystr '=valuestr;'])
112            else
113                eval(['Data.' keystr '='';'])
114            end
115            att_key{iatt}=keystr;
116        catch ME
117            att_key{iatt}=['attr_' num2str(iatt)];
118            Data.(att_key{iatt})=[];
119        end
120    end
121    Data.ListGlobalAttribute=att_key;
122
123    %%  -------- read dimension names-----------
124    ListDimNameNetcdf=cell(1,ndims);
125    dim_value=zeros(1,ndims);
126    for idim=1:ndims %loop on the dimensions of the netcdf file
127        [ListDimNameNetcdf{idim},dim_value(idim)] = netcdf.inqDim(nc,idim-1);%get name and value of each dimension
128    end
129    if ~isempty(ListDimNameNetcdf)
130        flag_used=zeros(1,ndims);%initialize the flag indicating the selected dimensions in the list (0=unused)
131    end
132 
133    %%  -------- read names of variables -----------
134    ListVarNameNetcdf=cell(1,nvars); %default
135    dimids=cell(1,nvars);
136    nbatt=zeros(1,nvars);
137    for ncvar=1:nvars %loop on the variables of the netcdf file
138        %get name, type, dimensions and attribute numbers of each variable
139        [ListVarNameNetcdf{ncvar},xtype,dimids{ncvar},nbatt(ncvar)] = netcdf.inqVar(nc,ncvar-1);
140    end 
141    testmulti=0;
142    if isequal(ListVarName,'*')||isempty(ListVarName)
143        var_index=1:nvars; %all the variables are selected in the netcdf file
144        Data.ListVarName=ListVarNameNetcdf;
145    else   %select input variables, if requested by the input ListVarName
146        ind_remove=[];
147        check_keep=ones(1,size(ListVarName,2));
148        for ivar=1:size(ListVarName,2) % check redondancy of variable names
149            if ~isempty(find(strcmp(ListVarName{1,ivar},ListVarName(1:ivar-1)), 1))
150                check_keep(ivar)=0;% the variable #ivar is already in the list
151            end
152        end
153        ListVarName=ListVarName(:,logical(check_keep));         
154        sizvar=size(ListVarName);
155        testmulti=(sizvar(1)>1);%test for multiple choice of variable ranked by order of priority
156        var_index=zeros(1,sizvar(2));%default
157        if testmulti %multiple choice of variable ranked by order of priority
158            for iline=1:sizvar(1)
159                search_index=find(strcmp(ListVarName{iline,1},ListVarNameNetcdf),1);%look for the first variable name in the list of netcdf variables
160                if ~isempty(search_index)
161                    break % go to the next line
162                end
163            end
164            ichoice=iline-1;%selected line number in the list of input names of variables
165        else
166            iline=1;
167        end
168        for ivar=1:sizvar(2)
169            search_index=find(strcmp(ListVarName{iline,ivar},ListVarNameNetcdf),1);%look for the variable name in the list of netcdf file
170            if ~isempty(search_index)
171                var_index(ivar)=search_index;%index of the netcdf list corresponding to the input list index ivar
172            end
173        end
174        var_detect=(var_index~=0);%=1 for detected variables         
175        list_index=find(var_index);% indices in the input list corresponding to a detected variable
176        var_index=var_index(list_index);% netcdf variable indices corresponding to the output list of read variable
177        Data.ListVarName=ListVarName(1,list_index);%the first line of ListVarName sets the output names of the variables
178    end
179     
180  %% get the dimensions and attributes associated to  variables
181    for ivar=1:length(var_index)
182        var_dim{ivar}=dimids{var_index(ivar)}+1; %netcdf dimension indices used by the variable #ivar
183        Data.VarDimName{ivar}=ListDimNameNetcdf(var_dim{ivar});
184        flag_used(var_dim{ivar})=ones(size(var_dim{ivar}));%flag_used =1 for the indices of used dimensions
185        for iatt=1:nbatt(var_index(ivar))
186            attname = netcdf.inqAttName(nc,var_index(ivar)-1,iatt-1);
187            valuestr= netcdf.getAtt(nc,var_index(ivar)-1,attname);
188            attname=regexprep(attname,{'\','/','\.','-',' '},{'','','','',''});%remove  '\','.' or '-' if exists
189            if strcmp(attname(1),'_')
190                attname(1)=[];
191            end
192            try
193            if ischar(valuestr)
194               % valuestr=regexprep(valuestr,{'\\','\/','\.','\-',' '},{'_','_','_','_','_'});%remove  '\','.' or '-' if exists
195                eval(['Data.VarAttribute{ivar}.' attname '=''' valuestr ''';'])
196            elseif isempty(valuestr)
197                eval(['Data.VarAttribute{ivar}.' attname '=[];'])
198            elseif isnumeric(valuestr)
199                eval(['Data.VarAttribute{ivar}.' attname '=valuestr;'])
200            end
201            catch ME
202                display(attname)
203                display(valuestr)
204                display(ME.message)         
205                eval(['Data.VarAttribute{ivar}.atrr_' num2str(iatt) '=''not read'';'])
206            end
207        end
208    end
209
210    %% select the dimensions used for the set of input variables
211    if ~isempty(var_index)     
212        dim_index=find(flag_used);%list of netcdf dimensions indices corresponding to used dimensions
213        Data.ListDimName=ListDimNameNetcdf(dim_index);
214        Data.DimValue=dim_value(dim_index);
215    end
216   
217    %% get the values of the input variables
218    if  ~isempty(ListVarName)
219        for ivar=1:length(var_index)
220            VarName=Data.ListVarName{ivar};
221            VarName=regexprep(VarName,'-',''); %suppress '-' if it exists in the netcdf variable name
222            eval(['Data.' VarName '=double(netcdf.getVar(nc,var_index(ivar)-1));'])%read the variable data
223        end
224    end
225   
226    %%  -------- close fle-----------
227    if testfile==1
228        netcdf.close(nc)
229    end
230   
231%% old netcdf library
232else
233    [Data,var_detect,ichoice]=nc2struct_toolbox(nc,varargin);
234end
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