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 |
|
---|
48 | function [Data,var_detect,ichoice]=nc2struct(nc,varargin)
|
---|
49 |
|
---|
50 | if isempty(varargin)
|
---|
51 | varargin{1}='*';
|
---|
52 | end
|
---|
53 | hhh=which('netcdf.open');% look for built-in matlab netcdf library
|
---|
54 |
|
---|
55 | if ~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 | att_key={};%default
|
---|
99 | % iatt_g=0;
|
---|
100 | Data.ListGlobalAttribute={};%default
|
---|
101 | for iatt=1:ngatts
|
---|
102 | keystr= netcdf.inqAttName(nc,netcdf.getConstant('NC_GLOBAL'),iatt-1);
|
---|
103 | valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),keystr);
|
---|
104 | keystr=regexprep(keystr,{'\','/','\.','-',' '},{'','','','',''});%remove '\','.' or '-' if exists
|
---|
105 | if strcmp(keystr(1),'_')
|
---|
106 | keystr(1)=[];
|
---|
107 | end
|
---|
108 | try
|
---|
109 | if ischar(valuestr) %& length(valuestr)<200 & double(valuestr)<=122 & double(valuestr)>=48 %usual characters
|
---|
110 | eval(['Data.' keystr '=''' valuestr ''';'])
|
---|
111 | elseif isnumeric(valuestr)
|
---|
112 | eval(['Data.' keystr '=valuestr;'])
|
---|
113 | else
|
---|
114 | eval(['Data.' keystr '='';'])
|
---|
115 | end
|
---|
116 | att_key{iatt}=keystr;
|
---|
117 | catch ME
|
---|
118 | att_key{iatt}=['attr_' num2str(iatt)];
|
---|
119 | eval(['Data.' att_key{iatt} '=[];'])
|
---|
120 | end
|
---|
121 | end
|
---|
122 | Data.ListGlobalAttribute=att_key;
|
---|
123 |
|
---|
124 | %% -------- read dimension names-----------
|
---|
125 | ListDimNameNetcdf={};
|
---|
126 | dim_value=[];
|
---|
127 | for idim=1:ndims %loop on the dimensions of the netcdf file
|
---|
128 | [ListDimNameNetcdf{idim},dim_value(idim)] = netcdf.inqDim(nc,idim-1);%get name and value of each dimension
|
---|
129 | end
|
---|
130 | if ~isempty(ListDimNameNetcdf)
|
---|
131 | flag_used=zeros(1,ndims);%initialize the flag indicating the selected dimensions in the list (0=unused)
|
---|
132 | end
|
---|
133 |
|
---|
134 | %% -------- read names of variables -----------
|
---|
135 | ListVarNameNetcdf={}; %default
|
---|
136 | dimids={};
|
---|
137 | nbatt=[];
|
---|
138 | for ncvar=1:nvars %loop on the variables of the netcdf file
|
---|
139 | %get name, type, dimensions and attribute numbers of each variable
|
---|
140 | [ListVarNameNetcdf{ncvar},xtype,dimids{ncvar},nbatt(ncvar)] = netcdf.inqVar(nc,ncvar-1);
|
---|
141 | end
|
---|
142 | testmulti=0;
|
---|
143 | if isequal(ListVarName,'*')||isempty(ListVarName)
|
---|
144 | var_index=1:nvars; %all the variables are selected in the netcdf file
|
---|
145 | Data.ListVarName=ListVarNameNetcdf;
|
---|
146 | else %select input variables, if requested by the input ListVarName
|
---|
147 | sizvar=size(ListVarName);
|
---|
148 | testmulti=(sizvar(1)>1);%test for multiple choice of variable ranked by order of priority
|
---|
149 | var_index=zeros(1,sizvar(2));%default
|
---|
150 | if testmulti %multiple choice of variable ranked by order of priority
|
---|
151 | for iline=1:sizvar(1)
|
---|
152 | search_index=find(strcmp(ListVarName{iline,1},ListVarNameNetcdf),1);%look for the first variable name in the list of netcdf variables
|
---|
153 | if ~isempty(search_index)
|
---|
154 | break % go to the next line
|
---|
155 | end
|
---|
156 | end
|
---|
157 | ichoice=iline-1;%selected line number in the list of input names of variables
|
---|
158 | else
|
---|
159 | iline=1;
|
---|
160 | end
|
---|
161 | for ivar=1:sizvar(2)
|
---|
162 | search_index=find(strcmp(ListVarName{iline,ivar},ListVarNameNetcdf),1);%look for the variable name in the list of netcdf file
|
---|
163 | if ~isempty(search_index)
|
---|
164 | var_index(ivar)=search_index;%index of the netcdf list corresponding to the input list index ivar
|
---|
165 | end
|
---|
166 | end
|
---|
167 | var_detect=(var_index~=0);%=1 for detected variables
|
---|
168 | list_index=find(var_index);% indices in the input list corresponding to a detected variable
|
---|
169 | var_index=var_index(list_index);% netcdf variable indices corresponding to the output list of read variable
|
---|
170 | Data.ListVarName=ListVarName(1,list_index);%the first line of ListVarName sets the output names of the variables
|
---|
171 | end
|
---|
172 |
|
---|
173 | %% get the dimensions and attributes associated to variables
|
---|
174 | for ivar=1:length(var_index)
|
---|
175 | var_dim{ivar}=dimids{var_index(ivar)}+1; %netcdf dimension indices used by the variable #ivar
|
---|
176 | Data.VarDimName{ivar}=ListDimNameNetcdf(var_dim{ivar});
|
---|
177 | flag_used(var_dim{ivar})=ones(size(var_dim{ivar}));%flag_used =1 for the indices of used dimensions
|
---|
178 | for iatt=1:nbatt(var_index(ivar))
|
---|
179 | attname = netcdf.inqAttName(nc,var_index(ivar)-1,iatt-1);
|
---|
180 | valuestr= netcdf.getAtt(nc,var_index(ivar)-1,attname);
|
---|
181 | attname=regexprep(attname,{'\','/','\.','-',' '},{'','','','',''});%remove '\','.' or '-' if exists
|
---|
182 | if strcmp(attname(1),'_')
|
---|
183 | attname(1)=[];
|
---|
184 | end
|
---|
185 | try
|
---|
186 | if ischar(valuestr)
|
---|
187 | % valuestr=regexprep(valuestr,{'\\','\/','\.','\-',' '},{'_','_','_','_','_'});%remove '\','.' or '-' if exists
|
---|
188 | eval(['Data.VarAttribute{ivar}.' attname '=''' valuestr ''';'])
|
---|
189 | elseif isempty(valuestr)
|
---|
190 | eval(['Data.VarAttribute{ivar}.' attname '=[];'])
|
---|
191 | elseif isnumeric(valuestr)
|
---|
192 | eval(['Data.VarAttribute{ivar}.' attname '=valuestr;'])
|
---|
193 | end
|
---|
194 | catch ME
|
---|
195 | display(attname)
|
---|
196 | display(valuestr)
|
---|
197 | display(ME.message)
|
---|
198 | eval(['Data.VarAttribute{ivar}.atrr_' num2str(iatt) '=''not read'';'])
|
---|
199 | end
|
---|
200 | end
|
---|
201 | end
|
---|
202 |
|
---|
203 | %% select the dimensions used for the set of input variables
|
---|
204 | if ~isempty(var_index)
|
---|
205 | dim_index=find(flag_used);%list of netcdf dimensions indices corresponding to used dimensions
|
---|
206 | Data.ListDimName=ListDimNameNetcdf(dim_index);
|
---|
207 | Data.DimValue=dim_value(dim_index);
|
---|
208 | end
|
---|
209 |
|
---|
210 | %% get the values of the input variables
|
---|
211 | if ~isempty(ListVarName)
|
---|
212 | for ivar=1:length(var_index)
|
---|
213 | VarName=Data.ListVarName{ivar};
|
---|
214 | VarName=regexprep(VarName,'-',''); %suppress '-' if it exists in the netcdf variable name
|
---|
215 | eval(['Data.' VarName '=double(netcdf.getVar(nc,var_index(ivar)-1));'])%read the variable data
|
---|
216 | end
|
---|
217 | end
|
---|
218 |
|
---|
219 | %% -------- close fle-----------
|
---|
220 | if testfile==1
|
---|
221 | netcdf.close(nc)
|
---|
222 | end
|
---|
223 |
|
---|
224 | %% old netcdf library
|
---|
225 | else
|
---|
226 | [Data,var_detect,ichoice]=nc2struct_toolbox(nc,varargin);
|
---|
227 | end |
---|