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,errormsg]=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 | % .VarType= integers giving the type of variable as coded by netcdf =2 for char, =4 for single,=( for double
|
---|
18 | % var_detect: vector with same length as the cell array ListVarName, = 1 for each detected variable and 0 else.
|
---|
19 | % var_detect=[] in the absence of input cell array
|
---|
20 | % ichoice: index of the selected line in the case of multiple choice
|
---|
21 | % (cell array of varible names with multiple lines) , =[] by default
|
---|
22 | %
|
---|
23 | % INPUT:
|
---|
24 | % nc: name of a NetCDF file (char string) or NetCDF object
|
---|
25 | % additional arguments:
|
---|
26 | % -no additional arguments: all the variables of the NetCDF file are read.
|
---|
27 | % -a cell array, ListVarName, made of char strings {'VarName1', 'VarName2',...} )
|
---|
28 | % if ListVarName=[] or {}, no variable value is read (only global attributes and list of variables and dimensions)
|
---|
29 | % if ListVarName is absent, or = '*', ALL the variables of the NetCDF file are read.
|
---|
30 | % if ListVarName is a cell array with n lines, the set of variables will be sought by order of priority in the list,
|
---|
31 | % while output names will be set by the first line
|
---|
32 | % - the string 'ListGlobalAttribute' followed by a list of attribute names: reads only these attributes (fast reading)
|
---|
33 | % - the string 'TimeVarName', a string (the name of the variable considered as time), an integer or vector with integer values
|
---|
34 | % representing time indices to select for each variable, the cell of other input variable names.
|
---|
35 | % - the string 'TimeDimName', a string (the name of the dimension considered as time), an integer or vector with integer values
|
---|
36 | % representing time indices to select for each variable, the cell of other input variable names.
|
---|
37 |
|
---|
38 | %=======================================================================
|
---|
39 | % Copyright 2008-2014, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France
|
---|
40 | % http://www.legi.grenoble-inp.fr
|
---|
41 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
|
---|
42 | %
|
---|
43 | % This file is part of the toolbox UVMAT.
|
---|
44 | %
|
---|
45 | % UVMAT is free software; you can redistribute it and/or modify
|
---|
46 | % it under the terms of the GNU General Public License as published
|
---|
47 | % by the Free Software Foundation; either version 2 of the license,
|
---|
48 | % or (at your option) any later version.
|
---|
49 | %
|
---|
50 | % UVMAT is distributed in the hope that it will be useful,
|
---|
51 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
|
---|
52 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
---|
53 | % GNU General Public License (see LICENSE.txt) for more details.
|
---|
54 | %=======================================================================
|
---|
55 |
|
---|
56 | function [Data,var_detect,ichoice,errormsg]=nc2struct(nc,varargin)
|
---|
57 | errormsg='';%default error message
|
---|
58 | if isempty(varargin)
|
---|
59 | varargin{1}='*';
|
---|
60 | end
|
---|
61 | hhh=which('netcdf.open');% look for built-in matlab NetCDF library
|
---|
62 |
|
---|
63 | if ~isequal(hhh,'')
|
---|
64 | %% default output
|
---|
65 | Data=[];%default
|
---|
66 | var_detect=[];%default
|
---|
67 | ichoice=[];%default
|
---|
68 |
|
---|
69 | %% open the NetCDF file for reading
|
---|
70 | if ischar(nc)
|
---|
71 | if exist(nc,'file')
|
---|
72 | try
|
---|
73 | nc=netcdf.open(nc,'NC_NOWRITE');
|
---|
74 | testfile=1;
|
---|
75 | catch ME
|
---|
76 | errormsg=['ERROR opening ' nc ': ' ME.message];
|
---|
77 | return
|
---|
78 | end
|
---|
79 | else
|
---|
80 | errormsg=['ERROR:file ' nc ' does not exist'];
|
---|
81 | return
|
---|
82 | end
|
---|
83 | else
|
---|
84 | testfile=0;
|
---|
85 | end
|
---|
86 |
|
---|
87 | %% short reading option for global attributes only, if the first argument is 'ListGlobalAttribute'
|
---|
88 | if isequal(varargin{1},'ListGlobalAttribute')
|
---|
89 | for ilist=2:numel(varargin)
|
---|
90 | valuestr=[];%default
|
---|
91 | try
|
---|
92 | valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),varargin{ilist});
|
---|
93 | catch ME
|
---|
94 | end
|
---|
95 | eval(['Data.' varargin{ilist} '=valuestr;'])
|
---|
96 | end
|
---|
97 | netcdf.close(nc)
|
---|
98 | return
|
---|
99 | end
|
---|
100 |
|
---|
101 | %% time variable or dimension
|
---|
102 | input_index=1;
|
---|
103 | CheckTimeVar=0;
|
---|
104 | TimeVarName='';
|
---|
105 | if isequal(varargin{1},'TimeVarName')
|
---|
106 | TimeVarName=varargin{2};
|
---|
107 | CheckTimeVar=1;
|
---|
108 | TimeIndex=varargin{3};
|
---|
109 | input_index=4;% list of varibles to read is at fourth argument
|
---|
110 | elseif isequal(varargin{1},'TimeDimName')
|
---|
111 | TimeDimName=varargin{2};
|
---|
112 | TimeIndex=varargin{3};
|
---|
113 | input_index=4;
|
---|
114 | end
|
---|
115 |
|
---|
116 | %% full reading: get the nbre of dimensions, variables, global attributes
|
---|
117 | ListVarName=varargin{input_index};
|
---|
118 | [ndims,nvars,ngatts]=netcdf.inq(nc);%nbre of dimensions, variables, global attributes, in the NetCDF file
|
---|
119 |
|
---|
120 | %% -------- read all global attributes (constants)-----------
|
---|
121 | Data.ListGlobalAttribute={};%default
|
---|
122 | att_key=cell(1,ngatts);%default
|
---|
123 | for iatt=1:ngatts
|
---|
124 | keystr= netcdf.inqAttName(nc,netcdf.getConstant('NC_GLOBAL'),iatt-1);
|
---|
125 | valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),keystr);
|
---|
126 | keystr=regexprep(keystr,{'\','/','\.','-',' '},{'','','','',''});%remove '\','.' or '-' if exists
|
---|
127 | if strcmp(keystr(1),'_')
|
---|
128 | keystr(1)=[];
|
---|
129 | end
|
---|
130 | try
|
---|
131 | if ischar(valuestr) %& length(valuestr)<200 & double(valuestr)<=122 & double(valuestr)>=48 %usual characters
|
---|
132 | eval(['Data.' keystr '=''' valuestr ''';'])
|
---|
133 | elseif isnumeric(valuestr)
|
---|
134 | eval(['Data.' keystr '=valuestr;'])
|
---|
135 | else
|
---|
136 | eval(['Data.' keystr '='';'])
|
---|
137 | end
|
---|
138 | att_key{iatt}=keystr;
|
---|
139 | catch ME
|
---|
140 | att_key{iatt}=['attr_' num2str(iatt)];
|
---|
141 | Data.(att_key{iatt})=[];
|
---|
142 | end
|
---|
143 | end
|
---|
144 | Data.ListGlobalAttribute=att_key;
|
---|
145 |
|
---|
146 | %% -------- read dimension names-----------
|
---|
147 | ListDimNameNetcdf=cell(1,ndims);
|
---|
148 | dim_value=zeros(1,ndims);
|
---|
149 | for idim=1:ndims %loop on the dimensions of the NetCDF file
|
---|
150 | [ListDimNameNetcdf{idim},dim_value(idim)] = netcdf.inqDim(nc,idim-1);%get name and value of each dimension
|
---|
151 | end
|
---|
152 | if ~isempty(ListDimNameNetcdf)
|
---|
153 | flag_used=zeros(1,ndims);%initialize the flag indicating the selected dimensions in the list (0=unused)
|
---|
154 | end
|
---|
155 | if isequal(varargin{1},'TimeDimName')% time dimension introduced
|
---|
156 | TimeDimIndex=find(strcmp(TimeDimName,ListDimNameNetcdf));
|
---|
157 | if isempty(TimeDimIndex)
|
---|
158 | errormsg=['requested time dimension ' varargin{2} ' not found'];
|
---|
159 | return
|
---|
160 | end
|
---|
161 | if dim_value(TimeDimIndex)<varargin{3}
|
---|
162 | errormsg=['requested time index ' num2str(varargin{3}) ' exceeds matrix dimension'];
|
---|
163 | return
|
---|
164 | end
|
---|
165 | end
|
---|
166 |
|
---|
167 | %% -------- read names of variables -----------
|
---|
168 | ListVarNameNetcdf=cell(1,nvars); %default
|
---|
169 | dimids=cell(1,nvars);
|
---|
170 | nbatt=zeros(1,nvars);
|
---|
171 | for ncvar=1:nvars %loop on the variables of the NetCDF file
|
---|
172 | %get name, type, dimensions and attribute numbers of each variable
|
---|
173 | [ListVarNameNetcdf{ncvar},xtype(ncvar),dimids{ncvar},nbatt(ncvar)] = netcdf.inqVar(nc,ncvar-1);
|
---|
174 | end
|
---|
175 | % testmulti=0;
|
---|
176 | if isequal(ListVarName,'*')||isempty(ListVarName)
|
---|
177 | var_index=1:nvars; %all the variables are selected in the NetCDF file
|
---|
178 | Data.ListVarName=ListVarNameNetcdf;
|
---|
179 | else %select input variables, if requested by the input ListVarName
|
---|
180 | check_keep=ones(1,size(ListVarName,2));
|
---|
181 | for ivar=1:size(ListVarName,2) % check redondancy of variable names
|
---|
182 | if ~isempty(find(strcmp(ListVarName{1,ivar},ListVarName(1:ivar-1)), 1))
|
---|
183 | check_keep(ivar)=0;% the variable #ivar is already in the list
|
---|
184 | end
|
---|
185 | end
|
---|
186 | ListVarName=ListVarName(:,logical(check_keep));
|
---|
187 | if size(ListVarName,1)>1 %multiple choice of variable ranked by order of priority
|
---|
188 | for iline=1:size(ListVarName,1)
|
---|
189 | search_index=find(strcmp(ListVarName{iline,1},ListVarNameNetcdf),1);%look for the first variable name in the list of NetCDF variables
|
---|
190 | if ~isempty(search_index)
|
---|
191 | break % go to the next line
|
---|
192 | end
|
---|
193 | end
|
---|
194 | ichoice=iline-1;%selected line number in the list of input names of variables
|
---|
195 | else
|
---|
196 | iline=1;
|
---|
197 | end
|
---|
198 | %ListVarName=ListVarName(iline,:);% select the appropriate option for input variable (lin ein the input name matrix)
|
---|
199 | if CheckTimeVar
|
---|
200 | TimeVarIndex=find(strcmp(TimeVarName,ListVarNameNetcdf),1); %look for the index of the time variable in the netcdf list
|
---|
201 | if isempty(TimeVarIndex)
|
---|
202 | errormsg='requested variable for time is missing';
|
---|
203 | return
|
---|
204 | end
|
---|
205 | TimeDimIndex=dimids{TimeVarIndex}(1)+1;
|
---|
206 | ListVarName=[ListVarName {TimeVarName}];
|
---|
207 | end
|
---|
208 | var_index=zeros(1,size(ListVarName,2));%default list of variable indices
|
---|
209 | for ivar=1:size(ListVarName,2)
|
---|
210 | search_index=find(strcmp(ListVarName{iline,ivar},ListVarNameNetcdf),1);%look for the variable name in the list of NetCDF file
|
---|
211 | if ~isempty(search_index)
|
---|
212 | var_index(ivar)=search_index;%index of the netcdf list corresponding to the input list index ivar
|
---|
213 | end
|
---|
214 | end
|
---|
215 | var_detect=(var_index~=0);%=1 for detected variables
|
---|
216 | list_index=find(var_index);% indices in the input list corresponding to a detected variable
|
---|
217 | var_index=var_index(list_index);% NetCDF variable indices corresponding to the output list of read variable
|
---|
218 | Data.ListVarName=ListVarName(1,list_index);%the first line of ListVarName sets the output names of the variables
|
---|
219 | end
|
---|
220 |
|
---|
221 | %% get the dimensions and attributes associated to variables
|
---|
222 | var_dim=cell(size(var_index));% initiate list of dimensions for variables
|
---|
223 | for ivar=1:length(var_index)
|
---|
224 | var_dim{ivar}=dimids{var_index(ivar)}+1; %netcdf dimension indices used by the variable #ivar
|
---|
225 | Data.VarDimName{ivar}=ListDimNameNetcdf(var_dim{ivar});
|
---|
226 | flag_used(var_dim{ivar})=ones(size(var_dim{ivar}));%flag_used =1 for the indices of used dimensions
|
---|
227 | for iatt=1:nbatt(var_index(ivar))
|
---|
228 | attname = netcdf.inqAttName(nc,var_index(ivar)-1,iatt-1);
|
---|
229 | valuestr= netcdf.getAtt(nc,var_index(ivar)-1,attname);
|
---|
230 | attname=regexprep(attname,{'\','/','\.','-',' '},{'','','','',''});%remove '\','.' or '-' if exists
|
---|
231 | if strcmp(attname(1),'_')
|
---|
232 | attname(1)=[];
|
---|
233 | end
|
---|
234 | try
|
---|
235 | if isempty(valuestr)
|
---|
236 | Data.VarAttribute{ivar}.(attname)=valuestr;
|
---|
237 | end
|
---|
238 | catch ME
|
---|
239 | display(attname)
|
---|
240 | display(valuestr)
|
---|
241 | display(ME.message)
|
---|
242 | Data.VarAttribute{ivar}.(['atrr_' num2str(iatt)])='not read';
|
---|
243 | end
|
---|
244 | end
|
---|
245 | end
|
---|
246 |
|
---|
247 | %% select the dimensions used for the set of input variables
|
---|
248 | if ~isempty(var_index)
|
---|
249 | dim_index=find(flag_used);%list of netcdf dimensions indices corresponding to used dimensions
|
---|
250 | Data.ListDimName=ListDimNameNetcdf(dim_index);
|
---|
251 | Data.DimValue=dim_value(dim_index);
|
---|
252 | if input_index==4% if a dimension is selected as time
|
---|
253 | Data.DimValue(TimeDimIndex)=numel(TimeIndex);
|
---|
254 | end
|
---|
255 | end
|
---|
256 |
|
---|
257 | %% get the values of the input variables
|
---|
258 | if ~isempty(ListVarName)
|
---|
259 | for ivar=1:length(var_index)
|
---|
260 | VarName=Data.ListVarName{ivar};
|
---|
261 | VarName=regexprep(VarName,'-','_'); %suppress '-' if it exists in the NetCDF variable name (leads to errors in matlab)
|
---|
262 | % CheckSub=0;
|
---|
263 | if input_index==4% if a dimension is selected as time
|
---|
264 | ind_vec=zeros(1,numel(var_dim{ivar}));% vector with zeros corresponding to al the dimensions of the variable VarName
|
---|
265 | ind_size=dim_value(var_dim{ivar});% vector giving the size (for each dimension) of the variable VarName
|
---|
266 | index_time=find(var_dim{ivar}==TimeDimIndex);
|
---|
267 | if ~isempty(index_time)
|
---|
268 | if ind_size(index_time)<max(TimeIndex)
|
---|
269 | errormsg=['requested index ' num2str(TimeIndex) ' exceeds matrix dimension'];
|
---|
270 | return
|
---|
271 | end
|
---|
272 | ind_vec(index_time)=TimeIndex-1;% selected index(or indices) to read
|
---|
273 | ind_size(index_time)=numel(TimeIndex);%length of the selected set of time indices
|
---|
274 | if numel(TimeIndex)==1 && ~strcmp(VarName,TimeVarName)
|
---|
275 | Data.VarDimName{ivar}(index_time)=[];% for a single selected time remove the time in the list of dimensions (except for tTime itself)
|
---|
276 | end
|
---|
277 | end
|
---|
278 | Data.(VarName)=double(netcdf.getVar(nc,var_index(ivar)-1,ind_vec,ind_size)); %read the variable data
|
---|
279 | Data.(VarName)=squeeze(Data.(VarName));%remove singeton dimension
|
---|
280 | else
|
---|
281 | Data.(VarName)=netcdf.getVar(nc,var_index(ivar)-1); %read the whole variable data
|
---|
282 | end
|
---|
283 | if xtype(var_index(ivar))==5
|
---|
284 | Data.(VarName)=double(Data.(VarName)); %transform to double for single pecision
|
---|
285 | end
|
---|
286 | end
|
---|
287 | end
|
---|
288 | Data.VarType=xtype(var_index);
|
---|
289 |
|
---|
290 | %% -------- close fle-----------
|
---|
291 | if testfile==1
|
---|
292 | netcdf.close(nc)
|
---|
293 | end
|
---|
294 |
|
---|
295 | %% old NetCDF library
|
---|
296 | else
|
---|
297 | [Data,var_detect,ichoice]=nc2struct_toolbox(nc,varargin);
|
---|
298 | end
|
---|