source: trunk/src/nc2struct.m @ 188

Last change on this file since 188 was 188, checked in by sommeria, 10 years ago

various bug repairs and cleaning

File size: 10.4 KB
RevLine 
[8]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%----------------------------------------------------------------------
[56]5% function [Data,var_detect,ichoice]=nc2struct(nc,varargin)
[8]6%
7% OUTPUT:
8%  Data: structure containing all the information of the netcdf file (or netcdf object)
[140]9%           with (optional)fields:
10%                    .ListGlobalAttribute: cell listing the names of the global attributes
[55]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)
[140]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
[8]21%INPUT:
[140]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',...} )
[56]26%         if ListVarName=[] or {}, no variables is read (only global attributes)
[140]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
[56]30%        - the string 'ListGlobalAttribute' followed by a list of attribute  names: reads only these attributes (fast reading)
[8]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)
[56]49
[55]50if isempty(varargin)
[56]51    varargin{1}='*';
[8]52end
53hhh=which('netcdf.open');% look for built-in matlab netcdf library
54
55if ~isequal(hhh,'')
[140]56    %% default output
57    Data=[];%default
58    var_detect=[];%default
[8]59    ichoice=[];%default
[140]60   
61    %% open the netcdf file for reading
[8]62    if ischar(nc)
63        if exist(nc,'file')
[150]64            try
[8]65            nc=netcdf.open(nc,'NC_NOWRITE');
66            testfile=1;
[150]67            catch errormsg
68              Data.Txt=['ERROR opening ' nc ': ' errormsg.identifier];
69              return
70            end
[8]71        else
72           Data.Txt=['ERROR:file ' nc ' does not exist'];
73           return
74        end
75    else
76        testfile=0;
77    end
[140]78   
79    %% short reading opion for global attributes only, if the first argument is 'ListGlobalAttribute'
[56]80    if isequal(varargin{1},'ListGlobalAttribute')
81        for ilist=2:numel(varargin)
[45]82            try
[56]83            valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),varargin{ilist});
[45]84            catch
85                valuestr=[];
86            end
[56]87            eval(['Data.' varargin{ilist} '=valuestr;'])
[8]88        end
89        netcdf.close(nc)
90       return
91    end
92
[140]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
[8]96   
[140]97    %%  -------- read all global attributes (constants)-----------
[8]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);
[140]103        indstr1=regexp(keystr,'\\','once');%detect '\\'
104        indstr2=regexp(keystr,'\.','once');%detect '\.'
[188]105        %indtitle=regexp(keystr,'title','once');%detect 'title'(bad characters)
106        if isempty(indstr1) && isempty(indstr2)%&&isempty(indtitle)
[8]107           valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),keystr);
[188]108           if ischar(valuestr) & length(valuestr)<200 & double(valuestr)<=122 & double(valuestr)>=48 %usual characters
[8]109                iatt_g=iatt_g+1;
[127]110                indstr1=regexp(keystr,'\\','once');%detect '\\'
111                indstr2=regexp(keystr,'\.','once');%detect '\.'
[8]112                if isempty(indstr1) && isempty(indstr2)
113                    eval(['Data.' keystr '=''' valuestr ''';'])
114                    att_key{iatt_g}=keystr;
115                end
116            elseif isempty(valuestr)
117                iatt_g=iatt_g+1;
118                eval(['Data.' keystr '=[];'])
119                att_key{iatt_g}=keystr;
120            elseif isnumeric(valuestr)
121                iatt_g=iatt_g+1;
122                eval(['Data.' keystr '=valuestr;'])
123                att_key{iatt_g}=keystr;
124            end
125        end
126    end
127    Data.ListGlobalAttribute=att_key;
128
[140]129    %%  -------- read dimension names-----------
130    ListDimNameNetcdf={};
[8]131    dim_value=[];
[140]132    for idim=1:ndims %loop on the dimensions of the netcdf file
133        [ListDimNameNetcdf{idim},dim_value(idim)] = netcdf.inqDim(nc,idim-1);%get name and value of each dimension
[8]134    end
[140]135    if ~isempty(ListDimNameNetcdf)
136        flag_used=zeros(1,ndims);%initialize the flag indicating the selected dimensions in the list (0=unused)
[8]137    end
138 
[140]139    %%  -------- read names of variables -----------
140    ListVarNameNetcdf={}; %default
[8]141    dimids={};
142    nbatt=[];
[140]143    for ncvar=1:nvars %loop on the variables of the netcdf file
144        %get name, type, dimensions and attribute numbers of each variable
145        [ListVarNameNetcdf{ncvar},xtype,dimids{ncvar},nbatt(ncvar)] = netcdf.inqVar(nc,ncvar-1);
[8]146    end 
147    testmulti=0;
[140]148    if isequal(ListVarName,'*')||isempty(ListVarName)
149        var_index=1:nvars; %all the variables are selected in the netcdf file
150        Data.ListVarName=ListVarNameNetcdf;
151    else   %select input variables, if requested by the input ListVarName
[8]152        sizvar=size(ListVarName);
[140]153        testmulti=(sizvar(1)>1);%test for multiple choice of variable ranked by order of priority
[8]154        var_index=zeros(1,sizvar(2));%default
[140]155        if testmulti %multiple choice of variable ranked by order of priority
[8]156            for iline=1:sizvar(1)
[140]157                search_index=find(strcmp(ListVarName{iline,1},ListVarNameNetcdf),1);%look for the first variable name in the list of netcdf variables
158                if ~isempty(search_index)
159                    break % go to the next line
[8]160                end
161            end
[140]162            ichoice=iline-1;%selected line number in the list of input names of variables
163        else
164            iline=1;
[8]165        end
[140]166        for ivar=1:sizvar(2)
167            search_index=find(strcmp(ListVarName{iline,ivar},ListVarNameNetcdf),1);%look for the variable name in the list of netcdf file
168            if ~isempty(search_index)
169                var_index(ivar)=search_index;%index of the netcdf list corresponding to the input list index ivar
[8]170            end
171        end
[140]172        var_detect=(var_index~=0);%=1 for detected variables         
173        list_index=find(var_index);% indices in the input list corresponding to a detected variable
174        var_index=var_index(list_index);% netcdf variable indices corresponding to the output list of read variable
175        Data.ListVarName=ListVarName(1,list_index);%the first line of ListVarName sets the output names of the variables
[8]176    end
[140]177     
178  %% get the dimensions and attributes associated to  variables
179    for ivar=1:length(var_index)
180        var_dim{ivar}=dimids{var_index(ivar)}+1; %netcdf dimension indices used by the variable #ivar
181        Data.VarDimName{ivar}=ListDimNameNetcdf(var_dim{ivar});
182        flag_used(var_dim{ivar})=ones(size(var_dim{ivar}));%flag_used =1 for the indices of used dimensions
[8]183        for iatt=1:nbatt(var_index(ivar))
184            attname = netcdf.inqAttName(nc,var_index(ivar)-1,iatt-1);
185            valuestr= netcdf.getAtt(nc,var_index(ivar)-1,attname);
186            if ischar(valuestr)
187                eval(['Data.VarAttribute{ivar}.' attname '=''' valuestr ''';'])
188            elseif isempty(valuestr)
189                eval(['Data.VarAttribute{ivar}.' attname '=[];'])
190            elseif isnumeric(valuestr)
191                eval(['Data.VarAttribute{ivar}.' attname '=valuestr;'])
192            end
193        end
194    end
195
[140]196    %% select the dimensions used for the set of input variables
197    if ~isempty(var_index)     
198        dim_index=find(flag_used);%list of netcdf dimensions indices corresponding to used dimensions
199        Data.ListDimName=ListDimNameNetcdf(dim_index);
200        Data.DimValue=dim_value(dim_index);
[8]201    end
[140]202   
203    %% get the values of the input variables
[8]204    if  ~isempty(ListVarName)
[140]205        for ivar=1:length(var_index)
[8]206            VarName=Data.ListVarName{ivar};
[140]207            VarName=regexprep(VarName,'-',''); %suppress '-' if it exists in the netcdf variable name
[100]208            eval(['Data.' VarName '=double(netcdf.getVar(nc,var_index(ivar)-1));'])%read the variable data
[8]209        end
210    end
[140]211   
212    %%  -------- close fle-----------
[8]213    if testfile==1
214        netcdf.close(nc)
215    end
[140]216   
217%% old netcdf library
[8]218else
219    [Data,var_detect,ichoice]=nc2struct_toolbox(nc,varargin);
220end
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