source: trunk/src/nc2struct.m @ 517

Last change on this file since 517 was 517, checked in by sommeria, 9 years ago

various bugs corrected. get_field now used in a passive way from uvmat: variable names are transferred from get_field to uvmat.

File size: 11.0 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
[404]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;
[227]67            catch ME
68              Data.Txt=['ERROR opening ' nc ': ' ME.message];
[150]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   
[227]79    %% short reading option for global attributes only, if the first argument is 'ListGlobalAttribute'
[56]80    if isequal(varargin{1},'ListGlobalAttribute')
81        for ilist=2:numel(varargin)
[227]82            valuestr=[];%default
[45]83            try
[56]84            valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),varargin{ilist});
[227]85            catch ME
[45]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
[227]99%     iatt_g=0;
[8]100    Data.ListGlobalAttribute={};%default
101    for iatt=1:ngatts
102        keystr= netcdf.inqAttName(nc,netcdf.getConstant('NC_GLOBAL'),iatt-1);
[227]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
[236]109            if ischar(valuestr) %& length(valuestr)<200 & double(valuestr)<=122 & double(valuestr)>=48 %usual characters
[227]110                eval(['Data.' keystr '=''' valuestr ''';'])
[8]111            elseif isnumeric(valuestr)
112                eval(['Data.' keystr '=valuestr;'])
[227]113            else
114                eval(['Data.' keystr '='';'])
[8]115            end
[227]116            att_key{iatt}=keystr;
117        catch ME
118            att_key{iatt}=['attr_' num2str(iatt)];
119            eval(['Data.' att_key{iatt} '=[];'])
[8]120        end
121    end
122    Data.ListGlobalAttribute=att_key;
123
[140]124    %%  -------- read dimension names-----------
125    ListDimNameNetcdf={};
[8]126    dim_value=[];
[140]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
[8]129    end
[140]130    if ~isempty(ListDimNameNetcdf)
131        flag_used=zeros(1,ndims);%initialize the flag indicating the selected dimensions in the list (0=unused)
[8]132    end
133 
[140]134    %%  -------- read names of variables -----------
135    ListVarNameNetcdf={}; %default
[8]136    dimids={};
137    nbatt=[];
[140]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);
[8]141    end 
142    testmulti=0;
[140]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
[517]147        ind_remove=[];
148        for ivar=1:numel(ListVarName) % check redondancy
149            if ~isempty(find(strcmp(ListVarName{ivar},ListVarName(1:ivar-1))))
150                ind_remove=[ind_remove ivar];
151            end
152        end
153        if ~isempty(ind_remove)
154            ListVarName(ind_remove)=[];
155        end           
[8]156        sizvar=size(ListVarName);
[140]157        testmulti=(sizvar(1)>1);%test for multiple choice of variable ranked by order of priority
[8]158        var_index=zeros(1,sizvar(2));%default
[140]159        if testmulti %multiple choice of variable ranked by order of priority
[8]160            for iline=1:sizvar(1)
[140]161                search_index=find(strcmp(ListVarName{iline,1},ListVarNameNetcdf),1);%look for the first variable name in the list of netcdf variables
162                if ~isempty(search_index)
163                    break % go to the next line
[8]164                end
165            end
[140]166            ichoice=iline-1;%selected line number in the list of input names of variables
167        else
168            iline=1;
[8]169        end
[140]170        for ivar=1:sizvar(2)
171            search_index=find(strcmp(ListVarName{iline,ivar},ListVarNameNetcdf),1);%look for the variable name in the list of netcdf file
172            if ~isempty(search_index)
173                var_index(ivar)=search_index;%index of the netcdf list corresponding to the input list index ivar
[8]174            end
175        end
[140]176        var_detect=(var_index~=0);%=1 for detected variables         
177        list_index=find(var_index);% indices in the input list corresponding to a detected variable
178        var_index=var_index(list_index);% netcdf variable indices corresponding to the output list of read variable
179        Data.ListVarName=ListVarName(1,list_index);%the first line of ListVarName sets the output names of the variables
[8]180    end
[140]181     
182  %% get the dimensions and attributes associated to  variables
183    for ivar=1:length(var_index)
184        var_dim{ivar}=dimids{var_index(ivar)}+1; %netcdf dimension indices used by the variable #ivar
185        Data.VarDimName{ivar}=ListDimNameNetcdf(var_dim{ivar});
186        flag_used(var_dim{ivar})=ones(size(var_dim{ivar}));%flag_used =1 for the indices of used dimensions
[8]187        for iatt=1:nbatt(var_index(ivar))
188            attname = netcdf.inqAttName(nc,var_index(ivar)-1,iatt-1);
189            valuestr= netcdf.getAtt(nc,var_index(ivar)-1,attname);
[227]190            attname=regexprep(attname,{'\','/','\.','-',' '},{'','','','',''});%remove  '\','.' or '-' if exists
191            if strcmp(attname(1),'_')
192                attname(1)=[];
193            end
194            try
[8]195            if ischar(valuestr)
[227]196               % valuestr=regexprep(valuestr,{'\\','\/','\.','\-',' '},{'_','_','_','_','_'});%remove  '\','.' or '-' if exists
[8]197                eval(['Data.VarAttribute{ivar}.' attname '=''' valuestr ''';'])
198            elseif isempty(valuestr)
199                eval(['Data.VarAttribute{ivar}.' attname '=[];'])
200            elseif isnumeric(valuestr)
201                eval(['Data.VarAttribute{ivar}.' attname '=valuestr;'])
202            end
[227]203            catch ME
204                display(attname)
205                display(valuestr)
206                display(ME.message)         
207                eval(['Data.VarAttribute{ivar}.atrr_' num2str(iatt) '=''not read'';'])
208            end
[8]209        end
210    end
211
[140]212    %% select the dimensions used for the set of input variables
213    if ~isempty(var_index)     
214        dim_index=find(flag_used);%list of netcdf dimensions indices corresponding to used dimensions
[421]215        Data.ListDimName=ListDimNameNetcdf(dim_index);
216        Data.DimValue=dim_value(dim_index);
[8]217    end
[140]218   
219    %% get the values of the input variables
[8]220    if  ~isempty(ListVarName)
[140]221        for ivar=1:length(var_index)
[8]222            VarName=Data.ListVarName{ivar};
[140]223            VarName=regexprep(VarName,'-',''); %suppress '-' if it exists in the netcdf variable name
[100]224            eval(['Data.' VarName '=double(netcdf.getVar(nc,var_index(ivar)-1));'])%read the variable data
[8]225        end
226    end
[140]227   
228    %%  -------- close fle-----------
[8]229    if testfile==1
230        netcdf.close(nc)
231    end
[140]232   
233%% old netcdf library
[8]234else
235    [Data,var_detect,ichoice]=nc2struct_toolbox(nc,varargin);
236end
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