source: trunk/src/struct2nc.m @ 932

Last change on this file since 932 was 930, checked in by sommeria, 5 years ago

extract functions updated

File size: 11.8 KB
Line 
1% 'struct2nc': create a netcdf file from a Matlab structure
2%---------------------------------------------------------------------
3% errormsg=struct2nc(flname,Data)
4%
5% OUTPUT:
6% errormsg=error message, =[]: default, no error
7%
8% INPUT:
9% flname: name of the netcdf file to create (must end with the extension '.nc')
10%  Data: structure containing all the information of the netcdf file (or netcdf object)
11%           with fields:
12%       (optional) .ListGlobalAttribute: list (cell array of character strings) of the names of the global attributes Att_1, Att_2...
13%                  .Att_1,Att_2...: values of the global attributes
14%      (requested) .ListVarName: list of the variable names Var_1, Var_2....(cell array of character strings).
15%      (requested) .VarDimName: list of dimension names for each element of .ListVarName (cell array of string cells)
16%       (optional) .VarAttribute: cell array of structures of the form .VarAttribute{ivar}.key=value, defining an attribute key name and value for the variable #ivar
17%      (requested) .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName
18
19%=======================================================================
20% Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
21%   http://www.legi.grenoble-inp.fr
22%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
23%
24%     This file is part of the toolbox UVMAT.
25%
26%     UVMAT is free software; you can redistribute it and/or modify
27%     it under the terms of the GNU General Public License as published
28%     by the Free Software Foundation; either version 2 of the license,
29%     or (at your option) any later version.
30%
31%     UVMAT is distributed in the hope that it will be useful,
32%     but WITHOUT ANY WARRANTY; without even the implied warranty of
33%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
34%     GNU General Public License (see LICENSE.txt) for more details.
35%=======================================================================
36
37function [errormsg,nc]=struct2nc(flname,Data,action)
38nc=[];
39% if ~ischar(flname)
40%     errormsg='invalid input for the netcf file name';
41%     return
42% end
43if ~exist('Data','var')
44     errormsg='no data  input for the netcdf file';
45    return
46end
47if ~exist('action','var')
48    action='one_input'; %fill the file with data and close it
49end
50
51
52%% check the validity of the input field structure
53[errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(Data);
54if ~isempty(errormsg)
55    errormsg=['error in struct2nc:invalid input structure_' errormsg];
56    return
57end
58ListVarName=Data.ListVarName;
59
60%% create the netcdf file with name flname in format NETCDF4
61if ischar(flname)
62    FilePath=fileparts(flname);
63    if ~strcmp(FilePath,'') && ~exist(FilePath,'dir')
64        errormsg=['directory ' FilePath ' needs to be created'];
65        return
66    end
67    cmode = netcdf.getConstant('NETCDF4');
68    cmode = bitor(cmode, netcdf.getConstant('CLASSIC_MODEL'));
69    cmode = bitor(cmode, netcdf.getConstant('CLOBBER'));
70    nc = netcdf.create(flname, cmode);
71else
72    nc=flname;
73end
74
75%% write global constants
76if isfield(Data,'ListGlobalAttribute')
77    keys=Data.ListGlobalAttribute;
78    for iattr=1:length(keys)
79        if isfield(Data,keys{iattr})
80             testvar=0;
81            for ivar=1:length(ListVarName)% eliminate possible global attributes with the same name as a variable
82                if isequal(ListVarName{ivar}, keys{iattr})
83                    testvar=1;
84                    break
85                end
86            end
87            if ~testvar               
88                eval(['cte=Data.' keys{iattr} ';'])
89                if (ischar(cte) ||isnumeric(cte)) &&  ~isempty(cte)%&& ~isequal(cte,'')
90                    %write constant only if it is numeric or char string, and not empty
91                    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),keys{iattr},cte)
92                end
93            end
94        end
95    end
96end
97
98%% create the dimensions
99dimid=zeros(1,length(ListDimName));
100for idim=1:length(ListDimName)
101     dimid(idim) = netcdf.defDim(nc,ListDimName{idim},DimValue(idim));
102end
103VarAttribute={}; %default
104testattr=0;
105if isfield(Data,'VarAttribute')
106    VarAttribute=Data.VarAttribute;
107    testattr=1;
108end
109
110
111%% create the variables
112varid=nan(1,length(Data.ListVarName));
113for ivar=1:length(ListVarName)
114    if isfield(Data,ListVarName{ivar})
115        VarClass=class(Data.(ListVarName{ivar}));
116        VarType='';
117        switch VarClass
118            case {'single','double'}
119                VarType='nc_float'; % store all floating reals as single
120            case {'uint8','int16','uint16','int32','uint32','int64','uint64'}
121                VarType='nc_int';
122            case  'logical'
123                VarType='nc_byte';
124        end
125        if ~isempty(VarType)
126            varid(ivar)=netcdf.defVar(nc,ListVarName{ivar},VarType,dimid(VarDimIndex{ivar}));%define variable
127        end
128    end
129end
130
131%% write variable attributes
132if testattr
133    for ivar=1:min(numel(VarAttribute),numel(ListVarName)) 
134        if isstruct(VarAttribute{ivar}) && ~isnan(varid(ivar))
135            attr_names=fields(VarAttribute{ivar});
136            for iattr=1:length(attr_names)
137                attr_val=VarAttribute{ivar}.(attr_names{iattr});
138                if ~isempty(attr_names{iattr})&& ~isempty(attr_val)&&~iscell(attr_val)
139                    netcdf.putAtt(nc,varid(ivar),attr_names{iattr},attr_val);
140                end
141            end
142        end
143    end
144end
145netcdf.endDef(nc); %put in data mode
146
147%% fill the variables with input data
148for ivar=1:length(ListVarName)
149    if ~isnan(varid(ivar))
150        VarVal=Data.(ListVarName{ivar});
151        %varval=values of the current variable
152        VarDimName=Data.VarDimName{ivar};
153        if ischar(VarDimName)
154            VarDimName={VarDimName};
155        end
156        siz=size(VarVal);
157        testrange=(numel(VarDimName)==1 && strcmp(VarDimName{1},ListVarName{ivar}) && numel(VarVal)==2);% case of a coordinate defined on a regular mesh by the first and last values.
158        testline=isequal(length(siz),2) && isequal(siz(1),1)&& isequal(siz(2), DimValue(VarDimIndex{ivar}));%matlab vector
159        %testcolumn=isequal(length(siz),2) && isequal(siz(1), DimValue(VarDimIndex{ivar}))&& isequal(siz(2),1);%matlab column vector
160        if testline || testrange
161            if testrange
162                VarVal=linspace(VarVal(1),VarVal(2),DimValue(VarDimIndex{ivar}));% restitute the whole array of coordinate values
163            end
164            netcdf.putVar(nc,varid(ivar), double(VarVal'));
165        else
166            netcdf.putVar(nc,varid(ivar), double(VarVal));
167        end     
168    end
169end
170if strcmp(action,'one_input')
171netcdf.close(nc)
172end
173
174%'check_field_structure': check the validity of the field struture representation consistant with the netcdf format
175%------------------------------------------------------------------------
176% [errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(Data)
177%
178% OUTPUT:
179% errormsg: error message which is not empty when the input structure does not have the right form
180% ListDimName: list of dimension names (cell array of cahr strings)
181% DimValue: list of dimension values (numerical array with the same dimension as ListDimName)
182% VarDimIndex: cell array of dimension index (in the list ListDimName) for each element of Data.ListVarName
183%
184% INPUT:
185% Data:   structure containing
186%         (optional) .ListGlobalAttribute: cell listing the names of the global attributes
187%                    .Att_1,Att_2... : values of the global attributes
188%         (requested)  .ListVarName: list of variable names to select (cell array of  char strings {'VarName1', 'VarName2',...} )
189%         (requested)  .VarDimName: list of dimension names for each element of .ListVarName (cell array of string cells)                         
190%         (requested) .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName
191
192
193function [errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(Data)
194errormsg='';
195ListDimName={};
196DimValue=[]; %default
197VarDimIndex={};
198if ~isstruct(Data)
199    errormsg='input field is not a structure';
200    return
201end
202if isfield(Data,'ListVarName') && iscell(Data.ListVarName)
203    nbfield=numel(Data.ListVarName);
204else
205    errormsg='input field does not contain the cell array of variable names .ListVarName';
206    return
207end
208%check dimension names
209if (isfield(Data,'VarDimName') && iscell(Data.VarDimName))
210    if  numel(Data.VarDimName)~=nbfield
211       errormsg=' .ListVarName and .VarDimName have different lengths';
212        return
213    end
214else
215    errormsg='input field does not contain the  cell array of dimension names .VarDimName';
216    return
217end
218nbdim=0;
219ListDimName={};
220
221%% main loop on the list of variables
222VarDimIndex=cell(1,nbfield);
223for ivar=1:nbfield
224    VarName=Data.ListVarName{ivar};
225    if ~isfield(Data,VarName)
226        errormsg=['the listed variable ' VarName ' is not found'];
227        return
228    end
229    sizvar=size(Data.(VarName));% sizvar = dimension of variable
230    DimCell=Data.VarDimName{ivar};
231    if ischar(DimCell)
232        DimCell={DimCell};%case of a single dimension name, defined by a string
233    elseif ~iscell(DimCell)
234        errormsg=['wrong format for .VarDimName{' num2str(ivar) ' (must be the cell of dimension names of the variable ' VarName];
235        return       
236    end
237    nbcoord=numel(sizvar);%nbre of coordinates for variable named VarName
238    testrange=0;
239    if numel(DimCell)==0
240        errormsg=['empty declared dimension .VarDimName{' num2str(ivar) '} for ' VarName];
241        return
242    elseif numel(DimCell)==1% one dimension declared
243        if nbcoord==2
244            if sizvar(1)==1
245                sizvar(1)=sizvar(2);
246            elseif sizvar(2)==1
247            else
248                errormsg=['1 dimension declared in .VarDimName{' num2str(ivar) '} inconsistent with the nbre of dimensions =2 of the variable ' VarName];
249                return
250            end
251            if sizvar(1)==2 && isequal(VarName,DimCell{1})
252                testrange=1;% test for a dimension variable representing a range
253            end
254        else
255            errormsg=['1 dimension declared in .VarDimName{' num2str(ivar) '} inconsistent with the nbre of dimensions =' num2str(nbcoord) ' of the variable ' VarName];
256            return
257        end
258    else
259        if numel(DimCell)>nbcoord
260            sizvar(nbcoord+1:numel(DimCell))=1;% case of singleton dimensions (not seen by the function size)
261        elseif nbcoord > numel(DimCell)
262            errormsg=['nbre of declared dimensions in .VarDimName{' num2str(ivar) '} smaller than the nbre of dimensions =' num2str(nbcoord) ' of the variable ' VarName];
263            return
264        end
265    end
266    DimIndex=[];
267    for idim=1:numel(DimCell) %loop on the coordinates of variable #ivar
268        DimName=DimCell{idim};
269        iprev=find(strcmp(DimName,ListDimName),1);%look for dimension name DimName in the current list
270        if isempty(iprev)% append the dimension name to the current list
271            nbdim=nbdim+1;
272            RangeTest(nbdim)=0; %default
273            if sizvar(idim)==2 && strcmp(DimName,VarName)%case of a coordinate defined by the two end values (regular spacing)
274                RangeTest(nbdim)=1; %to be updated for a later variable 
275            end
276            DimValue(nbdim)=sizvar(idim);
277            ListDimName{nbdim}=DimName;
278            DimIndex=[DimIndex nbdim];
279        else % DimName is detected in the current list of dimension names
280            if ~isequal(DimValue(iprev),sizvar(idim))
281                if isequal(DimValue(iprev),2)&& RangeTest(iprev)  % the dimension has been already detected as a range [min max]
282                    DimValue(iprev)=sizvar(idim); %update with actual value
283                elseif ~testrange               
284                    errormsg=['dimension declaration inconsistent with the size =[' num2str(sizvar) '] for ' VarName];
285                    return
286                end
287            end
288            DimIndex=[DimIndex iprev];
289        end
290    end
291    VarDimIndex{ivar}=DimIndex;
292end
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