source: trunk/src/struct2nc.m @ 1109

Last change on this file since 1109 was 1107, checked in by g7moreau, 3 years ago

Update Copyright to 2022

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[106]1% 'struct2nc': create a netcdf file from a Matlab structure
2%---------------------------------------------------------------------
[943]3% errormsg=struct2nc(flname,Data,action)
[106]4%
[811]5% OUTPUT:
[106]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
[943]18% action: if ='keep_open', don't close the file after creation, keep it open for further data input
[106]19
[809]20%=======================================================================
[1107]21% Copyright 2008-2022, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
[809]22%   http://www.legi.grenoble-inp.fr
23%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
24%
[106]25%     This file is part of the toolbox UVMAT.
[809]26%
[106]27%     UVMAT is free software; you can redistribute it and/or modify
[809]28%     it under the terms of the GNU General Public License as published
29%     by the Free Software Foundation; either version 2 of the license,
30%     or (at your option) any later version.
31%
[106]32%     UVMAT is distributed in the hope that it will be useful,
33%     but WITHOUT ANY WARRANTY; without even the implied warranty of
34%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
[809]35%     GNU General Public License (see LICENSE.txt) for more details.
36%=======================================================================
[106]37
[943]38function [errormsg,nc]=struct2nc(flname,Data,action,ListDimName,DimValue,VarDimIndex)
[930]39nc=[];
[943]40if ~ischar(flname)
41    errormsg='invalid input for the netcf file name';
42    return
43end
[1096]44FilePath=fileparts(flname);
45if ~strcmp(FilePath,'') && ~exist(FilePath,'dir')
46    errormsg=['directory ' FilePath ' needs to be created'];
47    return
48end
[106]49if ~exist('Data','var')
50     errormsg='no data  input for the netcdf file';
51    return
52end
[919]53
54%% check the validity of the input field structure
[943]55if ~ (exist('action','var') && strcmp(action,'keep_open'))
[1096]56    [errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(Data);
57    if ~isempty(errormsg)
58        errormsg=['error in struct2nc:invalid input structure_' errormsg];
59        return
60    end
[404]61end
62ListVarName=Data.ListVarName;
[919]63
64%% create the netcdf file with name flname in format NETCDF4
[1096]65cmode = netcdf.getConstant('NETCDF4');
66cmode = bitor(cmode, netcdf.getConstant('CLASSIC_MODEL'));
67cmode = bitor(cmode, netcdf.getConstant('CLOBBER'));
68nc = netcdf.create(flname, cmode);
[913]69
[919]70%% write global constants
[404]71if isfield(Data,'ListGlobalAttribute')
72    keys=Data.ListGlobalAttribute;
73    for iattr=1:length(keys)
74        if isfield(Data,keys{iattr})
75             testvar=0;
76            for ivar=1:length(ListVarName)% eliminate possible global attributes with the same name as a variable
77                if isequal(ListVarName{ivar}, keys{iattr})
78                    testvar=1;
79                    break
[106]80                end
[404]81            end
82            if ~testvar               
83                eval(['cte=Data.' keys{iattr} ';'])
84                if (ischar(cte) ||isnumeric(cte)) &&  ~isempty(cte)%&& ~isequal(cte,'')
85                    %write constant only if it is numeric or char string, and not empty
86                    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),keys{iattr},cte)
[106]87                end
88            end
89        end
90    end
[404]91end
[919]92
93%% create the dimensions
[404]94dimid=zeros(1,length(ListDimName));
95for idim=1:length(ListDimName)
96     dimid(idim) = netcdf.defDim(nc,ListDimName{idim},DimValue(idim));
97end
98VarAttribute={}; %default
99testattr=0;
100if isfield(Data,'VarAttribute')
101    VarAttribute=Data.VarAttribute;
102    testattr=1;
103end
[919]104
105
106%% create the variables
107varid=nan(1,length(Data.ListVarName));
[404]108for ivar=1:length(ListVarName)
[919]109    if isfield(Data,ListVarName{ivar})
[943]110        VarClass{ivar}=class(Data.(ListVarName{ivar}));
[919]111        VarType='';
[943]112        switch VarClass{ivar}
[919]113            case {'single','double'}
114                VarType='nc_float'; % store all floating reals as single
[944]115            case {'int8','uint8','int16','uint16','int32','uint32','int64','uint64'}
[919]116                VarType='nc_int';
[988]117            case 'logical'
[1033]118                VarType='nc_int';
119                Data.(ListVarName{ivar})=uint8(Data.(ListVarName{ivar}));
[919]120        end
121        if ~isempty(VarType)
122            varid(ivar)=netcdf.defVar(nc,ListVarName{ivar},VarType,dimid(VarDimIndex{ivar}));%define variable
123        end
124    end
[404]125end
[919]126
127%% write variable attributes
[404]128if testattr
129    for ivar=1:min(numel(VarAttribute),numel(ListVarName)) 
[919]130        if isstruct(VarAttribute{ivar}) && ~isnan(varid(ivar))
[404]131            attr_names=fields(VarAttribute{ivar});
132            for iattr=1:length(attr_names)
[526]133                attr_val=VarAttribute{ivar}.(attr_names{iattr});
134                if ~isempty(attr_names{iattr})&& ~isempty(attr_val)&&~iscell(attr_val)
[404]135                    netcdf.putAtt(nc,varid(ivar),attr_names{iattr},attr_val);
[106]136                end
137            end
138        end
139    end
[404]140end
141netcdf.endDef(nc); %put in data mode
[919]142
143%% fill the variables with input data
[943]144if ~(exist('action','var') && strcmp(action,'keep_open'))
145    for ivar=1:length(ListVarName)
146        if ~isnan(varid(ivar))
147            VarVal=Data.(ListVarName{ivar});
148            if strcmp(VarClass{ivar},'single')
149                VarVal=single(VarVal);
150            end
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 from the first and last values
163                end
164                netcdf.putVar(nc,varid(ivar), VarVal');
165            else
166                netcdf.putVar(nc,varid(ivar), VarVal);
167            end
[404]168        end
[106]169    end
170end
[943]171 netcdf.close(nc)
[938]172[success,errormsg] = fileattrib(flname ,'+w');% allow writing access for the group of users
[530]173%'check_field_structure': check the validity of the field struture representation consistant with the netcdf format
174%------------------------------------------------------------------------
[674]175% [errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(Data)
[530]176%
177% OUTPUT:
178% errormsg: error message which is not empty when the input structure does not have the right form
[674]179% ListDimName: list of dimension names (cell array of cahr strings)
180% DimValue: list of dimension values (numerical array with the same dimension as ListDimName)
181% VarDimIndex: cell array of dimension index (in the list ListDimName) for each element of Data.ListVarName
[530]182%
183% INPUT:
184% Data:   structure containing
185%         (optional) .ListGlobalAttribute: cell listing the names of the global attributes
186%                    .Att_1,Att_2... : values of the global attributes
187%         (requested)  .ListVarName: list of variable names to select (cell array of  char strings {'VarName1', 'VarName2',...} )
188%         (requested)  .VarDimName: list of dimension names for each element of .ListVarName (cell array of string cells)                         
189%         (requested) .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName
190
191
192function [errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(Data)
193errormsg='';
194ListDimName={};
195DimValue=[]; %default
196VarDimIndex={};
197if ~isstruct(Data)
198    errormsg='input field is not a structure';
199    return
200end
201if isfield(Data,'ListVarName') && iscell(Data.ListVarName)
202    nbfield=numel(Data.ListVarName);
203else
204    errormsg='input field does not contain the cell array of variable names .ListVarName';
205    return
206end
207%check dimension names
208if (isfield(Data,'VarDimName') && iscell(Data.VarDimName))
209    if  numel(Data.VarDimName)~=nbfield
210       errormsg=' .ListVarName and .VarDimName have different lengths';
211        return
212    end
213else
214    errormsg='input field does not contain the  cell array of dimension names .VarDimName';
215    return
216end
217nbdim=0;
218ListDimName={};
219
220%% main loop on the list of variables
[674]221VarDimIndex=cell(1,nbfield);
[530]222for ivar=1:nbfield
223    VarName=Data.ListVarName{ivar};
224    if ~isfield(Data,VarName)
225        errormsg=['the listed variable ' VarName ' is not found'];
226        return
227    end
228    sizvar=size(Data.(VarName));% sizvar = dimension of variable
229    DimCell=Data.VarDimName{ivar};
230    if ischar(DimCell)
231        DimCell={DimCell};%case of a single dimension name, defined by a string
232    elseif ~iscell(DimCell)
233        errormsg=['wrong format for .VarDimName{' num2str(ivar) ' (must be the cell of dimension names of the variable ' VarName];
[674]234        return       
[530]235    end
236    nbcoord=numel(sizvar);%nbre of coordinates for variable named VarName
237    testrange=0;
238    if numel(DimCell)==0
239        errormsg=['empty declared dimension .VarDimName{' num2str(ivar) '} for ' VarName];
240        return
241    elseif numel(DimCell)==1% one dimension declared
242        if nbcoord==2
243            if sizvar(1)==1
244                sizvar(1)=sizvar(2);
245            elseif sizvar(2)==1
246            else
247                errormsg=['1 dimension declared in .VarDimName{' num2str(ivar) '} inconsistent with the nbre of dimensions =2 of the variable ' VarName];
248                return
249            end
250            if sizvar(1)==2 && isequal(VarName,DimCell{1})
251                testrange=1;% test for a dimension variable representing a range
252            end
253        else
254            errormsg=['1 dimension declared in .VarDimName{' num2str(ivar) '} inconsistent with the nbre of dimensions =' num2str(nbcoord) ' of the variable ' VarName];
255            return
256        end
257    else
258        if numel(DimCell)>nbcoord
259            sizvar(nbcoord+1:numel(DimCell))=1;% case of singleton dimensions (not seen by the function size)
260        elseif nbcoord > numel(DimCell)
261            errormsg=['nbre of declared dimensions in .VarDimName{' num2str(ivar) '} smaller than the nbre of dimensions =' num2str(nbcoord) ' of the variable ' VarName];
262            return
263        end
264    end
265    DimIndex=[];
266    for idim=1:numel(DimCell) %loop on the coordinates of variable #ivar
267        DimName=DimCell{idim};
268        iprev=find(strcmp(DimName,ListDimName),1);%look for dimension name DimName in the current list
269        if isempty(iprev)% append the dimension name to the current list
270            nbdim=nbdim+1;
271            RangeTest(nbdim)=0; %default
272            if sizvar(idim)==2 && strcmp(DimName,VarName)%case of a coordinate defined by the two end values (regular spacing)
273                RangeTest(nbdim)=1; %to be updated for a later variable 
274            end
275            DimValue(nbdim)=sizvar(idim);
276            ListDimName{nbdim}=DimName;
277            DimIndex=[DimIndex nbdim];
278        else % DimName is detected in the current list of dimension names
279            if ~isequal(DimValue(iprev),sizvar(idim))
280                if isequal(DimValue(iprev),2)&& RangeTest(iprev)  % the dimension has been already detected as a range [min max]
281                    DimValue(iprev)=sizvar(idim); %update with actual value
282                elseif ~testrange               
283                    errormsg=['dimension declaration inconsistent with the size =[' num2str(sizvar) '] for ' VarName];
284                    return
285                end
286            end
287            DimIndex=[DimIndex iprev];
288        end
289    end
290    VarDimIndex{ivar}=DimIndex;
[801]291end
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