source: trunk/src/series/merge_proj.m @ 1061

Last change on this file since 1061 was 1061, checked in by g7moreau, 2 years ago
  • Update copyright to year 2019
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1%'merge_proj': concatene several fields from series, can project them on a regular grid in phys coordinates
2%------------------------------------------------------------------------
3% function ParamOut=merge_proj(Param)
4%------------------------------------------------------------------------
5%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
6%
7%OUTPUT
8% ParamOut: sets options in the GUI series.fig needed for the function
9%
10%INPUT:
11% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
12% In batch mode, Param is the name of the corresponding xml file containing the same information
13% when Param.Action.RUN=0 (as activated when the current Action is selected
14% in series), the function ouput paramOut set the activation of the needed GUI elements
15%
16% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
17% see the current structure Param)
18%    .InputTable: cell of input file names, (several lines for multiple input)
19%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
20%    .OutputSubDir: name of the subdirectory for data outputs
21%    .OutputDirExt: directory extension for data outputs
22%    .Action: .ActionName: name of the current activated function
23%             .ActionPath:   path of the current activated function
24%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
25%             .RUN =0 for GUI input, =1 for function activation
26%             .RunMode='local','background', 'cluster': type of function  use
27%             
28%    .IndexRange: set the file or frame indices on which the action must be performed
29%    .FieldTransform: .TransformName: name of the selected transform function
30%                     .TransformPath:   path  of the selected transform function
31%    .InputFields: sub structure describing the input fields withfields
32%              .FieldName: name(s) of the field
33%              .VelType: velocity type
34%              .FieldName_1: name of the second field in case of two input series
35%              .VelType_1: velocity type of the second field in case of two input series
36%              .Coord_y: name of y coordinate variable
37%              .Coord_x: name of x coordinate variable
38%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
39%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
40
41%=======================================================================
42% Copyright 2008-2019, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
43%   http://www.legi.grenoble-inp.fr
44%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
45%
46%     This file is part of the toolbox UVMAT.
47%
48%     UVMAT is free software; you can redistribute it and/or modify
49%     it under the terms of the GNU General Public License as published
50%     by the Free Software Foundation; either version 2 of the license,
51%     or (at your option) any later version.
52%
53%     UVMAT is distributed in the hope that it will be useful,
54%     but WITHOUT ANY WARRANTY; without even the implied warranty of
55%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
56%     GNU General Public License (see LICENSE.txt) for more details.
57%=======================================================================
58
59function ParamOut=merge_proj(Param)
60
61%% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed
62if isstruct(Param) && isequal(Param.Action.RUN,0)
63    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
64    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
65    ParamOut.NbSlice='off'; %nbre of slices ('off' by default)
66    ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
67    ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
68    ParamOut.FieldTransform = 'on';%can use a transform function
69    ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only)
70    ParamOut.ProjObject='on';%can use projection object(option 'off'/'on',
71    ParamOut.Mask='on';%can use mask option   (option 'off'/'on', 'off' by default)
72    ParamOut.OutputDirExt='.mproj';%set the output dir extension
73    ParamOut.OutputFileMode='NbInput';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
74      %check the input files
75    ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1)
76    first_j=[];
77    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
78    PairString='';
79    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
80    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
81    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
82        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
83    if ~exist(FirstFileName,'file')
84        msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
85    elseif isequal(size(Param.InputTable,1),1) && ~isfield(Param,'ProjObject')
86        msgbox_uvmat('WARNING','You may need a projection object of type plane for merge_proj')
87    end
88    return
89end
90
91%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
92ParamOut=[]; %default output
93RUNHandle=[];
94WaitbarHandle=[];
95%% read input parameters from an xml file if input is a file name (batch mode)
96checkrun=1;
97if ischar(Param)
98    Param=xml2struct(Param);% read Param as input file (batch case)
99    checkrun=0;
100else
101    hseries=findobj(allchild(0),'Tag','series');
102    RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
103    WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
104end
105
106%% define the directory for result file (with path=RootPath{1})
107OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
108
109if ~isfield(Param,'InputFields')
110    Param.InputFields.FieldName='';
111end
112
113%% root input file(s) name, type and index series
114RootPath=Param.InputTable(:,1);
115RootFile=Param.InputTable(:,3);
116SubDir=Param.InputTable(:,2);
117NomType=Param.InputTable(:,4);
118FileExt=Param.InputTable(:,5);
119
120hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
121% gives the series of input file names and indices set by the input parameters:
122[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
123% filecell{iview,fileindex}:
124%        iview: line in the table corresponding to a given file series
125%        fileindex: file index with i and j reshaped as a 1D array
126% i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j
127% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
128if ~isempty(hdisp),delete(hdisp),end;%end the waiting display
129
130NbView=numel(i1_series);%number of input file series (lines in InputTable)
131NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
132NbField_i=size(i1_series{1},2); %nb of fields for the i index
133NbField=NbField_j*NbField_i; %total number of fields
134
135%% determine the file type on each line from the first input file
136NcTypeOptions={'netcdf','civx','civdata'};
137for iview=1:NbView
138    if ~exist(filecell{iview,1}','file')
139        disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
140        return
141    end
142    [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1});
143    FileType{iview}=FileInfo{iview}.FileType;
144    if strcmp(FileType{iview},'civdata')&&  ~isfield(Param.InputFields,'VelType')
145        FileType{iview}='netcdf';
146    end
147    CheckImage{iview}=strcmp(FileInfo{iview}.FieldType,'image');% =1 for images
148    if CheckImage{iview}
149        ParamIn{iview}=MovieObject{iview};
150    else
151        ParamIn{iview}=Param.InputFields;
152    end
153    CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
154    if ~isempty(j1_series{iview})
155        frame_index{iview}=j1_series{iview};
156    else
157        frame_index{iview}=i1_series{iview};
158    end
159end
160if NbView >1 && max(cell2mat(CheckImage))>0 && ~isfield(Param,'ProjObject')
161    disp_uvmat('ERROR','projection on a common grid is needed to concatene images: use a Projection Object of type ''plane'' with ProjMode=''interp_lin''',checkrun)
162    return
163end
164
165%% calibration data and timing: read the ImaDoc files
166[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
167if size(time,1)>1
168    diff_time=max(max(diff(time)));
169    if diff_time>0
170        disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time) ': the mean time is chosen in result'],checkrun)
171    end   
172end
173if ~isempty(errormsg)
174    disp_uvmat('WARNING',errormsg,checkrun)
175end
176time=mean(time,1); %averaged time taken for the merged field
177
178%% coordinate transform or other user defined transform
179transform_fct='';%default fct handle
180if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
181    currentdir=pwd;
182    cd(Param.FieldTransform.TransformPath)
183    transform_fct=str2func(Param.FieldTransform.TransformName);
184    cd (currentdir)
185    if isfield(Param,'TransformInput')
186        for iview=1:NbView
187            XmlData{iview}.TransformInput=Param.TransformInput;
188        end
189    end       
190end
191%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
192 % EDIT FROM HERE
193
194%% check the validity of  input file types
195for iview=1:NbView
196    if ~isequal(CheckImage{iview},1)&&~isequal(CheckNc{iview},1)
197        disp_uvmat('ERROR','input set of input series: need  either netcdf either image series',checkrun)
198        return
199    end
200end
201
202%% output file type
203if min(cell2mat(CheckImage))==1 && (~Param.CheckObject || strcmp(Param.ProjObject.Type,'plane'))
204    FileExtOut='.png'; %image output (input and proj result = image)
205else
206    FileExtOut='.nc'; %netcdf output
207end
208if isempty(j1_series{1})
209    NomTypeOut='_1';
210else
211    NomTypeOut='_1_1';
212end
213%NomTypeOut=NomType;% output file index will indicate the first and last ref index in the series
214RootFileOut=RootFile{1};
215for iview=2:NbView
216    if ~strcmp(RootFile{iview},RootFile{1})
217        RootFileOut='mproj';
218        break
219    end
220end
221
222%% mask (TODO: case of multilevels)
223MaskData=cell(NbView,1);
224if Param.CheckMask
225    if ischar(Param.MaskTable)% case of a single mask (char chain)
226        Param.MaskTable={Param.MaskTable};
227    end
228    for iview=1:numel(Param.MaskTable)
229        if exist(Param.MaskTable{iview},'file')
230            [MaskData{iview},tild,errormsg] = read_field(Param.MaskTable{iview},'image');
231            if ~isempty(transform_fct) && nargin(transform_fct)>=2
232                MaskData{iview}=transform_fct(MaskData{iview},XmlData{iview});
233            end
234        end
235    end
236end
237
238%% Set field names and velocity types
239%use Param.InputFields for all views
240
241%% MAIN LOOP ON FIELDS
242%%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
243% for i_slice=1:NbSlice
244%     index_slice=i_slice:NbSlice:NbField;% select file indices of the slice
245%     NbFiles=0;
246%     nbmissing=0;
247
248    %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
249tstart=tic; %used to record the computing time
250CheckOverwrite=1;%default
251if isfield(Param,'CheckOverwrite')
252    CheckOverwrite=Param.CheckOverwrite;
253end
254for index=1:NbField
255        update_waitbar(WaitbarHandle,index/NbField)
256    if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
257        disp('program stopped by user')
258        return
259    end
260   
261     %% generating the name of the merged field
262    i1=i1_series{1}(index);
263    if ~isempty(i2_series{end})
264        i2=i2_series{end}(index);
265    else
266        i2=i1;
267    end
268    j1=1;
269    j2=1;
270    if ~isempty(j1_series{1})
271        j1=j1_series{1}(index);
272        if ~isempty(j2_series{end})
273            j2=j2_series{end}(index);
274        else
275            j2=j1;
276        end
277    end
278    OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFileOut,FileExtOut,NomTypeOut,i1,i2,j1,j2);
279    if ~CheckOverwrite && exist(OutputFile,'file')
280            disp(['existing output file ' OutputFile ' already exists, skip to next field'])
281            continue% skip iteration if the mode overwrite is desactivated and the result file already exists
282    end
283       
284    %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
285    Data=cell(1,NbView);%initiate the set Data
286    timeread=zeros(1,NbView);
287    for iview=1:NbView
288        %% reading input file(s)     
289        [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},ParamIn{iview},frame_index{iview}(index));
290        if ~isempty(errormsg)
291            disp_uvmat('ERROR',['ERROR in merge_proj/read_field/' errormsg],checkrun)
292            return
293        end
294       
295        ListVar=Data{iview}.ListVarName;
296        for ilist=1:numel(ListVar)
297            Data{iview}.(ListVar{ilist})=double(Data{iview}.(ListVar{ilist}));% transform all fields in double before all operations
298        end
299        % get the time defined in the current file if not already defined from the xml file
300        if isempty(time) && isfield(Data{iview},'Time')
301            timeread(iview)=Data{iview}.Time;
302        end
303        if ~isempty(NbSlice_calib)
304            Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
305        end
306       
307        %% transform the input field (e.g; phys) if requested (no transform involving two input fields)
308        if ~isempty(transform_fct)
309            if nargin(transform_fct)>=2
310                Data{iview}=transform_fct(Data{iview},XmlData{iview});
311            else
312                Data{iview}=transform_fct(Data{iview});
313            end
314        end
315       
316        %% calculate tps coefficients if needed
317
318        check_proj_tps= strcmp(FileType{iview},'civdata') && isfield(Param,'ProjObject')&&~isempty(Param.ProjObject)...
319            && strcmp(Param.ProjObject.ProjMode,'interp_tps')&&~isfield(Data{iview},'Coord_tps');
320        Data{iview}=tps_coeff_field(Data{iview},check_proj_tps);
321       
322        %% projection on object (gridded plane)
323        if Param.CheckObject
324            [Data{iview},errormsg]=proj_field(Data{iview},Param.ProjObject);
325            if ~isempty(errormsg)
326                disp_uvmat('ERROR',['ERROR in merge_proge/proj_field: ' errormsg],checkrun)
327                return
328            end
329        end
330       
331        %% mask
332        if Param.CheckMask && ~isempty(MaskData{iview})
333             [Data{iview},errormsg]=mask_proj(Data{iview},MaskData{iview});
334        end
335    end
336    %%%%%%%%%%%%%%%% END LOOP ON VIEWS %%%%%%%%%%%%%%%%
337
338    %% merge the NbView fields
339    [MergeData,errormsg]=merge_field(Data);
340    if ~isempty(errormsg)
341        disp_uvmat('ERROR',errormsg,checkrun);
342        return
343    end
344
345    %% time of the merged field: take the average of the different views
346    if ~isempty(time)
347        timeread=time(index);   
348    elseif ~isempty(find(timeread))% time defined from ImaDoc
349        timeread=mean(timeread(timeread~=0));% take average over times form the files (when defined)
350    else
351        timeread=index;% take time=file index
352    end
353
354 
355    %% recording the merged field
356    if strcmp(FileExtOut,'.png')    %output as image
357        if index==1
358            if strcmp(class(MergeData.A),'uint8')
359            BitDepth=8;
360            else
361              BitDepth=16; 
362            end
363            %write xml calibration file, using the first file
364            siz=size(MergeData.A);
365            npy=siz(1);
366            npx=siz(2);
367            if isfield(MergeData,'Coord_x') && isfield(MergeData,'Coord_y')
368                Rangx=MergeData.Coord_x;
369                Rangy=MergeData.Coord_y;
370            elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY')
371                Rangx=[MergeData.AX(1) MergeData.AX(end)];
372                Rangy=[MergeData.AY(1) MergeData.AY(end)];
373            else
374                Rangx=[0.5 npx-0.5];
375                Rangy=[npy-0.5 0.5];%default
376            end
377            pxcmx=(npx-1)/(Rangx(2)-Rangx(1));
378            pxcmy=(npy-1)/(Rangy(1)-Rangy(2));
379            T_x=-pxcmx*Rangx(1)+0.5;
380            T_y=-pxcmy*Rangy(2)+0.5;
381            GeometryCal.CalibrationType='rescale';
382            GeometryCal.CoordUnit=MergeData.CoordUnit;
383            GeometryCal.focal=1;
384            GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1];
385            GeometryCal.Tx_Ty_Tz=[T_x T_y 1];
386            ImaDoc.GeometryCalib=GeometryCal;
387            t=struct2xml(ImaDoc);
388            t=set(t,1,'name','ImaDoc');
389            save(t,[fileparts(OutputFile) '.xml'])
390        end
391        if BitDepth==8
392            imwrite(uint8(MergeData.A),OutputFile,'BitDepth',8)
393        else
394            imwrite(uint16(MergeData.A),OutputFile,'BitDepth',16)
395        end
396    else   %output as netcdf files
397        MergeData.ListGlobalAttribute={'Conventions','Project','InputFile_1','InputFile_end','NbCoord','NbDim'};
398        MergeData.Conventions='uvmat';
399        MergeData.NbCoord=2;
400        MergeData.NbDim=2;
401        % time interval of PIV
402        Dt=[];
403        if isfield(Data{1},'Dt')&& isnumeric(Data{1}.Dt)
404            Dt=Data{1}.Dt;
405        end
406        for iview =2:numel(Data)
407            if ~(isfield(Data{iview},'Dt')&& isequal(Data{iview}.Dt,Dt))
408                Dt=[];%dt not the same for all fields
409            end
410        end
411        if ~isempty(timeread)
412            MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'Time'}];
413            MergeData.Time=timeread;
414        end
415        % position of projection plane
416        if isfield(Data{1},'ProjObjectCoord')&& isfield(Data{1},'ProjObjectAngle')
417            ProjObjectCoord=Data{1}.ProjObjectCoord;
418            ProjObjectAngle=Data{1}.ProjObjectAngle;
419            for iview =2:numel(Data)
420                if ~(isfield(Data{iview},'ProjObjectCoord')&& isequal(Data{iview}.ProjObjectCoord,ProjObjectCoord))...
421                        ||~(isfield(Data{iview},'ProjObjectAngle')&& isequal(Data{iview}.ProjObjectAngle,ProjObjectAngle))
422                    ProjObjectCoord=[];%dt not the same for all fields
423                end
424            end
425            if ~isempty(ProjObjectCoord)
426                MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'ProjObjectCoord'} {'ProjObjectAngle'}];
427                MergeData.ProjObjectCoord=ProjObjectCoord;
428                MergeData.ProjObjectAngle=ProjObjectAngle;
429            end
430        end
431        % coord unit
432        if isfield(Data{1},'CoordUnit')
433            CoordUnit=Data{1}.CoordUnit;
434            for iview =2:numel(Data)
435                if ~(isfield(Data{iview},'CoordUnit')&& isequal(Data{iview}.CoordUnit,CoordUnit))
436                    CoordUnit=[];%CoordUnit not the same for all fields
437                end
438            end
439            if ~isempty(CoordUnit)
440                MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'CoordUnit'}];
441                MergeData.CoordUnit=CoordUnit;
442            end
443        end
444        % time unit
445        if isfield(Data{1},'TimeUnit')
446            TimeUnit=Data{1}.TimeUnit;
447            for iview =2:numel(Data)
448                if ~(isfield(Data{iview},'TimeUnit')&& isequal(Data{iview}.TimeUnit,TimeUnit))
449                    TimeUnit=[];%TimeUnit not the same for all fields
450                end
451            end
452            if ~isempty(TimeUnit)
453                MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'TimeUnit'}];
454                MergeData.TimeUnit=TimeUnit;
455            end
456        end
457        error=struct2nc(OutputFile,MergeData);%save result file
458        if isempty(error)
459            disp(['output file ' OutputFile ' written'])
460        else
461            disp(error)
462        end
463    end
464end
465ellapsed_time=toc(tstart);
466disp(['total ellapsed time ' num2str(ellapsed_time/60,2) ' minutes'])
467disp([ num2str(ellapsed_time/(60*NbField),3) ' minutes per iteration'])
468
469%'merge_field': concatene fields
470%------------------------------------------------------------------------
471function [MergeData,errormsg]=merge_field(Data)
472%% default output
473if isempty(Data)||~iscell(Data)
474    MergeData=[];
475    return
476end
477errormsg='';
478MergeData=Data{1};% merged field= first field by default, reproduces the global attributes of the first field
479NbView=length(Data);
480if NbView==1% if there is only one field, just reproduce it in MergeData
481    return
482end
483
484%% group the variables (fields of 'Data') in cells of variables with the same dimensions
485[CellInfo,NbDim,errormsg]=find_field_cells(Data{1});
486if ~isempty(errormsg)
487    return
488end
489
490%LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS
491for icell=1:length(CellInfo)
492    if NbDim(icell)~=1 % skip field cells which are of dim 1
493        switch CellInfo{icell}.CoordType
494            case 'scattered'  %case of input fields with unstructured coordinates: just concatene data
495                for ivar=CellInfo{icell}.VarIndex %  indices of the selected variables in the list FieldData.ListVarName
496                    VarName=Data{1}.ListVarName{ivar};
497                    for iview=2:NbView
498                        MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)];
499                    end
500                end
501            case 'grid'        %case of fields defined on a structured  grid
502                FFName='';
503                if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag)
504                    FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable
505                    MergeData.ListVarName(CellInfo{icell}.VarIndex_errorflag)=[];%remove error flag variable in MergeData (will use NaN instead)
506                    MergeData.VarDimName(CellInfo{icell}.VarIndex_errorflag)=[];
507                    MergeData.VarAttribute(CellInfo{icell}.VarIndex_errorflag)=[];
508                end
509                % select good data on each view
510                for ivar=CellInfo{icell}.VarIndex  %  indices of the selected variables in the list FieldData.ListVarName
511                    VarName=Data{1}.ListVarName{ivar};
512                    for iview=1:NbView
513                        if isempty(FFName)
514                            check_bad=isnan(Data{iview}.(VarName));%=0 for NaN data values, 1 else
515                        else
516                            check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else
517                        end
518                        Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
519                        if iview==1
520                            %MergeData.(VarName)=Data{1}.(VarName);% initiate MergeData with the first field
521                            MergeData.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
522                            NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point
523                        elseif size(Data{iview}.(VarName))~=size(MergeData.(VarName))
524                            errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object';
525                            return
526                        else                             
527                            MergeData.(VarName)=MergeData.(VarName) +double(Data{iview}.(VarName));%add data
528                            NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else
529                        end
530                    end
531                    MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point
532                    MergeData.(VarName)(NbAver==0)=NaN;% set to NaN the points with no good data
533                end
534        end
535    end
536end
537
538
539   
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