source: trunk/src/series/merge_proj_polar.m @ 977

Last change on this file since 977 was 977, checked in by g7moreau, 4 years ago
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1%'merge_proj': concatene several fields from series, project on a polar grid
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 2008-2017, 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_polar(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='on';% 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='on'; %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='off';% 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='off';%can use projection object(option 'off'/'on',
71    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
72    ParamOut.OutputDirExt='.polar';%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    end
86    return
87end
88
89%%%% specific input parameters
90% calculate the positions on which to interpolate
91radius_ref=450;% radius of the mountain top
92radius_shifted=-130:2:130;% radius shifted by the radius of the origin at the topography summit
93radius=radius_ref+radius_shifted;%radius from centre of the tank
94azimuth_arclength=(-150:2:400);%azimuth in arc length at origin position
95azimuth=pi/2-azimuth_arclength/radius_ref;%azimuth in radian
96[Radius,Azimuth]=meshgrid(radius,azimuth);
97XI=Radius.*cos(Azimuth);% set of x axis of the points where interpolqtion needs to be done
98YI=Radius.*sin(Azimuth)-radius_ref;% set of y axis of the points where interpolqtion needs to be done
99FieldNames={'vec(U,V)';'curl(U,V)';'div(U,V)'};
100HeadData.ListVarName= {'radius','azimuth'} ;
101HeadData.VarDimName={'radius','azimuth'};
102HeadData.VarAttribute={'coord_y','coord_x'} ;
103HeadData.radius=radius_shifted;
104HeadData.azimuth=azimuth_arclength;   
105thresh2=16; % square of the interpolation range
106
107%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
108ParamOut=[]; %default output
109RUNHandle=[];
110WaitbarHandle=[];
111%% read input parameters from an xml file if input is a file name (batch mode)
112checkrun=1;
113if ischar(Param)
114    Param=xml2struct(Param);% read Param as input file (batch case)
115    checkrun=0;
116else
117    hseries=findobj(allchild(0),'Tag','series');
118    RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
119    WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
120end
121
122%% root input file type
123RootPath=Param.InputTable(:,1);
124RootFile=Param.InputTable(:,3);
125SubDir=Param.InputTable(:,2);
126%NomType=Param.InputTable(:,4);
127FileExt=Param.InputTable(:,5);
128[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
129%%%%%%%%%%%%
130% The cell array filecell is the list of input file names, while
131% filecell{iview,fileindex}:
132%        iview: line in the table corresponding to a given file series
133%        fileindex: file index within  the file series,
134% 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
135% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
136%%%%%%%%%%%%
137% NbSlice=1;%default
138% if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
139%     NbSlice=Param.IndexRange.NbSlice;
140% end
141NbView=numel(i1_series);%number of input file series (lines in InputTable)
142NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
143NbField_i=size(i1_series{1},2); %nb of fields for the i index
144NbField=NbField_j*NbField_i; %total number of fields
145
146%% define the name for result file (with path=RootPath{1})
147OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
148% OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},'.nc','_1',i1_series{1}(1));
149% CheckOverwrite=1;%default
150% if isfield(Param,'CheckOverwrite')
151%     CheckOverwrite=Param.CheckOverwrite;
152% end
153% if ~CheckOverwrite && exist(OutputFile,'file')
154%     disp(['existing output file ' OutputFile ' already exists, skip to next field'])
155%     return% skip iteration if the mode overwrite is desactivated and the result file already exists
156% end
157
158if ~isfield(Param,'InputFields')
159    Param.InputFields.FieldName='';
160end
161
162
163%% determine the file type on each line from the first input file
164ImageTypeOptions={'image','multimage','mmreader','video'};
165NcTypeOptions={'netcdf','civx','civdata'};
166for iview=1:NbView
167    if ~exist(filecell{iview,1}','file')
168        disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
169        return
170    end
171    [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1});
172    FileType{iview}=FileInfo{iview}.FileType;
173    CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
174    if CheckImage{iview}
175        ParamIn{iview}=MovieObject{iview};
176    else
177        ParamIn{iview}=Param.InputFields;
178    end
179    CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
180    if ~isempty(j1_series{iview})
181        frame_index{iview}=j1_series{iview};
182    else
183        frame_index{iview}=i1_series{iview};
184    end
185end
186if NbView >1 && max(cell2mat(CheckImage))>0 && ~isfield(Param,'ProjObject')
187    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)
188    return
189end
190
191%% calibration data and timing: read the ImaDoc files
192[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
193if size(time,1)>1
194    diff_time=max(max(diff(time)));
195    if diff_time>0
196        disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time) ': the mean time is chosen in result'],checkrun)
197    end   
198end
199if ~isempty(errormsg)
200    disp_uvmat('WARNING',errormsg,checkrun)
201end
202time=mean(time,1); %averaged time taken for the merged field
203
204%% height z
205    % position of projection plane
206   
207ProjObjectCoord=XmlData{1}.GeometryCalib.SliceCoord;
208CoordUnit=XmlData{1}.GeometryCalib.CoordUnit;
209for iview =2:numel(XmlData)
210    if ~(isfield(XmlData{iview},'GeometryCalib')&& isequal(XmlData{iview}.GeometryCalib.SliceCoord,ProjObjectCoord))...
211        disp('error: geometric calibration missing or inconsistent plane positions')
212        return
213    end
214end
215
216
217%% coordinate transform or other user defined transform
218transform_fct='';%default fct handle
219if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
220        currentdir=pwd;
221        cd(Param.FieldTransform.TransformPath)
222        transform_fct=str2func(Param.FieldTransform.TransformName);
223        cd (currentdir)
224        if isfield(Param,'TransformInput')
225            for iview=1:NbView
226            XmlData{iview}.TransformInput=Param.TransformInput;
227            end
228        end       
229end
230%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
231 % EDIT FROM HERE
232
233%% check the validity of  input file types
234for iview=1:NbView
235    if ~isequal(CheckNc{iview},1)
236        disp_uvmat('ERROR','input files needs to be in netcdf (extension .nc)',checkrun)
237        return
238    end
239end
240
241% %% output file type
242if isempty(j1_series{1})
243    NomTypeOut='_1';
244else
245    NomTypeOut='_1_1';
246end
247RootFileOut=RootFile{1};
248for iview=2:NbView
249    if ~strcmp(RootFile{iview},RootFile{1})
250        RootFileOut='mproj';
251        break
252    end
253end
254
255
256%% MAIN LOOP ON FIELDS
257%%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
258% for i_slice=1:NbSlice
259%     index_slice=i_slice:NbSlice:NbField;% select file indices of the slice
260%     NbFiles=0;
261%     nbmissing=0;
262
263%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
264tstart=tic; %used to record the computing time
265CheckOverwrite=1;%default
266if isfield(Param,'CheckOverwrite')
267    CheckOverwrite=Param.CheckOverwrite;
268end
269
270for index=1:NbField
271    disp(['index=' num2str(index)])
272    disp(['ellapsed time ' num2str(toc(tstart)/60,4) ' minutes'])
273    update_waitbar(WaitbarHandle,index/NbField)
274    if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
275        disp('program stopped by user')
276        return
277    end
278   
279        %% generating the name of the merged field
280        i1=i1_series{1}(index);
281        if ~isempty(i2_series{end})
282            i2=i2_series{end}(index);
283        else
284            i2=i1;
285        end
286        j1=1;
287        j2=1;
288        if ~isempty(j1_series{1})
289            j1=j1_series{1}(index);
290            if ~isempty(j2_series{end})
291                j2=j2_series{end}(index);
292            else
293                j2=j1;
294            end
295        end
296       OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFileOut,'.nc',NomTypeOut,i1,i2,j1,j2);
297        if ~CheckOverwrite && exist(OutputFile,'file')
298            disp(['existing output file ' OutputFile ' already exists, skip to next field'])
299            continue% skip iteration if the mode overwrite is desactivated and the result file already exists
300        end
301   
302    %% z position
303    ZIndex=mod(i1_series{1}(index)-1,NbSlice_calib{1})+1;%Zindex for phys transform
304    ZPosNew=ProjObjectCoord(ZIndex,3);
305    if index==1
306        ZPos=ZPosNew;
307    else
308        if ZPosNew~=ZPos
309            disp('inconsistent z positions in the series')
310            return
311        end
312    end
313    % radius of the topography section at z position
314    ind_mask=[];
315    if ZPos<20
316        TopoRadius=40*sin(acos((20+ZPos)/40));
317        ind_mask=(XI'.*XI'+YI'.*YI')<TopoRadius*TopoRadius;% indidces of data to mask
318    end
319   
320    %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
321    Data=cell(1,NbView);%initiate the set Data
322    timeread=zeros(1,NbView);
323    for iview=1:NbView
324        %% reading input file(s)
325        [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},ParamIn{iview},frame_index{iview}(index));
326        if ~isempty(errormsg)
327            disp_uvmat('ERROR',['ERROR in merge_proj/read_field/' errormsg],checkrun)
328            return
329        end
330        ListVar=Data{iview}.ListVarName;
331        for ilist=1:numel(ListVar)
332            Data{iview}.(ListVar{ilist})=double(Data{iview}.(ListVar{ilist}));% transform all fields in double before all operations
333        end
334        % get the time defined in the current file if not already defined from the xml file
335        if ~isempty(time) && isfield(Data{iview},'Time')
336            timeread(iview)=Data{iview}.Time;
337        end
338        if ~isempty(NbSlice_calib)
339            Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
340        end
341       
342        %% transform the input field (e.g; phys) if requested (no transform involving two input fields)
343        if ~isempty(transform_fct)
344            if nargin(transform_fct)>=2
345                Data{iview}=transform_fct(Data{iview},XmlData{iview});
346            else
347                Data{iview}=transform_fct(Data{iview});
348            end
349        end
350       
351        %% calculate tps coefficients
352        Data{iview}=tps_coeff_field(Data{iview},1);
353       
354        %% projection on the polar grid
355        [DataOut,VarAttribute,errormsg]=calc_field_tps(Data{iview}.Coord_tps,Data{iview}.NbCentre,Data{iview}.SubRange,...
356            cat(3,Data{iview}.U_tps,Data{iview}.V_tps),FieldNames,cat(3,XI,YI));
357        % set to NaN interpolation points which are too far from any initial data (more than 2 CoordMesh)
358        Coord=permute(Data{iview}.Coord_tps,[1 3 2]);
359        Coord=reshape(Coord,size(Coord,1)*size(Coord,2),2);
360        if exist('scatteredInterpolant','file')%recent Matlab versions
361            F=scatteredInterpolant(Coord,Coord(:,1),'nearest');
362            G=scatteredInterpolant(Coord,Coord(:,2),'nearest');
363        else
364            F=TriScatteredInterp(Coord,Coord(:,1),'nearest');
365            G=TriScatteredInterp(Coord,Coord(:,2),'nearest');
366        end
367        Distx=F(XI,YI)-XI;% diff of x coordinates with the nearest measurement point
368        Disty=G(XI,YI)-YI;% diff of y coordinates with the nearest measurement point
369        Dist=Distx.*Distx+Disty.*Disty;
370        ListVarName=(fieldnames(DataOut))';
371        VarDimName=cell(size(ListVarName));
372        ProjData{iview}=HeadData;
373        ProjData{iview}.ListVarName= [ProjData{iview}.ListVarName ListVarName];
374        ProjData{iview}.VarDimName={'radius','azimuth'};
375        ProjData{iview}.VarAttribute=[{'coord_x'} {'coord_y'} VarAttribute];
376        for ivar=1:numel(ListVarName)
377            ProjData{iview}.VarDimName{ivar+2}={'radius','azimuth'};
378            VarName=ListVarName{ivar};
379            if ~isempty(thresh2)
380                DataOut.(VarName)(Dist>thresh2)=NaN;% put to NaN interpolated positions further than RangeInterp from initial data
381            end
382            ProjData{iview}.(VarName)=(DataOut.(VarName))';
383        end
384       
385    end
386    %%%%%%%%%%%%%%%% END LOOP ON VIEWS %%%%%%%%%%%%%%%%
387   
388    %% merge the NbView fields
389    [MergeData,errormsg]=merge_field(ProjData);
390    if ~isempty(errormsg)
391        disp_uvmat('ERROR',errormsg,checkrun);
392        return
393    end
394   
395   
396    %% time of the merged field: take the average of the different views
397    if ~isempty(time)
398        timeread=time(index);
399    elseif ~isempty(find(timeread))% time defined from ImaDoc
400        timeread=mean(timeread(timeread~=0));% take average over times form the files (when defined)
401    else
402        timeread=index;% take time=file index
403    end
404   
405    %% rotating the velocity vectors to the local axis of the polatr coordinates
406    Unew=MergeData.U.*sin(Azimuth')-MergeData.V.*cos(Azimuth');
407    Vnew=MergeData.U.*cos(Azimuth')+MergeData.V.*sin(Azimuth');
408    if ~isempty(ind_mask)
409        Unew(ind_mask)=NaN;
410        Vnew(ind_mask)=NaN;
411        MergeData.curl(ind_mask)=NaN;
412        MergeData.div(ind_mask)=NaN;
413    end
414    [npy,npx]=size(Unew);
415   
416    %% create the output file for the first iteration of the loop
417    if index==1
418        TimeData.ListGlobalAttribute={'Conventions','Project','CoordUnit','TimeUnit','ZPos','Time'};
419        TimeData.Conventions='uvmat';
420        TimeData.Project='2016_Circumpolar';
421        TimeData.CoordUnit='cm';
422        TimeData.TimeUnit='s';
423        TimeData.ZPos=ZPos;
424        TimeData.ListVarName={'radius','azimuth','U','V','curl','div'};
425        TimeData.VarDimName={'radius','azimuth',{'radius','azimuth'},{'radius','azimuth'}...
426            {'radius','azimuth'},{'radius','azimuth'}};
427        TimeData.VarAttribute{1}.Role='';
428        TimeData.VarAttribute{2}.Role='';
429        TimeData.VarAttribute{3}.Role='vector_x';
430        TimeData.VarAttribute{4}.Role='vector_y';
431        TimeData.VarAttribute{5}.Role='scalar';
432        TimeData.VarAttribute{6}.Role='scalar';
433       
434        TimeData.radius=radius_shifted;
435        TimeData.azimuth=azimuth_arclength;
436    end
437       
438        %% append data to the netcdf file for next iterations
439        TimeData.Time=timeread;
440       TimeData.U=Unew;
441       TimeData.V=Vnew;
442       TimeData.curl=MergeData.curl;
443       TimeData.div=MergeData.div;
444
445            [error,ncid]=struct2nc(OutputFile,TimeData);%save result file
446        if isempty(error)
447            disp(['output file ' OutputFile ' written'])
448        else
449            disp(error)
450        end
451            ellapsed_time=toc(tstart);
452    disp(['total ellapsed time ' num2str(ellapsed_time/60,2) ' minutes'])
453end
454
455ellapsed_time=toc(tstart);
456disp(['total ellapsed time ' num2str(ellapsed_time/60,2) ' minutes'])
457disp([ num2str(ellapsed_time/(60*NbField),3) ' minutes per iteration'])
458
459%'merge_field': concatene fields
460%------------------------------------------------------------------------
461function [MergeData,errormsg]=merge_field(Data)
462%% default output
463if isempty(Data)||~iscell(Data)
464    MergeData=[];
465    return
466end
467errormsg='';
468MergeData=Data{1};% merged field= first field by default, reproduces the global attributes of the first field
469NbView=length(Data);
470if NbView==1% if there is only one field, just reproduce it in MergeData
471    return
472end
473
474%% group the variables (fields of 'Data') in cells of variables with the same dimensions
475[CellInfo,NbDim,errormsg]=find_field_cells(Data{1});
476if ~isempty(errormsg)
477    return
478end
479
480%LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS
481for icell=1:length(CellInfo)
482    if NbDim(icell)~=1 % skip field cells which are of dim 1
483        switch CellInfo{icell}.CoordType
484            case 'scattered'  %case of input fields with unstructured coordinates: just concatene data
485                for ivar=CellInfo{icell}.VarIndex %  indices of the selected variables in the list FieldData.ListVarName
486                    VarName=Data{1}.ListVarName{ivar};
487                    for iview=2:NbView
488                        MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)];
489                    end
490                end
491            case 'grid'        %case of fields defined on a structured  grid
492                FFName='';
493                if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag)
494                    FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable
495                    MergeData.ListVarName(CellInfo{icell}.VarIndex_errorflag)=[];%remove error flag variable in MergeData (will use NaN instead)
496                    MergeData.VarDimName(CellInfo{icell}.VarIndex_errorflag)=[];
497                    MergeData.VarAttribute(CellInfo{icell}.VarIndex_errorflag)=[];
498                end
499                % select good data on each view
500                for ivar=CellInfo{icell}.VarIndex  %  indices of the selected variables in the list FieldData.ListVarName
501                    VarName=Data{1}.ListVarName{ivar};
502                    for iview=1:NbView
503                        if isempty(FFName)
504                            check_bad=isnan(Data{iview}.(VarName));%=0 for NaN data values, 1 else
505                        else
506                            check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else
507                        end
508                        Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
509                        if iview==1
510                            %MergeData.(VarName)=Data{1}.(VarName);% initiate MergeData with the first field
511                            MergeData.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
512                            NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point
513                        elseif size(Data{iview}.(VarName))~=size(MergeData.(VarName))
514                            errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object';
515                            return
516                        else
517                            MergeData.(VarName)=MergeData.(VarName) +double(Data{iview}.(VarName));%add data
518                            NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else
519                        end
520                    end
521                    MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point
522                    MergeData.(VarName)(NbAver==0)=NaN;% set to NaN the points with no good data
523                end
524        end
525        %         if isempty(FFName)
526        %             FFName='FF';
527        %         end
528        %         MergeData.(FFName)(NbAver~=0)=0;% flag to 1 undefined summed data
529        %         MergeData.(FFName)(NbAver==0)=1;% flag to 1 undefined summed data
530    end
531end
532
533
534   
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