source: trunk/src/series/merge_proj.m

Last change on this file was 1147, checked in by sommeria, 4 weeks ago

merge_proj repaired with multimask possibility

File size: 24.6 KB
Line 
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 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
43%   http://www.legi.grenoble-inp.fr
44%   Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.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    %%%%% list of possible transform functions (needed only for compilation)
70    if 0==1 %never satisfied but trigger compilation with the appropriate transform functions ('eval' inactive for compilation)
71        phys
72        phys_polar
73        sub_field
74    end
75
76    ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions
77    %%%%%%%%
78    ParamOut.ProjObject='on';%can use projection object(option 'off'/'on',
79    ParamOut.Mask='on';%can use mask option   (option 'off'/'on', 'off' by default)
80    ParamOut.OutputDirExt='.mproj';%set the output dir extension
81    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
82      %check the input files
83    ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1)
84    first_j=[];
85    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
86    PairString='';
87    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
88    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
89    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
90        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
91    if ~exist(FirstFileName,'file')
92        msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
93    end
94    return
95end
96
97%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
98ParamOut=[]; %default output
99RUNHandle=[];
100WaitbarHandle=[];
101%% read input parameters from an xml file if input is a file name (batch mode)
102checkrun=1;
103if ischar(Param)
104    Param=xml2struct(Param);% read Param as input file (batch case)
105    checkrun=0;
106else
107    hseries=findobj(allchild(0),'Tag','series');
108    RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
109    WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
110end
111
112%% define the directory for result file (with path=RootPath{1})
113OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
114
115if ~isfield(Param,'InputFields')
116    Param.InputFields.FieldName='';
117end
118
119%% root input file(s) name, type and index series
120RootPath=Param.InputTable(:,1);
121RootFile=Param.InputTable(:,3);
122SubDir=Param.InputTable(:,2);
123FileExt=Param.InputTable(:,5);
124
125hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
126% gives the series of input file names and indices set by the input parameters:
127[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
128% filecell{iview,fileindex}:
129%        iview: line in the table corresponding to a given file series
130%        fileindex: file index with i and j reshaped as a 1D array
131% 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
132% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
133if ~isempty(hdisp),delete(hdisp),end %end the waiting display
134
135NbView=numel(i1_series);%number of input file series (lines in InputTable)
136NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
137NbField_i=size(i1_series{1},2); %nb of fields for the i index
138NbField=NbField_j*NbField_i; %total number of fields
139
140%% determine the file type on each line from the first input file
141NcTypeOptions={'netcdf','civx','civdata','pivdata_fluidimage'};
142for iview=1:NbView
143    if ~exist(filecell{iview,1}','file')
144        disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
145        return
146    end
147    [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1});
148    FileType{iview}=FileInfo{iview}.FileType;
149    if strcmp(FileType{iview},'civdata')&&  ~isfield(Param.InputFields,'VelType')
150        FileType{iview}='netcdf';
151    end
152    CheckImage{iview}=strcmp(FileInfo{iview}.FieldType,'image');% =1 for images
153    if CheckImage{iview}
154        ParamIn{iview}=MovieObject{iview};
155    else
156        ParamIn{iview}=Param.InputFields;
157    end
158    CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
159    if ~isempty(j1_series{iview})
160        frame_index{iview}=j1_series{iview};
161    else
162        frame_index{iview}=i1_series{iview};
163    end
164end
165if NbView >1 && max(cell2mat(CheckImage))>0 && ~isfield(Param,'ProjObject')
166    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)
167    return
168end
169
170%% calibration data and timing: read the ImaDoc files
171[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
172if size(time,1)>1
173    diff_time=max(max(diff(time)));
174    if diff_time>0
175        disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time) ': the mean time is chosen in result'],checkrun)
176    end   
177end
178if ~isempty(errormsg)
179    disp_uvmat('WARNING',errormsg,checkrun)
180end
181time=mean(time,1); %averaged time taken for the merged field
182
183%% coordinate transform or other user defined transform
184transform_fct='';%default fct handle
185 checksub=0;
186if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
187    currentdir=pwd;
188    cd(Param.FieldTransform.TransformPath)
189    if strcmp(Param.FieldTransform.TransformName,'sub_field')
190        checksub=2;% the two into field series will be subtracted
191    end
192    transform_fct=str2func(Param.FieldTransform.TransformName);
193    cd (currentdir)
194    if isfield(Param,'TransformInput')
195        for iview=1:NbView
196            XmlData{iview}.TransformInput=Param.TransformInput;
197        end
198    end
199    if checksub>2 && NbView>2
200        disp_uvmat('WARNING',['only the two first input file series will be combined by ' Param.FieldTransform.TransformName],checkrun)
201    end
202end
203%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
204 % EDIT FROM HERE
205
206%% check the validity of  input file types
207for iview=1:NbView
208    if ~isequal(CheckImage{iview},1)&&~isequal(CheckNc{iview},1)
209        disp_uvmat('ERROR','input set of input series: need  either netcdf either image series',checkrun)
210        return
211    end
212end
213
214%% output file type
215if min(cell2mat(CheckImage))==1 && (~Param.CheckObject || strcmp(Param.ProjObject.Type,'plane'))
216    FileExtOut='.png'; %image output (input and proj result = image)
217else
218    FileExtOut='.nc'; %netcdf output
219end
220if isempty(j1_series{1})
221    NomTypeOut='_1';
222else
223    NomTypeOut='_1_1';
224end
225%NomTypeOut=NomType;% output file index will indicate the first and last ref index in the series
226RootFileOut=RootFile{1};
227for iview=2:NbView
228    if ~strcmp(RootFile{iview},RootFile{1})
229        RootFileOut='mproj';
230        break
231    end
232end
233
234
235%% Set field names and velocity types
236%use Param.InputFields for all views
237
238%% MAIN LOOP ON FIELDS
239%%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
240
241    %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
242tstart=tic; %used to record the computing time
243CheckOverwrite=1;%default
244if isfield(Param,'CheckOverwrite')
245    CheckOverwrite=Param.CheckOverwrite;
246end
247OutputPath=fullfile(Param.OutputPath,num2str(Param.Experiment),num2str(Param.Device));
248
249for index=1:NbField
250        update_waitbar(WaitbarHandle,index/NbField)
251    if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
252        disp('program stopped by user')
253        return
254    end
255   
256     %% generating the name of the merged field
257    i1=i1_series{1}(index);
258    if ~isempty(i2_series{end})
259        i2=i2_series{end}(index);
260    else
261        i2=i1;
262    end
263    j1=1;
264    j2=1;
265    if ~isempty(j1_series{1})
266        j1=j1_series{1}(index);
267        if ~isempty(j2_series{end})
268            j2=j2_series{end}(index);
269        else
270            j2=j1;
271        end
272    end
273    OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,FileExtOut,NomTypeOut,i1,i2,j1,j2);
274    if ~CheckOverwrite && exist(OutputFile,'file')
275            disp(['existing output file ' OutputFile ' already exists, skip to next field'])
276            continue% skip iteration if the mode overwrite is desactivated and the result file already exists
277    end
278       
279    %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
280    Data=cell(1,NbView);%initiate the set Data
281    timeread=zeros(1,NbView);
282    for iview=1:NbView
283        %% reading input file(s)     
284        [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},ParamIn{iview},frame_index{iview}(index));
285        if isempty(errormsg)
286            disp([filecell{iview,index} ' read OK'])
287        else
288            disp_uvmat('ERROR',['ERROR in merge_proj/read_field/' errormsg],checkrun)
289            return
290        end
291       
292        ListVar=Data{iview}.ListVarName;
293        for ilist=1:numel(ListVar)
294            Data{iview}.(ListVar{ilist})=double(Data{iview}.(ListVar{ilist}));% transform all fields in double before all operations
295        end
296        % get the time defined in the current file if not already defined from the xml file
297        if isempty(time) && isfield(Data{iview},'Time')
298            timeread(iview)=Data{iview}.Time;
299        end
300        if ~isempty(NbSlice_calib)
301            Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
302        end
303       
304        %% transform the input field iview (e.g; phys) if requested (no transform involving two input fields at this stage)
305        if ~isempty(transform_fct)&& checksub==0
306            if nargin(transform_fct)>=2
307                Data{iview}=transform_fct(Data{iview},XmlData{iview});
308            else
309                Data{iview}=transform_fct(Data{iview});
310            end
311        end
312       
313        %% calculate tps coefficients if needed
314
315        check_proj_tps= strcmp(FileType{iview},'civdata') && isfield(Param,'ProjObject')&&~isempty(Param.ProjObject)...
316            && strcmp(Param.ProjObject.ProjMode,'interp_tps')&&~isfield(Data{iview},'Coord_tps');
317        if check_proj_tps
318        Data{iview}=tps_coeff_field(Data{iview},check_proj_tps);
319        end
320       
321        %% projection on object (gridded plane)
322        if Param.CheckObject
323            [Data{iview},errormsg]=proj_field(Data{iview},Param.ProjObject);
324            if ~isempty(errormsg)
325                disp_uvmat('ERROR',['ERROR in merge_proge/proj_field: ' errormsg],checkrun)
326                return
327            end
328        end
329       
330        %% mask
331        if Param.CheckMask % introduce multilevel mask like for civ
332            NbSlice=Param.MaskTable{iview,2};
333            [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.MaskTable{iview,1});
334            i1_mask=mod(i1-1,NbSlice)+1;
335            maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask);
336            if ~exist(maskname,'file')
337                maskname=Param.MaskTable{iview,1};
338            end
339            [MaskData,~,errormsg] = read_field(maskname,'image');
340            if ~isempty(transform_fct) && nargin(transform_fct)>=2
341                MaskData=transform_fct(MaskData,XmlData{iview});
342            end
343            if  ~isempty(MaskData)
344                [Data{iview},errormsg]=mask_proj(Data{iview},MaskData);
345            end
346        end
347    end
348    %%%%%%%%%%%%%%%% END LOOP ON VIEWS %%%%%%%%%%%%%%%%
349
350    %% merge the NbView fields
351    if checksub==0
352        [MergeData,errormsg]=merge_field(Data);%concatene all the input field series by fct merge_data
353    else
354        MergeData=transform_fct(Data{1},XmlData{1},Data{2}); %combine the two input file series
355    % else
356    %     MergeData=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});%combine the two input file series with calibration parameters
357    end
358    if ~isempty(errormsg)
359        disp_uvmat('ERROR',errormsg,checkrun);
360        return
361    end
362
363    %% time of the merged field: take the average of the different views
364    if ~isempty(time)
365        timeread=time(index);   
366    elseif ~isempty(find(timeread))% time defined from ImaDoc
367        timeread=mean(timeread(timeread~=0));% take average over times form the files (when defined)
368    else
369        timeread=index;% take time=file index
370    end
371
372 
373    %% recording the merged field
374    if strcmp(FileExtOut,'.png')    %output as image
375        if index==1
376            if strcmp(class(MergeData.A),'uint8')
377            BitDepth=8;
378            else
379              BitDepth=16; 
380            end
381            %write xml calibration file, using the first file
382            siz=size(MergeData.A);
383            npy=siz(1);
384            npx=siz(2);
385            if isfield(MergeData,'Coord_x') && isfield(MergeData,'Coord_y')
386                Rangx=MergeData.Coord_x;
387                Rangy=MergeData.Coord_y;
388            elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY')
389                Rangx=[MergeData.AX(1) MergeData.AX(end)];
390                Rangy=[MergeData.AY(1) MergeData.AY(end)];
391            else
392                Rangx=[0.5 npx-0.5];
393                Rangy=[npy-0.5 0.5];%default
394            end
395            pxcmx=(npx-1)/(Rangx(2)-Rangx(1));
396            pxcmy=(npy-1)/(Rangy(1)-Rangy(2));
397            T_x=-pxcmx*Rangx(1)+0.5;
398            T_y=-pxcmy*Rangy(2)+0.5;
399            GeometryCal.CalibrationType='rescale';
400            GeometryCal.CoordUnit=MergeData.CoordUnit;
401            GeometryCal.focal=1;
402            GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1];
403            GeometryCal.Tx_Ty_Tz=[T_x T_y 1];
404            ImaDoc.GeometryCalib=GeometryCal;
405            t=struct2xml(ImaDoc);
406            t=set(t,1,'name','ImaDoc');
407            save(t,[fileparts(OutputFile) '.xml'])
408        end
409        if BitDepth==8
410            imwrite(uint8(MergeData.A),OutputFile,'BitDepth',8)
411        else
412            imwrite(uint16(MergeData.A),OutputFile,'BitDepth',16)
413        end
414    else   %output as netcdf files
415        MergeData.ListGlobalAttribute={'Conventions','Project','InputFile_1','InputFile_end','NbCoord','NbDim'};
416        MergeData.Conventions='uvmat';
417        MergeData.NbCoord=2;
418        MergeData.NbDim=2;
419        % time interval of PIV
420        Dt=[];
421        if isfield(Data{1},'Dt')&& isnumeric(Data{1}.Dt)
422            Dt=Data{1}.Dt;
423        end
424        for iview =2:numel(Data)
425            if ~(isfield(Data{iview},'Dt')&& isequal(Data{iview}.Dt,Dt))
426                Dt=[];%dt not the same for all fields
427            end
428        end
429        if ~isempty(timeread)
430            MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'Time'}];
431            MergeData.Time=timeread;
432        end
433        % position of projection plane
434        if isfield(Data{1},'ProjObjectCoord')&& isfield(Data{1},'ProjObjectAngle')
435            ProjObjectCoord=Data{1}.ProjObjectCoord;
436            ProjObjectAngle=Data{1}.ProjObjectAngle;
437            for iview =2:numel(Data)
438                if ~(isfield(Data{iview},'ProjObjectCoord')&& isequal(Data{iview}.ProjObjectCoord,ProjObjectCoord))...
439                        ||~(isfield(Data{iview},'ProjObjectAngle')&& isequal(Data{iview}.ProjObjectAngle,ProjObjectAngle))
440                    ProjObjectCoord=[];%dt not the same for all fields
441                end
442            end
443            if ~isempty(ProjObjectCoord)
444                MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'ProjObjectCoord'} {'ProjObjectAngle'}];
445                MergeData.ProjObjectCoord=ProjObjectCoord;
446                MergeData.ProjObjectAngle=ProjObjectAngle;
447            end
448        end
449        % coord unit
450        if isfield(Data{1},'CoordUnit')
451            CoordUnit=Data{1}.CoordUnit;
452            for iview =2:numel(Data)
453                if ~(isfield(Data{iview},'CoordUnit')&& isequal(Data{iview}.CoordUnit,CoordUnit))
454                    CoordUnit=[];%CoordUnit not the same for all fields
455                end
456            end
457            if ~isempty(CoordUnit)
458                MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'CoordUnit'}];
459                MergeData.CoordUnit=CoordUnit;
460            end
461        end
462        % time unit
463        if isfield(Data{1},'TimeUnit')
464            TimeUnit=Data{1}.TimeUnit;
465            for iview =2:numel(Data)
466                if ~(isfield(Data{iview},'TimeUnit')&& isequal(Data{iview}.TimeUnit,TimeUnit))
467                    TimeUnit=[];%TimeUnit not the same for all fields
468                end
469            end
470            if ~isempty(TimeUnit)
471                MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'TimeUnit'}];
472                MergeData.TimeUnit=TimeUnit;
473            end
474        end
475        error=struct2nc(OutputFile,MergeData);%save result file
476        if isempty(error)
477            disp(['output file ' OutputFile ' written'])
478        else
479            disp(error)
480        end
481    end
482end
483ellapsed_time=toc(tstart);
484disp(['total ellapsed time ' num2str(ellapsed_time/60,2) ' minutes'])
485disp([ num2str(ellapsed_time/(60*NbField),3) ' minutes per iteration'])
486
487%'merge_field': concatene fields
488%------------------------------------------------------------------------
489function [MergeData,errormsg]=merge_field(Data)
490%% default output
491if isempty(Data)||~iscell(Data)
492    MergeData=[];
493    return
494end
495errormsg='';
496MergeData=Data{1};% merged field= first field by default, reproduces the global attributes of the first field
497NbView=length(Data);
498if NbView==1% if there is only one field, just reproduce it in MergeData
499    return
500end
501
502%% group the variables (fields of 'Data') in cells of variables with the same dimensions
503[CellInfo,NbDim,errormsg]=find_field_cells(Data{1});
504if ~isempty(errormsg)
505    return
506end
507
508%LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS
509for icell=1:length(CellInfo)
510    if NbDim(icell)~=1 % skip field cells which are of dim 1
511        switch CellInfo{icell}.CoordType
512            case 'scattered'  %case of input fields with unstructured coordinates: just concatene data
513                for ivar=CellInfo{icell}.VarIndex %  indices of the selected variables in the list FieldData.ListVarName
514                    VarName=Data{1}.ListVarName{ivar};
515                    for iview=2:NbView
516                        MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)];
517                    end
518                end
519            case 'grid'        %case of fields defined on a structured  grid
520                FFName='';
521                if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag)
522                    FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable
523                    MergeData.ListVarName(CellInfo{icell}.VarIndex_errorflag)=[];%remove error flag variable in MergeData (will use NaN instead)
524                    MergeData.VarDimName(CellInfo{icell}.VarIndex_errorflag)=[];
525                    MergeData.VarAttribute(CellInfo{icell}.VarIndex_errorflag)=[];
526                end
527                % select good data on each view
528                for ivar=CellInfo{icell}.VarIndex  %  indices of the selected variables in the list FieldData.ListVarName
529                    VarName=Data{1}.ListVarName{ivar};
530                    for iview=1:NbView
531                        if isempty(FFName)
532                            check_bad=isnan(Data{iview}.(VarName));%=0 for NaN data values, 1 else
533                        else
534                            check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else
535                        end
536                        Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
537                        if iview==1
538                            %MergeData.(VarName)=Data{1}.(VarName);% initiate MergeData with the first field
539                            MergeData.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
540                            NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point
541                        elseif size(Data{iview}.(VarName))~=size(MergeData.(VarName))
542                            errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object';
543                            return
544                        else                             
545                            MergeData.(VarName)=MergeData.(VarName) +double(Data{iview}.(VarName));%add data
546                            NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else
547                        end
548                    end
549                    MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point
550                    MergeData.(VarName)(NbAver==0)=NaN;% set to NaN the points with no good data
551                end
552        end
553    end
554end
555
556
557   
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