source: trunk/src/series/merge_proj_polar.m @ 943

Last change on this file since 943 was 943, checked in by sommeria, 6 years ago

merge_proj_polar corrected

File size: 25.6 KB
Line 
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 2008-2016, 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
148OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},'.nc','_1',i1_series{1}(1));
149CheckOverwrite=1;%default
150if isfield(Param,'CheckOverwrite')
151    CheckOverwrite=Param.CheckOverwrite;
152end
153if ~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
156end
157
158if ~isfield(Param,'InputFields')
159    Param.InputFields.FieldName='';
160end
161
162%% prepare output file content
163%     TimeData.ListGlobalAttribute={'Conventions','Project','CoordUnit','TimeUnit','ZPos'};
164%     TimeData.Conventions='uvmat';
165%     TimeData.Project='2016_Circumpolar';
166%     TimeData.CoordUnit='cm';
167%     TimeData.TimeUnit='s';
168%     TimeData.ZPos=0;
169%     TimeData.ListVarName={'time','radius','azimuth','U','V','curl','div'};
170%     TimeData.VarDimName={'time','radius','azimuth',{'time','radius','azimuth'},{'time','radius','azimuth'}...
171%                         {'time','radius','azimuth'},{'time','radius','azimuth'}};
172%                     TimeData.VarAttribute{1}.Role='';
173%                     TimeData.VarAttribute{2}.Role='';
174%                     TimeData.VarAttribute{3}.Role='';
175%                     TimeData.VarAttribute{4}.Role='vector_x';
176%                     TimeData.VarAttribute{5}.Role='vector_y';
177%                     TimeData.VarAttribute{6}.Role='scalar';
178%                     TimeData.VarAttribute{7}.Role='scalar';
179%                     TimeData.time=nan(1,NbField);
180%                     TimeData.radius=radius_shifted;
181%                     TimeData.azimuth=azimuth_arclength;
182%                     nby=numel(radius);
183%                     nbx=numel(azimuth);
184%                     TimeData.U=nan(NbField,nby,nbx);
185%                     TimeData.V=nan(NbField,nby,nbx);
186%                     TimeData.curl=nan(NbField,nby,nbx);
187%                     TimeData.div=nan(NbField,nby,nbx);
188                   
189%     if ~isempty(timeread)
190%         MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'Time'}];
191%         MergeData.Time=timeread;
192%     end
193   
194    % time unit
195%     if isfield(Data{1},'TimeUnit')
196%         TimeUnit=Data{1}.TimeUnit;
197%         for iview =2:numel(Data)
198%             if ~(isfield(Data{iview},'TimeUnit')&& isequal(Data{iview}.TimeUnit,TimeUnit))
199%                 TimeUnit=[];%TimeUnit not the same for all fields
200%             end
201%         end
202%         if ~isempty(TimeUnit)
203%             MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'TimeUnit'}];
204%             MergeData.TimeUnit=TimeUnit;
205%         end
206%     end
207
208
209%% determine the file type on each line from the first input file
210ImageTypeOptions={'image','multimage','mmreader','video'};
211NcTypeOptions={'netcdf','civx','civdata'};
212for iview=1:NbView
213    if ~exist(filecell{iview,1}','file')
214        disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
215        return
216    end
217    [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1});
218    FileType{iview}=FileInfo{iview}.FileType;
219    CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
220    if CheckImage{iview}
221        ParamIn{iview}=MovieObject{iview};
222    else
223        ParamIn{iview}=Param.InputFields;
224    end
225    CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
226    if ~isempty(j1_series{iview})
227        frame_index{iview}=j1_series{iview};
228    else
229        frame_index{iview}=i1_series{iview};
230    end
231end
232if NbView >1 && max(cell2mat(CheckImage))>0 && ~isfield(Param,'ProjObject')
233    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)
234    return
235end
236
237%% calibration data and timing: read the ImaDoc files
238[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
239if size(time,1)>1
240    diff_time=max(max(diff(time)));
241    if diff_time>0
242        disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time) ': the mean time is chosen in result'],checkrun)
243    end   
244end
245if ~isempty(errormsg)
246    disp_uvmat('WARNING',errormsg,checkrun)
247end
248time=mean(time,1); %averaged time taken for the merged field
249
250%% height z
251    % position of projection plane
252   
253ProjObjectCoord=XmlData{1}.GeometryCalib.SliceCoord;
254CoordUnit=XmlData{1}.GeometryCalib.CoordUnit;
255for iview =2:numel(XmlData)
256    if ~(isfield(XmlData{iview},'GeometryCalib')&& isequal(XmlData{iview}.GeometryCalib.SliceCoord,ProjObjectCoord))...
257        disp('error: geometric calibration missing or inconsistent plane positions')
258        return
259    end
260end
261
262
263%% coordinate transform or other user defined transform
264transform_fct='';%default fct handle
265if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
266        currentdir=pwd;
267        cd(Param.FieldTransform.TransformPath)
268        transform_fct=str2func(Param.FieldTransform.TransformName);
269        cd (currentdir)
270        if isfield(Param,'TransformInput')
271            for iview=1:NbView
272            XmlData{iview}.TransformInput=Param.TransformInput;
273            end
274        end       
275end
276%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
277 % EDIT FROM HERE
278
279%% check the validity of  input file types
280for iview=1:NbView
281    if ~isequal(CheckNc{iview},1)
282        disp_uvmat('ERROR','input files needs to be in netcdf (extension .nc)',checkrun)
283        return
284    end
285end
286
287% %% output file type
288if isempty(j1_series{1})
289    NomTypeOut='_1';
290else
291    NomTypeOut='_1_1';
292end
293RootFileOut=RootFile{1};
294for iview=2:NbView
295    if ~strcmp(RootFile{iview},RootFile{1})
296        RootFileOut='mproj';
297        break
298    end
299end
300
301
302%% MAIN LOOP ON FIELDS
303%%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
304% for i_slice=1:NbSlice
305%     index_slice=i_slice:NbSlice:NbField;% select file indices of the slice
306%     NbFiles=0;
307%     nbmissing=0;
308
309%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
310tstart=tic; %used to record the computing time
311
312
313for index=1:NbField
314    disp(['index=' num2str(index)])
315    disp(['ellapsed time ' num2str(toc(tstart)/60,4) ' minutes'])
316    update_waitbar(WaitbarHandle,index/NbField)
317    if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
318        disp('program stopped by user')
319        return
320    end
321   
322        %% generating the name of the merged field
323        i1=i1_series{1}(index);
324        if ~isempty(i2_series{end})
325            i2=i2_series{end}(index);
326        else
327            i2=i1;
328        end
329        j1=1;
330        j2=1;
331        if ~isempty(j1_series{1})
332            j1=j1_series{1}(index);
333            if ~isempty(j2_series{end})
334                j2=j2_series{end}(index);
335            else
336                j2=j1;
337            end
338        end
339       OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFileOut,'.nc',NomTypeOut,i1,i2,j1,j2);
340        if ~CheckOverwrite && exist(OutputFile,'file')
341            disp(['existing output file ' OutputFile ' already exists, skip to next field'])
342            continue% skip iteration if the mode overwrite is desactivated and the result file already exists
343        end
344   
345    %% z position
346    ZIndex=mod(i1_series{1}(index)-1,NbSlice_calib{1})+1;%Zindex for phys transform
347    ZPosNew=ProjObjectCoord(ZIndex,3);
348    if index==1
349        ZPos=ZPosNew;
350    else
351        if ZPosNew~=ZPos
352            disp('inconsistent z positions in the series')
353            return
354        end
355    end
356    % radius of the topography section at z position
357    ind_mask=[];
358    if ZPos<20
359        TopoRadius=40*sin(acos((20+ZPos)/40));
360        ind_mask=(XI'.*XI'+YI'.*YI')<TopoRadius*TopoRadius;% indidces of data to mask
361    end
362   
363    %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
364    Data=cell(1,NbView);%initiate the set Data
365    timeread=zeros(1,NbView);
366    for iview=1:NbView
367        %% reading input file(s)
368        [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},ParamIn{iview},frame_index{iview}(index));
369        if ~isempty(errormsg)
370            disp_uvmat('ERROR',['ERROR in merge_proj/read_field/' errormsg],checkrun)
371            return
372        end
373        ListVar=Data{iview}.ListVarName;
374        for ilist=1:numel(ListVar)
375            Data{iview}.(ListVar{ilist})=double(Data{iview}.(ListVar{ilist}));% transform all fields in double before all operations
376        end
377        % get the time defined in the current file if not already defined from the xml file
378        if ~isempty(time) && isfield(Data{iview},'Time')
379            timeread(iview)=Data{iview}.Time;
380        end
381        if ~isempty(NbSlice_calib)
382            Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
383        end
384       
385        %% transform the input field (e.g; phys) if requested (no transform involving two input fields)
386        if ~isempty(transform_fct)
387            if nargin(transform_fct)>=2
388                Data{iview}=transform_fct(Data{iview},XmlData{iview});
389            else
390                Data{iview}=transform_fct(Data{iview});
391            end
392        end
393       
394        %% calculate tps coefficients
395        Data{iview}=tps_coeff_field(Data{iview},1);
396       
397        %% projection on the polar grid
398        [DataOut,VarAttribute,errormsg]=calc_field_tps(Data{iview}.Coord_tps,Data{iview}.NbCentre,Data{iview}.SubRange,...
399            cat(3,Data{iview}.U_tps,Data{iview}.V_tps),FieldNames,cat(3,XI,YI));
400        % set to NaN interpolation points which are too far from any initial data (more than 2 CoordMesh)
401        Coord=permute(Data{iview}.Coord_tps,[1 3 2]);
402        Coord=reshape(Coord,size(Coord,1)*size(Coord,2),2);
403        if exist('scatteredInterpolant','file')%recent Matlab versions
404            F=scatteredInterpolant(Coord,Coord(:,1),'nearest');
405            G=scatteredInterpolant(Coord,Coord(:,2),'nearest');
406        else
407            F=TriScatteredInterp(Coord,Coord(:,1),'nearest');
408            G=TriScatteredInterp(Coord,Coord(:,2),'nearest');
409        end
410        Distx=F(XI,YI)-XI;% diff of x coordinates with the nearest measurement point
411        Disty=G(XI,YI)-YI;% diff of y coordinates with the nearest measurement point
412        Dist=Distx.*Distx+Disty.*Disty;
413        ListVarName=(fieldnames(DataOut))';
414        VarDimName=cell(size(ListVarName));
415        ProjData{iview}=HeadData;
416        ProjData{iview}.ListVarName= [ProjData{iview}.ListVarName ListVarName];
417        ProjData{iview}.VarDimName={'radius','azimuth'};
418        ProjData{iview}.VarAttribute=[{'coord_x'} {'coord_y'} VarAttribute];
419        for ivar=1:numel(ListVarName)
420            ProjData{iview}.VarDimName{ivar+2}={'radius','azimuth'};
421            VarName=ListVarName{ivar};
422            if ~isempty(thresh2)
423                DataOut.(VarName)(Dist>thresh2)=NaN;% put to NaN interpolated positions further than RangeInterp from initial data
424            end
425            ProjData{iview}.(VarName)=(DataOut.(VarName))';
426        end
427       
428    end
429    %%%%%%%%%%%%%%%% END LOOP ON VIEWS %%%%%%%%%%%%%%%%
430   
431    %% merge the NbView fields
432    [MergeData,errormsg]=merge_field(ProjData);
433    if ~isempty(errormsg)
434        disp_uvmat('ERROR',errormsg,checkrun);
435        return
436    end
437   
438   
439    %% time of the merged field: take the average of the different views
440    if ~isempty(time)
441        timeread=time(index);
442    elseif ~isempty(find(timeread))% time defined from ImaDoc
443        timeread=mean(timeread(timeread~=0));% take average over times form the files (when defined)
444    else
445        timeread=index;% take time=file index
446    end
447   
448    %% rotating the velocity vectors to the local axis of the polatr coordinates
449    Unew=MergeData.U.*sin(Azimuth')-MergeData.V.*cos(Azimuth');
450    Vnew=MergeData.U.*cos(Azimuth')+MergeData.V.*sin(Azimuth');
451    if ~isempty(ind_mask)
452        Unew(ind_mask)=NaN;
453        Vnew(ind_mask)=NaN;
454        MergeData.curl(ind_mask)=NaN;
455        MergeData.div(ind_mask)=NaN;
456    end
457    [npy,npx]=size(Unew);
458   
459    %% create the output file for the first iteration of the loop
460    if index==1
461        TimeData.ListGlobalAttribute={'Conventions','Project','CoordUnit','TimeUnit','ZPos','Time'};
462        TimeData.Conventions='uvmat';
463        TimeData.Project='2016_Circumpolar';
464        TimeData.CoordUnit='cm';
465        TimeData.TimeUnit='s';
466        TimeData.ZPos=ZPos;
467        TimeData.ListVarName={'radius','azimuth','U','V','curl','div'};
468        TimeData.VarDimName={'radius','azimuth',{'radius','azimuth'},{'radius','azimuth'}...
469            {'radius','azimuth'},{'radius','azimuth'}};
470        TimeData.VarAttribute{1}.Role='';
471        TimeData.VarAttribute{2}.Role='';
472        TimeData.VarAttribute{3}.Role='vector_x';
473        TimeData.VarAttribute{4}.Role='vector_y';
474        TimeData.VarAttribute{5}.Role='scalar';
475        TimeData.VarAttribute{6}.Role='scalar';
476       
477        TimeData.radius=radius_shifted;
478        TimeData.azimuth=azimuth_arclength;
479    end
480       
481        %% append data to the netcdf file for next iterations
482        TimeData.Time=timeread;
483       TimeData.U=Unew;
484       TimeData.V=Vnew;
485       TimeData.curl=MergeData.curl;
486       TimeData.div=MergeData.div;
487
488            [error,ncid]=struct2nc(OutputFile,TimeData);%save result file
489        if isempty(error)
490            disp(['output file ' OutputFile ' written'])
491        else
492            disp(error)
493        end
494            ellapsed_time=toc(tstart);
495    disp(['total ellapsed time ' num2str(ellapsed_time/60,2) ' minutes'])
496end
497
498ellapsed_time=toc(tstart);
499disp(['total ellapsed time ' num2str(ellapsed_time/60,2) ' minutes'])
500disp([ num2str(ellapsed_time/(60*NbField),3) ' minutes per iteration'])
501
502%'merge_field': concatene fields
503%------------------------------------------------------------------------
504function [MergeData,errormsg]=merge_field(Data)
505%% default output
506if isempty(Data)||~iscell(Data)
507    MergeData=[];
508    return
509end
510errormsg='';
511MergeData=Data{1};% merged field= first field by default, reproduces the global attributes of the first field
512NbView=length(Data);
513if NbView==1% if there is only one field, just reproduce it in MergeData
514    return
515end
516
517%% group the variables (fields of 'Data') in cells of variables with the same dimensions
518[CellInfo,NbDim,errormsg]=find_field_cells(Data{1});
519if ~isempty(errormsg)
520    return
521end
522
523%LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS
524for icell=1:length(CellInfo)
525    if NbDim(icell)~=1 % skip field cells which are of dim 1
526        switch CellInfo{icell}.CoordType
527            case 'scattered'  %case of input fields with unstructured coordinates: just concatene data
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=2:NbView
531                        MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)];
532                    end
533                end
534            case 'grid'        %case of fields defined on a structured  grid
535                FFName='';
536                if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag)
537                    FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable
538                    MergeData.ListVarName(CellInfo{icell}.VarIndex_errorflag)=[];%remove error flag variable in MergeData (will use NaN instead)
539                    MergeData.VarDimName(CellInfo{icell}.VarIndex_errorflag)=[];
540                    MergeData.VarAttribute(CellInfo{icell}.VarIndex_errorflag)=[];
541                end
542                % select good data on each view
543                for ivar=CellInfo{icell}.VarIndex  %  indices of the selected variables in the list FieldData.ListVarName
544                    VarName=Data{1}.ListVarName{ivar};
545                    for iview=1:NbView
546                        if isempty(FFName)
547                            check_bad=isnan(Data{iview}.(VarName));%=0 for NaN data values, 1 else
548                        else
549                            check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else
550                        end
551                        Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
552                        if iview==1
553                            %MergeData.(VarName)=Data{1}.(VarName);% initiate MergeData with the first field
554                            MergeData.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
555                            NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point
556                        elseif size(Data{iview}.(VarName))~=size(MergeData.(VarName))
557                            errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object';
558                            return
559                        else
560                            MergeData.(VarName)=MergeData.(VarName) +double(Data{iview}.(VarName));%add data
561                            NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else
562                        end
563                    end
564                    MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point
565                    MergeData.(VarName)(NbAver==0)=NaN;% set to NaN the points with no good data
566                end
567        end
568        %         if isempty(FFName)
569        %             FFName='FF';
570        %         end
571        %         MergeData.(FFName)(NbAver~=0)=0;% flag to 1 undefined summed data
572        %         MergeData.(FFName)(NbAver==0)=1;% flag to 1 undefined summed data
573    end
574end
575
576
577   
Note: See TracBrowser for help on using the repository browser.