source: trunk/src/series/aver_stat.m @ 959

Last change on this file since 959 was 959, checked in by sommeria, 5 years ago

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1%'aver_stat': calculate field average over a time series
2%------------------------------------------------------------------------
3% function ParamOut=aver_stat(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=aver_stat(Param)
60
61%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
62if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN
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='on'; %nbre of slices ('off' by default)
66    ParamOut.VelType='two';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
67    ParamOut.FieldName='two';% 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.ProjObject='on';%can use projection object(option 'off'/'on',
70    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
71    ParamOut.OutputDirExt='.stat';%set the output dir extension
72    ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
73     % check for selection of a projection object
74    hseries=findobj(allchild(0),'Tag','series');% handles of the GUI series
75    if  ~isfield(Param,'ProjObject')
76        answer=msgbox_uvmat('INPUT_Y-N','use a projection object?');
77        if strcmp(answer,'Yes')
78            hhseries=guidata(hseries);
79            set(hhseries.CheckObject,'Visible','on')
80            set(hhseries.CheckObject,'Value',1)
81            Param.CheckObject=1;
82            series('CheckObject_Callback',hseries,[],hhseries); %file input with xml reading  in uvmat, show the image in phys coordinates
83        end
84    end
85    % introduce bin size for histograms
86    if isfield(Param,'CheckObject') && Param.CheckObject
87        SeriesData=get(hseries,'UserData');
88        if ismember(SeriesData.ProjObject.ProjMode,{'inside','outside'})
89            answer=msgbox_uvmat('INPUT_TXT','set bin size for histograms (or keep ''auto'' by default)?','auto');
90            ParamOut.ActionInput.VarMesh=str2num(answer);
91        end
92    end
93    % check the existence of the first and last file in the series
94    first_j=[];
95    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
96    last_j=[];
97    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
98    PairString='';
99    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
100    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
101    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
102        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
103    if ~exist(FirstFileName,'file')
104        msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
105    else
106        [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
107        LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
108        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
109        if ~exist(LastFileName,'file')
110             msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist'])
111        end
112    end
113    % determine volume scan mode
114        prompt = {'volume scan mode (Yes/No)'};
115    dlg_title = 'determine volume scan';
116    num_lines= 1;
117    def     = { 'No'};
118     answer=msgbox_uvmat('INPUT_Y-N','volume scan mode (OK/No)?');
119%     answer = inputdlg(prompt,dlg_title,num_lines,def);
120    if isempty(answer)
121        return
122    end
123    %check input consistency
124    if strcmp(answer,'Yes')
125            ParamOut.NbSlice=1;% set NbSlice to 1 ( for i index)
126            ParamOut.ActionInput.CheckVolume=1;
127    end
128    return
129end
130
131%%%%%%%%%%%%  STANDARD PART  %%%%%%%%%%%%
132ParamOut=[];%default output
133%% read input parameters from an xml file if input is a file name (batch mode)
134checkrun=1;
135if ischar(Param)
136    Param=xml2struct(Param);% read Param as input file (batch case)
137    checkrun=0;
138end
139hseries=findobj(allchild(0),'Tag','series');
140RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
141WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
142
143%% define the directory for result file (with path=RootPath{1})
144OutputDir=[Param.OutputSubDir Param.OutputDirExt];
145   
146%% root input file(s) name, type and index series
147RootPath=Param.InputTable(:,1);
148RootFile=Param.InputTable(:,3);
149SubDir=Param.InputTable(:,2);
150NomType=Param.InputTable(:,4);
151FileExt=Param.InputTable(:,5);
152hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
153[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
154if ~isempty(hdisp),delete(hdisp),end;
155%%%%%%%%%%%%
156% The cell array filecell is the list of input file names, while
157% filecell{iview,fileindex}:
158%        iview: line in the table corresponding to a given file series
159%        fileindex: file index within  the file series,
160% 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
161% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
162%%%%%%%%%%%%
163NbView=numel(i1_series);%number of input file series (lines in InputTable)
164NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
165NbField_i=size(i1_series{1},2); %nb of fields for the i index
166NbField=NbField_j*NbField_i; %total number of fields
167
168%% determine the file type on each line from the first input file
169ImageTypeOptions={'image','multimage','mmreader','video'};
170NcTypeOptions={'netcdf','civx','civdata'};
171for iview=1:NbView
172    if ~exist(filecell{iview,1}','file')
173        disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
174        return
175    end
176    [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1});
177    FileType{iview}=FileInfo{iview}.FileType;
178    CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
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
186
187%% calibration data and timing: read the ImaDoc files
188[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
189if size(time,1)>1
190    diff_time=max(max(diff(time)));
191    if diff_time>0
192        disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun)
193    end   
194end
195
196%% coordinate transform or other user defined transform
197transform_fct='';%default
198if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
199    addpath(Param.FieldTransform.TransformPath)
200    transform_fct=str2func(Param.FieldTransform.TransformName);
201    rmpath(Param.FieldTransform.TransformPath)
202    if isfield(Param,'TransformInput')
203            XmlData{1}.TransformInput=Param.TransformInput;
204    end     
205end
206
207%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
208 % EDIT FROM HERE
209
210%% check the validity of  input file types and set the output file type
211if CheckImage{1}
212    FileExtOut='.png'; % write result as .png images for image inputs
213elseif CheckNc{1}
214    FileExtOut='.nc';% write result as .nc files for netcdf inputs
215else
216    disp_uvmat('ERROR',['invalid file type input ' FileType{1}],checkrun)
217    return
218end
219if NbView==2 && ~isequal(CheckImage{1},CheckImage{2})
220    disp_uvmat('ERROR','input must be two image series or two netcdf file series',checkrun)
221    return
222end
223if isfield(Param,'ProjObject') && ~strcmp(Param.ProjObject.Type,'plane')
224      FileExtOut='.nc';% write result as .nc files (even for image input)
225end
226
227%% settings for the output file
228NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file
229first_i=i1_series{1}(1);
230last_i=i1_series{1}(end);
231if isempty(j1_series{1})% if there is no second index j
232    first_j=1;last_j=1;
233else
234    first_j=j1_series{1}(1);
235    last_j=j1_series{1}(end);
236end
237
238%% Set field names and velocity types
239InputFields{1}=[];%default (case of images)
240if NbView==2
241    InputFields{2}=[];%default (case of images)
242end
243if isfield(Param,'InputFields')
244    InputFields{1}=Param.InputFields;
245    if NbView==2
246        InputFields{2}=Param.InputFields;%default
247        if isfield(Param.InputFields,'FieldName_1')
248            InputFields{2}.FieldName=Param.InputFields.FieldName_1;
249            if isfield(Param.InputFields,'VelType_1')
250                InputFields{2}.VelType=Param.InputFields.VelType_1;
251            end
252        end
253    end
254end
255nbfiles=0;%counter of the successfully read files (bad files are skipped)
256VarMesh=[];
257if isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'})
258    if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'VarMesh')%case of histograms
259     VarMesh=Param.ActionInput.VarMesh;
260    else
261       VarMesh=[];
262       disp_uvmat('WARNING','automatic bin size for histograms, select aver_stat again to set the value',checkrun)
263    end
264end
265
266%% set volume scan
267NbSlice_j=1;
268index_series=1:size(filecell,2);
269first_j_out=first_j;
270last_j_out=last_j;
271if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'CheckVolume') ...
272        && Param.ActionInput.CheckVolume
273   index_j=Param.IndexRange.first_j:Param.IndexRange.incr_j:Param.IndexRange.last_j;
274   NbSlice_j=numel(index_j);
275   index_i=index_series(1:NbSlice_j:end);
276end
277
278%%% loop on slices (volume scan)
279for islice=index_j
280    if NbSlice_j>1
281    first_j_out=islice;
282    last_j_out=islice;
283   
284    end
285    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
286    %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
287    for index=index_i+index_j(islice)
288        update_waitbar(WaitbarHandle,index/NbField)
289        if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
290            disp('program stopped by user')
291            break
292        end
293       
294        %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
295        for iview=1:NbView
296            % reading input file(s)
297            %InputFile=fullfile_uvmat(RootPath{iview},SubDir{iview},RootFile{iview},FileExt{iview},NomType{iview},first_i,last_i,first_j_out,last_j_out);
298            [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
299            if ~isempty(errormsg)
300                errormsg=['error of input reading: ' errormsg];
301                break
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        end
307        %%%%%%%%%%%%%%%% end loop on views (input lines) %%%%%%%%%%%%%%%%
308       
309        if isempty(errormsg)
310            Field=Data{1}; % default input field structure
311            nbfiles=nbfiles+1; %increment the file counter
312            %% coordinate transform (or other user defined transform)
313            if ~isempty(transform_fct)
314                switch nargin(transform_fct)
315                    case 4
316                        if length(Data)==2
317                            Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});
318                        else
319                            Field=transform_fct(Data{1},XmlData{1});
320                        end
321                    case 3
322                        if length(Data)==2
323                            Field=transform_fct(Data{1},XmlData{1},Data{2});
324                        else
325                            Field=transform_fct(Data{1},XmlData{1});
326                        end
327                    case 2
328                        Field=transform_fct(Data{1},XmlData{1});
329                    case 1
330                        Field=transform_fct(Data{1});
331                end
332            end
333           
334            %% field projection on an object
335            if Param.CheckObject
336                if strcmp(Param.ProjObject.ProjMode,'interp_tps')
337                    Field=tps_coeff_field(Field,check_proj_tps);% calculate tps coefficients if needed
338                end
339                [Field,errormsg]=proj_field(Field,Param.ProjObject,VarMesh);
340                if ~isempty(errormsg)
341                    disp_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg],checkrun)
342                    return
343                end
344            end
345           
346            %%%%%%%%%%%% MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
347            if nbfiles==1 %first field
348                time_1=[];
349                if isfield(Field,'Time')
350                    time_1=Field.Time(1);
351                end
352                DataOut=Field;%outcome reproduces the first (projected) field by default
353                DataOut.Conventions='uvmat'; %suppress Conventions='uvmat/civdata' for civ input files
354                if isfield(Param,'ProjObject')&& ismember(Param.ProjObject.ProjMode,{'inside','outside'})%case of histograms
355                    for ivar=1:numel(Field.ListVarName)% list of variable names before projection (histogram)
356                        VarName=Field.ListVarName{ivar};
357                        if isfield(Data{1},VarName)
358                            DataOut.(VarName)=Field.(VarName);
359                            DataOut.([VarName 'Histo'])=zeros(size(DataOut.(VarName)));
360                            VarMesh=DataOut.(VarName)(2)-DataOut.(VarName)(1);
361                        end
362                    end
363                    disp(['mesh for histogram = ' num2str(VarMesh)])
364                else
365                    errorvar=zeros(numel(Field.ListVarName));%index of errorflag associated to each variable
366                    if isfield(Field,'VarAttribute')
367                        for ivar=1:numel(Field.ListVarName)
368                            VarName=Field.ListVarName{ivar};
369                            DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero
370                            NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero
371                           
372                            for iivar=1:length(Field.VarAttribute)
373                                if isequal(Field.VarDimName{iivar},Field.VarDimName{ivar})&& isfield(Field.VarAttribute{iivar},'Role')...
374                                        && strcmp(Field.VarAttribute{iivar}.Role,'errorflag')
375                                    errorvar(ivar)=iivar; % index of the errorflag variable corresponding to ivar
376                                end
377                            end
378                        end
379                        DataOut.ListVarName(errorvar(errorvar~=0))=[]; %remove errorflag from result
380                        DataOut.VarDimName(errorvar(errorvar~=0))=[]; %remove errorflag from result
381                        DataOut.VarAttribute(errorvar(errorvar~=0))=[]; %remove errorflag from result
382                    else
383                        for ivar=1:numel(Field.ListVarName)
384                            VarName=Field.ListVarName{ivar};
385                            DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero
386                            NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero
387                        end
388                    end
389                   
390                end
391            end   %current field
392            for ivar=1:length(DataOut.ListVarName)
393                VarName=DataOut.ListVarName{ivar};
394                sizmean=size(DataOut.(VarName));
395                siz=size(Field.(VarName));
396                if isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'})
397                    if isfield(Data{1},VarName)
398                        MaxValue=max(DataOut.(VarName));% current max of histogram absissa
399                        MinValue=min(DataOut.(VarName));% current min of histogram absissa
400                        %                     VarMesh=Field.VarAttribute{ivar}.Mesh;
401                        MaxIndex=round(MaxValue/VarMesh);
402                        MinIndex=round(MinValue/VarMesh);
403                        MaxIndex_new=round(max(Field.(VarName)/VarMesh));% max of the current field
404                        MinIndex_new=round(min(Field.(VarName)/VarMesh));
405                        if MaxIndex_new>MaxIndex% the variable max for the current field exceeds the previous one
406                            DataOut.(VarName)=[DataOut.(VarName) VarMesh*(MaxIndex+1:MaxIndex_new)];% append the new variable values
407                            DataOut.([VarName 'Histo'])=[DataOut.([VarName 'Histo']) zeros(1,MaxIndex_new-MaxIndex)]; % append the new histo values
408                        end
409                        if MinIndex_new <= MinIndex-1
410                            DataOut.(VarName)=[VarMesh*(MinIndex_new:MinIndex-1) DataOut.(VarName)];% insert the new variable values
411                            DataOut.([VarName 'Histo'])=[zeros(1,MinIndex-MinIndex_new) DataOut.([VarName 'Histo'])];% insert the new histo values
412                            ind_start=1;
413                        else
414                            ind_start=MinIndex_new-MinIndex+1;
415                        end
416                        DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_new-MinIndex_new)=...
417                            DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_new-MinIndex_new)+Field.([VarName 'Histo']);
418                    end
419                elseif ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean)
420                    disp_uvmat('ERROR',['unequal size of input field ' VarName ', need to project  on a grid'],checkrun)
421                    return
422                else
423                    if errorvar(ivar)==0
424                        check_bad=isnan(Field.(VarName));%=0 for NaN data values, 1 else
425                    else
426                        check_bad=isnan(Field.(VarName)) | Field.(Field.ListVarName{errorvar(ivar)})~=0;%=0 for NaN or error flagged data values, 1 else
427                    end
428                    Field.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
429                    DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum
430                    NbData.(VarName)=NbData.(VarName)+ ~check_bad;% records the number of data for each point
431                end
432            end
433            %%%%%%%%%%%%   END MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
434        else
435            disp(errormsg)
436        end
437    end
438    %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%%
439
440if ~(isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'}))
441    for ivar=1:length(Field.ListVarName)
442        VarName=Field.ListVarName{ivar};
443        DataOut.(VarName)=DataOut.(VarName)./NbData.(VarName); % normalize the mean
444    end
445end
446nbmissing=NbField-nbfiles;
447if nbmissing~=0
448    disp_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipped'],checkrun)
449end
450if isempty(time) % time is read from files
451    if isfield(Field,'Time')
452        time_end=Field.Time(1);%last time read
453        if ~isempty(time_1)
454            DataOut.Time=time_1;
455            DataOut.Time_end=time_end;
456        end
457    end
458else  % time from ImaDoc prevails if it exists
459    DataOut.Time=time(1);
460    DataOut.Time_end=time(end);
461end
462
463%% writing the result file
464OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j_out,last_j_out);
465if strcmp(FileExtOut,'.png') %case of images
466    if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16))
467        DataOut.A=uint16(DataOut.A);
468        imwrite(DataOut.A,OutputFile,'BitDepth',16); % case of 16 bit images
469    else
470        DataOut.A=uint8(DataOut.A);
471        imwrite(DataOut.A,OutputFile,'BitDepth',8); % case of 16 bit images
472    end
473    disp([OutputFile ' written']);
474else %case of netcdf  file , determine global attributes
475    errormsg=struct2nc(OutputFile,DataOut); %save result file
476    if isempty(errormsg)
477        disp([OutputFile ' written']);
478    else
479        disp(['error in writting result file: ' errormsg])
480    end
481end  % end averaging  loop
482end
483
484%% open the result file with uvmat (in RUN mode)
485if checkrun
486    uvmat(OutputFile)% open the last result file with uvmat
487end
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