source: trunk/src/series/aver_stat.m @ 984

Last change on this file since 984 was 984, checked in by sommeria, 4 years ago

introduce .cine in various functions, improve stero PIV

File size: 24.0 KB
Line 
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 2008-2017, 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=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': one output file per input file index, '=NbInput_i': one file per input file index i, '=NbSlice': one 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);
152
153hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
154% gives the series of input file names and indices set by the input parameters:
155[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
156% filecell{iview,fileindex}:
157%        iview: line in the table corresponding to a given file series
158%        fileindex: file index with i and j reshaped as a 1D array
159% 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
160% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
161if ~isempty(hdisp),delete(hdisp),end;%end the waiting display
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','cine_phantom'};
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
255
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
266NbSlice_j=1;% number of j slices =1 except fo volume scan
267index_series=1:size(filecell,2);
268index_j=1;
269
270%% set volume scan if requested
271first_j_out=first_j;%first j index to use  for the output file name
272last_j_out=last_j;%last j index to use for the output file name
273if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'CheckVolume') ...
274        && Param.ActionInput.CheckVolume
275    index_j=Param.IndexRange.first_j:Param.IndexRange.incr_j:Param.IndexRange.last_j;
276    NbSlice_j=numel(index_j);
277    index_series=1:NbSlice_j:size(filecell,2);
278end
279
280%% loop on j slices (volume scan)
281for islice=index_j
282    nbfiles=0;%counter of the successfully read files (bad files are skipped)
283    if NbSlice_j>1
284        first_j_out=islice;%first and last  j index to use  for the output file name are the current j index
285        last_j_out=islice;
286    end
287    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
288    %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
289    for index=index_series+index_j(islice)-index_j(1)
290        update_waitbar(WaitbarHandle,index/NbField)
291        if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
292            disp('program stopped by user')
293            break
294        end
295       
296        %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
297        for iview=1:NbView
298            % reading input file(s)
299            [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
300            if ~isempty(errormsg)
301                errormsg=['error of input reading: ' errormsg];
302                break% leave the loop on views in case of error
303            end
304            if ~isempty(NbSlice_calib)
305                Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
306            end
307        end
308        %%%%%%%%%%%%%%%% end loop on views (input lines) %%%%%%%%%%%%%%%%
309       
310        if ~isempty(errormsg)
311            disp(errormsg)
312            continue % go to next input field in case of error (file skipped in the average)
313        end
314        Field=Data{1}; % default input field structure
315        nbfiles=nbfiles+1; %increment the file counter
316       
317        %% coordinate transform (or other user defined transform)
318        if ~isempty(transform_fct)
319            switch nargin(transform_fct)
320                case 4
321                    if length(Data)==2
322                        Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});
323                    else
324                        Field=transform_fct(Data{1},XmlData{1});
325                    end
326                case 3
327                    if length(Data)==2
328                        Field=transform_fct(Data{1},XmlData{1},Data{2});
329                    else
330                        Field=transform_fct(Data{1},XmlData{1});
331                    end
332                case 2
333                    Field=transform_fct(Data{1},XmlData{1});
334                case 1
335                    Field=transform_fct(Data{1});
336            end
337        end
338       
339        %% field projection on an object
340        if Param.CheckObject
341            if strcmp(Param.ProjObject.ProjMode,'interp_tps')
342                Field=tps_coeff_field(Field,check_proj_tps);% calculate tps coefficients if needed
343            end
344            [Field,errormsg]=proj_field(Field,Param.ProjObject,VarMesh);
345            if ~isempty(errormsg)
346                disp_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg],checkrun)
347                return
348            end
349        end
350       
351        %%%%%%%%%%%% MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
352        if nbfiles==1 %first field
353            time_1=[];
354            if isfield(Field,'Time')
355                time_1=Field.Time(1);
356            end
357            DataOut=Field;%outcome reproduces the first (projected) field by default
358            DataOut.Conventions='uvmat'; %suppress Conventions='uvmat/civdata' for civ input files
359            if isfield(Param,'ProjObject')&& ismember(Param.ProjObject.ProjMode,{'inside','outside'})%case of histograms
360                for ivar=1:numel(Field.ListVarName)% list of variable names before projection (histogram)
361                    VarName=Field.ListVarName{ivar};
362                    if isfield(Data{1},VarName)
363                        DataOut.(VarName)=Field.(VarName);
364                        DataOut.([VarName 'Histo'])=zeros(size(DataOut.(VarName)));
365                        VarMesh=DataOut.(VarName)(2)-DataOut.(VarName)(1);
366                    end
367                end
368                disp(['mesh for histogram = ' num2str(VarMesh)])
369            else
370                errorvar=zeros(numel(Field.ListVarName));%index of errorflag associated to each variable
371                if isfield(Field,'VarAttribute')
372                    for ivar=1:numel(Field.ListVarName)
373                        VarName=Field.ListVarName{ivar};
374                        DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero
375                        NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero
376                       
377                        for iivar=1:length(Field.VarAttribute)
378                            if isequal(Field.VarDimName{iivar},Field.VarDimName{ivar})&& isfield(Field.VarAttribute{iivar},'Role')...
379                                    && strcmp(Field.VarAttribute{iivar}.Role,'errorflag')
380                                errorvar(ivar)=iivar; % index of the errorflag variable corresponding to ivar
381                            end
382                        end
383                    end
384                    DataOut.ListVarName(errorvar(errorvar~=0))=[]; %remove errorflag from result
385                    DataOut.VarDimName(errorvar(errorvar~=0))=[]; %remove errorflag from result
386                    DataOut.VarAttribute(errorvar(errorvar~=0))=[]; %remove errorflag from result
387                else
388                    for ivar=1:numel(Field.ListVarName)
389                        VarName=Field.ListVarName{ivar};
390                        DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero
391                        NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero
392                    end
393                end
394               
395            end
396        end   %current field
397        for ivar=1:length(DataOut.ListVarName)
398            VarName=DataOut.ListVarName{ivar};
399            sizmean=size(DataOut.(VarName));
400            siz=size(Field.(VarName));
401            if isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'})
402                if isfield(Data{1},VarName)
403                    MaxValue=max(DataOut.(VarName));% current max of histogram absissa
404                    MinValue=min(DataOut.(VarName));% current min of histogram absissa
405                    %                     VarMesh=Field.VarAttribute{ivar}.Mesh;
406                    MaxIndex=round(MaxValue/VarMesh);
407                    MinIndex=round(MinValue/VarMesh);
408                    MaxIndex_new=round(max(Field.(VarName)/VarMesh));% max of the current field
409                    MinIndex_new=round(min(Field.(VarName)/VarMesh));
410                    if MaxIndex_new>MaxIndex% the variable max for the current field exceeds the previous one
411                        DataOut.(VarName)=[DataOut.(VarName) VarMesh*(MaxIndex+1:MaxIndex_new)];% append the new variable values
412                        DataOut.([VarName 'Histo'])=[DataOut.([VarName 'Histo']) zeros(1,MaxIndex_new-MaxIndex)]; % append the new histo values
413                    end
414                    if MinIndex_new <= MinIndex-1
415                        DataOut.(VarName)=[VarMesh*(MinIndex_new:MinIndex-1) DataOut.(VarName)];% insert the new variable values
416                        DataOut.([VarName 'Histo'])=[zeros(1,MinIndex-MinIndex_new) DataOut.([VarName 'Histo'])];% insert the new histo values
417                        ind_start=1;
418                    else
419                        ind_start=MinIndex_new-MinIndex+1;
420                    end
421                    DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_new-MinIndex_new)=...
422                        DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_new-MinIndex_new)+Field.([VarName 'Histo']);
423                end
424            elseif ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean)
425                disp_uvmat('ERROR',['unequal size of input field ' VarName ', need to project  on a grid'],checkrun)
426                return
427            else
428                if errorvar(ivar)==0
429                    check_bad=isnan(Field.(VarName));%=0 for NaN data values, 1 else
430                else
431                    check_bad=isnan(Field.(VarName)) | Field.(Field.ListVarName{errorvar(ivar)})~=0;%=0 for NaN or error flagged data values, 1 else
432                end
433                Field.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
434                DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum
435                NbData.(VarName)=NbData.(VarName)+ ~check_bad;% records the number of data for each point
436            end
437        end
438        %%%%%%%%%%%%   END MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
439    end
440    %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%%
441   
442    if ~(isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'}))
443        for ivar=1:length(Field.ListVarName)
444            VarName=Field.ListVarName{ivar};
445            DataOut.(VarName)=DataOut.(VarName)./NbData.(VarName); % normalize the mean
446        end
447    end
448    nbmissing=numel(index_series+index_j(islice)-index_j(1))-nbfiles;
449    if nbmissing~=0
450        if NbSlice_j==1
451        disp_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipped'],checkrun)
452        else
453            disp(['WARNING: ' num2str(nbmissing) ' input files are missing or skipped in slice ' num2str(islice)])
454        end
455    end
456    if isempty(time) % time is read from files
457        if isfield(Field,'Time')
458            time_end=Field.Time(1);%last time read
459            if ~isempty(time_1)
460                DataOut.Time=time_1;
461                DataOut.Time_end=time_end;
462            end
463        end
464    else  % time from ImaDoc prevails if it exists
465        DataOut.Time=time(1);
466        DataOut.Time_end=time(end);
467    end
468   
469    %% writing the result file
470    OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j_out,last_j_out);
471    if strcmp(FileExtOut,'.png') %case of images
472        if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16))
473            DataOut.A=uint16(DataOut.A);
474            imwrite(DataOut.A,OutputFile,'BitDepth',16); % case of 16 bit images
475        else
476            DataOut.A=uint8(DataOut.A);
477            imwrite(DataOut.A,OutputFile,'BitDepth',8); % case of 16 bit images
478        end
479        disp([OutputFile ' written']);
480    else %case of netcdf  file , determine global attributes
481        errormsg=struct2nc(OutputFile,DataOut); %save result file
482        if isempty(errormsg)
483            disp([OutputFile ' written']);
484        else
485            disp(['error in writting result file: ' errormsg])
486        end
487    end  % end averaging  loop
488end
489
490%% open the result file with uvmat (in RUN mode)
491if checkrun
492    uvmat(OutputFile)% open the last result file with uvmat
493end
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