source: trunk/src/series/aver_stat.m @ 43

Last change on this file since 43 was 43, checked in by gostiaux, 11 years ago

improved use of movie input

File size: 19.6 KB
Line 
1function GUI_input=aver_stat(num_i1,num_i2,num_j1,num_j2,Series)
2%----------------------------------------------------------------------
3% --- make average on a series of files
4%----------------------------------------------------------------------
5%INPUT:
6%num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
7%num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
8%num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ )
9%num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ)
10%OTHER INPUTS given by the structure Series
11%  Series.Time:
12%  Series.GeometryCalib:%requests for the visibility of input windows in the GUI series  (activated directly by the selection in the menu ACTION)
13if ~exist('num_i1','var')
14    GUI_input={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one')
15        'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default)
16        'RootFile';'on';... %root input file name ('on' by default)
17        'FileExt';'on';... %input file extension ('on' by default)
18        'NomType';'on';...%type of file indexing ('on' by default)
19        'NbSlice';'on'; ...%nbre of slices ('off' by default)
20        'VelTypeMenu';'two';...% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
21        'FieldMenu';'two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
22        'CoordType'; 'on';...%can use a transform function
23        'GetObject';'on';...%can use projection object(option 'off'/'one'/'two',
24        %'GetMask';'on'...%can use mask option   
25        %'PARAMETER'; %options: name of the user defined parameter',repeat a line for each parameter
26               ''};
27        return
28end
29
30%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
31hseries=guidata(Series.hseries);%handles of the GUI series
32WaitbarPos=get(hseries.waitbar_frame,'Position');
33%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
34
35%projection object
36test_object=get(hseries.GetObject,'Value');
37if test_object%isfield(Series,'sethandles')
38    hset_object=findobj(allchild(0),'Name','set_object');
39    ProjObject=read_set_object(guidata(hset_object));
40    %answeryes=questdlg({['field series projected on ' Series.ProjObject.Style]});
41    answeryes=msgbox_uvmat('INPUT_Y-N',['field series projected on ' ProjObject.Style ' before averaging']);
42    if ~isequal(answeryes,'Yes')
43        return
44    end
45end
46
47%root input file and type
48if ~iscell(Series.RootPath)% case of a single input field series
49    num_i1={num_i1};num_j1={num_j1};num_i2={num_i2};num_j2={num_j2};
50    RootPath={Series.RootPath};
51    RootFile={Series.RootFile};
52    SubDir={Series.SubDir};
53    FileExt={Series.FileExt};
54    NomType={Series.NomType};
55else
56    RootPath=Series.RootPath;
57    RootFile=Series.RootFile;
58    SubDir=Series.SubDir;
59    NomType=Series.NomType;
60    FileExt=Series.FileExt;
61end   
62ext=FileExt{1};
63form=imformats(ext([2:end]));%test valid Matlab image formats
64testima=0;
65if ~isempty(form)||isequal(lower(ext),'.avi')||isequal(lower(ext),'.vol')
66    testima(1)=1;
67end
68if length(FileExt)>=2
69    ext_1=FileExt{2};
70    form=imformats(ext_1([2:end]));%test valid Matlab image formats
71    if ~isempty(form)||isequal(lower(ext_1),'.avi')||isequal(lower(ext_1),'.vol')
72        testima(2)=1;
73    end
74    if testima(2)~=testima(1)
75        msgbox_uvmat('ERROR','images and netcdf files cannot be compared')
76        return
77    end
78end
79
80%Number of input series: this function  accepts two input file series at most (then it operates on the difference of fields)
81nbview=length(RootPath);
82if nbview>2 
83    RootPath=RootPath(1:2);
84    set(hseries.RootPath,'String',RootPath)
85    SubDir=SubDir(1:2);
86    set(hseries.SubDir,'String',SubDir)
87    RootFile=RootFile(1:2);
88    set(hseries.RootFile,'String',RootFile)
89    NomType=NomType(1:2);
90    FileExt=FileExt(1:2);
91    set(hseries.FileExt,'String',FileExt)
92    nbview=2;
93end
94
95%determine image type
96hhh=which('mmreader');
97for iview=1:nbview
98    if isequal(FileExt{iview},'.nc')||isequal(FileExt{iview},'.cdf')
99        FileType{iview}='netcdf';
100    elseif isequal(lower(FileExt{iview}),'.avi')
101        if ~isequal(hhh,'')&& mmreader.isPlatformSupported()
102            MovieObject{iview}=mmreader(fullfile(RootPath{iview},[RootFile{iview} FileExt{iview}]));
103            FileType{iview}='movie';
104        else
105            FileType{iview}='avi';
106        end
107    elseif isequal(lower(FileExt{iview}),'.vol')
108        FileType{iview}='vol';
109    else
110       form=imformats(FileExt{iview}(2:end));
111       if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
112           if isequal(NomType{iview},'*');
113               FileType{iview}='multimage';
114           else
115               FileType{iview}='image';
116           end
117       end
118    end
119end
120
121% number of slices
122NbSlice=str2num(get(hseries.NbSlice,'String'));
123if isempty(NbSlice)
124    NbSlice=1;
125end
126NbSlice_name=num2str(NbSlice);
127
128% Field and velocity type (the same for the two views)
129Field_str=get(hseries.FieldMenu,'String');
130FieldName=[]; %default
131testfield=get(hseries.FieldMenu,'Visible');
132if isequal(testfield,'on')
133    val=get(hseries.FieldMenu,'Value');
134    FieldName=Field_str(val);%the same set of fields for all views
135    if isequal(FieldName,{'get_field...'})
136        hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI
137        if length(hget_field)>1
138            delete(hget_field(2:end))
139        elseif isempty(hget_field)
140           filename=...
141                 name_generator(fullfile(RootPath{1},RootFile{1}),num_i1{1}(1),num_j1{1}(1),FileExt{1},NomType{1},1,num_i2{1}(1),num_j2{1}(1),SubDir{1});
142           get_field(filename);
143           return
144        end
145        %hhget_field=guidata(hget_field);%handles of GUI elements in get_field
146        SubField=read_get_field(hget_field); %read the names of the variables to plot in the get_field GUI
147    end
148end
149%detect whether the two files are 'images' or 'netcdf'
150% testima=0;
151% testvol=0;
152testcivx=0;
153% testnc=0;
154FileExt=get(hseries.FileExt,'String');
155% test_movie=0;
156% for iview=1:nbview
157%      ext=FileExt{iview};
158%      form=imformats(ext([2:end]));
159%      if isequal(lower(ext),'.vol')
160%          testvol=testvol+1;
161%      elseif ~isempty(form)||isequal(lower(ext),'.avi')% if the extension corresponds to an image format recognized by Matlab
162%          testima=testima+1;
163%      elseif isequal(ext,'.nc')
164%          testnc=testnc+1;
165%      end
166% end
167% if testvol
168%     msgbox_uvmat('ERROR','volume images not implemented yet')
169%     return
170% end
171% if testnc~=nbview && testima~=nbview && testvol~=nbview
172%     msgbox_uvmat('ERROR','compare two image series or two netcdf files with the same fields as input')
173%     return
174% end
175if ~isequal(FieldName,{'get_field...'})
176    testcivx=isequal(FileType{1},'netcdf');
177end
178% if ~isequal(FieldName,{'get_field...'})
179%     if isequal(FieldName,{''}) && ~testima
180%         msgbox_uvmat('ERROR','an input field needs to be selected')
181%         return
182%     end
183%     testcivx=testnc;
184% end
185
186if testcivx
187    VelType_str=get(hseries.VelTypeMenu,'String');
188    VelType_val=get(hseries.VelTypeMenu,'Value');
189    VelType{1}=VelType_str{VelType_val};
190    if nbview==2
191        VelType_str=get(hseries.VelTypeMenu_1,'String');
192        VelType_val=get(hseries.VelTypeMenu_1,'Value');
193        VelType{2}=VelType_str{VelType_val};
194    end
195end
196
197%Calibration data and timing: read the ImaDoc files
198mode=''; %default
199timecell={};
200itime=0;
201NbSlice_calib={};
202for iview=1:nbview%Loop on views
203    XmlData{iview}=[];%default
204    filebase{iview}=fullfile(RootPath{iview},RootFile{iview});
205    if exist([filebase{iview} '.xml'],'file')
206        [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']);
207        if isfield(XmlData{iview},'Time')
208            itime=itime+1;
209            timecell{itime}=XmlData{iview}.Time;
210        end
211        if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord')
212            NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform
213            if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
214                msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
215            end
216        end
217    elseif exist([filebase{iview} '.civ'],'file')
218        [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']);
219        itime=itime+1;
220        timecell{itime}=time;
221        XmlData{iview}.Time=time;
222        GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
223        GeometryCalib.Tx=0;
224        GeometryCalib.Ty=0;
225        GeometryCalib.Tz=1;
226        GeometryCalib.dpx=1;
227        GeometryCalib.dpy=1;
228        GeometryCalib.sx=1;
229        GeometryCalib.Cx=0;
230        GeometryCalib.Cy=0;
231        GeometryCalib.f=1;
232        GeometryCalib.kappa1=0;
233        GeometryCalib.CoordUnit='cm';
234        XmlData{iview}.GeometryCalib=GeometryCalib;
235        if error==1
236            msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
237        end
238    end
239end
240
241%check coincidence in time
242multitime=0;
243if length(timecell)==0
244    time=[];
245elseif length(timecell)==1
246    time=timecell{1};
247elseif length(timecell)>1
248    multitime=1;
249    for icell=1:length(timecell)
250        if ~isequal(size(timecell{icell}),size(timecell{1}))
251            msgbox_uvmat('WARNING','inconsistent time array dimensions in ImaDoc fields, the time for the first series is used')
252            time=timecell{1};
253            multitime=0;
254            break
255        end
256    end
257end
258if multitime
259    for icell=1:length(timecell)
260        time(icell,:,:)=timecell{icell};
261    end
262    diff_time=max(max(diff(time)));
263    if diff_time>0
264        msgbox_uvmat('WARNING',['times of series differ by more than ' num2str(diff_time)])
265    end   
266end
267if size(time,2) < num_i2{1}(end) || size(time,3) < num_j2{1}(end)% ime array absent or too short in ImaDoc xml file'
268    time=[];
269end
270
271% Root name of output files (TO GENERALISE FOR TWO INPUT SERIES)
272subdir_result='aver_stat';
273if ~exist(fullfile(RootPath{1},subdir_result),'dir')
274    dircur=pwd; %record current working directory
275    cd(RootPath{1})% goes to the iamge directory
276    [m1,m2,m3]=mkdir(subdir_result);
277    if ~isequal(m2,'')
278         msgbox_uvmat('CONFIRMATION',m2);%error message for directory creation
279    end
280    cd(dircur) %back to the initial working directory
281end
282filebase_out=filebase{1};
283NomTypeOut=nomtype2pair(NomType{1},num_i2{end}(end)-num_i1{1}(1),num_j2{end}(end)-num_j1{1}(1));
284
285% coordinate transform or other user defined transform
286transform_fct=[];%default
287if isfield(Series,'transform_fct')
288    transform_fct=Series.transform_fct;
289end
290
291%slice loop
292siz=size(num_i1{1});
293lengthtot=siz(1)*siz(2);
294nbfield=floor(lengthtot/(siz(1)*NbSlice));%total number of i indexes (adjusted to an integer number of slices)
295nbfield_slice=nbfield*siz(1);% number of fields per slice
296
297for i_slice=1:NbSlice
298   S=0; %initiate the image sum S
299   nbfiles=0;
300   nbmissing=0;
301    %averaging loop
302   for ifile=i_slice:NbSlice:lengthtot
303        stopstate=get(hseries.RUN,'BusyAction');
304        if isequal(stopstate,'queue') % enable STOP command
305             update_waitbar(hseries.waitbar,WaitbarPos,ifile/lengthtot)
306             for iview=1:nbview
307                [filename]=...
308                           name_generator(filebase{iview},num_i1{iview}(ifile),num_j1{iview}(ifile),FileExt{iview},NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile),SubDir{iview});
309                if ~isequal(FileType{iview},'netcdf')               
310                    Data{iview}.ListVarName={'A'};
311                    Data{iview}.AName='image';
312                    switch FileType{iview}
313                        case 'movie'
314                            A=read(MovieObject{iview},num_i1{iview}(ifile));
315                        case 'avi'
316                            mov=aviread(filename,num_i1{iview}(ifile));
317                            A=frame2im(mov(1));
318                        case 'vol'
319                            A=imread(filename);
320                        case 'multimage'
321                            A=imread(filename,num_i1{iview}(ifile));
322                        case 'image'
323                            A=imread(filename);
324                    end
325                    Data{iview}.ListVarName={'coord_y','coord_x','A'}; %
326                    Atype{iview}=class(A);
327                    npy=size(A,1);
328                    npx=size(A,2);
329                    nbcolor=size(A,3);
330                    if nbcolor==3
331                         Data{iview}.VarDimName={'coord_y','coord_x',{'coord_y','coord_x','rgb'}};
332                    else
333                         Data{iview}.VarDimName={'coord_y','coord_x',{'coord_y','coord_x'}};
334                    end 
335                    Data{iview}.coord_y=[npy-0.5 0.5];
336                    Data{iview}.coord_x=[0.5 npx-0.5];
337                    Data{iview}.A=double(A);
338                    Data{iview}.CoordType='px';
339                elseif testcivx
340                    [Data{iview},VelTypeOut]=read_civxdata(filename,FieldName,VelType);
341                else
342                    [Data{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data               
343                    Data{iview}.VarAttribute=SubField.VarAttribute;
344                end
345                if isfield(Data{iview},'Txt')
346                    msgbox_uvmat('ERROR',['error of input reading: ' Data{iview}.Txt])
347                    return
348                end
349             end   
350             % coordinate transform (or other user defined transform)
351             if ~isempty(transform_fct)
352                 % z index
353                if ~isempty(NbSlice_calib)
354                    Data{iview}.ZIndex=mod(num_i1{iview}(ifile)-1,NbSlice_calib{1})+1;%Zindex for phys transform
355                end
356                if nbview==2
357                    [Data{1},Data{2}]=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});
358                    if isempty(Data{2})
359                        Data(2)=[];
360                    end
361                else
362                    Data{1}=transform_fct(Data{1},XmlData);
363                end
364             end     
365            if testcivx
366                    Data{iview}=calc_field(FieldName,Data{iview});%calculate field (vort..)
367            end
368            if length(Data)==2
369                [Field,errormsg]=sub_field(Data{1},Data{2}); %substract the two fields
370                if ~isempty(errormsg)
371                    msgbox_uvmat('ERROR',['error in aver_stat/sub_field:' errormsg])
372                    return
373                end
374            else
375                Field=Data{1};
376            end
377            if test_object
378                [Field,errormsg]=proj_field(Field,ProjObject);
379                 if ~isempty(errormsg)
380                    msgbox_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg])
381                    return
382                end
383             end                                                       
384                nbfiles=nbfiles+1;
385                if nbfiles==1 %first field
386                    time_1=[];
387                    if isfield(Field,'Time')
388                        time_1=Field.Time(1);
389                    end
390                    DataMean=Field;%default
391                else
392                    for ivar=1:length(Field.ListVarName)
393                        VarName=Field.ListVarName{ivar};
394                        eval(['sizmean=size(DataMean.' VarName ');']);
395                        eval(['siz=size(Field.' VarName ');']);
396                        if ~isequal(siz,sizmean)
397                           msgbox_uvmat('ERROR',['unequal size of input field ' VarName ', need to interpolate on a grid'])
398                           return
399                        else
400                            eval(['DataMean.' VarName '=DataMean.' VarName '+ Field.' VarName ';']); % update the sum
401                        end
402                    end
403                end
404%             else
405%                 nbmissing=nbmissing+1;
406%             end
407        end
408    end %end averaging loop
409    for ivar=1:length(Field.ListVarName)
410        VarName=Field.ListVarName{ivar};
411        eval(['DataMean.' VarName '=DataMean.' VarName '/nbfiles;']); % normalize the mean
412    end
413    if nbmissing~=0
414        msgbox_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipted'])
415    end
416    if isempty(time) % time read from files  prevails
417        time_end=[];
418        if isfield(Field,'Time')
419            time_end=Field.Time(1);%last time read
420            if ~isempty(time_1)
421                DataMean.Time=time_1;
422                DataMean.Time_end=time_end;
423            end
424        end
425    else  % time from ImaDoc prevails
426        DataMean.Time=time(1,num_i1{1}(1),num_j1{1}(1));
427        DataMean.Time_end=time(end,num_i1{end}(end),num_j1{end}(end));
428    end
429   
430    %writing the result file
431   if testima   
432%        if NbSlice==1
433        [filemean]=name_generator(filebase_out,num_i1{1}(1),num_j1{1}(1),'.png',NomTypeOut,1,num_i2{end}(end),num_j2{end}(end),subdir_result);
434%        else % label the file number by the slice # for simplicity
435%           [filemean]=name_generator(filebase_out,i_slice,1,'.png','_i');
436%        end
437        if exist(filemean,'file')
438            backupfile=filemean;
439            testexist=2;
440            while testexist==2
441                backupfile=[backupfile(1:end-4) '~.png'];
442                testexist=exist(backupfile,'file');
443            end
444            [success,message]=copyfile(filemean,backupfile);%make backup
445            if ~isequal(success,1)
446                msgbox_uvmat('ERROR',['previous file result ' filemean ' already exists, problem in backup'])
447                return
448            end
449        end
450        if isequal(Atype{1},'uint16')
451            imwrite(uint16(DataMean.A),filemean,'BitDepth',16);
452        else
453            imwrite(uint8(DataMean.A),filemean,'BitDepth',8);
454        end
455        display([filemean ' written']);
456    else %determine global attributes
457        DataMean.ListGlobalAttribute=[DataMean.ListGlobalAttribute {Series.Action}];
458        ActionKey='Action';
459        while isfield(DataMean,ActionKey)
460            ActionKey=[ActionKey '_1'];
461        end
462        eval(['DataMean.' ActionKey '=Series.Action;'])
463        DataMean.ListGlobalAttribute=[DataMean.ListGlobalAttribute {ActionKey}];
464        if isfield(DataMean,'Time')
465            DataMean.ListGlobalAttribute=[DataMean.ListGlobalAttribute {'Time','Time_end'}];
466        end 
467%         if NbSlice==1
468          filemean=name_generator(filebase_out,num_i1{1}(1),num_j1{1}(1),'.nc',NomTypeOut,1,num_i2{end}(end),num_j2{end}(end),subdir_result);
469%         else % label the file number by the slice # for simplicity
470%           [filemean]=name_generator(filebase_out,i_slice,1,'.nc','_i');
471%         end
472        if exist(filemean,'file')
473            backupfile=filemean;
474            testexist=2;
475            while testexist==2
476                backupfile=[backupfile(1:end-3) '~.nc'];
477                testexist=exist(backupfile,'file');
478            end
479            [success,message]=copyfile(filemean,backupfile);%make backup
480            if ~isequal(success,1)
481                msgbox_uvmat('ERROR',['previous file result ' filemean ' already exists, problem in backup'])
482                display(['previous file result ' filemean ' already exists, problem in backup'])
483                return
484            end
485        end
486        errormsg=struct2nc(filemean,DataMean); %save result file
487        if isempty(errormsg)
488            display([filemean ' written']);
489        else
490            msgbox_uvmat('ERROR',['error in writting result file: ' errormsg])
491            display(errormsg)
492        end
493   end
494end
495hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI
496delete(hget_field)
497uvmat(filemean)
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