source: trunk/src/series.m

Last change on this file was 1128, checked in by sommeria, 10 days ago

script_lavision added

File size: 181.2 KB
Line 
1%'series': master function associated to the GUI series.m for analysis field series 
2%------------------------------------------------------------------------
3% function varargout = series(varargin)
4% associated with the GUI series.fig
5%
6%INPUT
7% param: structure with input parameters (link with the GUI uvmat)
8%      .menu_coord_str: string for the TransformName (menu for coordinate transforms)
9%      .menu_coord_val: value for TransformName (menu for coordinate transforms)
10%      .FileName: input file name
11%      .FileName_1: second input file name
12%      .list_field: menu of input fields
13%      .index_fields: chosen index
14%      .civ1=0 or 1, .interp1,  ... : input civ field type
15%
16
17%=======================================================================
18% Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
19%   http://www.legi.grenoble-inp.fr
20%   Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr
21%
22%     This file is part of the toolbox UVMAT.
23%
24%     UVMAT is free software; you can redistribute it and/or modify
25%     it under the terms of the GNU General Public License as published
26%     by the Free Software Foundation; either version 2 of the license,
27%     or (at your option) any later version.
28%
29%     UVMAT is distributed in the hope that it will be useful,
30%     but WITHOUT ANY WARRANTY; without even the implied warranty of
31%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
32%     GNU General Public License (see LICENSE.txt) for more details.
33%=======================================================================
34
35%------------------------------------------------------------------------
36%------------------------------------------------------------------------
37%  I - MAIN FUNCTION series
38%------------------------------------------------------------------------
39%------------------------------------------------------------------------
40function varargout = series(varargin)
41
42% Begin initialization code - DO NOT EDIT
43gui_Singleton = 1;
44gui_State = struct('gui_Name',       mfilename, ...
45                   'gui_Singleton',  gui_Singleton, ...
46                   'gui_OpeningFcn', @series_OpeningFcn, ...
47                   'gui_OutputFcn',  @series_OutputFcn, ...
48                   'gui_LayoutFcn',  [] , ...
49                   'gui_Callback',   []);
50if nargin && ischar(varargin{1})
51    gui_State.gui_Callback = str2func(varargin{1});
52end
53
54if nargout
55    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
56else
57    gui_mainfcn(gui_State, varargin{:});
58end
59% End initialization code - DO NOT EDIT
60
61%--------------------------------------------------------------------------
62% --- Executes just before series is made visible.
63%--------------------------------------------------------------------------
64function series_OpeningFcn(hObject, eventdata, handles,Param)
65
66% Choose default command line output for series
67handles.output = hObject;
68% Update handles structure
69guidata(hObject, handles);
70
71%% initial settings
72% position and  size of the GUI at opening
73set(0,'Unit','points')
74ScreenSize=get(0,'ScreenSize'); % size of the current screen, in points (1/72 inch)
75Width=900; % prefered width of the GUI in points (1/72 inch)
76Height=624; % prefered height of the GUI in points (1/72 inch)
77%adjust to screen size (reduced by a min margin)
78RescaleFactor=min((ScreenSize(3)-80)/Width,(ScreenSize(4)-80)/Height);
79if RescaleFactor>1
80    RescaleFactor=min(RescaleFactor,1);
81end
82Width=Width*RescaleFactor;
83Height=Height*RescaleFactor;
84LeftX=80*RescaleFactor; % position of the left fig side, in pixels (put to the left side, with some margin)
85LowY=round(ScreenSize(4)/2-Height/2); % put at the middle height on the screen
86set(hObject,'Units','points')
87set(hObject,'Position',[LeftX LowY Width Height])% position and size of the GUI at opening
88
89% settings of table MinIndex_j
90set(handles.MinIndex_i,'ColumnFormat',{'numeric'})
91set(handles.MinIndex_i,'ColumnEditable',false)
92set(handles.MinIndex_i,'ColumnName',{'i min'})
93set(handles.MinIndex_i,'Data',[])% initiate Data to double (not cell)
94
95% settings of table MinIndex_j
96set(handles.MinIndex_j,'ColumnFormat',{'numeric'})
97set(handles.MinIndex_j,'ColumnEditable',false)
98set(handles.MinIndex_j,'ColumnName',{'j min'})
99set(handles.MinIndex_j,'Data',[])% initiate Data to double (not cell)
100
101% settings of table MaxIndex_i
102set(handles.MaxIndex_i,'ColumnFormat',{'numeric'})
103set(handles.MaxIndex_i,'ColumnEditable',false)
104set(handles.MaxIndex_i,'ColumnName',{'i max'})
105set(handles.MaxIndex_i,'Data',[])% initiate Data to double (not cell)
106
107% settings of table MaxIndex_j
108set(handles.MaxIndex_j,'ColumnFormat',{'numeric'})
109set(handles.MaxIndex_j,'ColumnEditable',false)
110set(handles.MaxIndex_j,'ColumnName',{'j max'})
111set(handles.MaxIndex_j,'Data',[])% initiate Data to double (not cell)
112
113% settings of table PairString
114set(handles.PairString,'ColumnName',{'pairs'})
115set(handles.PairString,'ColumnEditable',false)
116set(handles.PairString,'ColumnFormat',{'char'})
117set(handles.PairString,'Data',{''})
118
119% settings of table MaskTable
120%set(handles.MaskTable,'ColumnName',{'mask name'})
121set(handles.PairString,'ColumnEditable',false)
122set(handles.PairString,'ColumnFormat',{'char'})
123set(handles.PairString,'Data',{''})
124
125series_ResizeFcn(hObject, eventdata, handles)%resize table according to series GUI size
126set(hObject,'WindowButtonDownFcn',{'mouse_down'})%allows mouse action with right button (zoom for uicontrol display)
127set(hObject,'DeleteFcn',{@closefcn})%
128
129% check default input data
130if ~exist('Param','var')
131    Param=[]; % default
132end
133
134%% Read the parameter file series.xml, or created from series.xml.default if it does not exist
135SeriesData=[];
136[path_series,name,ext]=fileparts(which('series'));% path to the GUI series
137xmlfile=fullfile(path_series,'series.xml');
138if ~exist(xmlfile,'file')
139    [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);
140end
141if exist(xmlfile,'file')
142    SeriesData.SeriesParam=xml2struct(xmlfile);
143    if ~(isfield(SeriesData.SeriesParam,'ClusterParam')&& isfield(SeriesData.SeriesParam.ClusterParam,'LaunchCmdFcn'))
144        [success,message]=copyfile(xmlfile,fullfile(path_series,'series_old.xml'));% update the file series.xml inot correctly documented
145        delete(xmlfile);
146        [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);
147    end 
148    SeriesData.SeriesParam=xml2struct(xmlfile);
149end
150
151%% list of builtin functions in the menu ActionName
152ActionList={'check_data_files';'aver_stat';'time_series';'civ_series';'merge_proj'}; % WARNING: fits with nb_builtin_ACTION=4 in ActionName_callback
153NbBuiltinAction=numel(ActionList);
154set(handles.Action,'UserData',NbBuiltinAction)
155path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series'
156[path_series,name,ext]=fileparts(which('series')); % path to the GUI series
157path_series_fct=fullfile(path_series,'series'); % path of the functions in subdirectroy 'series'
158command = ['LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "l = x.split('':''); l = [s for s in l if ''matlab'' not in s]; print('':''.join(l))") ' ...
159            'python -c "import fluidimage"'];
160[code, ~] = system(command);
161if code==0
162    ActionExtList={'.m';'.sh';'.py (in dev.)'}; % default choice of extensions (Matlab fct .m or compiled version .sh
163else
164    ActionExtList={'.m';'.sh'};  % python options not installed
165end
166ActionPathList=cell(NbBuiltinAction,1); % initiate the cell matrix of Action fct paths
167ActionPathList(:)={path_series_fct}; % set the default path to series fcts to all list members
168RunModeList={'local';'background'}; % default choice of extensions (Matlab fct .m or compiled version .sh)
169[s,w]=system(SeriesData.SeriesParam.ClusterParam.ExistenceTest); % look for cluster system presence
170if isequal(s,0)
171    RunModeList=[RunModeList;{'cluster'}];
172    set(handles.MonitorCluster,'Visible','on'); % make visible button for access to Monika
173    set(handles.num_CPUTime,'Visible','on'); % make visible button for CPU time estimate for one ref index
174    set(handles.num_CPUTime,'String','')% default CPU time undefined
175    set(handles.CPUTime_txt,'Visible','on'); % make visible button for CPU time title
176end
177set(handles.RunMode,'String',RunModeList)% display the menu of available run modes, local, background or cluster manager
178
179%% list of builtin transform functions in the menu TransformName
180TransformList={'';'sub_field';'phys';'phys_polar'}; % WARNING: must fit with the corresponding menu in uvmat and nb_builtin_transform=4 in  TransformName_callback
181NbBuiltinTransform=numel(TransformList);
182path_transform_fct=fullfile(path_series,'transform_field');
183TransformPathList=cell(NbBuiltinTransform,1); % initiate the cell matrix of Action fct paths
184TransformPathList(:)={path_transform_fct}; % set the default path to series fcts to all list members
185SeriesData.TransformPath=path_transform_fct;% store the standard path for trqnsform functions (needed for compilation)
186
187%% get the user defined functions stored in the personal file uvmat_perso.mat
188dir_perso=prefdir;
189profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
190if exist(profil_perso,'file')
191    h=load (profil_perso);
192    %get the list of previous input files in the upper bar menu Open
193    if isfield(h,'MenuFile')
194        for ifile=1:min(length(h.MenuFile),5)
195            set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile});
196            set(handles.(['MenuFile_' num2str(ifile+5)]),'Label',h.MenuFile{ifile});
197        end
198    end
199    %get the menu of actions
200    if isfield(h,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser)
201        ActionList=[ActionList;h.ActionListUser];
202        ActionPathList=[ActionPathList;h.ActionPathListUser(:,1)];
203    end
204    %get the menu of transform fct
205    if isfield(h,'TransformListUser') && iscell(h.TransformListUser) && isfield(h,'TransformPathListUser') && iscell(h.TransformPathListUser)
206        TransformList=[TransformList;h.TransformListUser];
207        TransformPathList=[TransformPathList;h.TransformPathListUser];
208    end
209end
210
211%% selection of the input Action fct
212ActionCheckExist=true(size(ActionList)); % initiate the check of the path to the listed action fct
213for ilist=NbBuiltinAction+1:numel(ActionList)%check  the validity of the path of the user defined Action fct
214    ActionCheckExist(ilist)=exist(fullfile(ActionPathList{ilist},[ActionList{ilist} '.m']),'file');
215end
216ActionPathList=ActionPathList(ActionCheckExist,:); % suppress the menu options which are not valid anymore
217ActionList=ActionList(ActionCheckExist);
218set(handles.ActionName,'String',[ActionList;{'more...'}])
219set(handles.ActionName,'UserData',ActionPathList)
220ActionIndex=[];
221if isfield(Param,'ActionName')% copy the selected menu index transferred in Param from uvmat
222    ActionIndex=find(strcmp(Param.ActionName,ActionList),1);
223end
224if isempty(ActionIndex)
225    ActionIndex=1;
226end
227set(handles.ActionName,'Value',ActionIndex)
228set(handles.ActionPath,'String',ActionPathList{ActionIndex})
229set(handles.ActionExt,'Value',1)
230set(handles.ActionExt,'String',ActionExtList)
231
232%% selection of the input transform fct
233TransformCheckExist=true(size(TransformList));
234for ilist=NbBuiltinTransform+1:numel(TransformList)
235    TransformCheckExist(ilist)=exist(fullfile(TransformPathList{ilist},[TransformList{ilist} '.m']),'file');
236end
237TransformPathList=TransformPathList(TransformCheckExist);
238TransformList=TransformList(TransformCheckExist);
239set(handles.TransformName,'String',[TransformList;{'more...'}])
240set(handles.TransformName,'UserData',TransformPathList)
241TransformIndex=[];
242if isfield(Param,'TransformName')% copy the selected menu index transferred in Param from uvmat
243    TransformIndex=find(strcmp(Param.TransformName,TransformList),1);
244end
245if isempty(TransformIndex)
246    TransformIndex=1;
247end
248set(handles.TransformName,'Value',TransformIndex)
249set(handles.TransformPath,'String',TransformPathList{TransformIndex})
250   
251%% fields input initialisation
252if isfield(Param,'list_fields')&& isfield(Param,'index_fields') &&~isempty(Param.list_fields) &&~isempty(Param.index_fields)
253    set(handles.FieldName,'String',Param.list_fields); % list menu fields
254    set(handles.FieldName,'Value',Param.index_fields); % selected string index
255end
256if isfield(Param,'Coordinates')
257    if isfield(Param.Coordinates,'Coord_x')
258        set(handles.Coord_x,'String',Param.Coordinates.Coord_x)
259    end
260    if isfield(Param.Coordinates,'Coord_y')
261        set(handles.Coord_y,'String',Param.Coordinates.Coord_y)
262    end
263    if isfield(Param.Coordinates,'Coord_z')
264        set(handles.Coord_z,'String',Param.Coordinates.Coord_z)
265    end
266end
267
268%% introduce the input file name(s) if defined from input Param,
269set(handles.series,'UserData',SeriesData)% initiate Userdata
270if isfield(Param,'InputFile')
271   
272    %% fill the list of input file series
273    InputTable=[{Param.InputFile.RootPath},{Param.InputFile.SubDir},{Param.InputFile.RootFile},{Param.InputFile.NomType},{Param.InputFile.FileExt}];
274    if isempty(find(cellfun('isempty',InputTable)==0)) % if there is no input file, do not introduce input info
275        set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
276        return
277    end
278    TimeTable=[{Param.InputFile.TimeName},{[]},{[]},{[]},{[]}];
279    if isfield(Param.InputFile,'RootPath_1')
280        InputTable=[InputTable;[{Param.InputFile.RootPath_1},{Param.InputFile.SubDir_1},{Param.InputFile.RootFile_1},{Param.InputFile.NomType_1},{Param.InputFile.FileExt_1}]];
281        TimeTable=[TimeTable; [{Param.InputFile.TimeName_1},{[]},{[]},{[]},{[]}]];
282    end
283    set(handles.InputTable,'Data',InputTable)
284   
285    %% define the default path for the output files
286    [InputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
287    [InputPath,Experiment,ExperimentExt]=fileparts(InputPath);
288    set(handles.Device,'String',[Device DeviceExt])
289    set(handles.Experiment,'String',[Experiment ExperimentExt])
290    if ~isempty(regexp(InputTable{1,1},'(^http://)|(^https://)'))
291    set(handles.OutputPathBrowse,'Value',1)% an output folder needs to be specified for OpenDAP data
292    end
293
294    %update the output path if needed
295    if ~(isfield(SeriesData,'InputPath') && strcmp(SeriesData.InputPath,InputPath))
296    if get(handles.OutputPathBrowse,'Value')==1  % fix the output path in manual mode
297        OutputPathOld=get(handles.OutputPath,'String');
298        OutputPath=uigetdir(OutputPathOld,'pick a root folder for output data');
299        set(handles.OutputPath,'String',OutputPath)
300    else %reproduce the input path for output
301        set(handles.OutputPath,'String',InputPath)
302    end
303    end
304   
305    %% determine the selected reference field indices for pair display
306   
307    [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(Param.InputFile.FileIndex);
308    if isempty(i1)
309        i1=1;
310    end
311    if isempty(i2)
312        i2=i1;
313    end
314    ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
315    % set(handles.num_ref_i,'String',num2str(ref_i));
316    if isempty(j1)
317        j1=1;
318    end
319    if isempty(j2)
320        j2=j1;
321    end
322    ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
323    SeriesData.ref_i=ref_i;
324    SeriesData.ref_j=ref_j;
325    set(handles.series,'UserData',SeriesData)
326    update_rootinfo(handles,Param.HiddenData.i1_series{1},Param.HiddenData.i2_series{1},Param.HiddenData.j1_series{1},Param.HiddenData.j2_series{1},...
327        Param.HiddenData.FileInfo{1},Param.HiddenData.MovieObject{1},1)
328    if isfield(Param,'FileName_1')
329        %         display_file_name(handles,Param,2)
330        update_rootinfo(handles,Param.HiddenData.i1_series{2},Param.HiddenData.i2_series{2},Param.HiddenData.j1_series{2},Param.HiddenData.j2_series{2},...
331            Param.HiddenData.FileInfo{2},Param.HiddenData.MovieObject{2},2)
332    end
333    %% enable field and veltype menus, in accordance with the current action
334    ActionName_Callback([],[], handles)
335   
336    %% set length of waitbar
337    displ_time(handles)
338   
339else
340    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
341end
342if isfield(Param,'incr_i')
343    set(handles.num_incr_i,'String',num2str(Param.incr_i))
344else
345    set(handles.num_incr_i,'String','1')
346end
347if isfield(Param,'incr_j')
348    set(handles.num_incr_j,'String',num2str(Param.incr_j))
349else
350    set(handles.num_incr_j,'String','1')
351end
352
353%------------------------------------------------------------------------
354% --- Outputs from this function are returned to the command line.
355function varargout = series_OutputFcn(hObject, eventdata, handles)
356%------------------------------------------------------------------------
357varargout{1} = handles.output;
358
359%------------------------------------------------------------------------
360% --- executed when closing uvmat: delete or desactivate the associated figures if exist
361function closefcn(gcbo,eventdata)
362%------------------------------------------------------------------------
363
364% delete set_object_series if detected
365hh=findobj(allchild(0),'name','view_object_series');
366if ~isempty(hh)
367    delete(hh)
368end
369hh=findobj(allchild(0),'name','edit_object_series');
370if ~isempty(hh)
371    delete(hh)
372end
373
374%delete the bowser if detected
375hh=findobj(allchild(0),'tag','browser');
376if ~isempty(hh)
377    delete(hh)
378end
379
380
381%------------------------------------------------------------------------
382%------------------------------------------------------------------------
383%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
384% automatically sets the global properties when the rootfile name is introduced
385% then activate the view-field actionname if selected
386% it is activated either by clicking on the RootPath window or by the
387% browser
388%------------------------------------------------------------------------
389%------------------------------------------------------------------------
390% --- fct activated by the browser under 'Open'
391%------------------------------------------------------------------------ 
392function MenuBrowse_Callback(hObject, eventdata, handles)
393%% look for the previously opened file 'oldfile'
394InputTable=get(handles.InputTable,'Data');
395oldfile=InputTable{1,1};
396if isempty(oldfile)
397    % use a file name stored in prefdir
398    dir_perso=prefdir;
399    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
400    if exist(profil_perso,'file')
401        h=load (profil_perso);
402        if isfield(h,'RootPath') && ischar(h.RootPath)
403            oldfile=h.RootPath;
404        end
405    end
406end
407%% launch the browser
408fileinput=uigetfile_uvmat('pick an input file in the series',oldfile);
409hh=dir(fileinput);
410if numel(hh)>1
411    msgbox_uvmat('ERROR','invalid input, probably a broken link');
412else
413    if ~isempty(fileinput)
414        display_file_name(handles,fileinput,'one')
415    end
416end
417
418% --------------------------------------------------------------------
419function MenuBrowseAppend_Callback(hObject, eventdata, handles)
420
421%% look for the previously opened file 'oldfile'
422InputTable=get(handles.InputTable,'Data');
423RootPathCell=InputTable(:,1);
424if isempty(RootPathCell{1})% no input file in the table
425     MenuBrowse_Callback(hObject, eventdata, handles)%refresh the input table, not append
426     return
427end
428SubDirCell=InputTable(:,2);
429oldfile=fullfile(RootPathCell{1},SubDirCell{1});
430
431%% use a file name stored in prefdir
432dir_perso=prefdir;
433profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
434if exist(profil_perso,'file')
435    h=load (profil_perso);
436    if isfield(h,'RootPath') && ischar(h.RootPath)
437        oldfile=h.RootPath;
438    end
439end
440
441%% launch the browser
442fileinput=uigetfile_uvmat('pick a file to append in the input table',oldfile);
443hh=dir(fileinput);
444if numel(hh)>1
445    msgbox_uvmat('ERROR','invalid input, probably a broken link');
446else
447    if ~isempty(fileinput)
448        display_file_name(handles,fileinput,'append')
449    end
450end
451
452%------------------------------------------------------------------------
453% --- fct activated by selecting a previous file under the menu Open
454%------------------------------------------------------------------------
455function MenuFile_Callback(hObject, eventdata, handles)
456
457errormsg=display_file_name(handles,get(hObject,'Label'),'one');
458if ~isempty(errormsg)
459    set(hObject,'Label','')
460    MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
461        {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
462    str_find=strcmp(get(hObject,'Label'),MenuFile);
463    MenuFile(str_find)=[]; % suppress the input file to the list
464    for ifile=1:numel(MenuFile)
465        set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile});
466    end
467end
468
469%------------------------------------------------------------------------
470% --- fct activated by selecting a previous file under the menu Open/append
471%------------------------------------------------------------------------
472function MenuFile_append_Callback(hObject, eventdata, handles)
473
474InputTable=get(handles.InputTable,'Data');
475if isempty(InputTable{1,1})% no input file in the table
476    display_file_name(handles,get(hObject,'Label'),'one') %refresh the input table, not append
477else
478    display_file_name(handles,get(hObject,'Label'),'append')% append the selected file to the current list of InputTable
479end
480
481%------------------------------------------------------------------------
482% --- fct activated by the browser under 'Open campaign/Browse...'
483%------------------------------------------------------------------------
484function MenuBrowseCampaign_Callback(hObject, eventdata, handles)
485
486%% look for the previously opened file 'oldfile'
487InputTable=get(handles.InputTable,'Data');
488if ~isempty(InputTable)
489oldfile=[InputTable{1,1} InputTable{1,2}];
490else
491    % use a file name stored in prefdir
492    dir_perso=prefdir;
493    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
494    if exist(profil_perso,'file')
495        h=load (profil_perso);
496        if isfield(h,'MenuCampaign') && ~isempty(h.MenuCampaign)&& ischar(h.MenuCampaign{1})
497            oldfile=h.MenuCampaign{1};
498        end
499    end
500end
501InputTable{1,1}='...';
502set(handles.InputTable,'Data',InputTable)
503browse_data(oldfile,'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
504% NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
505% icount=0;
506% for iexp=1:numel(OutPut.Experiment)
507%     for idevice=1:numel(OutPut.DataSeries)
508%         icount=icount+1;
509%         InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp});
510%         InputTable{icount,2}=OutPut.DataSeries{idevice};
511%         if isempty(InputTable{icount,3})
512%             if icount>1
513%             InputTable{icount,3}=InputTable{icount-1,3};
514%             else
515%                 InputTable{icount,3}='';
516%             end
517%         end
518%         if isempty(InputTable{icount,4})
519%             if icount>1
520%             InputTable{icount,4}=InputTable{icount-1,4};
521%             else
522%                 InputTable{icount,4}='';
523%             end
524%         end
525%                 if isempty(InputTable{icount,5})
526%             if icount>1
527%             InputTable{icount,5}=InputTable{icount-1,5};
528%             else
529%                 InputTable{icount,5}='';
530%             end
531%         end
532%     end
533% end
534% if size(InputTable,1)>icount
535%     InputTable(icount+1:size(InputTable,1),:)=[];
536% end
537%REFRESH_Callback(hObject, eventdata, handles)
538
539% --------------------------------------------------------------------
540% function MenuCampaign_Callback(hObject, eventdata, handles)
541% % --------------------------------------------------------------------
542%
543% OutPut=browse_data(get(hObject,'Label'),'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
544% if ~isfield(OutPut,'Campaign')
545%     return
546% end
547% NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
548% icount=0;
549% InputTable=get(handles.InputTable,'Data');
550% for iexp=1:numel(OutPut.Experiment)
551%     for idevice=1:numel(OutPut.DataSeries)
552%         icount=icount+1;
553%         InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp});
554%         InputTable{icount,2}=OutPut.DataSeries{idevice};
555%         if isempty(InputTable{icount,3})
556%             if icount>1
557%                 InputTable{icount,3}=InputTable{icount-1,3};
558%             else
559%                 InputTable{icount,3}='';
560%             end
561%         end
562%         if isempty(InputTable{icount,4})
563%             if icount>1
564%                 InputTable{icount,4}=InputTable{icount-1,4};
565%             else
566%                 InputTable{icount,4}='';
567%             end
568%         end
569%         if isempty(InputTable{icount,5})
570%             if icount>1
571%                 InputTable{icount,5}=InputTable{icount-1,5};
572%             else
573%                 InputTable{icount,5}='';
574%             end
575%         end
576%     end
577% end
578% if size(InputTable,1)>icount
579%     InputTable(icount+1:size(InputTable,1),:)=[];
580% end
581% set(handles.InputTable,'Data',InputTable)
582% REFRESH_Callback(hObject, eventdata, handles)
583
584
585% --- Executes when selected cell(s) is changed in InputTable.
586function InputTable_CellSelectionCallback(hObject, eventdata, handles)
587iline=[];
588if ~isempty(eventdata.Indices)
589    iline=eventdata.Indices(1);
590end
591set(handles.InputLine,'String',num2str(iline));
592
593%------------------------------------------------------------------------
594% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
595%------------------------------------------------------------------------
596function InputTable_KeyPressFcn(hObject, eventdata, handles)
597set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
598set(handles.OutputSubDir,'BackgroundColor',[1 0 1])% set edit box OutputSubDir to magenta color to indicate that refresh may be needed
599xx=double(get(handles.series,'CurrentCharacter')); % get the keyboard character
600if ~isempty(xx)
601    switch xx
602        case 31 %downward arrow
603            InputTable=get(handles.InputTable,'Data');
604            iline=str2double(get(handles.InputLine,'String'));
605            if isequal(iline,size(InputTable,1))% arrow downward
606                InputTable=[InputTable;InputTable(iline,:)]; % create a new line as a copy of the last one
607                set(handles.InputTable,'Data',InputTable);
608            end
609        case 127  %key 'Suppress'
610            ClearLine_Callback(hObject, eventdata, handles)
611    end
612end
613
614%------------------------------------------------------------------------
615% --- Executes on button press in REFRESH.
616function REFRESH_Callback(hObject, eventdata, handles)
617%------------------------------------------------------------------------
618check_input_file_series(handles)
619
620%% enable field and veltype menus, in accordance with the current action
621ActionInput_Callback([],[], handles)
622
623%------------------------------------------------------------------------
624% --- check the input file series.
625function check_input_file_series(handles)
626%------------------------------------------------------------------------
627InputTable=get(handles.InputTable,'Data');
628set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
629set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
630drawnow
631empty_line=false(size(InputTable,1),1);
632for iline=1:size(InputTable,1)
633    empty_line(iline)= isempty(cell2mat(InputTable(iline,1:3)));%check the empty lines in the input table
634end
635if ~isempty(find(empty_line,1))
636    InputTable(empty_line,:)=[]; % remove empty lines
637    set(handles.InputTable,'Data',InputTable)
638    ListTable={'MinIndex_i','MaxIndex_i','MinIndex_j','MaxIndex_j','PairString','TimeTable'};
639    for ilist=1:numel(ListTable)
640        Table=get(handles.(ListTable{ilist}),'Data');
641        Table(empty_line,:)=[]; % remove empty lines
642        set(handles.(ListTable{ilist}),'Data',Table);
643    end
644    set(handles.series,'UserData',[])%refresh the stored info
645end
646nbview=size(InputTable,1);
647for iview=1:nbview
648    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
649    if ~exist(RootPath,'dir')
650        i1_series=[];
651        RootFile='';
652    else %scan the input folder
653        InputTable{iview,3}=regexprep(InputTable{iview,3},'^/','');%suppress '/' at the beginning of the input name
654        i1=str2num(get(handles.num_first_i,'String'));
655        j1=str2num(get(handles.num_first_j,'String'));
656        InputFile=fullfile_uvmat('','',InputTable{iview,3},InputTable{iview,5},InputTable{iview,4},i1,[],j1,[])
657            [RootPath,~,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=...
658                find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),InputFile);
659    end
660    % if no file is found, open a browser
661    if isempty(RootFile)&& isempty(i1_series)
662        fileinput=uigetfile_uvmat(['wrong input at line ' num2str(iview) ':pick a new input file'],RootPath);
663        if isempty(fileinput)
664            set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  back to red color
665            return
666        else
667            display_file_name(handles,fileinput,iview)
668        end
669    else
670       update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview)
671    end
672end
673
674%% update MinIndex_i and MaxIndex_i if the input table content has been reduced in line nbre
675MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
676set(handles.MinIndex_i,'Data',MinIndex_i_table(1:nbview,:));
677MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
678set(handles.MinIndex_j,'Data',MinIndex_j_table(1:nbview,:));
679MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
680
681set(handles.MaxIndex_i,'Data',MaxIndex_i_table(1:nbview,:));
682MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
683set(handles.MaxIndex_j,'Data',MaxIndex_j_table(1:nbview,:));
684PairString=get(handles.PairString,'Data'); % retrieve the min indices in the table MinIndex
685set(handles.PairString,'Data',PairString(1:nbview,:));
686TimeTable=get(handles.TimeTable,'Data'); % retrieve the min indices in the table MinIndex
687set(handles.TimeTable,'Data',TimeTable(1:nbview,:));
688
689%% set length of waitbar
690displ_time(handles)
691set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (indicate activation finished)
692set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch'
693
694
695
696%------------------------------------------------------------------------
697% --- Function called when a new file is opened, either by series_OpeningFcn or by the browser
698%------------------------------------------------------------------------
699% INPUT:
700% handles: handles of elements in the GUI
701% Param: structure of input parameters, including  input file name and path
702% iview: line index in the input table
703%       or 'one': refresh the list
704%         'append': add a new line to the input table
705function errormsg=display_file_name(handles,Param,iview)
706 
707set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
708drawnow
709errormsg=''; % default
710if ischar(Param)
711    fileinput=Param;
712else% input set when series is opened (called by the GUI uvmat)
713    fileinput=Param.FileName;
714end
715   
716%% get the input root name, indices, file extension and nomenclature NomType
717if isempty(regexp(fileinput,'^http')) && ~exist(fileinput,'file')
718    errormsg=['input file ' fileinput  ' does not exist'];
719    msgbox_uvmat('ERROR',errormsg)
720    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (refresh still needed)
721    return
722end
723
724%% detect root name, nomenclature and indices in the input file name:
725[FilePath,FileName,FileExt]=fileparts(fileinput);
726%%%%%%%%%%%%%%%%%%
727%TODO: case of input by uvmat: do not check agai the input seies %%%%%%%
728%%%%%%%%%%%%%%%%%%%
729% detect the file type, get the movie object if relevant, and look for the corresponding file series:
730% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
731[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
732FileType=FileInfo.FileType;
733if isempty(RootFile)&&isempty(i1_series)
734    errormsg='no input file in the series';
735    msgbox_uvmat('ERROR',errormsg)
736    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (end of activation)
737    return
738end
739if strcmp(FileType,'txt')
740    edit(fileinput)
741    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to  magenta color (end of activation)
742    return
743elseif strcmp(FileType,'xml')
744    editxml(fileinput)
745    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
746     return
747elseif strcmp(FileType,'figure')
748    open(fileinput)
749    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
750     return
751end
752
753%% enable other menus and uicontrols
754set(handles.RUN, 'Enable','On')
755set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
756set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
757drawnow
758
759
760%% fill the list of file series
761InputTable=get(handles.InputTable,'Data');
762SeriesData=get(handles.series,'UserData');
763
764if strcmp(iview,'append') % display the input data as a new line in the table
765    iview=size(InputTable,1)+1; % the next line in InputTable becomes the current line
766elseif strcmp(iview,'one') % refresh the list of  input  file series
767    iview=1; % the first line in InputTable becomes the current line
768    InputTable={'','','','',''};
769    set(handles.TimeTable,'Data',[{''},{[]},{[]},{[]},{[]}])
770    set(handles.MinIndex_i,'Data',[])
771    set(handles.MaxIndex_i,'Data',[])
772    set(handles.MinIndex_j,'Data',[])
773    set(handles.MaxIndex_j,'Data',[])
774    set(handles.PairString,'Data',{''})
775    SeriesData.CheckPair=0; % reset the list of input lines with pairs
776    SeriesData.i1_series={};
777    SeriesData.i2_series={};
778    SeriesData.j1_series={};
779    SeriesData.j2_series={};
780    SeriesData.FileType={};
781    SeriesData.FileInfo={};
782    SeriesData.Time={};
783end
784if isfield(SeriesData,'i1_series')
785    SeriesData.i1_series(iview+1:end)=[];
786    SeriesData.i2_series(iview+1:end)=[];
787    SeriesData.j1_series(iview+1:end)=[];
788    SeriesData.j2_series(iview+1:end)=[];
789    SeriesData.FileType(iview+1:end)=[];
790    SeriesData.FileInfo(iview+1:end)=[];
791    SeriesData.Time(iview+1:end)=[];
792end
793InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
794if iview >1
795    set(handles.InputLine,'String',num2str(iview))
796end
797set(handles.InputTable,'Data',InputTable)
798
799%% determine the selected reference field indices for pair display
800if isempty(i1)
801    i1=1;
802end
803if isempty(i2)
804    i2=i1;
805end
806ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
807% set(handles.num_ref_i,'String',num2str(ref_i));
808if isempty(j1)
809    j1=1;
810end
811if isempty(j2)
812    j2=j1;
813end
814ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
815SeriesData.ref_i=ref_i;
816SeriesData.ref_j=ref_j;
817
818%% update first and last indices if they do not exist
819Param=read_GUI(handles.series);
820first_j=[];
821if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
822last_j=[];
823if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
824PairString='';
825if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
826[i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
827FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
828    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
829if ~exist(FirstFileName,'file')
830    set(handles.num_first_i,'String',num2str(ref_i))
831    set(handles.num_first_j,'String',num2str(ref_j))
832end
833[i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
834LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
835    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
836if ~exist(LastFileName,'file')
837    set(handles.num_last_i,'String',num2str(ref_i))
838    set(handles.num_last_j,'String',num2str(ref_j))
839end
840
841%% update the list of recent files in the menubar and save it for future opening
842MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
843    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
844str_find=strcmp(fileinput,MenuFile);
845if isempty(find(str_find,1))
846    MenuFile=[{fileinput};MenuFile]; % insert the current file if not already in the list
847end
848for ifile=1:min(length(MenuFile),5)
849    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
850end
851dir_perso=prefdir;
852profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
853if exist(profil_perso,'file')
854    save (profil_perso,'MenuFile','-append'); % store the file names for future opening of uvmat
855else
856    save (profil_perso,'MenuFile','-V6'); % store the file names for future opening of uvmat
857end
858% save the opened file to initiate future opening
859SeriesData.RefFile{iview}=fileinput; % reference opening file for line iview
860SeriesData.Ref_i1=i1;
861SeriesData.Ref_i2=i2;
862SeriesData.Ref_j1=j1;
863SeriesData.Ref_j2=j2;
864
865%% define the path for the output files
866[InputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
867[InputPath,Experiment,ExperimentExt]=fileparts(InputPath);
868set(handles.Device,'String',[Device DeviceExt])
869set(handles.Experiment,'String',[Experiment ExperimentExt])
870if ~isempty(regexp(InputTable{1,1},'(^http://)|(^https://)'))
871    set(handles.OutputPathBrowse,'Value',1)% an output folder needs to be specified for OpenDAP data
872end
873
874%update the output path if needed
875if ~(isfield(SeriesData,'InputPath') && strcmp(SeriesData.InputPath,InputPath))
876    if get(handles.OutputPathBrowse,'Value')==1  % fix the output path in manual mode
877        OutputPathOld=get(handles.OutputPath,'String');
878        OutputPath=uigetdir(OutputPathOld,'pick a root folder for output data');
879        set(handles.OutputPath,'String',OutputPath)
880    else %reproduce the input path for output
881        set(handles.OutputPath,'String',InputPath)
882    end
883    SeriesData.InputPath=InputPath;
884end
885
886set(handles.series,'UserData',SeriesData)
887
888set(handles.InputTable,'BackgroundColor',[1 1 1])
889
890%% initiate input file series and refresh the current field view:     
891update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview);
892%% enable field and veltype menus, in accordance with the current action
893ActionName_Callback([],[], handles)
894
895%% set length of waitbar
896displ_time(handles)
897
898set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (end of activation)
899
900%------------------------------------------------------------------------
901% --- Update information about a new field series (indices to scan, timing,
902%     calibration from an xml file
903function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,VideoObject,iview)
904%------------------------------------------------------------------------
905InputTable=get(handles.InputTable,'Data');
906
907%% display the min and max indices for the whole file series
908if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
909    MinIndex_j=1; % index j set to 1 by default
910    MaxIndex_j=1;
911    MinIndex_i=find(i1_series(1,2,:), 1 )-1; % min ref index i detected in the series (corresponding to the first non-zero value of i1_series, except for zero index)
912    MaxIndex_i=find(i1_series(1,2,:),1,'last' )-1; % max ref index i detected in the series (corresponding to the last non-zero value of i1_series)
913else
914    ref_i=squeeze(max(i1_series(1,:,:),[],2)); % select ref_j index for each ref_i
915    ref_j=squeeze(max(j1_series(1,:,:),[],3)); % select ref_i index for each ref_j
916     MinIndex_i=min(find(ref_i))-1;
917     MaxIndex_i=max(find(ref_i))-1;
918     MaxIndex_j=max(find(ref_j))-1;
919     MinIndex_j=min(find(ref_j))-1;
920    diff_j_max=diff(ref_j);
921    diff_i_max=diff(ref_i);
922    if ~isempty(diff_i_max) && isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max)))
923        set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to dispaly by default
924    end
925    if ~isempty(diff_j_max) && isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max)))
926        set(handles.num_incr_j,'String',num2str(diff_j_max(1)))
927    end
928end
929if isequal(MinIndex_i,-1)
930    MinIndex_i=0;
931end
932if isequal(MinIndex_j,-1)
933    MinIndex_j=0;
934end
935MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
936MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
937MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
938MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
939if ~isempty(MinIndex_i)&&~isempty(MaxIndex_i)
940    MinIndex_i_table(iview,1)=MinIndex_i;
941    MaxIndex_i_table(iview,1)=MaxIndex_i;
942end
943if ~isempty(MinIndex_j)&&~isempty(MaxIndex_j)
944    MinIndex_j_table(iview,1)=MinIndex_j;
945    MaxIndex_j_table(iview,1)=MaxIndex_j;
946end
947set(handles.MinIndex_i,'Data',MinIndex_i_table)%display the min indices in the table MinIndex
948set(handles.MinIndex_j,'Data',MinIndex_j_table)%display the max indices in the table MaxIndex
949set(handles.MaxIndex_i,'Data',MaxIndex_i_table)%display the min indices in the table MinIndex
950set(handles.MaxIndex_j,'Data',MaxIndex_j_table)%display the max indices in the table MaxIndex
951SeriesData=get(handles.series,'UserData');
952
953%% adjust the first and last indices for the selected series, only if requested by the bounds
954% i index, compare input to min index i
955first_i=str2num(get(handles.num_first_i,'String')); % retrieve previous first i
956% ref_i=str2num(get(handles.num_ref_i,'String')); % index i given by the input field
957ref_i=1;
958if isfield(SeriesData,'ref_i')
959    ref_i=SeriesData.ref_i;
960end
961if isempty(first_i)
962    first_i=ref_i; % first_i updated by the input value
963elseif first_i < MinIndex_i
964    first_i=MinIndex_i; % first_i set to the min i index (restricted by oter input lines)
965elseif first_i >MaxIndex_i
966    first_i=MaxIndex_i; % first_i set to the max i index (restricted by oter input lines)
967end
968% j index,  compare input to min index j
969first_j=str2num(get(handles.num_first_j,'String'));
970ref_j=1;
971if isfield(SeriesData,'ref_j')
972    ref_j=SeriesData.ref_j;
973end
974if isempty(first_j)
975    first_j=ref_j; % first_j updated by the input value
976elseif first_j<MinIndex_j
977    first_j=MinIndex_j; % first_j set to the min j index (restricted by oter input lines)
978elseif first_j >MaxIndex_j
979    first_j=MaxIndex_j; % first_j set to the max j index (restricted by oter input lines)
980end
981% i index, compare input to max index i
982last_i=str2num(get(handles.num_last_i,'String'));
983if isempty(last_i)
984    last_i=ref_i;
985elseif last_i > MaxIndex_i
986    last_i=MaxIndex_i;
987elseif last_i<first_i
988    last_i=first_i;
989end
990% j index, compare input to max index j
991last_j=str2num(get(handles.num_last_j,'String'));
992if isempty(last_j)
993    last_j=ref_j;
994elseif last_j>MaxIndex_j
995    last_j=MaxIndex_j;
996elseif last_j<first_j
997    last_j=first_j;
998end
999set(handles.num_first_i,'String',num2str(first_i));
1000set(handles.num_first_j,'String',num2str(first_j));
1001set(handles.num_last_i,'String',num2str(last_i));
1002set(handles.num_last_j,'String',num2str(last_j));
1003
1004%% number of slices set by default
1005NbSlice=[]; % default
1006% read  value set by the first series for the append mode (iwiew >1)
1007if iview>1 && strcmp(get(handles.num_NbSlice,'Visible'),'on')
1008    NbSlice=str2double(get(handles.num_NbSlice,'String'));
1009end
1010
1011%% default time settings
1012TimeUnit='';
1013% read  value set by the first series for the append mode (iwiew >1)
1014if iview>1
1015    TimeUnit=get(handles.TimeUnit,'String');
1016end
1017TimeName='';
1018Time=[]; % default
1019TimeMin=[];
1020TimeFirst=[];
1021TimeLast=[];
1022TimeMax=[];
1023
1024%%  read image documentation file if found
1025XmlData=[];
1026check_calib=0;
1027XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
1028if ~isempty(XmlFileName)
1029    [XmlData,errormsg]=imadoc2struct(XmlFileName);
1030    if ~isempty(errormsg)
1031        msgbox_uvmat('WARNING',['error in reading ' XmlFileName ': ' errormsg]);
1032    end
1033    % read time if available
1034    if isfield(XmlData,'Time')
1035        Time=XmlData.Time;
1036        TimeName='xml';
1037    end
1038    if isfield(XmlData,'Camera')
1039        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
1040            if iview>1 && ~isempty(TimeUnit) && ~strcmp(TimeUnit,XmlData.Camera.TimeUnit)
1041                msgbox_uvmat('WARNING','inconsistent time unit with the first field series');
1042            end
1043            TimeUnit=XmlData.Camera.TimeUnit;
1044        end
1045    end
1046    % number of slices
1047    if isfield(XmlData,'TranslationMotor')&& isfield(XmlData.TranslationMotor,'NbSlice')
1048        NbSlice_motor=XmlData.TranslationMotor.NbSlice;
1049        if ~isempty(NbSlice) && ~isequal(NbSlice_motor,NbSlice)
1050                msgbox_uvmat('WARNING','inconsistent Z numbers of Z indices');
1051        else
1052            NbSlice=NbSlice_motor;
1053        end
1054    end
1055end
1056if ~isempty(NbSlice)
1057set(handles.num_NbSlice,'String',num2str(NbSlice))
1058set(handles.num_NbSlice,'Visible','on')
1059end
1060
1061%% read timing  from the current file (prioritary)
1062if ~isempty(VideoObject)% case of movies
1063    imainfo=get(VideoObject);
1064    if isfield(imainfo,'NumFrames')
1065        imainfo.NumberOfFrames=imainfo.NumFrames;
1066    end
1067    if isempty(j1_series) % frame index along i
1068        Time=zeros(imainfo.NumberOfFrames+1,2);
1069        Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
1070    else
1071        Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
1072    end
1073    TimeName='video';
1074end
1075
1076
1077%% determine the min and max times: case of Netcdf files will be treated later in FieldName_Callback
1078if ~isempty(TimeName)
1079    TimeMin=Time(MinIndex_i+1,MinIndex_j+1);
1080    if size(Time)>=[first_i+1 first_j+1]
1081        TimeFirst=Time(first_i+1,first_j+1);
1082    end
1083    if size(Time)>=[last_i+1 last_j+1]
1084        TimeLast=Time(last_i+1,last_j+1);
1085    end
1086    if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1]
1087        TimeMax=Time(MaxIndex_i+1,MaxIndex_j+1);
1088    end
1089end
1090
1091%% update the time table
1092TimeTable=get(handles.TimeTable,'Data');
1093TimeTable{iview,1}=TimeName;
1094TimeTable{iview,2}=TimeMin;
1095TimeTable{iview,3}=TimeFirst;
1096TimeTable{iview,4}=TimeLast;
1097TimeTable{iview,5}=TimeMax;
1098set(handles.TimeTable,'Data',TimeTable)
1099
1100%% update the series info in 'UserData'
1101SeriesData.i1_series{iview}=i1_series;
1102SeriesData.i2_series{iview}=i2_series;
1103SeriesData.j1_series{iview}=j1_series;
1104SeriesData.j2_series{iview}=j2_series;
1105SeriesData.FileType{iview}=FileInfo.FileType;
1106SeriesData.FileInfo{iview}=FileInfo;
1107SeriesData.Time{iview}=Time;
1108
1109SeriesData.TimeName=TimeName;
1110
1111if check_calib
1112    SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib;
1113end
1114set(handles.series,'UserData',SeriesData)
1115
1116%% update pair menus
1117hset_pair=findobj(allchild(0),'Tag','set_pairs');
1118if ~isempty(hset_pair), delete(hset_pair); end % delete the GUI set_pair if opened
1119CheckPair= ~isempty(i2_series)||~isempty(j2_series); % check whether index pairs need to be defined
1120PairString=get(handles.PairString,'Data');
1121if CheckPair% if pairs need to be display for line iview
1122    [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series);
1123    Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,ModeMenu{ModeValue},Time,TimeUnit,ref_i,ref_j,TimeName,InputTable(iview,:),FileInfo);
1124    PairString{iview,1}=Menu{1};
1125else
1126    PairString{iview,1}=''; % no pair for #iview
1127end
1128set(handles.PairString,'Data',PairString)
1129if isempty(find(cellfun('isempty',get(handles.PairString,'Data'))==0, 1))% if all lines of pairs are empty
1130    set(handles.PairString,'Visible','off')
1131    set(handles.SetPairs,'Visible','off')
1132else
1133    set(handles.PairString,'Visible','on')
1134    set(handles.SetPairs,'Visible','on')
1135end
1136
1137
1138%% display the set of existing files as an image
1139set(handles.FileStatus,'Units','pixels')
1140Position=get(handles.FileStatus,'Position');
1141set(handles.FileStatus,'Units','normalized')
1142%xI=0.5:Position(3)-0.5;
1143nbview=numel(SeriesData.i1_series);
1144j_max=cell(1,nbview);
1145MaxIndex_i=ones(1,nbview); % default
1146MinIndex_i=ones(1,nbview); % default
1147for iline=1:nbview
1148    pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); % max on pair index
1149    j_max{iline}=max(pair_max,[],1); % max on j index
1150    if ~isempty(j_max{iline})
1151    MaxIndex_i(iline)=find(j_max{iline}, 1, 'last' )-1; % max ref index i
1152    MinIndex_i(iline)=find(j_max{iline}, 1 )-1; % min ref index i
1153    end
1154end
1155MinIndex_i=min(MinIndex_i);
1156MaxIndex_i=max(MaxIndex_i);
1157range_index=MaxIndex_i-MinIndex_i+1;
1158range_y=max(1,floor(Position(4)/nbview));
1159npx=floor(Position(3));
1160file_indices=MinIndex_i+floor(((0.5:npx-0.5)/npx)*range_index)+1;
1161CData=zeros(nbview*range_y,npx); % initiate the image representing the existing files
1162for iline=1:nbview
1163    ind_y=1+(iline-1)*range_y:iline*range_y;
1164    LineData=zeros(size(file_indices));
1165    file_select=file_indices(file_indices<=numel(j_max{iline}));
1166    ind_select=file_indices<=numel(j_max{iline});
1167    LineData(ind_select)=j_max{iline}(file_select)~=0;
1168    CData(ind_y,:)=ones(size(ind_y'))*LineData;
1169end
1170CData=cat(3,zeros(size(CData)),CData,zeros(size(CData))); % make color images r=0,g,b=0
1171set(handles.FileStatus,'CData',CData);
1172
1173%-----------------------------------------------------------guide -------------
1174%------------------------------------------------------------------------
1175%  III - FUNCTIONS ASSOCIATED TO THE FRAME IndexRange
1176%------------------------------------------------------------------------
1177
1178
1179% ---- determine the menu to put in mode and advice a default choice
1180%------------------------------------------------------------------------
1181function [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series)
1182%------------------------------------------------------------------------   
1183ModeMenu={''};
1184if isempty(j2_series)% no j pair
1185    ModeValue=1;
1186    if ~isempty(i2_series)
1187        ModeMenu={'series(Di)'}; % pair menu with only option Di
1188    end
1189else %existence of j pairs
1190    pair_max=squeeze(max(i1_series,[],1)); % max on pair index
1191    j_max=max(pair_max,[],1);
1192    MaxIndex_i=find(j_max, 1, 'last' )-1; % max ref index i
1193    MinIndex_i=find(j_max, 1 )-1; % min ref index i
1194    i_max=max(pair_max,[],2);
1195    MaxIndex_j=find(i_max, 1, 'last' )-1; % max ref index i
1196    MinIndex_j=find(i_max, 1 )-1; % min ref index i
1197    if MaxIndex_j==MinIndex_j
1198        ModeValue=1;
1199        ModeMenu={'bursts'};
1200    elseif MaxIndex_i==MinIndex_i
1201        ModeValue=1;
1202        ModeMenu={'series(Dj)'};
1203    else
1204        ModeMenu={'bursts';'series(Dj)'};
1205        if (MaxIndex_j-MinIndex_j)>10
1206            ModeValue=2; % set mode to series(Dj) if more than 10 j values
1207        else
1208            ModeValue=1;
1209        end
1210    end
1211end
1212
1213
1214%------------------------------------------------------------------------
1215%fill the menu of possible pairs as input
1216function displ_pair=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo)
1217%------------------------------------------------------------------------
1218displ_pair={};
1219if isempty(TimeUnit)
1220    dtunit='e-03';
1221else
1222    dtunit=['m' TimeUnit];
1223end
1224switch mode
1225    case 'series(Di)'
1226        diff_i=i2_series-i1_series;
1227        min_diff=min(diff_i(diff_i>0));
1228        max_diff=max(diff_i(diff_i>0));
1229        for ipair=min_diff:max_diff
1230            if ~isempty(find(diff_i==ipair,1))% if the considered difference exists as input
1231                pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1232                if size(time,1)>=ref_i+ceil(ipair/2)
1233                    if ref_i<=floor(ipair/2)
1234                        ref_i=floor(ipair/2)+1; % shift ref_i to get the first pair
1235                    end
1236                    Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1237                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1238                end
1239                displ_pair=[displ_pair;{pair_string}];
1240            end
1241        end
1242        if ~isempty(displ_pair)
1243            displ_pair=[displ_pair;{'Di=*|*'}];
1244        end
1245    case 'series(Dj)'
1246        if isempty(j2_series)
1247            msgbox_uvmat('ERROR','no j1-j2 pair available')
1248            return
1249        end
1250        diff_j=j2_series-j1_series;
1251        min_diff=min(diff_j(diff_j>0));
1252        max_diff=max(diff_j(diff_j>0));
1253        for ipair=min_diff:max_diff
1254            if numel(diff_j(diff_j==ipair))>0
1255                pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1256                if ~isempty(time)
1257                    if ref_j<=floor(ipair/2)
1258                        ref_j=floor(ipair/2)+1; % shift ref_i to get the first pair
1259                    end
1260                    Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1261                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1262                end
1263                displ_pair=[displ_pair;{pair_string}];
1264            end
1265        end
1266        if ~isempty(displ_pair)
1267            displ_pair=[displ_pair;{'Dj=*|*'}];
1268        end
1269    case 'bursts'
1270        if isempty(j2_series)
1271            msgbox_uvmat('ERROR','no j1-j2 pair available')
1272            return
1273        end
1274        %diff_j=j2_series-j1_series;
1275        min_j1=min(j1_series(j1_series>0));
1276        max_j1=max(j1_series(j1_series>0));
1277        min_j2=min(j2_series(j2_series>0));
1278        max_j2=max(j2_series(j2_series>0));
1279        for pair1=min_j1:min(max_j1,min_j1+20)
1280            for pair2=min_j2:min(max_j2,min_j2+20)
1281                if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1282                    pair_string=['j= ' num2str(pair1) '-' num2str(pair2)];
1283                    [TimeValue,DtValue]=get_time(ref_i,[],pair_string,InputTable,FileInfo,TimeName,'Dt');
1284                    %Dt=time(ref_i,pair2+1)-time(ref_i,pair1+1);
1285                    pair_string=[pair_string ', Dt=' num2str(DtValue) ' ' dtunit];
1286                    displ_pair=[displ_pair;{pair_string}];
1287                end
1288            end
1289        end
1290        if ~isempty(displ_pair)
1291            displ_pair=[displ_pair;{'j=*-*'}];
1292        end
1293end
1294
1295%------------------------------------------------------------------------
1296function num_first_i_Callback(hObject, eventdata, handles)
1297%------------------------------------------------------------------------
1298num_last_i_Callback(hObject, eventdata, handles)
1299
1300%------------------------------------------------------------------------
1301function num_last_i_Callback(hObject, eventdata, handles)
1302%------------------------------------------------------------------------
1303SeriesData=get(handles.series,'UserData');
1304if ~isfield(SeriesData,'Time')
1305    SeriesData.Time{1}=[];
1306end
1307displ_time(handles);
1308
1309%------------------------------------------------------------------------
1310function num_first_j_Callback(hObject, eventdata, handles)
1311%------------------------------------------------------------------------
1312 num_last_j_Callback(hObject, eventdata, handles)
1313
1314%------------------------------------------------------------------------
1315function num_last_j_Callback(hObject, eventdata, handles)
1316%------------------------------------------------------------------------
1317% first_j=str2num(get(handles.num_first_j,'String'));
1318% last_j=str2num(get(handles.num_last_j,'String'));
1319% ref_j=ceil((first_j+last_j)/2);
1320% set(handles.num_ref_j,'String', num2str(ref_j))
1321% num_ref_j_Callback(hObject, eventdata, handles)
1322SeriesData=get(handles.series,'UserData');
1323if ~isfield(SeriesData,'Time')
1324    SeriesData.Time{1}=[];
1325end
1326displ_time(handles);
1327
1328%------------------------------------------------------------------------
1329% ---- find the times corresponding to the first and last indices of a series
1330function displ_time(handles)
1331%------------------------------------------------------------------------
1332SeriesData=get(handles.series,'UserData'); %
1333if ~isfield(SeriesData,'Time')
1334    return
1335end
1336PairString=get(handles.PairString,'Data');
1337ref_i_1=str2num(get(handles.num_first_i,'String')); % first reference index
1338ref_i_2=str2num(get(handles.num_last_i,'String')); % last reference index
1339ref_j_1=[];ref_j_2=[];
1340if strcmp(get(handles.num_first_j,'Visible'),'on')
1341ref_j_1=str2num(get(handles.num_first_j,'String'));
1342ref_j_2=str2num(get(handles.num_last_j,'String'));
1343end
1344[i1_1,i2_1,j1_1,j2_1] = get_file_index(ref_i_1,ref_j_1,PairString);
1345[i1_2,i2_2,j1_2,j2_2] = get_file_index(ref_i_2,ref_j_2,PairString);
1346TimeTable=get(handles.TimeTable,'Data');
1347%%%%%%
1348%TODO: read time in netcdf file, see ActionName_Callback
1349%%%%%%%
1350%Pairs=get(handles.PairString,'Data');
1351for iview=1:size(TimeTable,1)
1352    if size(SeriesData.Time,1)<iview
1353        break
1354    end
1355    TimeTable{iview,3}=[];
1356    TimeTable{iview,4}=[];
1357    if size(SeriesData.Time{iview},1)>=i2_2+1 && (isempty(ref_j_1)||size(SeriesData.Time{iview},2)>=j2_2+1)
1358        if isempty(ref_j_1)
1359            time_first=(SeriesData.Time{iview}(i1_1+1,2)+SeriesData.Time{iview}(i2_1+1,2))/2;
1360            time_last=(SeriesData.Time{iview}(i1_2+1,2)+SeriesData.Time{iview}(i2_2+1,2))/2;
1361        else
1362            time_first=(SeriesData.Time{iview}(i1_1+1,j1_1+1)+SeriesData.Time{iview}(i2_1+1,j2_1+1))/2;
1363            time_last=(SeriesData.Time{iview}(i1_2+1,j1_2+1)+SeriesData.Time{iview}(i2_2+1,j2_1+1))/2;
1364        end
1365        TimeTable{iview,3}=time_first; % TODO: take into account pairs
1366        TimeTable{iview,4}=time_last; % TODO: take into account pairs
1367    end
1368end
1369set(handles.TimeTable,'Data',TimeTable)
1370
1371%% set the waitbar position with respect to the min and max in the series
1372MinIndex_i=min(get(handles.MinIndex_i,'Data'));
1373MaxIndex_i=max(get(handles.MaxIndex_i,'Data'));
1374pos_first=(ref_i_1-MinIndex_i)/(MaxIndex_i-MinIndex_i+1);
1375pos_last=(ref_i_2-MinIndex_i+1)/(MaxIndex_i-MinIndex_i+1);
1376if isempty(pos_first), pos_first=0; end
1377if isempty(pos_last), pos_last=1; end
1378Position=get(handles.Waitbar,'Position'); % position of the waitbar:= [ x,y, width, height]
1379Position_status=get(handles.FileStatus,'Position');
1380Position(1)=Position_status(1)+Position_status(3)*pos_first;
1381Position(3)=max(Position_status(3)*(pos_last-pos_first),0.001); % width must remain positive
1382set(handles.Waitbar,'Position',Position)
1383update_waitbar(handles.Waitbar,0)
1384
1385%------------------------------------------------------------------------
1386% --- Executes when selected cell(s) is changed in PairString.
1387function PairString_CellSelectionCallback(hObject, eventdata, handles)
1388%------------------------------------------------------------------------   
1389if numel(eventdata.Indices)>=1
1390    PairString=get(hObject,'Data');
1391    if ~isempty(PairString{eventdata.Indices(1)})
1392        SetPairs_Callback(hObject, eventdata.Indices(1), handles)
1393    end
1394end
1395
1396%-------------------------------------
1397function enable_i(handles,state)
1398set(handles.i_txt,'Visible',state)
1399set(handles.num_first_i,'Visible',state)
1400set(handles.num_last_i,'Visible',state)
1401set(handles.num_incr_i,'Visible',state)
1402
1403%-----------------------------------
1404function enable_j(handles,state)
1405set(handles.j_txt,'Visible',state)
1406set(handles.num_first_j,'Visible',state)
1407set(handles.num_last_j,'Visible',state)
1408set(handles.num_incr_j,'Visible',state)
1409set(handles.MinIndex_j,'Visible',state)
1410set(handles.MaxIndex_j,'Visible',state)
1411
1412
1413%%%%%%%%%%%%%%%%%%%%
1414%%  MAIN ActionName FUNCTIONS
1415%%%%%%%%%%%%%%%%%%%%
1416%------------------------------------------------------------------------
1417% --- Executes on button press in RUN.
1418%------------------------------------------------------------------------
1419function RUN_Callback(hObject, eventdata, handles)
1420
1421%% settings of the button RUN
1422if ~isequal(get(handles.ActionInput,'BackgroundColor'),[1 0 0])
1423    msgbox_uvmat('ERROR','first activate the button ActionInput')
1424    return
1425end
1426set(handles.RUN,'BusyAction','queue'); % activation of STOP button will set BusyAction to 'cancel'
1427set(handles.RUN, 'Enable','Off')% avoid further RUN action until the current one is finished
1428set(handles.RUN,'BackgroundColor',[1 1 0])%show activation of RUN by yellow color
1429drawnow
1430set(handles.status,'Value',0)% desable status display if relevant
1431status_Callback([], eventdata, handles)
1432
1433%% launch action
1434errormsg=launch_action(handles);
1435if ~isempty(errormsg)
1436     msgbox_uvmat('ERROR',errormsg)
1437end
1438
1439%% reset the GUI series
1440update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate launching is finished
1441set(handles.RUN, 'Enable','On')
1442set(handles.RUN,'BackgroundColor',[1 0 0])
1443set(handles.RUN, 'Value',0)
1444
1445%------------------------------------------------------------------------
1446% --- called by RUN_Callback
1447%------------------------------------------------------------------------
1448% The calculations are launched in three different ways:
1449% RunMode='local': calculation on the local Matlab session, will prevent other actions during that time.
1450% RunMode='background': calculation on the local computer, but in a new Matlab session (with no graphic output).
1451% RunMode='cluster': calculations dispatched in a cluster, using a managing system, 'oar, 'sge, or 'sgb'.
1452% In the latter case, the calculation is split in 'packets' of i index (all j indices are contained in a single packet).
1453% This splitting is possible only if the different calculations in the series are independent. Otherwise the action
1454% function imposes a number of processes NbSlice in input, for instance NbSlice=1 for a time series.
1455% If NbSlice is not imposed, the splitting in packets (jobs) is determined
1456% so that a job is optimum length AdvisedJobCPUTime), and the total job number in any case smaller
1457% than MaxJobNumber (these parameters are defined in the file series.xml in
1458% accordance with the management strategy for the cluster). The jobs are
1459% dispatched in parallel into NbCore processors by the cluster managing system.
1460
1461function errormsg=launch_action(handles)
1462errormsg=''; % default
1463
1464%% read the data on the GUI series
1465Param=read_GUI_series(handles); % displayed parameters
1466SeriesData=get(handles.series,'UserData'); % hidden parameters
1467if isfield(SeriesData,'TransformInput')
1468    Param.TransformInput=SeriesData.TransformInput;
1469end
1470if isfield(SeriesData,'ProjObject')
1471    Param.ProjObject=SeriesData.ProjObject;
1472end
1473if ~isfield(SeriesData,'i1_series')
1474    errormsg='The input field series needs to be refreshed: press REFRESH';
1475    return
1476end
1477if isfield(Param,'InputFields')&& isfield(Param.InputFields,'FieldName')&& isequal(Param.InputFields.FieldName,'add_field...')
1478    errormsg='input field name(s) not defined, select add_field...';
1479    return
1480end
1481
1482%% select the Action mode, 'local', 'background' or 'cluster' (if available)
1483RunMode='local'; % default (needed for first opening of the GUI series)
1484if isfield(Param.Action,'RunMode')
1485    RunMode=Param.Action.RunMode;
1486    Param.Action=rmfield(Param.Action,'RunMode'); % remove from the recorded xml file to avoid interference during ImportConfig
1487    Param.RunMode=RunMode; % keep track of the mode
1488end
1489ActionExt='.m'; % default
1490if isfield(Param.Action,'ActionExt')
1491    ActionExt=Param.Action.ActionExt; % '.m', '.sh' (compiled)  or '.py' (Python)
1492    Param.Action=rmfield(Param.Action,'ActionExt'); % remove from the recorded xml file to avoid interference during ImportConfig
1493end
1494ActionName=Param.Action.ActionName;
1495ActionPath=Param.Action.ActionPath;
1496path_series=fileparts(which('series'));
1497
1498%% create the Action fct handle if RunMode option = 'local'
1499if strcmp(RunMode,'local')
1500    if ~isequal(ActionPath,path_series)
1501        eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1502        if ~exist(ActionPath,'dir')
1503            errormsg=['The prescribed function path ' ActionPath ' does not exist'];
1504            return
1505        end
1506        if ~isequal(spath,ActionPath)
1507            addpath(ActionPath)% add the prescribed path if not the current one
1508        end
1509    end
1510    eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1511    if ~isequal(ActionPath,path_series)
1512        rmpath(ActionPath)% add the prescribed path if not the current one
1513    end
1514end
1515
1516%% Get  parameters from series.xml
1517errormsg=''; % default error message
1518ActionFullName=fullfile(get(handles.ActionPath,'String'),ActionName);
1519
1520%% If a compiled version has been selected (ext .sh) check wether it needs to be recompiled
1521if strcmp(ActionExt,'.sh')
1522    TransformPath='';
1523    if isfield(SeriesData,'TransformPath')
1524        TransformPath=SeriesData.TransformPath;
1525        if isfield(SeriesData,'TransformList')
1526            TransformList=get(handles.TransformName,'String');
1527            TransformIndex=get(handles.TransformName,'Value');
1528            TransformName=TransformList{TransformIndex};
1529            if ~ismember(TransformName,SeriesData.TransformList)
1530                TransformPath='';
1531            end
1532        end
1533    end
1534    if ~isempty(TransformPath)&&...
1535          ~strcmp(TransformPath,get(handles.TransformPath,'String'))% if the transform is not in paths set for compilation
1536        msgbox_uvmat('ERROR', 'compilation not available for this transform function, select .m')
1537        return
1538    end
1539    set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
1540    set(handles.ActionExt,'BackgroundColor',[1 1 0])
1541    [mcrmajor, mcrminor] = mcrversion;   
1542    MCRROOT = ['MCRROOT',int2str(mcrmajor),int2str(mcrminor)];
1543    RunTime = getenv('MCRROOT'); % Just variable MCRROOT with no version in it's name
1544    if strcmp(RunTime,'')
1545        RunTime = getenv(MCRROOT); % Use specialize MCRROOT with version
1546    end
1547    ActionNameVersion=[ActionName '_' MCRROOT];
1548    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']);
1549    % compile the .m file if the .sh file does not exist yet
1550    if ~exist(ActionFullName,'file')
1551        answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
1552        if strcmp(answer,'Yes')
1553            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1554            path_uvmat=fileparts(which('series'));
1555            currentdir=pwd;
1556            cd(get(handles.ActionPath,'String'))% go to the directory of Action
1557            addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1558            compile(ActionName,TransformPath)
1559            cd(currentdir)
1560        else
1561            errormsg='Action launch interrupted';
1562            return
1563        end       
1564    else
1565        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']));
1566        m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
1567        if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
1568            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1569            drawnow
1570            answer=msgbox_uvmat('INPUT_Y-N',[ActionNameVersion '.sh needs to be updated: recompile now?']);
1571            if strcmp(answer,'Yes')
1572                path_uvmat=fileparts(which('series'));
1573                currentdir=pwd;
1574                cd(get(handles.ActionPath,'String'))% go to the directory of Action
1575                addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1576                addpath(fullfile(path_uvmat,'transform_field'))% add the path to transform functions to run the fct 'compile'
1577                compile(ActionName,TransformPath)
1578                cd(currentdir)
1579            end
1580        end
1581    end
1582
1583    set(handles.ActionExt,'BackgroundColor',[1 1 1])
1584     set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch
1585end
1586
1587%% set nbre of cluster cores and processes:
1588% NbCore is the number of computer processors used
1589% NbProcess is the number of independent processes in which the required calculation is split.
1590% switch RunMode
1591%     case {'local','background'}
1592%         NbCore=1; % no need to split the calculation
1593%     case 'cluster'
1594%         %proposed number of cores to reserve in the cluster
1595%         NbCoreAdvised=SeriesData.SeriesParam.ClusterParam.NbCoreAdvised;
1596%         NbCoreMax=min(NbProcess,SeriesData.SeriesParam.ClusterParam.NbCoreMax);
1597%         if NbCoreMax~=1
1598%             if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1599%                 warning_string=', preferably use .sh option to save Matlab licences';
1600%             else
1601%                 warning_string=')';
1602%             end
1603%             answer=msgbox_uvmat('INPUT_TXT',['Number of cores (max ' num2str(NbCoreMax) ', ' warning_string],num2str(NbCoreAdvised));
1604%             if isempty(answer)
1605%                 errormsg='Action launch interrupted by user';
1606%                 return
1607%             end
1608%             NbCore=str2double(answer);
1609%             if NbCore > NbCoreMax
1610%                 NbCore=NbCoreMax;
1611%             end
1612%         else
1613%             NbCore=1;
1614%         end
1615% end
1616if ~isfield(Param.IndexRange,'NbSlice')
1617    Param.IndexRange.NbSlice=[];
1618end
1619OutputPath=get(handles.OutputPath,'String');
1620
1621%% Look for processing on multiple experiments set by the GUI browse_data
1622NbExp=1;% initiate the number of experiments set by the GUI browse_data, =1 otherwise
1623if get(handles.Replicate,'Value')
1624    hh=findobj(allchild(0),'Tag','browse_data');
1625    if isempty(hh)
1626        set(handles.Replicate,'Value',0)
1627    else
1628        set(handles.Replicate,'BackgroundColor',[1 1 0])%paint Relicate button in yellow
1629        BrowseData=guidata(hh);
1630        SourceDir=get(BrowseData.SourceDir,'String');
1631        ListExp=get(BrowseData.ListExperiments,'String');
1632        ExpIndices=get(BrowseData.ListExperiments,'Value');
1633        ListExp=ListExp(ExpIndices);
1634        ListDevices=get(BrowseData.ListDevices,'String');
1635        DeviceIndices=get(BrowseData.ListDevices,'Value');
1636        ListDevices=ListDevices(DeviceIndices);
1637        ListDataSeries=get(BrowseData.DataSeries,'String');
1638        DataSeriesIndices=get(BrowseData.DataSeries,'Value');
1639        ListDataSeries=ListDataSeries(DataSeriesIndices);
1640        NbExp=0; % counter of the number of experiments set by the GUI browse_data
1641        for iexp=1:numel(ListExp)
1642            if ~isempty(regexp(ListExp{iexp},'^\+/'))% if it is a folder
1643               %if strcmp(get(BrowseData.DataSeries,'enable'),'off') %case of a multiple input line for series
1644%                     NbExp=NbExp+1;
1645%                     ExpIndex{NbExp}=iexp;
1646%                     for idevice=1:numel(ListDevices)
1647%                         lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),...
1648%                             regexprep(ListDevices{idevice},'^\+/',''));
1649%                         lpathout=fullfile(OutputPath,regexprep(ListExp{iexp},'^\+/',''),...
1650%                             regexprep(ListDevices{idevice},'^\+/',''));
1651%                         ldir=regexprep(ListDataSeries{idevice},'^\+/','');
1652%                         ListPath{idevice,NbExp}=lpath;
1653%                         ListPathOut{idevice,NbExp}=lpathout;
1654%                         ListSubdir{idevice,NbExp}=ldir;
1655%                     end
1656                %else
1657                    for idevice=1:numel(ListDevices)
1658                        if ~isempty(regexp(ListDevices{idevice},'^\+/'))% if it is a folder
1659                            for isubdir=1:numel(ListDataSeries)
1660                                if ~isempty(regexp(ListDataSeries{isubdir},'^\+/'))% if it is a folder
1661                                    lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),...
1662                                        regexprep(ListDevices{idevice},'^\+/',''));
1663                                    lpathout= fullfile(OutputPath,regexprep(ListExp{iexp},'^\+/',''),...
1664                                        regexprep(ListDevices{idevice},'^\+/',''));
1665                                    ldir= regexprep(ListDataSeries{isubdir},'^\+/','');
1666                                    if exist(fullfile(lpath,ldir),'dir')
1667                                        NbExp=NbExp+1;
1668                                        ExpIndex(NbExp)=ExpIndices(iexp);
1669                                        DeviceIndex(NbExp)=DeviceIndices(idevice);
1670                                        ListPath{NbExp}=lpath;
1671                                        ListPathOut{NbExp}=lpathout;
1672                                        ListDeviceOut{NbExp}=regexprep(ListDevices{idevice},'^\+/','');
1673                                        ListExpOut{NbExp}=regexprep(ListExp{iexp},'^\+/','');
1674                                        ListSubdir{NbExp}=ldir;
1675                                    end
1676                                end
1677                            end
1678                        end
1679                    end
1680%                 end
1681            end
1682        end
1683        answer=msgbox_uvmat('INPUT_Y-N-Cancel',['replicate the processing on ' num2str(NbExp) ' data series']);
1684        if strcmp(answer,'Cancel')||strcmp(answer,'No')
1685            return
1686        end
1687    end
1688end
1689
1690%%%%%%%%%%%%%%%%%%% LOOP ON EXPERIMENTS POSSIBLY SET BY THE GUI browse_data, NbExp=1 otherwise %%%%%%%%%
1691
1692for iexp=1:NbExp
1693    if get(handles.Replicate,'Value')
1694        if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1695            disp('program stopped by user')
1696            return
1697        end
1698        set(BrowseData.ListExperiments,'Value',ExpIndex(iexp))
1699        set(BrowseData.ListDevices,'Value',DeviceIndex(iexp))
1700        Param.InputTable(:,1)=ListPath(:,iexp);
1701        Param.InputTable(:,2)=ListSubdir(:,iexp);
1702        OutputSubDir=unique(ListSubdir(:,iexp));
1703        Param.OutputSubDir=OutputSubDir{1};
1704        if numel(OutputSubDir)>1% case
1705            for iout=2:numel(OutputSubDir)
1706                Param.OutputSubDir=[Param.OutputSubDir '-' OutputSubDir{iout}];
1707            end               
1708        end       
1709    end
1710    [xx,ExpName]=fileparts(Param.InputTable{1,1});
1711    Param.IndexRange.first_i=str2num(get(handles.num_first_i,'String'));%reset the firrst_i and last_i for multiple experiments, modified by the splitting into NbProcess
1712    Param.IndexRange.last_i=str2num(get(handles.num_last_i,'String'));
1713   
1714    %% create the output data directory if needed, after checking its existence
1715    OutputDir='';
1716    answer='';
1717    if isfield(Param,'OutputSubDir')&& isfield(Param,'OutputDirExt')% possibly update the output dir if it already exists
1718        PathOut=get(handles.OutputPath,'String');
1719        if ~exist(PathOut,'dir') % test if  the dir  already exist
1720            PathOut=uigetdir(PathOut,'pick the output root path');
1721            set(handles.OutputPath,'String',PathOut);
1722        end
1723        if get(handles.Replicate,'Value')
1724        PathExpOut=fileparts(ListPath{iexp});
1725        PathExpDeviceOut=ListPath{iexp};
1726        else
1727            PathExpOut=fullfile(PathOut,get(handles.Experiment,'String'));
1728            PathExpDeviceOut=fullfile(PathExpOut,get(handles.Device,'String'))
1729        end
1730        if ~exist(PathExpOut,'dir')
1731            [tild,msg1]=mkdir(PathExpOut);
1732            if ~strcmp(msg1,'')
1733                errormsg=['cannot create ' PathExpOut ': ' msg1]; % error message for directory creation
1734                return
1735            end
1736        end
1737        if ~exist(PathExpDeviceOut,'dir')
1738            [tild,msg1]=mkdir(PathExpDeviceOut);
1739            if ~strcmp(msg1,'')
1740                errormsg=['cannot create ' PathExpDeviceOut ': ' msg1]; % error message for directory creation
1741                return
1742            end
1743        end
1744
1745        SubDirOut=[Param.OutputSubDir Param.OutputDirExt];
1746        SubDirOutNew=SubDirOut;
1747        detect=exist(fullfile(PathExpDeviceOut,SubDirOutNew),'dir'); % test if  the dir  already exist
1748        check_create=1; % need to create the result directory by default
1749        CheckOverwrite=1;
1750        if isfield(Param,'CheckOverwrite')
1751            CheckOverwrite=Param.CheckOverwrite;% will overwrite previous data if it is equal to 1
1752        end
1753        while detect
1754            if CheckOverwrite
1755                comment=', possibly overwrite previous data';
1756            else
1757                comment=', will complement existing result files (no overwriting)';
1758            end
1759            answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(PathExpDeviceOut,SubDirOutNew) comment]);
1760            if strcmp(answer,'Cancel')
1761                break
1762            elseif strcmp(answer,'Yes')
1763                detect=0;
1764                check_create=0;
1765            else
1766                r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names'); % detect whether name ends by a number
1767                if isempty(r)
1768                    r(1).root=[SubDirOutNew '_'];
1769                    r(1).num1='0';
1770                end
1771                SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)]; % increment the index by 1 or put 1
1772                detect=exist(fullfile(PathExpDeviceOut,SubDirOutNew),'dir'); % test if  the dir  already exists
1773                check_create=1;
1774            end
1775        end
1776        if strcmp(answer,'Cancel')
1777            continue
1778        end
1779        Param.OutputDirExt=regexprep(SubDirOutNew,['^' Param.OutputSubDir],'');
1780        Param.OutputRootFile=Param.InputTable{1,3}; % the first sorted RootFile taken for output
1781        OutputDir=fullfile(PathExpDeviceOut,[Param.OutputSubDir Param.OutputDirExt]); % full name (with path) of output directory
1782        if check_create    % create output directory if it does not exist
1783            [tild,msg1]=mkdir(OutputDir);
1784            if ~strcmp(msg1,'')
1785                errormsg=['cannot create ' OutputDir ': ' msg1]; % error message for directory creation
1786                return
1787            end
1788        end
1789       
1790    elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir
1791        OutputDir=Param.ActionInput.LogPath;
1792    end
1793    if isfield(Param,'OutputSubDir')&& isfield(Param,'OutputDirExt')
1794        set(handles.OutputSubDir,'String',Param.OutputSubDir)
1795        set(handles.OutputDirExt,'String',Param.OutputDirExt)
1796        drawnow
1797    end
1798    if get(handles.Replicate,'Value')
1799        set(handles.InputTable,'Data',Param.InputTable)
1800        set(handles.OutputPath,'String',OutputPath)
1801         set(handles.Experiment,'String',ListExpOut{iexp})
1802        set(handles.Device,'String',ListDeviceOut{iexp})
1803        Param.Experiment=ListExpOut{iexp};
1804        Param.Device=ListDeviceOut{iexp};
1805        check_input_file_series(handles)     
1806    end
1807    DirXml=fullfile(OutputDir,'0_XML');
1808    if ~exist(DirXml,'dir')
1809        [~,msg1]=mkdir(DirXml);
1810        if ~strcmp(msg1,'')
1811            errormsg=['cannot create ' DirXml ': ' msg1]; % error message for directory creation
1812            return
1813        end
1814        [success,msg] = fileattrib(DirXml,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
1815        if success==0
1816            msgbox_uvmat('WARNING',{['unable to set group write access to ' DirXml ':']; msg}); % error message for directory creation
1817        end
1818    end
1819    OutputNomType=nomtype2pair(Param.InputTable{1,4}); % nomenclature for output files
1820   
1821    %% get the set of reference input field indices
1822    first_i=1; % first i index to process
1823    last_i=1; % last i index to process
1824    incr_i=1; % increment step in i index
1825    first_j=1; % first j index to process
1826    last_j=1; % last j index to process
1827    incr_j=1; % increment step in j index
1828    if isfield(Param.IndexRange,'first_i')
1829        first_i=Param.IndexRange.first_i;
1830        incr_i=Param.IndexRange.incr_i;
1831        last_i=Param.IndexRange.last_i;
1832    end
1833    if isfield(Param.IndexRange,'incr_j')
1834        first_j=Param.IndexRange.first_j;
1835        last_j=Param.IndexRange.last_j;
1836        incr_j=Param.IndexRange.incr_j;
1837    end
1838    if last_i < first_i || last_j < first_j
1839        errormsg= 'series/Run_Callback:last field index must be larger or equal to the first one';
1840        return
1841    end
1842    %incr_i must be defined, =1 by default, if NbSlice is active
1843    if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice)
1844        incr_i=1;
1845        set(handles.num_incr_i,'String','1')
1846    end
1847    % case of no increment i defined: processing is done on the available files found in i1_series
1848    if isempty(incr_i)
1849        if isempty(incr_j)
1850            [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1851            ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1852            ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1853            ref_j=ref_j-1;
1854            ref_i=ref_i-1;
1855        else
1856            ref_j=first_j:incr_j:last_j;
1857            [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1858            ref_i=ref_i-1;
1859            ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1860        end
1861        % increment i is defined: processing is done on first_i:incr_i:last_i;
1862    else
1863        ref_i=first_i:incr_i:last_i;
1864        if isempty(incr_j)% automatic finding of the existing j indices
1865            [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1866            ref_j=ref_j-1;
1867            ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1868        else
1869            ref_j=first_j:incr_j:last_j;
1870        end
1871    end
1872    nbfield_j=numel(ref_j); % number of j indices
1873    BlockLength=numel(ref_i); % by default, job involves the full set of i field indicesNbProcess
1874    NbProcess=1;
1875    NbCore=1;
1876    switch RunMode
1877        case 'cluster'
1878            if (isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime) && isnumeric(Param.Action.CPUTime))
1879                CPUTime=Param.Action.CPUTime; % Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j
1880            else
1881                answer=msgbox_uvmat('INPUT_TXT','estimate the CPU time(in minutes) for each value of index i:' ,'');
1882                CPUTime=str2num(answer);
1883                set(handles.num_CPUTime,'String',answer)
1884                Param.Action.CPUTime=CPUTime;
1885            end
1886            JobNumberMax=SeriesData.SeriesParam.ClusterParam.JobNumberMax;
1887            JobCPUTimeAdvised=SeriesData.SeriesParam.ClusterParam.JobCPUTimeAdvised;
1888            if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined
1889                BlockLength= ceil(JobCPUTimeAdvised/(CPUTime*nbfield_j)); % iterations are grouped in sets with length BlockLength  such that the typical CPU time of a job is JobCPUTimeAdvised.
1890                BlockLength=max(BlockLength,ceil(numel(ref_i)*NbExp/JobNumberMax)); % possibly increase the BlockLength to have less than MaxJobNumber jobs
1891                NbProcess=ceil(numel(ref_i)/BlockLength) ; % nbre of processes sent to oar
1892            else
1893                NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1894            end
1895
1896            %         %proposed number of cores to reserve in the cluster
1897            NbCoreAdvised=SeriesData.SeriesParam.ClusterParam.NbCoreAdvised;
1898            NbCoreMax=min(NbProcess,SeriesData.SeriesParam.ClusterParam.NbCoreMax);% reduces the number of cores if it exceeds the number of processes
1899            if NbCoreMax~=1
1900                if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1901                    warning_string=', preferably use .sh option to save Matlab licences';
1902                else
1903                    warning_string=')';
1904                end
1905                answer=msgbox_uvmat('INPUT_TXT',['Number of cores (max ' num2str(NbCoreMax) ', ' warning_string],num2str(NbCoreAdvised));
1906                if isempty(answer)
1907                    errormsg='Action launch interrupted by user';
1908                    return
1909                end
1910                NbCore=str2double(answer);
1911                if NbCore > NbCoreMax
1912                    NbCore=NbCoreMax;
1913                end
1914            end
1915        otherwise
1916            if ~isempty(Param.IndexRange.NbSlice)
1917                NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1918            end
1919    end
1920
1921    %% record nbre of output files and starting time for computation for status
1922    StatusData=get(handles.status,'UserData');
1923    if isfield(StatusData,'OutputFileMode')
1924        switch StatusData.OutputFileMode
1925            case 'NbInput'
1926                StatusData.NbOutputFile=numel(ref_i)*nbfield_j;
1927            case 'NbInput_i'
1928                StatusData.NbOutputFile=numel(ref_i);
1929            case 'NbSlice'
1930                StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
1931        end
1932    end
1933    StatusData.TimeStart=now;
1934    set(handles.status,'UserData',StatusData)
1935
1936    %% case of a function in Python
1937    if strcmp(ActionExt, '.py (in dev.)')
1938        fprintf([
1939            '\n' ...
1940            '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ...
1941            'The option .py is used. It is still in development.\n' ...
1942            'To try it, first install pyper and the most recent version of fluidimage\n' ...
1943            '(see https://bitbucket.org/fluiddyn/fluidimage).\n' ...
1944            'Warning: there is no direct correspondance between UVMAT and fluidimage parameters\n' ...
1945            '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n'])
1946        RunMode = 'python';
1947    end
1948   
1949   
1950    %% direct processing on the current Matlab session or creation of command files
1951    filexml=cell(1,NbProcess); % initialisation of the names of the files containing the processing parameters
1952    extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process
1953    for iprocess=1:NbProcess
1954        extxml{iprocess}='.xml';
1955    end
1956    for iprocess=1:NbProcess
1957        if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1958            disp('program stopped by user')
1959            return
1960        end
1961        Param.IndexRange.incr_slice=incr_i;
1962        if isempty(Param.IndexRange.NbSlice)
1963            Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1964            if Param.IndexRange.first_i>last_i
1965                NbProcess=iprocess-1; % leave the loop, we are at the end of the calculation
1966                break
1967            end
1968            Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
1969        else %multislices (then incr_i is not empty)
1970            Param.IndexRange.first_i= first_i+iprocess-1;
1971            Param.IndexRange.incr_slice=incr_i*Param.IndexRange.NbSlice;
1972        end
1973        for ilist=1:size(Param.InputTable,1)
1974            Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/'); % correct path name for PCWIN system
1975        end
1976       
1977        if isfield(Param,'OutputSubDir')
1978            t=struct2xml(Param);
1979            t=set(t,1,'name','Series');
1980            extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,...
1981                Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1982            filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess});
1983            try
1984                save(t, filexml{iprocess}); % save the xml file containing the processing parameters
1985            catch ME
1986                if ~strcmp (RunMode,'local')
1987                    errormsg=['error writting ' filexml{iprocess} ': ' ME.message];
1988                    return
1989                end
1990            end
1991        end
1992        if strcmp (RunMode,'local')
1993            switch ActionExt
1994                case '.m'
1995                    h_fun(Param); % direct launching
1996                   
1997                case '.sh'
1998                    switch computer
1999                        case {'PCWIN','PCWIN64'} %Windows system
2000                            filexml=regexprep(filexml,'\\','\\\\'); % add '\' so that '\' are left as characters
2001                            system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); % TODO: adapt to DOS system
2002                        case {'GLNX86','GLNXA64','MACI64'}%Linux  system
2003                            system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]);
2004                    end
2005            end
2006        end
2007    end
2008   
2009    if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python')
2010        %% processing on a different session of the same computer (background) or cluster, create executable files
2011        batch_file_list=cell(NbProcess,1); % initiate the list of executable files
2012        DirExe=fullfile(OutputDir,'0_EXE'); % directory name for executable files
2013        switch computer
2014            case {'PCWIN','PCWIN64'} %Windows system
2015                ExeExt='.bat';
2016            case {'GLNX86','GLNXA64','MACI64'}%Linux  system
2017                ExeExt='.sh';
2018        end
2019        %create subdirectory for executable files
2020        if ~exist(DirExe,'dir')
2021            [tild,msg1]=mkdir(DirExe);
2022            if ~strcmp(msg1,'')
2023                errormsg=['cannot create ' DirExe ': ' msg1]; % error message for directory creation
2024                return
2025            end
2026            [success,msg] = fileattrib(DirExe,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2027            if success==0
2028                msgbox_uvmat('WARNING',{['unable to set group write access to ' DirExe ':']; msg}); % error message for directory creation
2029            end
2030        end
2031        %create subdirectory for log files
2032        DirLog=fullfile(OutputDir,'0_LOG');
2033        if ~exist(DirLog,'dir')
2034            [tild,msg1]=mkdir(DirLog);
2035            if ~strcmp(msg1,'')
2036                errormsg=['cannot create ' DirLog ': ' msg1]; % error message for directory creation
2037                return
2038            end
2039            [success,msg] = fileattrib(DirLog,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2040            if success==0
2041                msgbox_uvmat('WARNING',{['unable to set group write access to ' DirLog ':']; msg}); % error message for directory creation
2042            end
2043        end
2044       
2045        %create the executable file
2046        file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,...
2047            first_i,last_i,first_j,last_j);
2048        file_exe_global=fullfile(OutputDir,'0_EXE',file_exe_global);
2049        filelog_global=fullfile_uvmat('','',Param.InputTable{1,3},'.log',OutputNomType,...
2050            first_i,last_i,first_j,last_j);
2051        filelog_global=fullfile(OutputDir,'0_LOG',filelog_global);
2052       
2053        for iprocess=1:NbProcess
2054            %create the executable file
2055            batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt));
2056           
2057            % set the log file name
2058            filelog{iprocess}=fullfile(OutputDir,'0_LOG',regexprep(extxml{iprocess},'.xml$','.log'));
2059        end
2060    end
2061   
2062    %% launch the executable files for background or cluster processing
2063   
2064    switch RunMode
2065       
2066        case 'background'
2067            [fid,message]=fopen(file_exe_global,'w');
2068            if isequal(fid,-1)
2069                errormsg=['creation of ' file_exe_global ':' message];
2070                return
2071            end
2072            switch ActionExt
2073                case '.m'% Matlab function
2074                    switch computer
2075                        case {'GLNX86','GLNXA64','MACI64'}
2076                            matlab_ver = ver('MATLAB');
2077                            matlab_version = matlab_ver.Version;
2078                            cmd=[...
2079                                '#!/bin/bash\n'...
2080                                'source /etc/profile\n'...
2081                                'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
2082                                'time_start=$(date +%%s)\n'...
2083                                'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog_global ''' <<END_MATLAB\n'...
2084                                'addpath(''' path_series ''');\n'...
2085                                'addpath(''' Param.Action.ActionPath ''');\n'];
2086                            for iprocess=1:NbProcess
2087                                cmd=[cmd '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'];
2088                            end
2089                            cmd=[cmd  'exit\n' 'END_MATLAB\n'...
2090                                'time_end=$(date +%%s)\n'...
2091                                'echo "global time = " $(($time_end - $time_start)) >> ''' filelog_global '''\n'];
2092                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
2093                            fclose(fid); % close the executable filefilelog_global
2094                            system(['chmod +x ' file_exe_global]); % set the file to executable
2095                        case {'PCWIN','PCWIN64'}
2096                            cmd=['matlab -automation -logfile ' regexprep(filelog{iprocess},'\\','\\\\')...
2097                                ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
2098                                'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');'];
2099                            for iprocess=1:NbProcess
2100                                cmd=[cmd '' Param.Action.ActionName  '( ''' regexprep(filexml{iprocess},'\\','\\\\') ''');']
2101                            end
2102                            cmd=[cmd ';exit"'];
2103                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
2104                            fclose(fid); % close the executable file
2105                    end
2106                    system([file_exe_global ' &'])% directly execute the command file
2107                case '.sh' % compiled Matlab function
2108                    for iprocess=1:NbProcess
2109                        switch computer
2110                            case {'GLNX86','GLNXA64','MACI64'}
2111                                [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
2112                                if isequal(fid,-1)
2113                                    errormsg=['creation of .bat file: ' message];
2114                                    return
2115                                end
2116                                cmd=['#!/bin/bash \n '...
2117                                    '#$ -cwd \n '...
2118                                    'hostname && date \n '...
2119                                    'umask 002 \n'...
2120                                    ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
2121                                fprintf(fid,cmd); % fill the executable file with the  char string cmd
2122                                fclose(fid); % close the executable file
2123                                system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
2124                                system([batch_file_list{iprocess} ' &'])% directly execute the command file
2125                            case {'PCWIN','PCWIN64'}
2126                                msgbox_uvmat('ERROR','option for compiled Matlab functions not implemented for Windows system')
2127                                return
2128                        end
2129                    end
2130                    msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched in background for ' ExpName ': press STATUS to see results'])
2131            end
2132           
2133        case 'cluster' % option 'oar-parexec' used
2134            %create subdirectory for oar commands
2135            for iprocess=1:NbProcess
2136                [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
2137                if isequal(fid,-1)
2138                    errormsg=['creation of .bat file: ' message];
2139                    return
2140                end
2141                if  strcmp(ActionExt,'.sh')
2142                    cmd=['#!/bin/bash \n '...
2143                        '#$ -cwd \n '...
2144                        'hostname && date \n '...
2145                        'umask 002 \n'...
2146                        ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
2147                else
2148                    matlab_ver = ver('MATLAB');
2149                    matlab_version = matlab_ver.Version;
2150                    cmd=[...
2151                        '#!/bin/bash\n'...
2152                        'source /etc/profile\n'...
2153                        'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
2154                        'matlab -nodisplay -nosplash -nojvm -singleCompThread -logfile ''' filelog{iprocess} ''' <<END_MATLAB\n'...
2155                        'addpath(''' path_series ''');\n'...
2156                        'addpath(''' Param.Action.ActionPath ''');\n'...
2157                        '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'...
2158                        'exit\n'...
2159                        'END_MATLAB\n'];
2160                end
2161                fprintf(fid,cmd); % fill the executable file with the  char string cmd
2162                fclose(fid); % close the executable file
2163                system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
2164            end
2165            DIR_CLUSTER=fullfile(OutputDir,'0_CLUSTER');
2166            if exist(DIR_CLUSTER,'dir')% delete the content of the dir 0_LOG to allow new input
2167                curdir=pwd;
2168                cd(DIR_CLUSTER)
2169                delete('*')
2170                cd(curdir)
2171            else
2172                [tild,msg1]=mkdir(DIR_CLUSTER);
2173                if ~strcmp(msg1,'')
2174                    errormsg=['cannot create ' DIR_CLUSTER ': ' msg1]; % error message for directory creation
2175                    return
2176                end
2177            end
2178            % create file containing the list of jobs
2179            ListProcess=fullfile(DIR_CLUSTER,'job_list.txt'); % name of the file containing the list of executables
2180            [fid,errormsg]=fopen(ListProcess,'w'); % open it for writting
2181            if isempty(errormsg)
2182            for iprocess=1:length(batch_file_list)
2183                fprintf(fid,[batch_file_list{iprocess} '\n']); % write list of exe files
2184            end
2185            fclose(fid);
2186            system(['chmod +x ' ListProcess]); % set the file to executable
2187            else
2188                errormsg=['error for writting the executable file:' errormsg];
2189            end       
2190            CPUTimeProcess=CPUTime*BlockLength*nbfield_j; % estimated CPU time for one individual process (in minutes)
2191            LaunchCmdFcn=SeriesData.SeriesParam.ClusterParam.LaunchCmdFcn;
2192            oar_command=feval(LaunchCmdFcn,ListProcess,ActionFullName,DirLog,NbProcess, NbCore,CPUTimeProcess)
2193            [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window
2194            filename_oarcommand=fullfile(DIR_CLUSTER,'0_cluster_command'); % keep track of the command in file '0-OAR/0_cluster_command'
2195            [fid,errormsg]=fopen(filename_oarcommand,'w');
2196            if ~isempty(errormsg)
2197                msgbox_uvmat('ERROR',['cannot create ' filename_oarcommand ': ' errormsg])
2198                return
2199            end
2200            fprintf(fid,oar_command); % store the command
2201            fprintf(fid,result); % store the result (job ID number)
2202            fclose(fid);
2203            if status==0
2204                msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched for ' ExpName ' as ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
2205            else
2206                msgbox_uvmat('ERROR',result)
2207            end
2208            %     case 'cluster_pbs' % for LMFA Kepler machine:  trqnsferred to fct
2209           
2210            %         %create subdirectory for pbs command and log files
2211            %         DirPBS=fullfile(OutputDir,'0_PBS'); % todo : common name OAR/PBS
2212            %         if exist(DirPBS,'dir')% delete the content of the dir 0_LOG to allow new input
2213            %             curdir=pwd;
2214            %             cd(DirPBS)
2215            %             delete('*')
2216            %             cd(curdir)
2217            %         else
2218            %             [tild,msg1]=mkdir(DirPBS);
2219            %             if ~strcmp(msg1,'')
2220            %                 errormsg=['cannot create ' DirPBS ': ' msg1]; % error message for directory creation
2221            %                 return
2222            %             end
2223            %         end
2224            %         max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h)
2225            %         walltime_onejob=1800; % seconds, max estimated time for asingle file index value
2226            %         ListProcess=fullfile(DirPBS,'job_list.txt'); % create name of the global executable file
2227            %         fid=fopen(ListProcess,'w');
2228            %         for iprocess=1:length(batch_file_list)
2229            %             fprintf(fid,[batch_file_list{iprocess} '\n']); % list of exe files
2230            %         end
2231            %         fclose(fid);
2232            %         system(['chmod +x ' ListProcess]); % set the file to executable
2233            %         pbs_command=['qsub -n CIVX '...
2234            %             '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
2235            %             '-l /core=' num2str(NbCore) ','...
2236            %             'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
2237            %             '-E ' regexprep(ListProcess,'\.txt\>','.stderr') ' '...
2238            %             '-O ' regexprep(ListProcess,'\.txt\>','.log') ' '...
2239            %             extra_qstat ' '...
2240            %             '"oar-parexec -s -f ' ListProcess ' '...
2241            %             '-l ' ListProcess '.log"'];
2242            %         filename_oarcommand=fullfile(DirPBS,'pbs_command');
2243            %         fid=fopen(filename_oarcommand,'w');
2244            %         fprintf(fid,pbs_command);
2245            %         fclose(fid);
2246            %         fprintf(pbs_command); % display in command line
2247            %         %system(pbs_command);
2248            %         msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster'])
2249           
2250        case 'cluster_sge' % for PSMN % TODO: use the standard 'cluster' config with an external fct
2251            % Au PSMN, on ne cr??e pas 1 job avec plusieurs c??urs, mais N jobs de 1 c??urs
2252            % o?? N < 1000.
2253            %create subdirectory for pbs command and log files
2254           
2255            DirSGE=fullfile(OutputDir,'0_SGE');
2256            if exist(DirSGE,'dir')% delete the content of the dir 0_LOG to allow new input
2257                curdir=pwd;
2258                cd(DirSGE)
2259                delete('*')
2260                cd(curdir)
2261            else
2262                [tild,msg1]=mkdir(DirSGE);
2263                if ~strcmp(msg1,'')
2264                    errormsg=['cannot create ' DirSGE ': ' msg1]; % error message for directory creation
2265                    return
2266                end
2267            end
2268            maxImgsPerJob = ceil(length(batch_file_list)/NbCore);
2269            disp(['Max number of jobs: ' num2str(NbCore)])
2270            disp(['Images per job: ' num2str(maxImgsPerJob)])
2271           
2272            iprocess = 1;
2273            imgsInJob = [];
2274            currJobIndex = 1;
2275            done = 0;
2276            while(~done)
2277                if(iprocess <= length(batch_file_list))
2278                    imgsInJob = [imgsInJob, iprocess];
2279                end
2280                if((numel(imgsInJob) >= maxImgsPerJob) || (iprocess == length(batch_file_list)))
2281                    cmd=['#!/bin/sh \n'...
2282                        '#$ -cwd \n'...
2283                        'hostname && date\n']
2284                    for ii=1:numel(imgsInJob)
2285                        cmd=[cmd ActionFullName ' /softs/matlab ' filexml{imgsInJob(ii)} '\n'];
2286                    end
2287                    [fid, message] = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w');
2288                    fprintf(fid, cmd);
2289                    fclose(fid);
2290                    system(['chmod +x ' DirSGE '/job' num2str(currJobIndex) '.sh'])
2291                    sge_command=['qsub -N civ_' num2str(currJobIndex) ' '...
2292                        '-q ' qstat_Queue ' '...
2293                        '-e ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2294                        '-o ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2295                        fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])];
2296                    fprintf(sge_command); % display in command line
2297                    [status, result] = system(sge_command);
2298                    fprintf(result);
2299                    currJobIndex = currJobIndex + 1;
2300                    imgsInJob = [];
2301                end
2302                if(iprocess == length(batch_file_list))
2303                    done = 1;
2304                end
2305                iprocess = iprocess + 1;
2306            end
2307            msgbox_uvmat('CONFIRMATION',[num2str(currJobIndex-1) ' jobs launched on queue ' qstat_Queue '.'])
2308        case 'python'
2309            command = ['LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "l = x.split('':''); l = [s for s in l if ''matlab'' not in s]; print('':''.join(l))") ' ...
2310                'python -m fluidimage.run_from_xml ' filexml{iprocess}];
2311            fprintf(['command:\n' command '\n\n'])
2312            system(command, '-echo');
2313    end
2314    if exist(OutputDir,'dir')
2315        [SUCCESS,MESSAGE,MESSAGEID] = fileattrib (OutputDir);
2316        if MESSAGE.GroupWrite~=1
2317            [success,msg] = fileattrib(OutputDir,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2318            if success==0
2319                msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg}); % error message for directory creation
2320            end
2321        end
2322    end
2323end
2324set(handles.Replicate,'BackgroundColor',[0 1 0])
2325
2326%------------------------------------------------------------------------
2327function STOP_Callback(hObject, eventdata, handles)
2328%------------------------------------------------------------------------
2329set(handles.RUN, 'BusyAction','cancel')
2330set(handles.RUN,'BackgroundColor',[1 0 0])
2331set(handles.RUN,'enable','on')
2332set(handles.RUN, 'Value',0)
2333
2334%------------------------------------------------------------------------
2335% --- read parameters from the GUI series
2336%------------------------------------------------------------------------
2337function Param=read_GUI_series(handles)
2338
2339%% read raw parameters from the GUI series
2340Param=read_GUI(handles.series);
2341
2342%% clean the output structure by removing unused information
2343if isfield(Param,'Pairs')
2344    Param=rmfield(Param,'Pairs'); % info Pairs not needed for output
2345end
2346if isfield(Param,'InputLine')
2347    Param=rmfield(Param,'InputLine');
2348end
2349if isfield(Param,'EditObject')
2350    Param=rmfield(Param,'EditObject');
2351end
2352Param.IndexRange.TimeSource=Param.IndexRange.TimeTable{end,1};
2353Param.IndexRange=rmfield(Param.IndexRange,'TimeTable');
2354empty_line=false(size(Param.InputTable,1),1);
2355for iline=1:size(Param.InputTable,1)
2356    empty_line(iline)=isempty(cell2mat(Param.InputTable(iline,1:3)));
2357end
2358Param.InputTable(empty_line,:)=[];
2359
2360%------------------------------------------------------------------------
2361% --- Executes on selection change in ActionName.
2362function ActionName_Callback(hObject, ActionPath, handles)
2363%------------------------------------------------------------------------
2364
2365%% stop any ongoing series processing
2366if isequal(get(handles.RUN,'Value'),1)
2367    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
2368    if strcmp(answer,'Yes')
2369        STOP_Callback(hObject, [], handles)
2370    else
2371        return
2372    end
2373end
2374set(handles.ActionName,'BackgroundColor',[1 1 0])
2375huigetfile=findobj(allchild(0),'tag','status_display');
2376if ~isempty(huigetfile)
2377    delete(huigetfile)
2378end
2379drawnow
2380
2381%% get Action name and path
2382NbBuiltinAction=get(handles.Action,'UserData'); % nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
2383ActionList=get(handles.ActionName,'String'); % list menu fields
2384ActionIndex=get(handles.ActionName,'Value');
2385if ~isequal(ActionIndex,1)% if we are not just opening series
2386    InputTable=get(handles.InputTable,'Data');
2387    if isempty(InputTable{1,4})
2388        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
2389        return
2390    end
2391end
2392ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2393ActionPathList=get(handles.ActionName,'UserData'); % list of recorded paths to functions of the list ActionName
2394
2395%% add a new function to the menu if 'more...' has been selected in the menu ActionName
2396if isequal(ActionName,'more...')
2397    if ~ischar(ActionPath)
2398        ActionPath=get(handles.ActionPath,'String');
2399    end
2400    [FileName, PathName] = uigetfile( ...
2401        {'*.m', ' (*.m)';
2402        '*.m',  '.m files '; ...
2403        '*.*', 'All Files (*.*)'}, ...
2404        'Pick a series processing function ',ActionPath);
2405    if length(FileName)<2
2406        return
2407    end
2408    [tild,ActionName,ActionExt]=fileparts(FileName);
2409   
2410    % insert the choice in the menu ActionName
2411    ActionIndex=find(strcmp(ActionName,ActionList),1); % look for the selected function in the menu Action
2412    PathName=regexprep(PathName,'/$','');
2413    if ~isempty(ActionIndex) && ~strcmp(ActionPathList{ActionIndex},PathName)%compare the path to the existing fct
2414        ActionIndex=[]; % the selected path is different than the recorded one
2415    end
2416    if isempty(ActionIndex)%the qselected fct (with selected path) does not exist in the menu
2417        ActionIndex= length(ActionList);
2418        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)]; % the selected function is appended in the menu, before the last item 'more...'
2419         ActionPathList=[ActionPathList; PathName];
2420    end
2421   
2422    % record the file extension and extend the path list if it is a new extension
2423    ActionExtList=get(handles.ActionExt,'String');
2424    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
2425    if isempty(ActionExtIndex)
2426        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
2427    end
2428
2429    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
2430    if length(ActionList)>NbBuiltinAction+5; % nb_builtin_ACTION=nbre of functions always remaining in the initial menu
2431        nbremove=length(ActionList)-NbBuiltinAction-5;
2432        ActionList(NbBuiltinAction+1:end-5)=[];
2433        ActionPathList(NbBuiltinAction+1:end-4,:)=[];
2434        ActionIndex=ActionIndex-nbremove;
2435    end
2436   
2437    % record action menu, choice and path
2438    set(handles.ActionName,'Value',ActionIndex)
2439    set(handles.ActionName,'String',ActionList)
2440       set(handles.ActionName,'UserData',ActionPathList);
2441    set(handles.ActionExt,'Value',ActionExtIndex)
2442       
2443    %record the user defined menu additions in personal file profil_perso
2444    dir_perso=prefdir;
2445    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2446    if NbBuiltinAction+1<=numel(ActionList)-1
2447        ActionListUser=ActionList(NbBuiltinAction+1:numel(ActionList)-1);
2448        ActionPathListUser=ActionPathList(NbBuiltinAction+1:numel(ActionList)-1);
2449        ActionExtListUser={};
2450        if numel(ActionExtList)>2
2451            ActionExtListUser=ActionExtList(3:end);
2452        end
2453        if exist(profil_perso,'file')
2454            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
2455        else
2456            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
2457        end
2458    end
2459end
2460
2461%% check the current ActionPath to the selected function
2462ActionPath=ActionPathList{ActionIndex}; % current recorded path
2463set(handles.ActionPath,'String',ActionPath); % show the path to the senlected function
2464
2465%% reinitialise the waitbar
2466update_waitbar(handles.Waitbar,0)
2467
2468%% Put the first line of the selected Action fct as tooltip help
2469try
2470    [fid,errormsg] =fopen([ActionName '.m']);
2471    InputText=textscan(fid,'%s',1,'delimiter','\n');
2472    fclose(fid);
2473    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
2474end
2475set(handles.ActionName,'BackgroundColor',[1 1 1])
2476set(handles.ActionInput,'BackgroundColor',[1 0 1])% set ActionInput button to magenta color to indicate that input refr
2477set(handles.num_CPUTime,'String','')
2478
2479% --- Executes on button press in ActionInput.
2480function ActionInput_Callback(hObject, eventdata, handles)
2481
2482set(handles.ActionInput,'BackgroundColor',[1 1 0])
2483SeriesData=get(handles.series,'UserData'); % info on the input file series
2484
2485%% create the function handle for Action
2486ActionPath=get(handles.ActionPath,'String');
2487ActionList=get(handles.ActionName,'String');
2488ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2489if ~exist(ActionPath,'dir')
2490    ActionName_Callback(handles.ActionName, ActionPath, handles)% update the function
2491    return
2492end
2493current_dir=pwd; % current working dir
2494cd(ActionPath)
2495h_fun=str2func(ActionName);% create the function handle for the function ActionName
2496cd(current_dir)
2497
2498%% Activate the Action fct to adapt the configuration of the GUI series and bring specific parameters in SeriesData
2499Param=read_GUI_series(handles); % read the parameters from the GUI series
2500Param.Action.RUN=0;
2501Param.SeriesData=SeriesData;
2502ParamOut=h_fun(Param); % run the selected Action function to get the relevant input
2503
2504
2505%% Visibility of VelType and VelType_1 menus asked by ActionName
2506VelTypeRequest=1; % VelType requested by default
2507VelTypeRequest_1=1; % VelType requested by default
2508if isfield(ParamOut,'VelType')
2509    VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'});
2510    VelTypeRequest_1=strcmp( ParamOut.VelType,'two');
2511end
2512FieldNameRequest=0;  %hidden by default
2513FieldNameRequest_1=0;  %hidden by default
2514if isfield(ParamOut,'FieldName')
2515    FieldNameRequest=ismember(ParamOut.FieldName,{'on','one','two'});
2516    FieldNameRequest_1=strcmp( ParamOut.FieldName,'two');
2517end
2518
2519%% Detect the types of input files and set menus and default options in 'VelType'
2520if ~isfield(SeriesData,'FileType')
2521    SeriesData.FileType={'none'};
2522end
2523iview_civ=find( strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));
2524iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)); % all nc files, icluding civ
2525FieldList=get(handles.FieldName,'String'); % previous list as default
2526if ~iscell(FieldList),FieldList={FieldList};end
2527FieldList_1=get(handles.FieldName_1,'String'); % previous list as default
2528if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
2529CheckPivData_1=0; % indicate whether FieldName_1 has been updated with civ data, 0 by default
2530handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title];
2531if VelTypeRequest && numel(iview_civ)>=1
2532    menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)});
2533    set(handles.VelType,'Value',1)% set first choice by default
2534    set(handles.VelType,'String',[{'*'};menu])
2535    set(handles.VelType,'Visible','on')
2536    set(handles.VelType_title,'Visible','on')
2537    FieldList=set_field_list('U','V'); % standard menu for civx data
2538    if max(get(handles.FieldName,'Value'))>numel(FieldList)
2539        set(handles.FieldName,'Value',1); % velocity vector choice by default
2540    end
2541    if  VelTypeRequest_1 && numel(iview_civ)>=2
2542        menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});
2543        set(handles.VelType_1,'Value',1)% set first choice by default
2544        set(handles.VelType_1,'String',[{'*'};menu])
2545        set(handles.VelType_1,'Visible','on')
2546        set(handles.VelType_title_1,'Visible','on')
2547        FieldList_1=[set_field_list('U','V');{'C'};{'add_field...'}]; % standard menu for civx data
2548        CheckPivData_1=1;
2549        set(handles.FieldName_1,'Value',1); % velocity vector choice by default
2550    else
2551        set(handles.VelType_1,'Visible','off')
2552        set(handles.VelType_title_1,'Visible','off')
2553    end
2554else
2555    set(handles.VelType,'Visible','off')
2556    set(handles.VelType_title,'Visible','off')
2557end
2558
2559%% Detect the types of input files and set menus and default options in 'FieldName'
2560if (FieldNameRequest || VelTypeRequest) && numel(iview_netcdf)>=1
2561    set(handles.InputFields,'Visible','on')% set the frame InputFields visible
2562    if FieldNameRequest && isfield(SeriesData.FileInfo{iview_netcdf(1)},'ListVarName')
2563        set(handles.FieldName,'Visible','on')
2564        set(handles.Field_text,'Visible','on')
2565        ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName;
2566        ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2567        for ilist=1:numel(ind_var)
2568            if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2569                FieldList={}; % previous choice not consistent with new input field
2570                set(handles.FieldName,'Value',1)
2571                break
2572            end
2573        end
2574        if ~isempty(FieldList)iview_netcdf
2575            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2576                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2577                FieldList={};
2578                set(handles.Coord_x,'String','')
2579                set(handles.Coord_y,'String','')
2580            end
2581            Coord_z=get(handles.Coord_z,'String');
2582            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))REFRESH
2583                FieldList={};
2584                set(handles.Coord_z,'String','')
2585            end
2586        end
2587    else
2588        set(handles.FieldName,'Visible','off')
2589        set(handles.Field_text,'Visible','off')
2590    end
2591    set(handles_coord,'Visible','on')
2592    if isempty(find(strcmp('add_field...',FieldList)))
2593        FieldList=[FieldList;{'add_field...'}];%add 'add_field...' to the menu FieldName if it is not already
2594    end
2595    if FieldNameRequest_1 && numel(iview_netcdf)>=2
2596        set(handles.FieldName_1,'Visible','on')
2597        set(handles.Field_text_1,'Visible','on')
2598        if CheckPivData_1==0        % not civ input made
2599            FieldList_1={'add_field...'}
2600            ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName;
2601            ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2602            for ilist=1:numel(ind_var)
2603                if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2604                    %FieldList_1={}; % previous choice not consistent with new input field
2605                    set(handles.FieldName_1,'Value',1)
2606                    break
2607                end
2608            end
2609            warn_coord=0;
2610            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2611                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2612                warn_coord=1;
2613            end
2614            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2615                FieldList_1={'add_field...'};
2616                warn_coord=1;
2617            end
2618            if warn_coord
2619                msgbox_uvmat('WARNING','coordinate names do not exist in the second netcdf input file')
2620            end
2621           
2622            set(handles.FieldName_1,'Visible','on')
2623            set(handles.FieldName_1,'Value',1)
2624            set(handles.FieldName_1,'String',FieldList_1)
2625        end
2626    else
2627        set(handles.FieldName_1,'Visible','off')
2628    end
2629    if isempty(FieldList)
2630        set(handles.Field_text,'Visible','off')
2631        set(handles.FieldName,'Visible','off')
2632    else
2633        set(handles.Field_text,'Visible','on')
2634        set(handles.FieldName,'Visible','on')
2635        set(handles.FieldName,'String',FieldList)
2636    end
2637else
2638    set(handles.InputFields,'Visible','off')
2639end
2640
2641%% Introduce visibility of file overwrite option
2642if isfield(ParamOut,'CheckOverwriteVisible')&& strcmp(ParamOut.CheckOverwriteVisible,'on')
2643    set(handles.CheckOverwrite,'Visible','on')
2644else
2645    set(handles.CheckOverwrite,'Visible','off')
2646end
2647
2648%% Check whether alphabetical sorting of input Subdir is allowed by the Action fct  (for multiples series entries)
2649if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Param.InputTable,1)>1
2650    [tild,iview]=sort(Param.InputTable(:,2)); % subdirectories sorted in alphabetical order
2651    set(handles.InputTable,'Data',Param.InputTable(iview,:));
2652    MinIndex_i=get(handles.MinIndex_i,'Data');
2653    MinIndex_j=get(handles.MinIndex_j,'Data');
2654    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2655    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2656    set(handles.MinIndex_i,'Data',MinIndex_i(iview,:));
2657    set(handles.MinIndex_j,'Data',MinIndex_j(iview,:));
2658    set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:));
2659    set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));
2660    TimeTable=get(handles.TimeTable,'Data');
2661    if size(TimeTable,1)<size(Param.InputTable,1)%if the time table is not complete, copy the missing lines from the previous ones
2662        for iline=size(TimeTable,1)+1:size(Param.InputTable,1)
2663            TimeTable(iline,:)=TimeTable(iline-1,:);
2664        end
2665    end
2666    set(handles.TimeTable,'Data',TimeTable(iview,:));% sort the time tables
2667    PairString=get(handles.PairString,'Data');
2668    set(handles.PairString,'Data',PairString(iview,:));
2669end
2670
2671%% Impose the whole input file index range if requested
2672if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on')
2673    MinIndex_i=get(handles.MinIndex_i,'Data');
2674    MinIndex_j=get(handles.MinIndex_j,'Data');
2675    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2676    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2677    set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line)
2678    set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line)
2679    set(handles.num_incr_i,'String','1')
2680    set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line)
2681    set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line)
2682    set(handles.num_incr_j,'String','1')
2683else  % check index ranges
2684    first_i=1;last_i=1;first_j=1;last_j=1;
2685    if isfield(Param.IndexRange,'first_i')
2686        first_i=Param.IndexRange.first_i;
2687        last_i=Param.IndexRange.last_i;
2688    end
2689    if isfield(Param.IndexRange,'first_j')
2690        first_j=Param.IndexRange.first_j;
2691        last_j=Param.IndexRange.last_j;
2692    end
2693    if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
2694            set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end
2695end
2696
2697%% enable or desable j index visibility
2698status_j='on'; % default
2699if isfield(SeriesData,'j1_series') && isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)) % case of empty j indices
2700    status_j='off'; % no j index needed
2701elseif strcmp(get(handles.PairString,'Visible'),'on')
2702    check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j')); % =0 for burst case, 1 otherwise
2703    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
2704        status_j='off'; % no j index needed for bust case
2705    end
2706end
2707enable_j(handles,status_j) % no j index needed
2708if isfield(ParamOut,'j_index_1')&& isfield(ParamOut,'j_index_2')%strcmp(ParamOut.Desable_j_index,'on')
2709    %status_j='off';
2710    set(handles.num_first_j,'String',num2str(ParamOut.j_index_1))
2711    set(handles.num_last_j,'String',num2str(ParamOut.j_index_2))
2712    set(handles.num_first_j,'enable','off')
2713    set(handles.num_last_j,'enable','off')
2714    set(handles.num_incr_j,'visible','off')
2715else
2716    set(handles.num_first_j,'enable','on')
2717    set(handles.num_last_j,'enable','on')
2718    set(handles.num_incr_j,'visible',status_j)
2719end
2720
2721%% NbSlice visibility
2722if isfield(ParamOut,'OutputFileMode')&& strcmp(ParamOut.OutputFileMode,'NbSlice')
2723    ParamOut.NbSlice='on';
2724end
2725if isfield(ParamOut,'NbSlice') && (strcmp(ParamOut.NbSlice,'on')||isnumeric(ParamOut.NbSlice))
2726    set(handles.num_NbSlice,'Visible','on')
2727    set(handles.NbSlice_title,'Visible','on')
2728else
2729    set(handles.num_NbSlice,'Visible','off')
2730    set(handles.NbSlice_title,'Visible','off')
2731end
2732if isfield(ParamOut,'NbSlice') && isnumeric(ParamOut.NbSlice)
2733    set(handles.num_NbSlice,'String',num2str(ParamOut.NbSlice))
2734    set(handles.num_NbSlice,'Enable','off'); % NbSlice set by the activation of the Action function
2735else
2736    set(handles.num_NbSlice,'Enable','on'); % NbSlice can be modified on the GUI series
2737end
2738
2739%% Visibility of FieldTransform menu
2740FieldTransformVisible='off';  %hidden by default
2741if isfield(ParamOut,'FieldTransform')
2742    if ~strcmp(ParamOut.FieldTransform,'off')
2743    FieldTransformVisible='on'; 
2744    end
2745    if iscell(ParamOut.FieldTransform)
2746        SeriesData.TransformList=ParamOut.FieldTransform;
2747    end
2748    TransformName_Callback([],[], handles)
2749end
2750set(handles.FieldTransform,'Visible',FieldTransformVisible)
2751if isfield(ParamOut,'TransformPath')% record the path of transform function requested for compilation
2752    set(handles.TransformPath,'UserData',ParamOut.TransformPath)
2753else
2754    set(handles.TransformPath,'UserData',[])
2755end
2756
2757%% Visibility of projection object
2758ProjObjectVisible='off';  %hidden by default
2759if isfield(ParamOut,'ProjObject')
2760    ProjObjectVisible=ParamOut.ProjObject;
2761end
2762set(handles.CheckObject,'Visible',ProjObjectVisible)
2763if ~get(handles.CheckObject,'Value')
2764    ProjObjectVisible='off';
2765end
2766set(handles.ProjObjectName,'Visible',ProjObjectVisible)
2767set(handles.DeleteObject,'Visible',ProjObjectVisible)
2768set(handles.ViewObject,'Visible',ProjObjectVisible)
2769set(handles.EditObject,'Visible',ProjObjectVisible)
2770
2771%% Visibility of mask input
2772MaskVisible='off';  %hidden by default
2773if isfield(ParamOut,'Mask')
2774    MaskVisible=ParamOut.Mask;
2775end
2776set(handles.CheckMask,'Visible',MaskVisible);
2777%% Setting of expected iteration time
2778if isfield(ParamOut,'CPUTime')
2779    set(handles.num_CPUTime,'String',num2str(ParamOut.CPUTime));
2780end
2781
2782%% definition of the path for the output files
2783InputTable=get(handles.InputTable,'Data');
2784[OutputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
2785[OutputPath,Experiment,ExperimentExt]=fileparts(OutputPath);
2786set(handles.Device,'String',[Device DeviceExt])
2787set(handles.Device,'Visible','on')
2788set(handles.Device_title,'Visible','on')
2789set(handles.Experiment,'String',[Experiment ExperimentExt])
2790set(handles.Experiment,'Visible','on')
2791set(handles.Experiment_title,'Visible','on')
2792set(handles.Experiment_title,'Visible','on')
2793set(handles.OutputPath,'Visible','on')
2794set(handles.OutputPathBrowse,'Visible','on')
2795   
2796%% definition of the subdirectory containing the output files
2797
2798if  ~(isfield(SeriesData,'ActionName') && strcmp(ActionName,SeriesData.ActionName))
2799    OutputDirExt='.series'; % default
2800    if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
2801        OutputDirExt=ParamOut.OutputDirExt;
2802    end
2803    set(handles.OutputDirExt,'String',OutputDirExt)
2804end
2805OutputDirVisible='off';
2806OutputSubDirMode='auto'; % default
2807SubDirOut='';
2808if isfield(ParamOut,'OutputSubDirMode')
2809    OutputSubDirMode=ParamOut.OutputSubDirMode;
2810end
2811switch OutputSubDirMode
2812    case 'auto' % default
2813        OutputDirVisible='on';
2814        SubDir=InputTable(1:end,2); % set of subdirectories
2815        SubDirOut=SubDir{1};
2816        if numel(SubDir)>1
2817            for ilist=2:numel(SubDir)
2818                SubDirOut=[SubDirOut '-' regexprep(SubDir{ilist},'^/','')];
2819            end
2820        end
2821    case 'one'
2822        OutputDirVisible='on';
2823        SubDirOut=InputTable{1,2}; % use the first subdir name (+OutputDirExt) as output  subdirectory
2824    case 'two'
2825        OutputDirVisible='on';   
2826        SubDir=InputTable(1:2,2); % set of subdirectories
2827        SubDirOut=SubDir{1};
2828        if numel(SubDir)>1
2829                SubDirOut=[SubDirOut '-' regexprep(SubDir{2},'^/','')];
2830        end
2831    case 'last'
2832        OutputDirVisible='on';
2833        SubDirOut=InputTable{end,2}; % use the last subdir name (+OutputDirExt) as output  subdirectory
2834end
2835set(handles.OutputSubDir,'String',SubDirOut)
2836set(handles.OutputSubDir,'BackgroundColor',[1 1 1])% set edit box to white color to indicate refreshment
2837set(handles.OutputDirExt,'Visible',OutputDirVisible)
2838set(handles.OutputSubDir,'Visible',OutputDirVisible)
2839% set(handles.OutputDir_title,'Visible',OutputDirVisible)
2840SeriesData.ActionName=ActionName; % record ActionName for next use
2841
2842
2843%% visibility of the run mode (local or background or cluster)
2844if strcmp(OutputSubDirMode,'none')
2845    RunModeVisible='off'; % only local mode available if no output file is produced
2846else
2847    RunModeVisible='on';
2848end
2849set(handles.RunMode,'Visible',RunModeVisible)
2850set(handles.ActionExt,'Visible',RunModeVisible)
2851set(handles.RunMode_title,'Visible',RunModeVisible)
2852set(handles.ActionExt_title,'Visible',RunModeVisible)
2853
2854
2855%% Expected nbre of output files
2856if isfield(ParamOut,'OutputFileMode')
2857    StatusData.OutputFileMode=ParamOut.OutputFileMode;
2858    set(handles.status,'UserData',StatusData)
2859end
2860
2861%% definition of an additional parameter set, determined by an ancillary GUI
2862if isfield(ParamOut,'ActionInput')
2863%     set(handles.ActionInput,'Visible','on')
2864    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
2865    SeriesData.ActionInput=ParamOut.ActionInput;
2866else
2867%     set(handles.ActionInput,'Visible','off')
2868    if isfield(SeriesData,'ActionInput')
2869        SeriesData=rmfield(SeriesData,'ActionInput');
2870    end
2871end
2872set(handles.series,'UserData',SeriesData)
2873set(handles.ActionInput,'BackgroundColor',[1 0 0])
2874
2875
2876%------------------------------------------------------------------------
2877% --- Executes on button press in RefreshField.
2878function RefreshField_Callback(hObject, eventdata, handles)
2879%------------------------------------------------------------------------
2880set(handles.FieldName,'String',{'add_field...'});
2881set(handles.FieldName,'Value',1);
2882FieldName_Callback(hObject, eventdata, handles)
2883
2884
2885%------------------------------------------------------------------------
2886% --- Executes on selection change in FieldName.
2887function FieldName_Callback(hObject, eventdata, handles)
2888%------------------------------------------------------------------------
2889FieldListInit=get(handles.FieldName,'String');
2890field_index=get(handles.FieldName,'Value');
2891field=FieldListInit{field_index(1)};
2892if isequal(field,'add_field...')
2893    FieldListInit(field_index(1))=[];
2894    SeriesData=get(handles.series,'UserData');
2895    % input line for which the field choice is relevant
2896    iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ
2897    hget_field=findobj(allchild(0),'name','get_field');
2898    if ~isempty(hget_field)
2899        delete(hget_field)%delete opened versions of get_field
2900    end
2901    Param=read_GUI(handles.series);
2902    InputTable=Param.InputTable(iview,:);
2903    % check the existence of the first file in the series
2904    first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1; % default setting for index j
2905    if isfield(Param.IndexRange,'first_j') % if index j is used     
2906        first_j=Param.IndexRange.first_j;
2907        last_j=Param.IndexRange.last_j;
2908        MinIndex_j=Param.IndexRange.MinIndex_j(iview);
2909        MaxIndex_j=Param.IndexRange.MaxIndex_j(iview);
2910    end
2911    PairString='';
2912    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end
2913    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2914    LineIndex=iview(1);
2915    if numel(iview)>1     
2916        answer=msgbox_uvmat('INPUT_TXT',['select the line of the input table:' num2str(iview)] ,num2str(iview(1)));
2917        LineIndex=str2num(answer);
2918    end
2919    FirstFileName=fullfile_uvmat(InputTable{LineIndex,1},InputTable{LineIndex,2},InputTable{LineIndex,3},...
2920        InputTable{LineIndex,5},InputTable{LineIndex,4},i1,i2,j1,j2);
2921    if exist(FirstFileName,'file') || ~isempty(regexp(InputTable{LineIndex,1},'^http'))
2922        ParamIn.Title='get_field: pick input variables and coordinates for series processing';
2923        ParamIn.SeriesInput=1;
2924        GetFieldData=get_field(FirstFileName,ParamIn);
2925        FieldList={};
2926        if isfield(GetFieldData,'FieldOption')% if a field has been selected
2927        switch GetFieldData.FieldOption
2928            case 'vectors'
2929                UName=GetFieldData.PanelVectors.vector_x;
2930                VName=GetFieldData.PanelVectors.vector_y;
2931                YName={GetFieldData.Coordinates.Coord_y};
2932                FieldList={['vec(' UName ',' VName ')'];...
2933                    ['norm(' UName ',' VName ')'];...
2934                    UName;VName};
2935                set(handles.VelType,'Visible','off')
2936            case {'scalar'}
2937                FieldList=GetFieldData.PanelScalar.scalar;
2938                YName={GetFieldData.Coordinates.Coord_y};
2939                if ischar(FieldList)
2940                    FieldList={FieldList};
2941                end
2942                set(handles.VelType,'Visible','off')
2943            case 'civdata...'
2944                FieldList=[set_field_list('U','V') ;{'C'}];
2945                set(handles.FieldName,'Value',1) % set menu to 'velocity
2946                XName='X';
2947                YName='y';
2948                set(handles.VelType,'Visible','on')
2949        end
2950        set(handles.FieldName,'Value',1)
2951        set(handles.FieldName,'String',[FieldListInit; FieldList; {'add_field...'}]);
2952        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2953           if ~isempty(regexp(FieldList{1},'^vec'))
2954                set(handles.FieldName,'Value',1)
2955           else
2956                set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
2957           end
2958            XName=GetFieldData.Coordinates.Coord_x;
2959            YName=GetFieldData.Coordinates.Coord_y;
2960            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2961            % get the time info                     
2962            TimeTable=get(handles.TimeTable,'Data');
2963            switch TimeNameStr
2964                case 'file index'
2965                    TimeName='';
2966                case 'attribute'
2967                    TimeName=['att:' GetFieldData.Time.TimeName];
2968                    % update the time table
2969                    TimeTable{LineIndex,2}=get_time(Param.IndexRange.MinIndex_i(LineIndex),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Min time     
2970                    TimeTable{LineIndex,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % first time             
2971                    TimeTable{LineIndex,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % last time                     
2972                    TimeTable{LineIndex,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Max time
2973                case 'variable'
2974                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2975                    set(handles.NomType,'String','*')
2976                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2977                    set(handles.FileIndex,'String','')
2978                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2979                case 'matrix_index'
2980                    TimeName=['dim:' GetFieldData.Time.TimeName];
2981                    set(handles.NomType,'String','*')
2982                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2983                    set(handles.FileIndex,'String','')
2984                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2985            end
2986            TimeTable{LineIndex,1}=TimeName;
2987            set(handles.TimeTable,'Data',TimeTable);
2988        end
2989        set(handles.Coord_x,'String',XName)
2990        set(handles.Coord_y,'String',YName)
2991        set(handles.Coord_x,'Visible','on')
2992        set(handles.Coord_y,'Visible','on')
2993        end
2994    else
2995        msgbox_uvmat('ERROR',[FirstFileName ' does not exist'])
2996    end
2997end
2998
2999
3000function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
3001[i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
3002FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2);
3003Data=nc2struct(FileName,[]);
3004TimeValue=[];
3005DtValue=[];
3006if isequal(FileInfo.FileType,'civdata')
3007    if ismember(TimeName,{'civ1','filter1'})
3008        if isfield(Data,'Civ1_Time')
3009        TimeValue=Data.Civ1_Time;
3010        end
3011        if isfield(Data,'Civ1_Dt')
3012        DtValue=Data.Civ1_Dt;
3013        end
3014    else
3015        if isfield(Data,'Civ2_Time')
3016        TimeValue=Data.Civ2_Time;
3017        end
3018        if isfield(Data,'Civ2_Dt')
3019        DtValue=Data.Civ2_Dt;
3020        end
3021    end
3022else
3023    if ~isempty(TimeName)&& isfield(Data,TimeName)
3024        TimeValue=Data.(TimeName);
3025    end
3026    if exist('DtName','var') && isfield(Data,DtName)
3027        DtValue=Data.(DtName);
3028    end
3029end
3030
3031%------------------------------------------------------------------------
3032% --- Executes on selection change in FieldName_1.
3033function FieldName_1_Callback(hObject, eventdata, handles)
3034%------------------------------------------------------------------------
3035field_str=get(handles.FieldName_1,'String');
3036field_index=get(handles.FieldName_1,'Value');
3037field=field_str{field_index(1)};
3038if strcmp(field,'add_field...')
3039    %iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ
3040    hget_field=findobj(allchild(0),'name','get_field');
3041    if ~isempty(hget_field)
3042        delete(hget_field)%delete opened versions of get_field
3043    end
3044    Param=read_GUI(handles.series);
3045    InputTable=Param.InputTable(2,:);
3046    % check the existence of the first file in the series
3047    first_j=[];
3048    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
3049    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
3050    PairString='';
3051    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
3052    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
3053    FirstFileName=fullfile_uvmat(Param.InputTable{2,1},Param.InputTable{2,2},Param.InputTable{2,3},...
3054        Param.InputTable{2,5},Param.InputTable{2,4},i1,i2,j1,j2);
3055    if exist(FirstFileName,'file')
3056        ParamIn.SeriesInput=1;
3057        GetFieldData=get_field(FirstFileName,ParamIn);
3058        FieldList={};
3059        switch GetFieldData.FieldOption
3060            case 'vectors'
3061                UName=GetFieldData.PanelVectors.vector_x;
3062                VName=GetFieldData.PanelVectors.vector_y;
3063                FieldList={['vec(' UName ',' VName ')'];...
3064                    ['norm(' UName ',' VName ')'];...
3065                    UName;VName};
3066            case {'scalar','pick variables'}
3067                FieldList=GetFieldData.PanelScalar.scalar;
3068                if ischar(FieldList)
3069                    FieldList={FieldList};
3070                end
3071            case '1D plot'
3072
3073            case 'civdata...'
3074                FieldList=set_field_list('U','V','C');
3075                set(handles.FieldName,'Value',2) % set menu to 'velocity
3076        end
3077%         if ~strcmp(GetFieldData.FieldOption,'civdata...')
3078%             TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
3079%             switch TimeNameStr
3080%                 case 'file index'
3081%                     set(handles.TimeName,'String','');
3082%                 case 'attribute'
3083%                     set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
3084%                 case 'variable'
3085%                     set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
3086%                     set(handles.NomType,'String','*')
3087%                     set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
3088%                     set(handles.FileIndex,'String','')
3089%                     ParamIn.TimeVarName=GetFieldData.Time.TimeName;
3090%                 case 'matrix_index'
3091%                     set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]);
3092%                     set(handles.NomType,'String','*')
3093%                     set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
3094%                     set(handles.FileIndex,'String','')
3095%                     ParamIn.TimeDimName=GetFieldData.Time.TimeName;
3096%             end
3097%         end
3098        set(handles.FieldName_1,'Value',1)
3099        set(handles.FieldName_1,'String',[FieldList; {'add_field...'}]);
3100    end
3101end   
3102
3103
3104%%%%%%%%%%%%%
3105function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
3106indsel=ind_i;
3107indiff=diff(ind_i); % test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
3108indiff=[1 indiff last_i-ind_i(end)+1]; % for testing gaps with the imposed bounds
3109if ~isempty(indiff)
3110    indiff2=diff(indiff);
3111    indiffp=[indiff2 1];
3112    indiffm=[1 indiff2];
3113    ind_multi_m=find((indiff==0)&(indiffm<0))-1; % indices of first members of multiplets
3114    ind_multi_p=find((indiff==0)&(indiffp>0)); % indices of last members of multiplets
3115    %for each multiplet, select the most recent file
3116    ind_remove=[];
3117    for i=1:length(ind_multi_m)
3118        ind_pairs=ind_multi_m(i):ind_multi_p(i);
3119        for imulti=1:length(ind_pairs)
3120            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date); % dates of creation
3121        end
3122        [datenew,indsort2]=sort(datepair); % sort the multiplet by creation date
3123        ind_s=indsort2(1:end-1); %
3124        ind_remove=[ind_remove ind_pairs(ind_s)]; % remove these indices, leave the last one
3125    end
3126end
3127
3128%------------------------------------------------------------------------
3129% --- determine the list of index pairstring of processing file
3130function [num_i1,num_i2,num_j1,num_j2,num_i_out,num_j_out]=find_file_indices(num_i,num_j,ind_shift,NomType,mode)
3131%------------------------------------------------------------------------
3132num_i1=num_i; % set of first image numbers by default
3133num_i2=num_i;
3134num_j1=num_j;
3135num_j2=num_j;
3136num_i_out=num_i;
3137num_j_out=num_j;
3138% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
3139if isequal(mode,'series(Di)')
3140    num_i1_line=num_i+ind_shift(3); % set of first image numbers
3141    num_i2_line=num_i+ind_shift(4);
3142    % adjust the first and last field number
3143        indsel=find(num_i1_line >= 1);
3144    num_i_out=num_i(indsel);
3145    num_i1_line=num_i1_line(indsel);
3146    num_i2_line=num_i2_line(indsel);
3147    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
3148    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
3149    [xx,num_i1]=meshgrid(num_j,num_i1_line);
3150    [xx,num_i2]=meshgrid(num_j,num_i2_line);
3151elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
3152    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
3153        num_j1=ind_shift(1)*ones(size(num_i));
3154        num_j2=ind_shift(2)*ones(size(num_i));
3155    else
3156        num_j1_col=num_j+ind_shift(1); % set of first image numbers
3157        num_j2_col=num_j+ind_shift(2);
3158        % adjust the first field number
3159        indsel=find((num_j1_col >= 1));   
3160        num_j_out=num_j(indsel);
3161        num_j1_col=num_j1_col(indsel);
3162        num_j2_col=num_j2_col(indsel);
3163        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
3164        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
3165    end   
3166end
3167
3168%------------------------------------------------------------------------
3169% --- Executes on button press in CheckObject.
3170function CheckObject_Callback(hObject, eventdata, handles)
3171%------------------------------------------------------------------------
3172hset_object=findobj(allchild(0),'tag','set_object'); % find the set_object interface handle
3173if get(handles.CheckObject,'Value')
3174    SeriesData=get(handles.series,'UserData');
3175    if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject)% a projection object is already loaded in the GUI series
3176        set(handles.ViewObject,'Value',1)
3177        ViewObject_Callback(hObject, eventdata, handles)
3178    else
3179        if ishandle(hset_object)% a projection object is already displayed in a GUI set_object
3180            uistack(hset_object,'top')% show the GUI set_object if opened
3181        else
3182            %get the object file
3183            InputTable=get(handles.InputTable,'Data');
3184            defaultname=InputTable{1,1};
3185            if isempty(defaultname)
3186                defaultname={''};
3187            end
3188            fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml');
3189            if isempty(fileinput)% exit if no object file is selected
3190                set(handles.CheckObject,'Value',0)
3191                return
3192            end
3193            %read the file
3194            data=xml2struct(fileinput);
3195            if ~isfield(data,'Type')
3196                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
3197                set(handles.CheckObject,'Value',0)
3198                return
3199            end
3200            if ~isfield(data,'ProjMode')
3201                data.ProjMode='none';
3202            end
3203            hset_object=set_object(data); % call the set_object interface
3204            set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat
3205        end
3206        ProjObject=read_GUI(hset_object);
3207        set(handles.ProjObjectName,'String',ProjObject.Name); % display the object name
3208        SeriesData=get(handles.series,'UserData');
3209        SeriesData.ProjObject=ProjObject;
3210        set(handles.series,'UserData',SeriesData);
3211    end
3212    set(handles.EditObject,'Visible','on');
3213    set(handles.DeleteObject,'Visible','on');
3214    set(handles.ViewObject,'Visible','on');
3215    set(handles.ProjObjectName,'Visible','on');
3216else
3217    set(handles.EditObject,'Visible','off');
3218    set(handles.DeleteObject,'Visible','off');
3219    set(handles.ViewObject,'Visible','off');
3220    if ~ishandle(hset_object)
3221        set(handles.ViewObject,'Value',0);
3222    end
3223    set(handles.ProjObjectName,'Visible','off');
3224end
3225
3226%------------------------------------------------------------------------
3227% --- Executes on button press in ViewObject.
3228%------------------------------------------------------------------------
3229function ViewObject_Callback(hObject, eventdata, handles)
3230
3231UserData=get(handles.series,'UserData');
3232hset_object=findobj(allchild(0),'Tag','set_object');
3233if ~isempty(hset_object)
3234    delete(hset_object)% refresh set_object if already opened
3235end
3236hset_object=set_object(UserData.ProjObject);
3237set(hset_object,'Name','view_object_series')
3238
3239
3240%------------------------------------------------------------------------
3241% --- Executes on button press in EditObject.
3242function EditObject_Callback(hObject, eventdata, handles)
3243%------------------------------------------------------------------------
3244if get(handles.EditObject,'Value')
3245    set(handles.ViewObject,'Value',0)
3246    UserData=get(handles.series,'UserData');
3247    if isfield(UserData,'ProjObject')
3248    hset_object=set_object(UserData.ProjObject);
3249    set(hset_object,'Name','edit_object_series')
3250    set(get(hset_object,'Children'),'Enable','on')
3251    else
3252        msgbox_uvmat('ERROR','no projection object available');
3253    end
3254else
3255    hset_object=findobj(allchild(0),'Tag','set_object');
3256    if ~isempty(hset_object)
3257        set(get(hset_object,'Children'),'Enable','off')
3258    end
3259end
3260
3261%------------------------------------------------------------------------
3262% --- Executes on button press in DeleteObject.
3263function DeleteObject_Callback(hObject, eventdata, handles)
3264%------------------------------------------------------------------------
3265SeriesData=get(handles.series,'UserData');
3266SeriesData.ProjObject=[];
3267set(handles.series,'UserData',SeriesData)
3268set(handles.ProjObjectName,'String','')
3269set(handles.ProjObjectName,'Visible','off')
3270set(handles.CheckObject,'Value',0)
3271set(handles.ViewObject,'Visible','off')
3272set(handles.EditObject,'Visible','off')
3273hset_object=findobj(allchild(0),'name','set_object_series');
3274if ~isempty(hset_object)
3275    delete(hset_object)
3276end
3277set(handles.DeleteObject,'Visible','off')
3278
3279%------------------------------------------------------------------------
3280% --- Executed when CheckMask is activated
3281%------------------------------------------------------------------------
3282function CheckMask_Callback(hObject, eventdata, handles)
3283
3284if get(handles.CheckMask,'Value')
3285    InputTable=get(handles.InputTable,'Data');
3286    nbview=size(InputTable,1);
3287    MaskTable=cell(nbview,1); % default
3288    ListMask=cell(nbview,1); % default
3289    MaskData=get(handles.MaskTable,'Data');
3290    MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1); % complement if undefined lines
3291    for iview=1:nbview
3292        ListMask{iview,1}=num2str(iview);
3293        RootPath=InputTable{iview,1};
3294        if ~isempty(RootPath)
3295            if isempty(MaskData{iview})
3296                SubDir=InputTable{iview,2};
3297                MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']); % take the root part of SubDir, before the first dot '.'
3298                if exist(MaskPath,'dir')
3299                    ListStruct=dir(MaskPath); % look for a mask file
3300                    ListCells=struct2cell(ListStruct); % transform dir struct to a cell arrray
3301                    check_dir=cell2mat(ListCells(4,:)); % =1 for directories, =0 for files
3302                    ListFiles=ListCells(1,:); % list of file and dri names
3303                    ListFiles=ListFiles(~check_dir); % list of file names (excluding dir)
3304                    mdetect=0;
3305                    if ~isempty(ListFiles)
3306                        for ifile=1:numel(ListFiles)
3307                            [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0);
3308                            if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series)
3309                                mdetect=1;
3310                                MaskName=ListFiles{ifile};
3311                            end
3312                            if ~strcmp(MaskFile{ifile},MaskFile{1})
3313                                mdetect=0; % cancel detection test in case of multiple masks, use the brower for selection
3314                                break
3315                            end
3316                        end
3317                    end
3318                    if mdetect==1
3319                        MaskName=fullfile(MaskPath,'mask_1.png');
3320                    else
3321                        MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image');
3322                    end
3323                else
3324                    MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3325                end
3326                MaskTable{iview,1}=MaskName ;
3327                ListMask{iview,1}=num2str(iview);
3328            end
3329        end
3330    end
3331    set(handles.MaskTable,'Data',MaskTable)
3332    set(handles.MaskTable,'Visible','on')
3333    set(handles.MaskBrowse,'Visible','on')
3334    set(handles.ListMask,'Visible','on')
3335    set(handles.ListMask,'String',ListMask)
3336    set(handles.ListMask,'Value',1)
3337else
3338    set(handles.MaskTable,'Visible','off')
3339    set(handles.MaskBrowse,'Visible','off')
3340    set(handles.ListMask,'Visible','off')
3341end
3342
3343%------------------------------------------------------------------------
3344% --- Executes on button press in MaskBrowse.
3345%------------------------------------------------------------------------
3346function MaskBrowse_Callback(hObject, eventdata, handles)
3347
3348InputTable=get(handles.InputTable,'Data');
3349iview=get(handles.ListMask,'Value');
3350RootPath=InputTable{iview,1};
3351MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3352if ~isempty(MaskName)
3353    MaskTable=get(handles.MaskTable,'Data');
3354    MaskTable{iview,1}=MaskName ;
3355    set(handles.MaskTable,'Data',MaskTable)
3356end
3357
3358%------------------------------------------------------------------------
3359% --- Executes when selected cell(s) is changed in MaskTable.
3360%------------------------------------------------------------------------
3361function MaskTable_CellSelectionCallback(hObject, eventdata, handles)
3362
3363if numel(eventdata.Indices)>=1
3364set(handles.ListMask,'Value',eventdata.Indices(1))
3365end
3366
3367%-------------------------------------------------------------------
3368function MenuHelp_Callback(hObject, eventdata, handles)
3369%-------------------------------------------------------------------
3370
3371
3372% path_to_uvmat=which ('uvmat'); % check the path of uvmat
3373% pathelp=fileparts(path_to_uvmat);
3374% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
3375% if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
3376% else
3377%     addpath (fullfile(pathelp,'uvmat_doc'))
3378%     web([helpfile '#series'])
3379% end
3380
3381%-------------------------------------------------------------------
3382% --- Executes on selection change in TransformName.
3383function TransformName_Callback(hObject, eventdata, handles)
3384%----------------------------------------------------------------------
3385TransformList=get(handles.TransformName,'String');
3386TransformIndex=get(handles.TransformName,'Value');
3387TransformName=TransformList{TransformIndex};
3388TransformPathList=get(handles.TransformName,'UserData');
3389nb_builtin_transform=4;
3390
3391%% browse transform functions with the input menu option more...
3392if isequal(TransformName,'more...')% browse transform functions     
3393    FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
3394    if isempty(FileName)
3395        return     %browser closed without choice
3396    end
3397    [TransformPath,TransformName,TransformExt]=fileparts(FileName); % removes extension .m
3398    if ~strcmp(TransformExt,'.m')
3399        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3400        return
3401    end
3402     % insert the choice in the menu
3403    TransformIndex=find(strcmp(TransformName,TransformList),1); % look for the selected function in the menu Action
3404    if isempty(TransformIndex)%the input string does not exist in the menu
3405        TransformIndex= length(TransformList);
3406        TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)]; % the selected function is appended in the menu, before the last item 'more...'
3407        set(handles.TransformName,'String',TransformList)
3408        TransformPathList=[TransformPathList;{TransformPath}];
3409    else% the input function already exist, we update its path (possibly new)
3410        TransformPathList{TransformIndex}=TransformPath; %
3411        set(handles.TransformName,'Value',TransformIndex)
3412    end
3413   % save the new menu in the personal file 'uvmat_perso.mat'
3414   dir_perso=prefdir; % personal Matalb directory
3415   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3416   if exist(profil_perso,'file')
3417       for ilist=nb_builtin_transform+1:numel(TransformPathList)
3418           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
3419           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
3420       end
3421       TransformPathListUser=TransformPathListUser';
3422       TransformListUser=TransformListUser';
3423       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); % store the root name for future opening of uvmat
3424   end
3425end
3426
3427%% display the current function path
3428set(handles.TransformPath,'String',TransformPathList{TransformIndex}); % show the path to the senlected function
3429set(handles.TransformName,'UserData',TransformPathList);
3430
3431%% create the function handle of the selected fct
3432if ~isempty(TransformName)
3433    if ~exist(TransformPathList{TransformIndex},'dir')
3434        msgbox_uvmat('ERROR',['The prescribed transform function path ' TransformPathList{TransformIndex} ' does not exist']);
3435        return
3436    end
3437    current_dir=pwd; % current working dir
3438    cd(TransformPathList{TransformIndex})
3439    transform_handle=str2func(TransformName);
3440    cd(current_dir)
3441    Field.Action.RUN=0;% indicate that the transform fct is called only to get input param
3442    SeriesData=get(handles.series,'UserData');
3443    ParamIn=[];
3444    if isfield(SeriesData,'TransformInput')
3445        ParamIn.TransformInput=SeriesData.TransformInput;
3446    end
3447    DataOut=feval(transform_handle,Field,ParamIn);% execute the transform fct to get its input parameters
3448    if isfield(DataOut,'TransformInput')%  used to add transform parameters at selection of the transform fct
3449        SeriesData.TransformInput=DataOut.TransformInput;
3450        set(handles.series,'UserData',SeriesData)
3451    end
3452end
3453
3454%------------------------------------------------------------------------
3455% --- fct activated by the upper bar menu ExportConfig
3456%------------------------------------------------------------------------
3457function MenuDisplayConfig_Callback(hObject, eventdata, handles)
3458
3459global Param
3460Param=read_GUI_series(handles);
3461evalin('base','global Param')%make CurData global in the workspace
3462display('current series config :')
3463evalin('base','Param') %display CurData in the workspace
3464commandwindow; % brings the Matlab command window to the front
3465
3466%------------------------------------------------------------------------
3467% --- fct activated by the upper bar menu InportConfig: import
3468%     menu settings from an xml file (stored in /0_XML for each run)
3469%------------------------------------------------------------------------
3470function MenuImportConfig_Callback(hObject, eventdata, handles)
3471
3472%% use a browser to choose the xml file containing the processing config
3473InputTable=get(handles.InputTable,'Data');
3474oldfile=InputTable{1,1}; % current path in InputTable
3475if isempty(oldfile)
3476    % use a file name stored in prefdir
3477    dir_perso=prefdir;
3478    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3479    if exist(profil_perso,'file')
3480        h=load (profil_perso);
3481        if isfield(h,'RootPath') && ischar(h.RootPath)
3482            oldfile=h.RootPath;
3483        end
3484    end
3485end
3486filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml'); % get the xml file containing processing parameters
3487if isempty(filexml), return, end % quit function if an xml file has not been opened
3488
3489%% fill the GUI series with the content of the xml file
3490[Param,RootTag,errormsg]=xml2struct(filexml); % read the input xml file as a Matlab structure
3491if ~isempty(errormsg)
3492    msgbox_uvmat('ERROR',errormsg);
3493    return
3494end
3495% ask to stop current Action if button RUN is in action (another process is already running)
3496if isequal(get(handles.RUN,'Value'),1)
3497    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
3498    if strcmp(answer,'Yes')
3499        STOP_Callback(hObject, eventdata, handles)
3500    else
3501        return
3502    end
3503end
3504Param.Action.RUN=0; % desactivate the input RUN=1
3505
3506fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
3507SeriesData=get(handles.series,'UserData');
3508if isfield(Param,'InputFields')
3509    ListField=Param.InputFields.FieldName;
3510    if ischar(ListField),ListField={ListField}; end
3511    set(handles.FieldName,'String',[ListField;{'add_field...'}])
3512     set(handles.FieldName,'Value',1:numel(ListField))
3513     set(handles.FieldName,'Visible','on')
3514end       
3515if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
3516%     set(handles.ActionInput,'Visible','on')
3517%     set(handles.ActionInput,'Value',0)
3518    Param.ActionInput.ConfigSource=filexml; % record the source of config for future info
3519    SeriesData.ActionInput=Param.ActionInput;
3520end
3521if isfield(Param,'TransformInput')%  introduce  parameters specific to a transform fct
3522    SeriesData.TransformInput=Param.TransformInput;
3523end
3524if isfield(Param,'ProjObject') %introduce projection object if relevant
3525    SeriesData.ProjObject=Param.ProjObject;
3526end
3527set(handles.series,'UserData',SeriesData)
3528if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
3529    set(handles.ProjObjectName,'String',Param.ProjObject.Name)
3530    set(handles.ViewObject,'Visible','on')
3531    set(handles.EditObject,'Visible','on')
3532    set(handles.DeleteObject,'Visible','on')
3533else     
3534    set(handles.ProjObjectName,'String','')
3535    set(handles.ProjObjectName,'Visible','off')
3536    set(handles.ViewObject,'Visible','off')
3537    set(handles.EditObject,'Visible','off')
3538    set(handles.DeleteObject,'Visible','off')     
3539end     
3540set(handles.REFRESH,'BackgroundColor',[1 0 1]); % paint REFRESH button in magenta to indicate that it should be activated
3541
3542
3543%------------------------------------------------------------------------
3544% --- Executes when the GUI series is resized.
3545%------------------------------------------------------------------------
3546function series_ResizeFcn(hObject, eventdata, handles)
3547
3548%% input table
3549set(handles.InputTable,'Unit','pixel')
3550Pos=get(handles.InputTable,'Position');
3551set(handles.InputTable,'Unit','normalized')
3552ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
3553ColumnWidth=num2cell(ColumnWidth);
3554set(handles.InputTable,'ColumnWidth',ColumnWidth)
3555
3556%% MinIndex_j and MaxIndex_i
3557unit=get(handles.MinIndex_i,'Unit');
3558set(handles.MinIndex_i,'Unit','pixel')
3559Pos=get(handles.MinIndex_i,'Position');
3560set(handles.MinIndex_i,'Unit',unit)
3561set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18})
3562set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18})
3563set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18})
3564set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18})
3565
3566%% TimeTable
3567set(handles.TimeTable,'Unit','pixel')
3568Pos=get(handles.TimeTable,'Position');
3569set(handles.TimeTable,'Unit','normalized')
3570% ColumnWidth=get(handles.TimeTable,'ColumnWidth');
3571ColumnWidth=num2cell(floor([0.2 0.2 0.2 0.2 0.2]*(Pos(3)-20)));
3572set(handles.TimeTable,'ColumnWidth',ColumnWidth)
3573
3574
3575%% PairString
3576set(handles.PairString,'Unit','pixel')
3577Pos=get(handles.PairString,'Position');
3578set(handles.PairString,'Unit','normalized')
3579set(handles.PairString,'ColumnWidth',{Pos(3)-5})
3580
3581%% MaskTable
3582% % set(handles.MaskTable,'Unit','pixel')
3583% % Pos=get(handles.MaskTable,'Position');
3584% % set(handles.MaskTable,'Unit','normalized')
3585% % set(handles.MaskTable,'ColumnWidth',{Pos(3)-5})
3586
3587%------------------------------------------------------------------------
3588% --- Executes on button press in status.
3589%------------------------------------------------------------------------
3590function status_Callback(hObject, eventdata, handles)
3591
3592if get(handles.status,'Value')
3593    set(handles.status,'BackgroundColor',[1 1 0])
3594    drawnow
3595    Param=read_GUI(handles.series);
3596    RootPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device);
3597    if ~isfield(Param,'OutputSubDir')   
3598        msgbox_uvmat('ERROR','no standard sub-directory definition for output files, use a browser to check the output')
3599        set(handles.status,'BackgroundColor',[0 1 0])
3600        return
3601    end
3602    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt]; % subdirectory for output files
3603    OutputDir=fullfile(RootPath,OutputSubDir);
3604    if exist(OutputDir,'dir')
3605        uigetfile_uvmat('status_display',OutputDir)
3606    else
3607        msgbox_uvmat('ERROR','output folder not created yet: calculation did not start')
3608        set(handles.status,'BackgroundColor',[0 1 0])
3609    end
3610else
3611    %% delete current display fig if selection is off
3612    set(handles.status,'BackgroundColor',[0 1 0])
3613    hfig=findobj(allchild(0),'name','status_display');
3614    if ~isempty(hfig)
3615        delete(hfig)
3616    end
3617    return
3618end
3619
3620
3621%------------------------------------------------------------------------   
3622% launched by selecting a file on the list
3623%------------------------------------------------------------------------
3624function view_file(hObject, eventdata)
3625
3626list=get(hObject,'String');
3627index=get(hObject,'Value');
3628rootroot=get(hObject,'UserData');
3629selectname=list{index};
3630ind_dot=regexp(selectname,'\.\.\.');
3631if ~isempty(ind_dot)
3632    selectname=selectname(1:ind_dot-1);
3633end
3634FullSelectName=fullfile(rootroot,selectname);
3635if exist(FullSelectName,'dir')% a directory has been selected
3636    ListFiles=dir(FullSelectName);
3637    ListDisplay=cell(numel(ListFiles),1);
3638    for ilist=2:numel(ListDisplay)% suppress the first line '.'
3639        ListDisplay{ilist-1}=ListFiles(ilist).name;
3640    end
3641    set(hObject,'Value',1)
3642    set(hObject,'String',ListDisplay)
3643    if strcmp(selectname,'..')
3644        FullSelectName=fileparts(fileparts(FullSelectName));
3645    end
3646    set(hObject,'UserData',FullSelectName)
3647    hfig=get(hObject,'parent');
3648    htitlebox=findobj(hfig,'tag','titlebox');   
3649    set(htitlebox,'String',FullSelectName)
3650elseif exist(FullSelectName,'file')%visualise the vel field if it exists
3651    FileInfo=get_file_info(FullSelectName);   
3652    if strcmp(FileInfo.FileType,'txt')
3653        edit(FullSelectName)
3654    elseif strcmp(FileInfo.FileType,'xml')
3655        editxml(FullSelectName)
3656    else
3657        uvmat(FullSelectName)
3658    end
3659    set(gcbo,'Value',1)
3660end
3661
3662
3663%------------------------------------------------------------------------   
3664% launched by refreshing the status figure
3665%------------------------------------------------------------------------
3666function refresh_GUI(hfig)
3667
3668htitlebox=findobj(hfig,'tag','titlebox');
3669hlist=findobj(hfig,'tag','list');
3670hseries=findobj(allchild(0),'tag','series');
3671hstatus=findobj(hseries,'tag','status');
3672StatusData=get(hstatus,'UserData');
3673OutputDir=get(htitlebox,'String');
3674if ischar(OutputDir),OutputDir={OutputDir};end
3675ListFiles=dir(OutputDir{1});
3676if numel(ListFiles)<1
3677    return
3678end
3679ListFiles(1)=[]; % removes the first line ='.'
3680ListDisplay=cell(numel(ListFiles),1);
3681testrecent=0;
3682datnum=zeros(numel(ListDisplay),1);
3683for ilist=1:numel(ListDisplay)
3684    ListDisplay{ilist}=ListFiles(ilist).name;
3685      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
3686            datnum(ilist)=ListFiles(ilist).datenum; % only available in recent matlab versions
3687            testrecent=1;
3688       end
3689end
3690set(hlist,'String',ListDisplay)
3691
3692%% Look at date of creation
3693ListDisplay=ListDisplay(datnum~=0);
3694datnum=datnum(datnum~=0); % keep the non zero values corresponding to existing files
3695NbOutputFile=[];
3696if isempty(datnum)
3697    if testrecent
3698        message='no civ result created yet';
3699    else
3700        message='';
3701    end
3702else
3703    [first,indfirst]=min(datnum);
3704    [last,indlast]=max(datnum);
3705    NbOutputFile_str='?';
3706    NbOutputFile=[];
3707    if isfield(StatusData,'NbOutputFile')
3708        NbOutputFile=StatusData.NbOutputFile;
3709        NbOutputFile_str=num2str(NbOutputFile);
3710    end
3711    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
3712        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
3713end
3714set(htitlebox,'String', [OutputDir{1};message])
3715
3716%% update the waitbar
3717hwaitbar=findobj(hfig,'tag','waitbar');
3718if ~isempty(NbOutputFile)
3719    BarPosition=get(hwaitbar,'Position');
3720    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
3721    set(hwaitbar,'Position',BarPosition)
3722end
3723
3724%------------------------------------------------------------------------
3725% --- Executes on selection change in ActionExt.
3726%------------------------------------------------------------------------
3727function ActionExt_Callback(hObject, eventdata, handles)
3728
3729ActionExtList=get(handles.ActionExt,'String');
3730ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
3731if strcmp(ActionExt,'.py (in dev.)')
3732    set(handles.RunMode,'Value',2)
3733end
3734
3735
3736function num_NbSlice_Callback(hObject, eventdata, handles)
3737NbSlice=str2num(get(handles.num_NbSlice,'String'));
3738
3739%------------------------------------------------------------------------
3740% --- set the visibility of relevant velocity type menus:
3741function menu=set_veltype_display(Civ,FileType)
3742%------------------------------------------------------------------------
3743if ~exist('FileType','var')
3744    FileType='civx';
3745end
3746switch FileType
3747    case 'civx'
3748        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3749        if isequal(Civ,0)
3750            imax=0;
3751        elseif isequal(Civ,1) || isequal(Civ,2)
3752            imax=1;
3753        elseif isequal(Civ,3)
3754            imax=3;
3755        elseif isequal(Civ,4) || isequal(Civ,5)
3756            imax=4;
3757        elseif isequal(Civ,6) %patch2
3758            imax=6;
3759        end
3760    case 'civdata'
3761        menu={'civ1';'filter1';'civ2';'filter2'};
3762        if isequal(Civ,0)
3763            imax=0;
3764        elseif isequal(Civ,1) || isequal(Civ,2)
3765            imax=1;
3766        elseif isequal(Civ,3)
3767            imax=2;
3768        elseif isequal(Civ,4) || isequal(Civ,5)
3769            imax=3;
3770        else%if isequal(Civ,6) %patch2
3771            imax=4;
3772        end
3773end
3774menu=menu(1:imax);
3775
3776
3777% --- Executes on mouse motion over figure - except title and menu.
3778% function series_WindowButtonMotionFcn(hObject, eventdata, handles)
3779% set(hObject,'Pointer','arrow');
3780
3781
3782% --- Executes on button press in SetPairs.
3783function SetPairs_Callback(hObject, eventdata, handles)
3784
3785%% delete previous occurrence of 'set_pairs'
3786hfig=findobj(allchild(0),'Tag','set_pairs');
3787if ~isempty(hfig)
3788delete(hfig)
3789end
3790
3791%% create the GUI set_pairs
3792set(0,'Unit','points')
3793ScreenSize=get(0,'ScreenSize'); % get the size of the screen, to put the fig on the upper right
3794Width=220; % fig width in points (1/72 inch)
3795Height=min(0.8*ScreenSize(4),300);
3796Left=ScreenSize(3)- Width-40; % right edge close to the right, with margin=40
3797Bottom=ScreenSize(4)-Height-40; % put fig at top right
3798hfig=findobj(allchild(0),'Tag','set_slice');
3799if ~isempty(hfig),delete(hfig), end; % delete existing version of the GUI
3800hfig=figure('name','set_pairs','tag','set_pairs','MenuBar','none','NumberTitle','off','Unit','points','Position',[Left,Bottom,Width,Height]);
3801BackgroundColor=get(hfig,'Color');
3802SeriesData=get(handles.series,'UserData');
3803TimeUnit=get(handles.TimeUnit,'String');
3804PairString=get(handles.PairString,'Data');
3805ListViewLines=find(cellfun('isempty',PairString)==0); % find list of non empty pairs
3806ListViewMenu=cell(numel(ListViewLines),1);
3807%iview=get(handles.PairString,'Value');
3808iview=[];
3809for ilist=1:numel(ListViewLines)
3810    ListViewMenu{ilist}=num2str(ListViewLines(ilist));
3811end
3812if isempty(iview)
3813    ListViewValue=numel(ListViewLines); % we work by default on the pair option for the last line which requires pairs
3814    iview=ListViewLines(end);
3815else
3816    ListViewValue=find(ListViewLines==iview);
3817end
3818ref_i=str2num(get(handles.num_first_i,'String'));
3819ref_j=1; % default
3820if strcmp(get(handles.num_first_j,'String'),'Visible')
3821    ref_j=str2num(get(handles.num_first_j,'String'));
3822end
3823[ModeMenu,ModeValue]=update_mode(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j2_series{1});
3824InputTable=get(handles.InputTable,'Data');
3825displ_pair=update_listpair(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j1_series{1},SeriesData.j2_series{1},ModeMenu{ModeValue},...
3826                                                 SeriesData.Time{1},TimeUnit,ref_i,ref_j,SeriesData.TimeName,InputTable,SeriesData.FileInfo{1});
3827for iline=1:size(InputTable,1)
3828    viewcell{iline}=num2str(iline);
3829end
3830viewcell=viewcell';
3831ModeMenu={'bursts';'series(Dj)'};
3832ModeValue=1;                                               
3833                   %i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo                             
3834% first raw of the GUI
3835uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,...
3836    'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right'); % title
3837uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.54 0.8 0.3 0.2],'BackgroundColor',[1 1 1],...
3838    'Callback',@(hObject,eventdata)ListView_Callback(hObject,eventdata),'String',viewcell,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3839    'Tag','ListView','TooltipString','''ListView'':choice of the file series w for pair display');
3840% second raw of the GUI
3841uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.79 0.7 0.1],'BackgroundColor',BackgroundColor,...
3842    'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3843uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.05 0.62 0.9 0.2],'BackgroundColor',[1 1 1],...
3844    'Callback',@(hObject,eventdata)Mode_Callback(hObject,eventdata),'String',ModeMenu,'Value',ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3845    'Tag','Mode','TooltipString','''Mode'': choice of the image pair mode');
3846% third raw
3847uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.6 0.7 0.1],'BackgroundColor',BackgroundColor,...
3848    'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3849uicontrol('Style','listbox','Units','normalized', 'Position', [0.05 0.42 0.9 0.2],'BackgroundColor',[1 1 1],...
3850    'Callback',@(hObject,eventdata)ListPair_Callback(hObject,eventdata),'String',displ_pair,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3851    'Tag','ListPair','TooltipString','''ListPair'': menu for selecting the image pair');
3852uicontrol('Style','text','Units','normalized', 'Position', [0.1 0.22 0.8 0.1],'BackgroundColor',BackgroundColor,...
3853    'String','ref_i           ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center'); % title
3854uicontrol('Style','edit','Units','normalized', 'Position', [0.15 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3855    'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),'String',num2str(ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3856    'Tag','num_ref_i','TooltipString','''num_ref_i'': reference field index i used to display dt in ''list_pair_civ''');
3857uicontrol('Style','edit','Units','normalized', 'Position', [0.55 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3858    'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),'String',num2str(ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3859    'Tag','num_ref_j','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ''');
3860uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.01 0.01 0.3 0.12],'BackgroundColor',[0 1 0],...
3861    'Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),'String','OK','FontUnits','points','FontSize',12,'FontWeight','bold',...
3862    'Tag','OK','TooltipString','''OK'': validate the choice');
3863%  last raw  of the GUI: pushbuttons
3864% uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.35 0.01 0.3 0.15],'BackgroundColor',[0 1 0],'String','OK','Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),...
3865%     'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''OK'': apply the output to the current field series in uvmat');
3866drawnow
3867
3868%------------------------------------------------------------------------
3869function ListView_Callback(hObject,eventdata)
3870Mode_Callback(hObject,eventdata)
3871
3872%------------------------------------------------------------------------   
3873function Mode_Callback(hObject,eventdata)
3874%% get input info
3875hseries=findobj(allchild(0),'tag','series'); % handles of the GUI series
3876hhseries=guidata(hseries); % handles of the elements in the GUI series
3877TimeUnit=get(hhseries.TimeUnit,'String');
3878SeriesData=get(hseries,'UserData');
3879mode_list=get(hObject,'String');
3880mode=mode_list{get(hObject,'Value')};
3881hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3882iview=get(hListView,'Value');
3883i1_series=SeriesData.i1_series{iview};
3884i2_series=SeriesData.i2_series{iview};
3885j1_series=SeriesData.j1_series{iview};
3886j2_series=SeriesData.j2_series{iview};
3887
3888%% enable j index visibility after the new choice
3889
3890if strcmp(mode,'series(Dj)')
3891   status_j='on'; % default
3892else
3893       status_j='off'; % no j index needed for bust case
3894end
3895enable_j(hhseries,status_j) % no j index needed
3896
3897%% get the reference indices for the time interval Dt
3898href_i=findobj(get(hObject,'parent'),'Tag','ref_i');
3899ref_i=[];ref_j=[];
3900if strcmp(get(href_i,'Visible'),'on')
3901    ref_i=str2num(get(href_i,'String'));
3902end
3903if isempty(ref_i)
3904    ref_i=1;
3905end
3906if isempty(ref_j)
3907    ref_j=1;
3908end
3909
3910%% update the menu ListPair
3911Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo);
3912hlist_pairs=findobj(get(hObject,'parent'),'Tag','ListPair');
3913set(hlist_pairs,'Value',1)% set the first choice by default in ListPair
3914set(hlist_pairs,'String',Menu)% set the menu in ListPair
3915ListPair_Callback(hlist_pairs,[])% apply the default choice in ListPair
3916
3917%-------------------------------------------------------------
3918% --- Executes on selection in ListPair.
3919function ListPair_Callback(hObject,eventdata)
3920%------------------------------------------------------------
3921list_pair=get(hObject,'String'); % get the menu of image pairs
3922if isempty(list_pair)
3923    string='';
3924else
3925    string=list_pair{get(hObject,'Value')};
3926   % string=regexprep(string,',.*',''); % removes time indication (after ',')
3927end
3928hseries=findobj(allchild(0),'tag','series');
3929hPairString=findobj(hseries,'tag','PairString');
3930PairString=get(hPairString,'Data');
3931hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3932iview=get(hListView,'Value');
3933PairString{iview,1}=string;
3934% report the selected pair string to the table PairString
3935set(hPairString,'Data',PairString)
3936
3937
3938%------------------------------------------------------------------------
3939function num_ref_i_Callback(hObject, eventdata)
3940%------------------------------------------------------------------------
3941Mode_Callback([],[])
3942
3943%------------------------------------------------------------------------
3944function num_ref_j_Callback(hObject, eventdata)
3945%------------------------------------------------------------------------
3946Mode_Callback([],[])
3947
3948%------------------------------------------------------------------------
3949function OK_Callback(hObject, eventdata)
3950%------------------------------------------------------------------------
3951delete(get(hObject,'parent'))
3952
3953
3954%------------------------------------------------------------------------
3955% --- Executes on button press in ClearLine.
3956%------------------------------------------------------------------------
3957function ClearLine_Callback(hObject, eventdata, handles)
3958InputTable=get(handles.InputTable,'Data');
3959iline=str2double(get(handles.InputLine,'String'));
3960if size(InputTable,1)>1
3961    InputTable(iline,:)=[]; % suppress the current line if not the first
3962    set(handles.InputTable,'Data',InputTable);
3963end
3964set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refr
3965
3966
3967% --- Executes on button press in MonitorCluster.
3968function MonitorCluster_Callback(hObject, eventdata, handles)
3969
3970[rr,ss]=system('oarstat |grep N=UVmat');% check the list of jobs launched with uvmat
3971if isempty(ss)
3972   disp( 'no job presently submitted with uvmat')
3973else
3974    disp('format: R/W=run/wait, time lapsed, R=nbre of cores,W=walltime')
3975    disp(ss)
3976end
3977
3978
3979function OutputSubDir_Callback(hObject, eventdata, handles)
3980set(handles.OutputSubDir,'BackgroundColor',[1 1 1])
3981
3982
3983% --- Executes on button press in CheckOverwrite.
3984function CheckOverwrite_Callback(hObject, eventdata, handles)
3985
3986% --- Executes on button press in TestCPUTime.
3987function TestCPUTime_Callback(hObject, eventdata, handles)
3988% hObject    handle to TestCPUTime (see GCBO)
3989% eventdata  reserved - to be defined in a future version of MATLAB
3990% handles    structure with handles and user data (see GUIDATA)
3991
3992
3993% --- Executes on button press in DiskQuota.
3994function DiskQuota_Callback(hObject, eventdata, handles)
3995SeriesData=get(handles.series,'UserData');
3996system(SeriesData.SeriesParam.DiskQuotaCmd)
3997
3998
3999% --- Executes on button press in Replicate.
4000function Replicate_Callback(hObject, eventdata, handles)
4001if get(handles.Replicate,'Value')
4002    InputTable=get(handles.InputTable,'Data');
4003    for ilist=1:size(InputTable,1)
4004        InputDir{ilist}=fullfile(InputTable{ilist,1},InputTable{ilist,2});
4005    end
4006    browse_data(InputDir)
4007else
4008    hh=findobj(allchild(0),'Tag','browse_data');
4009    if ~isempty(hh)
4010        delete(hh)
4011    end
4012end
4013
4014
4015
4016
4017function OutputPath_Callback(hObject, eventdata, handles)
4018
4019
4020function Experiment_Callback(hObject, eventdata, handles)
4021
4022
4023function Device_Callback(hObject, eventdata, handles)
4024
4025
4026% --- Executes on button press in OutputPathBrowse.
4027function OutputPathBrowse_Callback(hObject, eventdata, handles)
4028CheckValue=get(handles.OutputPathBrowse,'Value');
4029if CheckValue
4030OutputPath=uigetdir(get(handles.OutputPath,'String'));
4031set(handles.OutputPath,'String',OutputPath)
4032else
4033    InputTable=get(handles.InputTable,'Data');
4034    set(handles.OutputPath,'String',InputTable{1,1})
4035end
4036
4037
4038
4039function Mask_Callback(hObject, eventdata, handles)
4040% hObject    handle to Mask (see GCBO)
4041% eventdata  reserved - to be defined in a future version of MATLAB
4042% handles    structure with handles and user data (see GUIDATA)
4043
4044% Hints: get(hObject,'String') returns contents of Mask as text
4045%        str2double(get(hObject,'String')) returns contents of Mask as a double
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