source: trunk/src/series.m @ 951

Last change on this file since 951 was 951, checked in by sommeria, 5 years ago

bugs repaired

File size: 160.9 KB
RevLine 
[867]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%
[924]16
17%=======================================================================
18% Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
19%   http://www.legi.grenoble-inp.fr
20%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
21%
[867]22%     This file is part of the toolbox UVMAT.
[924]23%
[867]24%     UVMAT is free software; you can redistribute it and/or modify
[924]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%
[867]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
[924]32%     GNU General Public License (see LICENSE.txt) for more details.
33%=======================================================================
[867]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
120set(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%% list of builtin functions in the mebu ActionName
135ActionList={'check_data_files';'aver_stat';'time_series';'civ_series';'merge_proj'};% WARNING: fits with nb_builtin_ACTION=4 in ActionName_callback
136NbBuiltinAction=numel(ActionList);
137set(handles.Action,'UserData',NbBuiltinAction)
138[path_series,name,ext]=fileparts(which('series'));% path to the GUI series
139path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series'
[872]140[code, message] = system...
[942]141    ('LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "p.split('':'') |... [s for s in p if ''matlab'' not in s] | '':''.join(p)") python -c "import fluidimage"');
[872]142if code==0
143    ActionExtList={'.m';'.sh';'.py (in dev.)'};% default choice of extensions (Matlab fct .m or compiled version .sh
144else
[880]145    ActionExtList={'.m';'.sh'};  % python options not installed
[872]146end
[867]147ActionPathList=cell(NbBuiltinAction,1);%initiate the cell matrix of Action fct paths
148ActionPathList(:)={path_series_fct}; %set the default path to series fcts to all list members
149RunModeList={'local';'background'};% default choice of extensions (Matlab fct .m or compiled version .sh)
150[s,w]=system('oarstat');% look for cluster system 'oar'
151if isequal(s,0)
152    RunModeList=[RunModeList;{'cluster_oar'}];
[880]153    set(handles.MonitorCluster,'Visible','on'); % make visible button for access to Monika
[914]154    set(handles.num_CPUTime,'Visible','on'); % make visible button for access to Monika
155    set(handles.CPUTime_txt,'Visible','on'); % make visible button for access to Monika
[867]156end
[882]157[s,w]=system('qstat --version');% look for cluster system 'sge'
[867]158if isequal(s,0)
[882]159    if regexp(w,'^pbs')
160        RunModeList=[RunModeList;{'cluster_pbs'}];
161    else
162        RunModeList=[RunModeList;{'cluster_sge'}];
163    end
[867]164end
165set(handles.RunMode,'String',RunModeList)
166
167%% list of builtin transform functions in the menu TransformName
168TransformList={'';'sub_field';'phys';'phys_polar'};% WARNING: must fit with the corresponding menu in uvmat and nb_builtin_transform=4 in  TransformName_callback
169NbBuiltinTransform=numel(TransformList);
170path_transform_fct=fullfile(path_series,'transform_field');
171TransformPathList=cell(NbBuiltinTransform,1);%initiate the cell matrix of Action fct paths
172TransformPathList(:)={path_transform_fct}; %set the default path to series fcts to all list members
173
174%% get the user defined functions stored in the personal file uvmat_perso.mat
175dir_perso=prefdir;
176profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
177if exist(profil_perso,'file')
178    h=load (profil_perso);
179    %get the list of previous input files in the upper bar menu Open
180    if isfield(h,'MenuFile')
181        for ifile=1:min(length(h.MenuFile),5)
182            set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile});
183            set(handles.(['MenuFile_' num2str(ifile+5)]),'Label',h.MenuFile{ifile});
184        end
185    end
186    %get the list of previous campaigns in the upper bar menu Open campaign
187    if isfield(h,'MenuCampaign')
188        for ifile=1:min(length(h.MenuCampaign),5)
189            set(handles.(['MenuCampaign_' num2str(ifile)]),'Label',h.MenuCampaign{ifile});
190        end
191    end
192    %get the menu of actions
[872]193%     if isfield(h,'ActionExtListUser') && iscell(h.ActionExtListUser)
194%         ActionExtList=[ActionExtList; h.ActionExtListUser];
195%     end
[867]196    if isfield(h,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser)
197        ActionList=[ActionList;h.ActionListUser];
198        ActionPathList=[ActionPathList;h.ActionPathListUser(:,1)];
199    end
200    %get the menu of transform fct
201    if isfield(h,'TransformListUser') && iscell(h.TransformListUser) && isfield(h,'TransformPathListUser') && iscell(h.TransformPathListUser)
202        TransformList=[TransformList;h.TransformListUser];
203        TransformPathList=[TransformPathList;h.TransformPathListUser];
204    end
205end
206
207%% selection of the input Action fct
208ActionCheckExist=true(size(ActionList));%initiate the check of the path to the listed action fct
209for ilist=NbBuiltinAction+1:numel(ActionList)%check  the validity of the path of the user defined Action fct
210    ActionCheckExist(ilist)=exist(fullfile(ActionPathList{ilist},[ActionList{ilist} '.m']),'file');
211end
212ActionPathList=ActionPathList(ActionCheckExist,:);% suppress the menu options which are not valid anymore
213ActionList=ActionList(ActionCheckExist);
214set(handles.ActionName,'String',[ActionList;{'more...'}])
215set(handles.ActionName,'UserData',ActionPathList)
216ActionIndex=[];
217if isfield(Param,'ActionName')% copy the selected menu index transferred in Param from uvmat
218    ActionIndex=find(strcmp(Param.ActionName,ActionList),1);
219end
220if isempty(ActionIndex)
221    ActionIndex=1;
222end
223set(handles.ActionName,'Value',ActionIndex)
224set(handles.ActionPath,'String',ActionPathList{ActionIndex})
225set(handles.ActionExt,'Value',1)
226set(handles.ActionExt,'String',ActionExtList)
227
228%% selection of the input transform fct
229TransformCheckExist=true(size(TransformList));
230for ilist=NbBuiltinTransform+1:numel(TransformList)
231    TransformCheckExist(ilist)=exist(fullfile(TransformPathList{ilist},[TransformList{ilist} '.m']),'file');
232end
233TransformPathList=TransformPathList(TransformCheckExist);
234TransformList=TransformList(TransformCheckExist);
235set(handles.TransformName,'String',[TransformList;{'more...'}])
236set(handles.TransformName,'UserData',TransformPathList)
237TransformIndex=[];
238if isfield(Param,'TransformName')% copy the selected menu index transferred in Param from uvmat
239    TransformIndex=find(strcmp(Param.TransformName,TransformList),1);
240end
241if isempty(TransformIndex)
242    TransformIndex=1;
243end
244set(handles.TransformName,'Value',TransformIndex)
245set(handles.TransformPath,'String',TransformPathList{TransformIndex})
246   
247%% fields input initialisation
248if isfield(Param,'list_fields')&& isfield(Param,'index_fields') &&~isempty(Param.list_fields) &&~isempty(Param.index_fields)
249    set(handles.FieldName,'String',Param.list_fields);% list menu fields
250    set(handles.FieldName,'Value',Param.index_fields);% selected string index
251end
[869]252if isfield(Param,'Coordinates')
253    if isfield(Param.Coordinates,'Coord_x')
254        set(handles.Coord_x,'String',Param.Coordinates.Coord_x)
255    end
256    if isfield(Param.Coordinates,'Coord_y')
257        set(handles.Coord_y,'String',Param.Coordinates.Coord_y)
258    end
259    if isfield(Param.Coordinates,'Coord_z')
260        set(handles.Coord_z,'String',Param.Coordinates.Coord_z)
261    end
[867]262end
[869]263% if isfield(Param,'Coord_x_str') && ischar(Param.Coord_x_str)
264%         set(handles.Coord_x,'String',Param.Coord_x_str);% list menu fields
265% end
266% if isfield(Param,'Coord_y_str')&& ischar(Param.Coord_y_str)
267%         set(handles.Coord_y,'String',Param.Coord_y_str);% list menu fields
268% end
[867]269
270%% introduce the input file name(s) if defined from input Param,
[886]271set(handles.series,'UserData',[])% initiate Userdata
[867]272if isfield(Param,'InputFile')
273   
274    %% fill the list of file series
275    InputTable=[{Param.InputFile.RootPath},{Param.InputFile.SubDir},{Param.InputFile.RootFile},{Param.InputFile.NomType},{Param.InputFile.FileExt}];
[909]276    if isempty(find(cellfun('isempty',InputTable)==0));% if there is no input file, do not introduce input info
277        set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
278        return
279    end
[867]280    TimeTable=[{Param.InputFile.TimeName},{[]},{[]},{[]},{[]}];
281    if isfield(Param.InputFile,'RootPath_1')
282        InputTable=[InputTable;[{Param.InputFile.RootPath_1},{Param.InputFile.SubDir_1},{Param.InputFile.RootFile_1},{Param.InputFile.NomType_1},{Param.InputFile.FileExt_1}]];
283        TimeTable=[TimeTable; [{Param.InputFile.TimeName_1},{[]},{[]},{[]},{[]}]];
284    end
285    set(handles.InputTable,'Data',InputTable)
286    %% determine the selected reference field indices for pair display
287   
288    [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(Param.InputFile.FileIndex);
289    if isempty(i1)
290        i1=1;
291    end
292    if isempty(i2)
293        i2=i1;
294    end
295    ref_i=floor((i1+i2)/2);% reference image number corresponding to the file
296    % set(handles.num_ref_i,'String',num2str(ref_i));
297    if isempty(j1)
298        j1=1;
299    end
300    if isempty(j2)
301        j2=j1;
302    end
303    ref_j=floor((j1+j2)/2);% reference image number corresponding to the file
304    SeriesData.ref_i=ref_i;
305    SeriesData.ref_j=ref_j;
306    set(handles.series,'UserData',SeriesData)
307    update_rootinfo(handles,Param.HiddenData.i1_series{1},Param.HiddenData.i2_series{1},Param.HiddenData.j1_series{1},Param.HiddenData.j2_series{1},...
308        Param.HiddenData.FileInfo{1},Param.HiddenData.MovieObject{1},1)
[869]309    if isfield(Param,'FileName_1')
[867]310        %         display_file_name(handles,Param,2)
311        update_rootinfo(handles,Param.HiddenData.i1_series{2},Param.HiddenData.i2_series{2},Param.HiddenData.j1_series{2},Param.HiddenData.j2_series{2},...
312            Param.HiddenData.FileInfo{2},Param.HiddenData.MovieObject{2},2)
313    end
314    %% enable field and veltype menus, in accordance with the current action
[869]315    ActionName_Callback([],[], handles)
316   
317    %% set length of waitbar
318    displ_time(handles)
319   
[867]320else
321    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
322end
323if isfield(Param,'incr_i')
324    set(handles.num_incr_i,'String',num2str(Param.incr_i))
325else
326    set(handles.num_incr_i,'String','1')
327end
328if isfield(Param,'incr_j')
329    set(handles.num_incr_j,'String',num2str(Param.incr_j))
330else
331    set(handles.num_incr_j,'String','1')
332end
333
334%------------------------------------------------------------------------
335% --- Outputs from this function are returned to the command line.
336function varargout = series_OutputFcn(hObject, eventdata, handles)
337%------------------------------------------------------------------------
338varargout{1} = handles.output;
339
340%------------------------------------------------------------------------
341% --- executed when closing uvmat: delete or desactivate the associated figures if exist
342function closefcn(gcbo,eventdata)
343%------------------------------------------------------------------------
344
345% delete set_object_series if detected
346hh=findobj(allchild(0),'name','view_object_series');
347if ~isempty(hh)
348    delete(hh)
349end
350hh=findobj(allchild(0),'name','edit_object_series');
351if ~isempty(hh)
352    delete(hh)
353end
354
355%delete the bowser if detected
356hh=findobj(allchild(0),'tag','browser');
357if ~isempty(hh)
358    delete(hh)
359end
360
361
362%------------------------------------------------------------------------
363%------------------------------------------------------------------------
364%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
365% automatically sets the global properties when the rootfile name is introduced
366% then activate the view-field actionname if selected
367% it is activated either by clicking on the RootPath window or by the
368% browser
369%------------------------------------------------------------------------
370%------------------------------------------------------------------------
371% --- fct activated by the browser under 'Open'
372%------------------------------------------------------------------------ 
373function MenuBrowse_Callback(hObject, eventdata, handles)
374%% look for the previously opened file 'oldfile'
375InputTable=get(handles.InputTable,'Data');
376oldfile=InputTable{1,1};
377if isempty(oldfile)
378    % use a file name stored in prefdir
379    dir_perso=prefdir;
380    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
381    if exist(profil_perso,'file')
382        h=load (profil_perso);
383        if isfield(h,'RootPath') && ischar(h.RootPath)
384            oldfile=h.RootPath;
385        end
386    end
387end
388%% launch the browser
389fileinput=uigetfile_uvmat('pick an input file in the series',oldfile);
390hh=dir(fileinput);
391if numel(hh)>1
392    msgbox_uvmat('ERROR','invalid input, probably a broken link');
393else
394    if ~isempty(fileinput)
395        display_file_name(handles,fileinput,'one')
396    end
397end
398
399% --------------------------------------------------------------------
400function MenuBrowseAppend_Callback(hObject, eventdata, handles)
401
402%% look for the previously opened file 'oldfile'
403InputTable=get(handles.InputTable,'Data');
404RootPathCell=InputTable(:,1);
405if isempty(RootPathCell{1})% no input file in the table
406     MenuBrowse_Callback(hObject, eventdata, handles)%refresh the input table, not append
407     return
408end
409SubDirCell=InputTable(:,2);
410oldfile=fullfile(RootPathCell{1},SubDirCell{1});
411
412%% use a file name stored in prefdir
413dir_perso=prefdir;
414profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
415if exist(profil_perso,'file')
416    h=load (profil_perso);
417    if isfield(h,'RootPath') && ischar(h.RootPath)
418        oldfile=h.RootPath;
419    end
420end
421
422%% launch the browser
423fileinput=uigetfile_uvmat('pick a file to append in the input table',oldfile);
424hh=dir(fileinput);
425if numel(hh)>1
426    msgbox_uvmat('ERROR','invalid input, probably a broken link');
427else
428    if ~isempty(fileinput)
429        display_file_name(handles,fileinput,'append')
430    end
431end
432
433%------------------------------------------------------------------------
434% --- fct activated by selecting a previous file under the menu Open
435%------------------------------------------------------------------------
436function MenuFile_Callback(hObject, eventdata, handles)
437
438errormsg=display_file_name(handles,get(hObject,'Label'),'one');
439if ~isempty(errormsg)
440    set(hObject,'Label','')
441    MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
442        {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
443    str_find=strcmp(get(hObject,'Label'),MenuFile);
444    MenuFile(str_find)=[];% suppress the input file to the list
445    for ifile=1:numel(MenuFile)
446        set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile});
447    end
448end
449
450%------------------------------------------------------------------------
451% --- fct activated by selecting a previous file under the menu Open/append
452%------------------------------------------------------------------------
453function MenuFile_append_Callback(hObject, eventdata, handles)
454
455InputTable=get(handles.InputTable,'Data');
456if isempty(InputTable{1,1})% no input file in the table
457    display_file_name(handles,get(hObject,'Label'),'one') %refresh the input table, not append
458else
459    display_file_name(handles,get(hObject,'Label'),'append')% append the selected file to the current list of InputTable
460end
461
462%------------------------------------------------------------------------
463% --- fct activated by the browser under 'Open campaign/Browse...'
464%------------------------------------------------------------------------
465function MenuBrowseCampaign_Callback(hObject, eventdata, handles)
466
467%% look for the previously opened file 'oldfile'
468InputTable=get(handles.InputTable,'Data');
[937]469if ~isempty(InputTable)
[934]470oldfile=fullfile(InputTable{1,1},InputTable{1,2});
[937]471else
[867]472    % use a file name stored in prefdir
473    dir_perso=prefdir;
474    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
475    if exist(profil_perso,'file')
476        h=load (profil_perso);
[937]477        if isfield(h,'MenuCampaign') && ~isempty(h.MenuCampaign)&& ischar(h.MenuCampaign{1})
478            oldfile=h.MenuCampaign{1};
[867]479        end
480    end
481end
[934]482
483OutPut=browse_data(oldfile,'on','on');% open the GUI browse_data to get select a campaign dir, experiment and device
484NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
485icount=0;
486for iexp=1:numel(OutPut.Experiment)
487    for idevice=1:numel(OutPut.DataSeries)
488        icount=icount+1;
489        InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp});
490        InputTable{icount,2}=OutPut.DataSeries{idevice};
491        if isempty(InputTable{icount,3})
492            if icount>1
493            InputTable{icount,3}=InputTable{icount-1,3};
494            else
495                InputTable{icount,3}='';
496            end
497        end
498        if isempty(InputTable{icount,4})
499            if icount>1
500            InputTable{icount,4}=InputTable{icount-1,4};
501            else
502                InputTable{icount,4}='';
503            end
504        end
505                if isempty(InputTable{icount,5})
506            if icount>1
507            InputTable{icount,5}=InputTable{icount-1,5};
508            else
509                InputTable{icount,5}='';
510            end
511        end
[867]512    end
513end
[934]514if size(InputTable,1)>icount
515    InputTable(icount+1:size(InputTable,1),:)=[];
516end
517set(handles.InputTable,'Data',InputTable)
518REFRESH_Callback(hObject, eventdata, handles)
[867]519
520% --------------------------------------------------------------------
521function MenuCampaign_Callback(hObject, eventdata, handles)
522% --------------------------------------------------------------------
[937]523
[935]524OutPut=browse_data(get(hObject,'Label'),'on','on');% open the GUI browse_data to get select a campaign dir, experiment and device
[867]525if ~isfield(OutPut,'Campaign')
526    return
527end
[935]528NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
529icount=0;
530InputTable=get(handles.InputTable,'Data');
531for iexp=1:numel(OutPut.Experiment)
532    for idevice=1:numel(OutPut.DataSeries)
533        icount=icount+1;
534        InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp});
535        InputTable{icount,2}=OutPut.DataSeries{idevice};
536        if isempty(InputTable{icount,3})
537            if icount>1
538                InputTable{icount,3}=InputTable{icount-1,3};
539            else
540                InputTable{icount,3}='';
541            end
[867]542        end
[935]543        if isempty(InputTable{icount,4})
544            if icount>1
545                InputTable{icount,4}=InputTable{icount-1,4};
546            else
547                InputTable{icount,4}='';
548            end
549        end
550        if isempty(InputTable{icount,5})
551            if icount>1
552                InputTable{icount,5}=InputTable{icount-1,5};
553            else
554                InputTable{icount,5}='';
555            end
556        end
[867]557    end
558end
[935]559if size(InputTable,1)>icount
560    InputTable(icount+1:size(InputTable,1),:)=[];
[867]561end
[935]562set(handles.InputTable,'Data',InputTable)
563REFRESH_Callback(hObject, eventdata, handles)
[867]564
565
566% --- Executes when selected cell(s) is changed in InputTable.
567function InputTable_CellSelectionCallback(hObject, eventdata, handles)
568iline=[];
569if ~isempty(eventdata.Indices)
570    iline=eventdata.Indices(1);
571end
572set(handles.InputLine,'String',num2str(iline));
573% set(handles.InputTable,'UserData',iline);
574
575%------------------------------------------------------------------------
576% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
577%------------------------------------------------------------------------
578function InputTable_KeyPressFcn(hObject, eventdata, handles)
579set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
[880]580set(handles.OutputSubDir,'BackgroundColor',[1 0 1])% set edit box OutputSubDir to magenta color to indicate that refresh may be needed
[867]581xx=double(get(handles.series,'CurrentCharacter')); %get the keyboard character
582if ~isempty(xx)
583    switch xx
584        case 31 %downward arrow
585            InputTable=get(handles.InputTable,'Data');
586            iline=str2double(get(handles.InputLine,'String'));
587            if isequal(iline,size(InputTable,1))% arrow downward
588                InputTable=[InputTable;InputTable(iline,:)];% create a new line as a copy of the last one
589                set(handles.InputTable,'Data',InputTable);
590            end
591        case 127  %key 'Suppress'
592            ClearLine_Callback(hObject, eventdata, handles)
593    end
594end
595
596%------------------------------------------------------------------------
597% --- Executes on button press in REFRESH.
598function REFRESH_Callback(hObject, eventdata, handles)
599%------------------------------------------------------------------------
600InputTable=get(handles.InputTable,'Data');
601set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
602set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
603drawnow
604empty_line=false(size(InputTable,1),1);
605for iline=1:size(InputTable,1)
606    empty_line(iline)= isempty(cell2mat(InputTable(iline,1:3)));
607end
608if ~isempty(find(empty_line));
609    InputTable(empty_line,:)=[];%remove empty lines
610    set(handles.InputTable,'Data',InputTable)
611    ListTable={'MinIndex_i','MaxIndex_i','MinIndex_j','MaxIndex_j','PairString','TimeTable'};
612    for ilist=1:numel(ListTable)
613        Table=get(handles.(ListTable{ilist}),'Data');
614        Table(empty_line,:)=[];%remove empty lines
615        set(handles.(ListTable{ilist}),'Data',Table);
616    end
617    set(handles.series,'UserData',[])%refresh the stored info
618end
[883]619nbview=size(InputTable,1);
620for iview=1:nbview
[867]621    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
622    if ~exist(RootPath,'dir')
623        i1_series=[];
624        RootFile='';
625    else %scan the input folder
[914]626        [RootPath,~,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=...
[867]627            find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]);
628    end
629    % if no file is found, open a browser
630    if isempty(RootFile)&& isempty(i1_series)
631        fileinput=uigetfile_uvmat(['wrong input at line ' num2str(iview) ':pick a new input file'],RootPath);
632        if isempty(fileinput)
633            set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  back to red color
634            return
635        else
636            display_file_name(handles,fileinput,iview)
637        end
638    else
639       update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview)
640    end
641end
[883]642
643%% update MinIndex_i and MaxIndex_i if the input table content has been reduced in line nbre
644MinIndex_i_table=get(handles.MinIndex_i,'Data');%retrieve the min indices in the table MinIndex
645set(handles.MinIndex_i,'Data',MinIndex_i_table(1:nbview,:));
646MinIndex_j_table=get(handles.MinIndex_j,'Data');%retrieve the min indices in the table MinIndex
647set(handles.MinIndex_j,'Data',MinIndex_j_table(1:nbview,:));
648MaxIndex_i_table=get(handles.MaxIndex_i,'Data');%retrieve the min indices in the table MinIndex
649set(handles.MaxIndex_i,'Data',MaxIndex_i_table(1:nbview,:));
650MaxIndex_j_table=get(handles.MaxIndex_j,'Data');%retrieve the min indices in the table MinIndex
651set(handles.MaxIndex_j,'Data',MaxIndex_j_table(1:nbview,:));
652PairString=get(handles.PairString,'Data');%retrieve the min indices in the table MinIndex
653set(handles.PairString,'Data',PairString(1:nbview,:));
654TimeTable=get(handles.TimeTable,'Data');%retrieve the min indices in the table MinIndex
655set(handles.TimeTable,'Data',TimeTable(1:nbview,:));
656
[867]657%% enable field and veltype menus, in accordance with the current action
658ActionName_Callback([],[], handles)
659
660%% set length of waitbar
661displ_time(handles)
662
663set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (indicate activation finished)
664set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch'
665
666%------------------------------------------------------------------------
667% --- Function called when a new file is opened, either by series_OpeningFcn or by the browser
668%------------------------------------------------------------------------
669% INPUT:
670% handles: handles of elements in the GUI
671% Param: structure of input parameters, including  input file name and path
672% iview: line index in the input table
673%       or 'one': refresh the list
674%         'append': add a new line to the input table
675function errormsg=display_file_name(handles,Param,iview)
676 
677set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
678drawnow
679errormsg='';%default
680if ischar(Param)
681    fileinput=Param;
682else% input set when series is opened (called by the GUI uvmat)
683    fileinput=Param.FileName;
684end
685   
686%% get the input root name, indices, file extension and nomenclature NomType
687if ~exist(fileinput,'file')
688    errormsg=['input file ' fileinput  ' does not exist'];
689    msgbox_uvmat('ERROR',errormsg)
690    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (refresh still needed)
691    return
692end
693
694%% detect root name, nomenclature and indices in the input file name:
695[FilePath,FileName,FileExt]=fileparts(fileinput);
696%%%%%%%%%%%%%%%%%%
697%TODO: case of input by uvmat: do not check agai the input seies %%%%%%%
698%%%%%%%%%%%%%%%%%%%
699% detect the file type, get the movie object if relevant, and look for the corresponding file series:
700% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
701[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
702FileType=FileInfo.FileType;
703if isempty(RootFile)&&isempty(i1_series)
704    errormsg='no input file in the series';
705    msgbox_uvmat('ERROR',errormsg)
706    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (end of activation)
707    return
708end
709if strcmp(FileType,'txt')
710    edit(fileinput)
711    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to  magenta color (end of activation)
712    return
713elseif strcmp(FileType,'xml')
714    editxml(fileinput)
715    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
716     return
717elseif strcmp(FileType,'figure')
718    open(fileinput)
719    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
720     return
721end
722
723%% enable other menus and uicontrols
[937]724% set(handles.MenuOpenCampaign,'Enable','on')
[867]725set(handles.MenuCampaign_1,'Enable','on')
726set(handles.MenuCampaign_2,'Enable','on')
727set(handles.MenuCampaign_3,'Enable','on')
728set(handles.MenuCampaign_4,'Enable','on')
729set(handles.MenuCampaign_5,'Enable','on')
730set(handles.RUN, 'Enable','On')
731set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
732set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
733drawnow
734
735
736%% fill the list of file series
737InputTable=get(handles.InputTable,'Data');
738SeriesData=get(handles.series,'UserData');
739if strcmp(iview,'append') % display the input data as a new line in the table
740    iview=size(InputTable,1)+1;% the next line in InputTable becomes the current line
741%     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
742elseif strcmp(iview,'one') % refresh the list of  input  file series
743    iview=1; %the first line in InputTable becomes the current line
744    InputTable={'','','','',''};
745%     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
746    set(handles.TimeTable,'Data',[{''},{[]},{[]},{[]},{[]}])
747    set(handles.MinIndex_i,'Data',[])
748    set(handles.MaxIndex_i,'Data',[])
749    set(handles.MinIndex_j,'Data',[])
750    set(handles.MaxIndex_j,'Data',[])
751    set(handles.PairString,'Data',{''})
752    SeriesData.CheckPair=0;%reset the list of input lines with pairs
753    SeriesData.i1_series={};
754    SeriesData.i2_series={};
755    SeriesData.j1_series={};
756    SeriesData.j2_series={};
757    SeriesData.FileType={};
758    SeriesData.FileInfo={};
759    SeriesData.Time={};
760end
[883]761if isfield(SeriesData,'i1_series')
762    SeriesData.i1_series(iview+1:end)=[];
[867]763    SeriesData.i2_series(iview+1:end)=[];
764    SeriesData.j1_series(iview+1:end)=[];
765    SeriesData.j2_series(iview+1:end)=[];
766    SeriesData.FileType(iview+1:end)=[];
767    SeriesData.FileInfo(iview+1:end)=[];
768    SeriesData.Time(iview+1:end)=[];
[883]769end
770InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
[867]771if iview >1
772    set(handles.InputLine,'String',num2str(iview))
773end
774set(handles.InputTable,'Data',InputTable)
775
776%% determine the selected reference field indices for pair display
777if isempty(i1)
778    i1=1;
779end
780if isempty(i2)
781    i2=i1;
782end
783ref_i=floor((i1+i2)/2);% reference image number corresponding to the file
784% set(handles.num_ref_i,'String',num2str(ref_i));
785if isempty(j1)
786    j1=1;
787end
788if isempty(j2)
789    j2=j1;
790end
791ref_j=floor((j1+j2)/2);% reference image number corresponding to the file
792SeriesData.ref_i=ref_i;
793SeriesData.ref_j=ref_j;
794
795%% update first and last indices if they do not exist
796Param=read_GUI(handles.series);
797first_j=[];
798if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
799last_j=[];
800if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
801PairString='';
802if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
803[i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
804FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
805    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
806if ~exist(FirstFileName,'file')
807    set(handles.num_first_i,'String',num2str(ref_i))
808    set(handles.num_first_j,'String',num2str(ref_j))
809end
810[i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
811LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
812    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
813if ~exist(LastFileName,'file')
814    set(handles.num_last_i,'String',num2str(ref_i))
815    set(handles.num_last_j,'String',num2str(ref_j))
816end
817
818%% update the list of recent files in the menubar and save it for future opening
819MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
820    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
821str_find=strcmp(fileinput,MenuFile);
822if isempty(find(str_find,1))
823    MenuFile=[{fileinput};MenuFile];%insert the current file if not already in the list
824end
825for ifile=1:min(length(MenuFile),5)
826    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
827end
828dir_perso=prefdir;
829profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
830if exist(profil_perso,'file')
831    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
832else
833    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
834end
835% save the opened file to initiate future opening
836SeriesData.RefFile{iview}=fileinput;% reference opening file for line iview
837SeriesData.Ref_i1=i1;
838SeriesData.Ref_i2=i2;
839SeriesData.Ref_j1=j1;
840SeriesData.Ref_j2=j2;
841set(handles.series,'UserData',SeriesData)
842
843set(handles.InputTable,'BackgroundColor',[1 1 1])
844
845%% initiate input file series and refresh the current field view:     
846update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview);
847%% enable field and veltype menus, in accordance with the current action
848ActionName_Callback([],[], handles)
849
850%% set length of waitbar
851displ_time(handles)
852
853set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (end of activation)
854
855%------------------------------------------------------------------------
856% --- Update information about a new field series (indices to scan, timing,
857%     calibration from an xml file
858function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,VideoObject,iview)
859%------------------------------------------------------------------------
860InputTable=get(handles.InputTable,'Data');
861
862%% display the min and max indices for the whole file series
863if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
864    MinIndex_j=1;% index j set to 1 by default
865    MaxIndex_j=1;
866    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)
867    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)
868else
869    ref_i=squeeze(max(i1_series(1,:,:),[],2));% select ref_j index for each ref_i
870    ref_j=squeeze(max(j1_series(1,:,:),[],3));% select ref_i index for each ref_j
871     MinIndex_i=min(find(ref_i))-1;
872     MaxIndex_i=max(find(ref_i))-1;
873     MaxIndex_j=max(find(ref_j))-1;
874     MinIndex_j=min(find(ref_j))-1;
875    diff_j_max=diff(ref_j);
876    diff_i_max=diff(ref_i);
877    if ~isempty(diff_i_max) && isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max)))
878        set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to dispaly by default
879    end
880    if ~isempty(diff_j_max) && isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max)))
881        set(handles.num_incr_j,'String',num2str(diff_j_max(1)))
882    end
883end
884if isequal(MinIndex_i,-1)
885    MinIndex_i=0;
886end
887if isequal(MinIndex_j,-1)
888    MinIndex_j=0;
889end
890MinIndex_i_table=get(handles.MinIndex_i,'Data');%retrieve the min indices in the table MinIndex
891MinIndex_j_table=get(handles.MinIndex_j,'Data');%retrieve the min indices in the table MinIndex
892MaxIndex_i_table=get(handles.MaxIndex_i,'Data');%retrieve the min indices in the table MinIndex
893MaxIndex_j_table=get(handles.MaxIndex_j,'Data');%retrieve the min indices in the table MinIndex
894if ~isempty(MinIndex_i)&&~isempty(MaxIndex_i)
895    MinIndex_i_table(iview,1)=MinIndex_i;
896    MaxIndex_i_table(iview,1)=MaxIndex_i;
897end
898if ~isempty(MinIndex_j)&&~isempty(MaxIndex_j)
899    MinIndex_j_table(iview,1)=MinIndex_j;
900    MaxIndex_j_table(iview,1)=MaxIndex_j;
901end
902set(handles.MinIndex_i,'Data',MinIndex_i_table)%display the min indices in the table MinIndex
903set(handles.MinIndex_j,'Data',MinIndex_j_table)%display the max indices in the table MaxIndex
904set(handles.MaxIndex_i,'Data',MaxIndex_i_table)%display the min indices in the table MinIndex
905set(handles.MaxIndex_j,'Data',MaxIndex_j_table)%display the max indices in the table MaxIndex
906SeriesData=get(handles.series,'UserData');
907
908%% adjust the first and last indices for the selected series, only if requested by the bounds
909% i index, compare input to min index i
910first_i=str2num(get(handles.num_first_i,'String'));%retrieve previous first i
911% ref_i=str2num(get(handles.num_ref_i,'String'));%index i given by the input field
912ref_i=1;
913if isfield(SeriesData,'ref_i')
[937]914    ref_i=SeriesData.ref_i;
[867]915end
916if isempty(first_i)
917    first_i=ref_i;% first_i updated by the input value
918elseif first_i < MinIndex_i
919    first_i=MinIndex_i; % first_i set to the min i index (restricted by oter input lines)
920elseif first_i >MaxIndex_i
921    first_i=MaxIndex_i;% first_i set to the max i index (restricted by oter input lines)
922end
923% j index,  compare input to min index j
924first_j=str2num(get(handles.num_first_j,'String'));
925ref_j=1;
926if isfield(SeriesData,'ref_j')
[937]927    ref_j=SeriesData.ref_j;
[867]928end
929if isempty(first_j)
930    first_j=ref_j;% first_j updated by the input value
931elseif first_j<MinIndex_j
932    first_j=MinIndex_j; % first_j set to the min j index (restricted by oter input lines)
933elseif first_j >MaxIndex_j
934    first_j=MaxIndex_j; % first_j set to the max j index (restricted by oter input lines)
935end
936% i index, compare input to max index i
937last_i=str2num(get(handles.num_last_i,'String'));
938if isempty(last_i)
939    last_i=ref_i;
940elseif last_i > MaxIndex_i
941    last_i=MaxIndex_i;
942elseif last_i<first_i
943    last_i=first_i;
944end
945% j index, compare input to max index j
946last_j=str2num(get(handles.num_last_j,'String'));
947if isempty(last_j)
948    last_j=ref_j;
949elseif last_j>MaxIndex_j
950    last_j=MaxIndex_j;
951elseif last_j<first_j
952    last_j=first_j;
953end
[937]954set(handles.num_first_i,'String',num2str(first_i));
[867]955set(handles.num_first_j,'String',num2str(first_j));
[937]956set(handles.num_last_i,'String',num2str(last_i));
[867]957set(handles.num_last_j,'String',num2str(last_j));
958
959%% number of slices set by default
[937]960NbSlice=[];%default
[867]961% read  value set by the first series for the append mode (iwiew >1)
962if iview>1 && strcmp(get(handles.num_NbSlice,'Visible'),'on')
[937]963    NbSlice=str2double(get(handles.num_NbSlice,'String'));
[867]964end
965
966%% default time settings
967TimeUnit='';
968% read  value set by the first series for the append mode (iwiew >1)
[937]969if iview>1
[867]970    TimeUnit=get(handles.TimeUnit,'String');
971end
972TimeName='';
973Time=[];%default
974TimeMin=[];
975TimeFirst=[];
976TimeLast=[];
977TimeMax=[];
978
979%%  read image documentation file if found
980XmlData=[];
981check_calib=0;
982XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
983if ~isempty(XmlFileName)
984    [XmlData,errormsg]=imadoc2struct(XmlFileName);
985    if ~isempty(errormsg)
[937]986        msgbox_uvmat('WARNING',['error in reading ' XmlFileName ': ' errormsg]);
[867]987    end
988    % read time if available
989    if isfield(XmlData,'Time')
[937]990        Time=XmlData.Time;
[867]991        TimeName='xml';
[951]992%                         if XmlData.Time(1,:)==XmlData.Time(2,:)% case starting with index 1
993%                     sizDti=size(XmlData.Time,1)-1;%size of the time vector explicitly defined in the xml file
994%                     ind_start=1;
995%                 else
996%                     sizDti=size(XmlData.Time,1);% case starting with index 0
997%                     ind_start=0;
998%                 end
999%         % complement the input if the whole time series is not defined
1000%             if size(i1_series,3)>size(XmlData.Time,1)-ind_start %only the first time interval is defined, extrapolate to the whole series
1001%                 Dti_total=XmlData.Time(end)-XmlData.Time(1);%total time interval covered by the time vector
1002%                 missing_indices=sizDti+1+ind_start:size(i1_series,3)+1;% remaining set of frame indices for which time needs to be found
1003%                 repeat_nbre=1+floor((missing_indices-sizDti-ind_start)/(sizDti-1));% number of repetitions of Dti
1004%                 time_indices=1+mod(missing_indices-sizDti-1,sizDti-1);
1005%                 for j=1:size(XmlData.Time,2)
1006%                 Time(missing_indices,j)=XmlData.Time(time_indices,j)+repeat_nbre'*Dti_total;
1007%                 end
1008%                 % update the xml file with NbDti
1009%                 t=xmltree(XmlFileName);
1010%                 uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti')
1011%                 if isempty(uid_NbDti)
1012%                     uid_BurstTiming=find(t,'ImaDoc/Camera/BurstTiming')
1013%                     [t,uid_NbDti]=add(t,uid_BurstTiming,'element','NbDti');
1014%                 end
1015%                 [t,uid_NbDti]=add(t,uid_NbDti,'chardata',num2str(repeat_nbre(end)-1));
1016%                 save(t,XmlFileName)
1017%             end
[867]1018    end
1019    if isfield(XmlData,'Camera')
[937]1020        %         if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
1021        %             if iview>1 && ~isempty(NbSlice) && ~strcmp(NbSlice,XmlData.Camera.NbSlice)
1022        %                 msgbox_uvmat('WARNING','inconsistent number of slices with the first field series');
1023        %             end
1024        %             NbSlice=XmlData.Camera.NbSlice;% Nbre of slices from camera
1025        %         end
[867]1026        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
1027            if iview>1 && ~isempty(TimeUnit) && ~strcmp(TimeUnit,XmlData.Camera.TimeUnit)
1028                msgbox_uvmat('WARNING','inconsistent time unit with the first field series');
1029            end
1030            TimeUnit=XmlData.Camera.TimeUnit;
1031        end
1032    end
1033    % number of slices
[937]1034    if isfield(XmlData,'TranslationMotor')&& isfield(XmlData.TranslationMotor,'NbSlice')
1035        NbSlice_motor=XmlData.TranslationMotor.NbSlice;
1036        if ~isempty(NbSlice) && ~isequal(NbSlice_motor,NbSlice)
1037                msgbox_uvmat('WARNING','inconsistent Z numbers of Z indices');
1038        else
1039            NbSlice=NbSlice_motor;
1040        end
1041    end
1042   
[867]1043    if isfield(XmlData,'GeometryCalib')
1044        check_calib=1;
1045        if isfield(XmlData.GeometryCalib,'SliceCoord')
1046            siz=size(XmlData.GeometryCalib.SliceCoord);
[937]1047            if ~isempty(NbSlice)&& ~isequal(size(1),NbSlice)
1048                msgbox_uvmat('WARNING','inconsistent numbers of Z indices between motor and calibration');
1049            else
[867]1050                NbSlice=siz(1);
1051            end
1052        end
1053    end
1054end
[937]1055if ~isempty(NbSlice)
1056set(handles.num_NbSlice,'String',num2str(NbSlice))
1057set(handles.num_NbSlice,'Visible','on')
1058end
[867]1059
1060%% read timing  from the current file (prioritary)
1061if ~isempty(VideoObject)% case of movies
1062    imainfo=get(VideoObject);
1063    if isempty(j1_series); %frame index along i
1064        Time=zeros(imainfo.NumberOfFrames+1,2);
1065        Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
1066    else
1067        Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
1068    end
1069    TimeName='video';
1070end
1071
1072
1073%% determine the min and max times: case of Netcdf files will be treated later in FieldName_Callback
1074if ~isempty(TimeName)
1075    TimeMin=Time(MinIndex_i+1,MinIndex_j+1);
1076    if size(Time)>=[first_i+1 first_j+1]
1077        TimeFirst=Time(first_i+1,first_j+1);
1078    end
1079    if size(Time)>=[last_i+1 last_j+1]
1080        TimeLast=Time(last_i+1,last_j+1);
1081    end
1082    if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1];
1083        TimeMax=Time(MaxIndex_i+1,MaxIndex_j+1);
1084    end
1085end
1086
1087%% update the time table
1088TimeTable=get(handles.TimeTable,'Data');
1089TimeTable{iview,1}=TimeName;
1090TimeTable{iview,2}=TimeMin;
1091TimeTable{iview,3}=TimeFirst;
1092TimeTable{iview,4}=TimeLast;
1093TimeTable{iview,5}=TimeMax;
1094set(handles.TimeTable,'Data',TimeTable)
1095
1096%% update the series info in 'UserData'
1097SeriesData.i1_series{iview}=i1_series;
1098SeriesData.i2_series{iview}=i2_series;
1099SeriesData.j1_series{iview}=j1_series;
1100SeriesData.j2_series{iview}=j2_series;
1101SeriesData.FileType{iview}=FileInfo.FileType;
1102SeriesData.FileInfo{iview}=FileInfo;
1103SeriesData.Time{iview}=Time;
1104% if ~isempty(TimeName)
1105%     SeriesData.TimeSource=TimeSource;
1106% end
1107if check_calib
1108    SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib;
1109end
1110set(handles.series,'UserData',SeriesData)
1111
1112%% update pair menus
1113hset_pair=findobj(allchild(0),'Tag','set_pairs');
1114if ~isempty(hset_pair), delete(hset_pair); end % delete the GUI set_pair if opened
1115CheckPair= ~isempty(i2_series)||~isempty(j2_series); % check whether index pairs need to be defined
1116PairString=get(handles.PairString,'Data');
1117if CheckPair% if pairs need to be display for line iview
1118    [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series);
1119    Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,ModeMenu{ModeValue},Time,TimeUnit,ref_i,ref_j,TimeName,InputTable(iview,:),FileInfo);
1120    PairString{iview,1}=Menu{1};
1121else
1122    PairString{iview,1}='';%no pair for #iview
1123end
1124set(handles.PairString,'Data',PairString)
1125if isempty(find(cellfun('isempty',get(handles.PairString,'Data'))==0, 1))% if all lines of pairs are empty
1126    set(handles.PairString,'Visible','off')
1127    set(handles.SetPairs,'Visible','off')
1128else
1129    set(handles.PairString,'Visible','on')
1130    set(handles.SetPairs,'Visible','on')
1131end
1132
1133
1134%% display the set of existing files as an image
1135set(handles.FileStatus,'Units','pixels')
1136Position=get(handles.FileStatus,'Position');
1137set(handles.FileStatus,'Units','normalized')
1138%xI=0.5:Position(3)-0.5;
1139nbview=numel(SeriesData.i1_series);
1140j_max=cell(1,nbview);
1141MaxIndex_i=ones(1,nbview);%default
1142MinIndex_i=ones(1,nbview);%default
1143for iline=1:nbview
1144    pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); %max on pair index
1145    j_max{iline}=max(pair_max,[],1);%max on j index
1146    if ~isempty(j_max{iline})
1147    MaxIndex_i(iline)=max(find(j_max{iline}))-1;% max ref index i
1148    MinIndex_i(iline)=min(find(j_max{iline}))-1;% min ref index i
1149    end
1150end
1151MinIndex_i=min(MinIndex_i);
1152MaxIndex_i=max(MaxIndex_i);
1153range_index=MaxIndex_i-MinIndex_i+1;
1154range_y=max(1,floor(Position(4)/nbview));
1155npx=floor(Position(3));
1156file_indices=MinIndex_i+floor(((0.5:npx-0.5)/npx)*range_index)+1;
1157CData=zeros(nbview*range_y,npx);% initiate the image representing the existing files
1158for iline=1:nbview
1159    ind_y=1+(iline-1)*range_y:iline*range_y;
1160    LineData=zeros(size(file_indices));
1161    file_select=file_indices(file_indices<=numel(j_max{iline}));
1162    ind_select=find(file_indices<=numel(j_max{iline}));
1163    LineData(ind_select)=j_max{iline}(file_select)~=0;
1164    CData(ind_y,:)=ones(size(ind_y'))*LineData;
1165end
1166CData=cat(3,zeros(size(CData)),CData,zeros(size(CData)));%make color images r=0,g,b=0
1167set(handles.FileStatus,'CData',CData);
1168
1169%-----------------------------------------------------------guide -------------
1170%------------------------------------------------------------------------
1171%  III - FUNCTIONS ASSOCIATED TO THE FRAME IndexRange
1172%------------------------------------------------------------------------
1173
1174
1175% ---- determine the menu to put in mode and advice a default choice
1176%------------------------------------------------------------------------
1177function [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series)
1178%------------------------------------------------------------------------   
1179ModeMenu={''};
1180if isempty(j2_series)% no j pair
1181    ModeValue=1;
1182    if ~isempty(i2_series)
1183        ModeMenu={'series(Di)'}; % pair menu with only option Di
1184    end
1185else %existence of j pairs
1186    pair_max=squeeze(max(i1_series,[],1)); %max on pair index
1187    j_max=max(pair_max,[],1);
1188    MaxIndex_i=find(j_max, 1, 'last' )-1;% max ref index i
1189    MinIndex_i=find(j_max, 1 )-1;% min ref index i
1190    i_max=max(pair_max,[],2);
1191    MaxIndex_j=find(i_max, 1, 'last' )-1;% max ref index i
1192    MinIndex_j=find(i_max, 1 )-1;% min ref index i
1193    if MaxIndex_j==MinIndex_j
1194        ModeValue=1;
1195        ModeMenu={'bursts'};
1196    elseif MaxIndex_i==MinIndex_i
1197        ModeValue=1;
1198        ModeMenu={'series(Dj)'};
1199    else
1200        ModeMenu={'bursts';'series(Dj)'};
1201        if (MaxIndex_j-MinIndex_j)>10
1202            ModeValue=2;%set mode to series(Dj) if more than 10 j values
1203        else
1204            ModeValue=1;
1205        end
1206    end
1207end
1208
1209
1210%------------------------------------------------------------------------
1211function displ_pair=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo)
1212%------------------------------------------------------------------------
1213displ_pair={};
1214if isempty(TimeUnit)
1215    dtunit='e-03';
1216else
1217    dtunit=['m' TimeUnit];
1218end
1219switch mode
1220    case 'series(Di)'
1221        diff_i=i2_series-i1_series;
1222        min_diff=min(diff_i(diff_i>0));
1223        max_diff=max(diff_i(diff_i>0));
1224        for ipair=min_diff:max_diff
1225            if numel(diff_i(diff_i==ipair))>0
1226                pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1227                if ~isempty(time)
1228                    if ref_i<=floor(ipair/2)
1229                        ref_i=floor(ipair/2)+1;% shift ref_i to get the first pair
1230                    end
1231                    Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1232                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1233                end
1234                displ_pair=[displ_pair;{pair_string}];
1235            end
1236        end
1237        if ~isempty(displ_pair)
1238            displ_pair=[displ_pair;{'Di=*|*'}];
1239        end
1240    case 'series(Dj)'
1241        if isempty(j2_series)
1242            msgbox_uvmat('ERROR','no j1-j2 pair available')
1243            return
1244        end
1245        diff_j=j2_series-j1_series;
1246        min_diff=min(diff_j(diff_j>0));
1247        max_diff=max(diff_j(diff_j>0));
1248        for ipair=min_diff:max_diff
1249            if numel(diff_j(diff_j==ipair))>0
1250                pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1251                if ~isempty(time)
1252                    if ref_j<=floor(ipair/2)
1253                        ref_j=floor(ipair/2)+1;% shift ref_i to get the first pair
1254                    end
1255                    Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1256                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1257                end
1258                displ_pair=[displ_pair;{pair_string}];
1259            end
1260        end
1261        if ~isempty(displ_pair)
1262            displ_pair=[displ_pair;{'Dj=*|*'}];
1263        end
1264    case 'bursts'
1265        if isempty(j2_series)
1266            msgbox_uvmat('ERROR','no j1-j2 pair available')
1267            return
1268        end
1269        %diff_j=j2_series-j1_series;
1270        min_j1=min(j1_series(j1_series>0));
1271        max_j1=max(j1_series(j1_series>0));
1272        min_j2=min(j2_series(j2_series>0));
1273        max_j2=max(j2_series(j2_series>0));
1274        for pair1=min_j1:min(max_j1,min_j1+20)
1275            for pair2=min_j2:min(max_j2,min_j2+20)
1276                if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1277                    pair_string=['j= ' num2str(pair1) '-' num2str(pair2)];
1278                    [TimeValue,DtValue]=get_time(ref_i,[],pair_string,InputTable,FileInfo,TimeName,'Dt');
1279                    %Dt=time(ref_i,pair2+1)-time(ref_i,pair1+1);
1280                    pair_string=[pair_string ', Dt=' num2str(DtValue) ' ' dtunit];
1281                    displ_pair=[displ_pair;{pair_string}];
1282                end
1283            end
1284        end
1285        if ~isempty(displ_pair)
1286            displ_pair=[displ_pair;{'j=*-*'}];
1287        end
1288end
1289
1290%------------------------------------------------------------------------
1291function num_first_i_Callback(hObject, eventdata, handles)
1292%------------------------------------------------------------------------
1293num_last_i_Callback(hObject, eventdata, handles)
1294
1295%------------------------------------------------------------------------
1296function num_last_i_Callback(hObject, eventdata, handles)
1297%------------------------------------------------------------------------
1298SeriesData=get(handles.series,'UserData');
1299if ~isfield(SeriesData,'Time')
1300    SeriesData.Time{1}=[];
1301end
1302displ_time(handles);
1303
1304%------------------------------------------------------------------------
1305function num_first_j_Callback(hObject, eventdata, handles)
1306%------------------------------------------------------------------------
1307 num_last_j_Callback(hObject, eventdata, handles)
1308
1309%------------------------------------------------------------------------
1310function num_last_j_Callback(hObject, eventdata, handles)
1311%------------------------------------------------------------------------
1312% first_j=str2num(get(handles.num_first_j,'String'));
1313% last_j=str2num(get(handles.num_last_j,'String'));
1314% ref_j=ceil((first_j+last_j)/2);
1315% set(handles.num_ref_j,'String', num2str(ref_j))
1316% num_ref_j_Callback(hObject, eventdata, handles)
1317SeriesData=get(handles.series,'UserData');
1318if ~isfield(SeriesData,'Time')
1319    SeriesData.Time{1}=[];
1320end
1321displ_time(handles);
1322
1323%------------------------------------------------------------------------
1324% ---- find the times corresponding to the first and last indices of a series
1325function displ_time(handles)
1326%------------------------------------------------------------------------
1327SeriesData=get(handles.series,'UserData');%
1328if ~isfield(SeriesData,'Time')
1329    return
1330end
1331PairString=get(handles.PairString,'Data');
1332ref_i_1=str2num(get(handles.num_first_i,'String'));%first reference index
1333ref_i_2=str2num(get(handles.num_last_i,'String'));%last reference index
1334ref_j_1=[];ref_j_2=[];
1335if strcmp(get(handles.num_first_j,'Visible'),'on')
1336ref_j_1=str2num(get(handles.num_first_j,'String'));
1337ref_j_2=str2num(get(handles.num_last_j,'String'));
1338end
1339[i1_1,i2_1,j1_1,j2_1] = get_file_index(ref_i_1,ref_j_1,PairString);
1340[i1_2,i2_2,j1_2,j2_2] = get_file_index(ref_i_2,ref_j_2,PairString);
1341TimeTable=get(handles.TimeTable,'Data');
1342%%%%%%
1343%TODO: read time in netcdf file, see ActionName_Callback
1344%%%%%%%
1345%Pairs=get(handles.PairString,'Data');
1346for iview=1:size(TimeTable,1)
1347    if size(SeriesData.Time,1)<iview
1348        break
1349    end
1350    TimeTable{iview,3}=[];
1351    TimeTable{iview,4}=[];
1352    if size(SeriesData.Time{iview},1)>=i2_2+1 && (isempty(ref_j_1)||size(SeriesData.Time{iview},2)>=j2_2+1)
1353        if isempty(ref_j_1)
1354            time_first=(SeriesData.Time{iview}(i1_1+1,2)+SeriesData.Time{iview}(i2_1+1,2))/2;
1355            time_last=(SeriesData.Time{iview}(i1_2+1,2)+SeriesData.Time{iview}(i2_2+1,2))/2;
1356        else
1357            time_first=(SeriesData.Time{iview}(i1_1+1,j1_1+1)+SeriesData.Time{iview}(i2_1+1,j2_1+1))/2;
1358            time_last=(SeriesData.Time{iview}(i1_2+1,j1_2+1)+SeriesData.Time{iview}(i2_2+1,j2_1+1))/2;
1359        end
1360        TimeTable{iview,3}=time_first; %TODO: take into account pairs
1361        TimeTable{iview,4}=time_last; %TODO: take into account pairs
1362    end
1363end
1364set(handles.TimeTable,'Data',TimeTable)
1365
1366%% set the waitbar position with respect to the min and max in the series
1367MinIndex_i=min(get(handles.MinIndex_i,'Data'));
1368MaxIndex_i=max(get(handles.MaxIndex_i,'Data'));
1369pos_first=(ref_i_1-MinIndex_i)/(MaxIndex_i-MinIndex_i+1);
1370pos_last=(ref_i_2-MinIndex_i+1)/(MaxIndex_i-MinIndex_i+1);
1371if isempty(pos_first), pos_first=0; end
1372if isempty(pos_last), pos_last=1; end
1373Position=get(handles.Waitbar,'Position');% position of the waitbar:= [ x,y, width, height]
1374Position_status=get(handles.FileStatus,'Position');
1375Position(1)=Position_status(1)+Position_status(3)*pos_first;
1376Position(3)=max(Position_status(3)*(pos_last-pos_first),0.001);% width must remain positive
1377set(handles.Waitbar,'Position',Position)
1378update_waitbar(handles.Waitbar,0)
1379
1380%------------------------------------------------------------------------
1381% --- Executes when selected cell(s) is changed in PairString.
1382function PairString_CellSelectionCallback(hObject, eventdata, handles)
1383%------------------------------------------------------------------------   
1384if numel(eventdata.Indices)>=1
1385    PairString=get(hObject,'Data');
1386    if ~isempty(PairString{eventdata.Indices(1)})
1387        SetPairs_Callback(hObject, eventdata.Indices(1), handles)
1388    end
1389end
1390
1391%-------------------------------------
1392function enable_i(handles,state)
1393set(handles.i_txt,'Visible',state)
1394set(handles.num_first_i,'Visible',state)
1395set(handles.num_last_i,'Visible',state)
1396set(handles.num_incr_i,'Visible',state)
1397
1398%-----------------------------------
1399function enable_j(handles,state)
1400set(handles.j_txt,'Visible',state)
1401set(handles.num_first_j,'Visible',state)
1402set(handles.num_last_j,'Visible',state)
1403set(handles.num_incr_j,'Visible',state)
1404set(handles.MinIndex_j,'Visible',state)
1405set(handles.MaxIndex_j,'Visible',state)
1406
1407
1408%%%%%%%%%%%%%%%%%%%%
1409%%  MAIN ActionName FUNCTIONS
1410%%%%%%%%%%%%%%%%%%%%
1411%------------------------------------------------------------------------
1412% --- Executes on button press in RUN.
1413%------------------------------------------------------------------------
1414function RUN_Callback(hObject, eventdata, handles)
1415
1416%% settings of the button RUN
1417set(handles.RUN,'BusyAction','queue');% activation of STOP button will set BusyAction to 'cancel'
1418set(handles.RUN, 'Enable','Off')% avoid further RUN action until the current one is finished
1419set(handles.RUN,'BackgroundColor',[1 1 0])%show activation of RUN by yellow color
1420drawnow
1421set(handles.status,'Value',0)% desable status display if relevant
1422status_Callback([], eventdata, handles)
1423
1424%% launch action
1425errormsg=launch_action(handles);
1426if ~isempty(errormsg)
1427     msgbox_uvmat('ERROR',errormsg)
1428end
1429
1430%% reset the GUI series
1431update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate launching is finished
1432set(handles.RUN, 'Enable','On')
1433set(handles.RUN,'BackgroundColor',[1 0 0])
1434set(handles.RUN, 'Value',0)
1435
1436%------------------------------------------------------------------------
1437% --- called by RUN_Callback
1438%------------------------------------------------------------------------
1439function errormsg=launch_action(handles)
1440errormsg='';%default
1441
1442%% read the data on the GUI series
1443Param=read_GUI_series(handles);%displayed parameters
1444SeriesData=get(handles.series,'UserData');%hidden parameters
[883]1445if isfield(SeriesData,'TransformInput')
1446    Param.TransformInput=SeriesData.TransformInput;
1447end
[867]1448if ~isfield(SeriesData,'i1_series')
1449    errormsg='The input field series needs to be refreshed: press REFRESH';
1450    return
1451end
[940]1452if isfield(Param,'InputFields')&& isfield(Param.InputFields,'FieldName')&& isequal(Param.InputFields.FieldName,'get_field...')
[867]1453    errormsg='input field name(s) not defined, select get_field...';
1454    return
1455end
1456
1457%% select the Action mode, 'local', 'background' or 'cluster' (if available)
1458RunMode='local';%default (needed for first opening of the GUI series)
1459if isfield(Param.Action,'RunMode')
1460    RunMode=Param.Action.RunMode;
1461    Param.Action=rmfield(Param.Action,'RunMode');%remove from the recorded xml file to avoid interference during ImportConfig
1462end
1463ActionExt='.m';%default
1464if isfield(Param.Action,'ActionExt')
1465    ActionExt=Param.Action.ActionExt;% '.m', '.sh' (compiled)  or '.py' (Python)
1466    Param.Action=rmfield(Param.Action,'ActionExt');%remove from the recorded xml file to avoid interference during ImportConfig
1467end
1468ActionName=Param.Action.ActionName;
1469ActionPath=Param.Action.ActionPath;
1470path_series=fileparts(which('series'));
1471
1472%% create the Action fct handle if RunMode option = 'local'
1473if strcmp(RunMode,'local')
1474    if ~isequal(ActionPath,path_series)
1475        eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1476        if ~exist(ActionPath,'dir')
1477            errormsg=['The prescribed function path ' ActionPath ' does not exist'];
1478            return
1479        end
1480        if ~isequal(spath,ActionPath)
1481            addpath(ActionPath)% add the prescribed path if not the current one
1482        end
1483    end
1484    eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1485    if ~isequal(ActionPath,path_series)
1486        rmpath(ActionPath)% add the prescribed path if not the current one
1487    end
1488end
1489
[918]1490%% Get  PARAM.xml (not used at this stage)
[867]1491errormsg='';%default error message
1492xmlfile=fullfile(path_series,'PARAM.xml');
1493if ~exist(xmlfile,'file')
1494    [success,message]=copyfile(fullfile(path_series,'PARAM.xml.default'),xmlfile);
1495end
1496if strcmp(ActionExt,'.sh')
1497    if exist(xmlfile,'file')
1498        s=xml2struct(xmlfile);
1499        if strcmp(RunMode,'cluster_oar') && isfield(s,'BatchParam')
1500            if isfield(s.BatchParam,'NbCore')
1501                NbCore=s.BatchParam.NbCore;
1502            end
1503        elseif (strcmp(RunMode,'background')||strcmp(RunMode,'local')) && isfield(s,'RunParam')
1504            if isfield(s.RunParam,'NbCore')
1505                NbCore=s.RunParam.NbCore;
1506            end
1507        end
1508    end
1509end
[928]1510ActionFullName=fullfile(get(handles.ActionPath,'String'),ActionName);
[934]1511
1512%% If a compiled version has been selected (ext .sh) check wether it needs to be recompiled
[867]1513if strcmp(ActionExt,'.sh')
1514    TransformPath='';
1515    if ~isempty(get(handles.ActionExt,'UserData'))
1516        TransformPath=get(handles.ActionExt,'UserData');
1517    end
1518    set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
1519    set(handles.ActionExt,'BackgroundColor',[1 1 0])
[923]1520    [mcrmajor, mcrminor] = mcrversion;   
1521    MCRROOT = ['MCRROOT',int2str(mcrmajor),int2str(mcrminor)];
[895]1522    RunTime = getenv(MCRROOT);
1523    ActionNameVersion=[ActionName '_' MCRROOT];
1524    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']);
[934]1525    % compile the .m file if the .sh file does not exist yet
[867]1526    if ~exist(ActionFullName,'file')
1527        answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
1528        if strcmp(answer,'Yes')
1529            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1530            path_uvmat=fileparts(which('series'));
1531            currentdir=pwd;
1532            cd(get(handles.ActionPath,'String'))% go to the directory of Action
1533            addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1534            compile(ActionName,TransformPath)
1535            cd(currentdir)
[880]1536        else
1537            errormsg='Action launch interrupted';
1538            return
[867]1539        end       
1540    else
[895]1541        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']));
[867]1542        m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
1543        if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
1544            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1545            drawnow
[895]1546            answer=msgbox_uvmat('INPUT_Y-N',[ActionNameVersion '.sh needs to be updated: recompile now?']);
[867]1547            if strcmp(answer,'Yes')
1548                path_uvmat=fileparts(which('series'));
1549                currentdir=pwd;
1550                cd(get(handles.ActionPath,'String'))% go to the directory of Action
1551                addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1552                addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile'
1553                compile(ActionName,TransformPath)
1554                cd(currentdir)
1555            end
1556        end
1557    end
[934]1558
[867]1559    set(handles.ActionExt,'BackgroundColor',[1 1 1])
1560     set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch
1561end
1562
[897]1563%% set nbre of cluster cores and processes:
1564% NbCore is the number of computer processors used
[917]1565% NbProcess is the number of independent processes in which the required calculation is split.
[867]1566switch RunMode
1567    case {'local','background'}
1568        NbCore=1;% no need to split the calculation
1569    case 'cluster_oar'
[935]1570        %%%%% TEST A REMETTRE%%%%%
1571 %       if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1572%             NbCore=1;% one core used only (limitation of Matlab licences)
1573%             answer=msgbox_uvmat('INPUT_Y-N','Number of cores =1: select the compiled version .sh for multi-core processing. Proceed with the .m version?');
1574%             if ~strcmp(answer,'Yes')
1575%                 errormsg='Action launch interrupted by user';
1576%                 return
1577%             end
1578%             extra_oar='';
1579 %       else
[867]1580            answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''});
[896]1581            if isempty(answer)
1582                                errormsg='Action launch interrupted by user';
1583                return
1584            end
[867]1585            NbCore=str2double(answer{1});
1586            extra_oar=answer{2};
[935]1587 %       end
[882]1588    case 'cluster_pbs'
1589        if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1590            NbCore=1;% one core used only (limitation of Matlab licences)
1591            answer=msgbox_uvmat('INPUT_Y-N','Number of cores =1: select the compiled version .sh for multi-core processing. Proceed with the .m version?');
1592            if ~strcmp(answer,'Yes')
1593                errormsg='Action launch interrupted';
1594                return
1595            end
1596            extra_oar='';
1597        else
1598            answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''});
1599            NbCore=str2double(answer{1});
1600            %extra_oar=answer{2};%TODO : fix this for LMFA cluster. Maybe
1601            %extrs_oar and extra_pbs are not the best names
1602        end
[867]1603end
1604if ~isfield(Param.IndexRange,'NbSlice')
1605    Param.IndexRange.NbSlice=[];
1606end
1607
1608%% create the output data directory if needed
1609OutputDir='';
1610if isfield(Param,'OutputSubDir')
1611    SubDirOut=[get(handles.OutputSubDir,'String') Param.OutputDirExt];
1612    SubDirOutNew=SubDirOut;
1613    detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exist
1614    check_create=1; %need to create the result directory by default
[905]1615    CheckOverwrite=1;
1616    if isfield(Param,'CheckOverwrite')
1617        CheckOverwrite=Param.CheckOverwrite;
1618    end
[867]1619    while detect
[905]1620        if CheckOverwrite
[904]1621            comment=', possibly overwrite previous data';
1622        else
1623            comment=', will complement existing result files (no overwriting)';
1624        end
1625        answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(Param.InputTable{1,1},SubDirOutNew) comment]);
[867]1626        if strcmp(answer,'Cancel')
1627            return
1628        elseif strcmp(answer,'Yes')
1629            detect=0;
1630            check_create=0;
1631        else
1632            r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names');%detect whether name ends by a number
1633            if isempty(r)
1634                r(1).root=[SubDirOutNew '_'];
1635                r(1).num1='0';
1636            end
1637            SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1
1638            detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exists
1639            check_create=1;
1640        end
1641    end
1642    Param.OutputDirExt=regexprep(SubDirOutNew,Param.OutputSubDir,'');
1643    Param.OutputRootFile=Param.InputTable{1,3};% the first sorted RootFile taken for output
1644    set(handles.OutputDirExt,'String',Param.OutputDirExt)
1645    OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]);% full name (with path) of output directory
1646    if check_create    % create output directory if it does not exist
1647        [tild,msg1]=mkdir(OutputDir);
1648        if ~strcmp(msg1,'')
1649            errormsg=['cannot create ' OutputDir ': ' msg1];%error message for directory creation
1650            return
1651        end
1652    end
1653   
1654elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir
1655    OutputDir=Param.ActionInput.LogPath;   
1656end
1657DirXml=fullfile(OutputDir,'0_XML');
1658if ~exist(DirXml,'dir')
[935]1659    [~,msg1]=mkdir(DirXml);
[867]1660    if ~strcmp(msg1,'')
1661        errormsg=['cannot create ' DirXml ': ' msg1];%error message for directory creation
1662        return
1663    end
1664end
1665OutputNomType=nomtype2pair(Param.InputTable{1,4});% nomenclature for output files
1666
[897]1667%% get the set of reference input field indices
1668first_i=1;% first i index to process
1669last_i=1;% last i index to process
1670incr_i=1;% increment step in i index
1671first_j=1;% first j index to process
1672last_j=1;% last j index to process
1673incr_j=1;% increment step in j index
[867]1674if isfield(Param.IndexRange,'first_i')
1675    first_i=Param.IndexRange.first_i;
1676    incr_i=Param.IndexRange.incr_i;
1677    last_i=Param.IndexRange.last_i;
1678end
1679if isfield(Param.IndexRange,'first_j')
1680    first_j=Param.IndexRange.first_j;
1681    last_j=Param.IndexRange.last_j;
1682    incr_j=Param.IndexRange.incr_j;
1683end
[932]1684if last_i < first_i || last_j < first_j
[867]1685    errormsg= 'series/Run_Callback:last field index must be larger or equal to the first one';
1686    return
1687end
1688%incr_i must be defined, =1 by default, if NbSlice is active
1689if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice)
1690    incr_i=1;
1691    set(handles.num_incr_i,'String','1')
1692end
[897]1693% case of no increment i defined: processing is done on the available files found in i1_series
[867]1694if isempty(incr_i)
1695    if isempty(incr_j)
1696        [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1697        ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1698        ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1699        ref_j=ref_j-1;
1700        ref_i=ref_i-1;
1701    else
1702        ref_j=first_j:incr_j:last_j;
1703        [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1704        ref_i=ref_i-1;
1705        ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1706    end
[932]1707    % increment i is defined: processing is done on first_i:incr_i:last_i;
[867]1708else
1709    ref_i=first_i:incr_i:last_i;
[904]1710    if isempty(incr_j)% automatic finding of the existing j indices
[867]1711        [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1712        ref_j=ref_j-1;
1713        ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1714    else
1715        ref_j=first_j:incr_j:last_j;
1716    end
1717end
[914]1718CPUTime=1;% job time estimated at 1 min per iteration (on index i and j) by default
[906]1719if isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime)
1720    CPUTime=Param.Action.CPUTime;%Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j
[904]1721end
1722nbfield_j=numel(ref_j); % number of j indices
[932]1723BlockLength=numel(ref_i);% by default, job involves the full set of i field indices
[910]1724NbProcess=1;
1725switch RunMode
1726    case {'cluster_oar','cluster_pbs'}
1727        if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined
[932]1728            BlockLength= ceil(20/(CPUTime*nbfield_j));% short iterations are grouped such that the minimum time of a process is 20 min.
1729            BlockLength=max(BlockLength,ceil(numel(ref_i)/500));% possibly increase the BlockLength to have less than 500 jobs
1730            NbProcess=ceil(numel(ref_i)/BlockLength) ; % nbre of processes sent to oar
[910]1731        else
1732            NbProcess=Param.IndexRange.NbSlice;% the parameter NbSlice sets the nbre of run processes
1733            NbCore=min(NbCore,NbProcess);% reduces the number of cores if it exceeds the number of processes
1734        end
[917]1735    otherwise
[932]1736        if ~isempty(Param.IndexRange.NbSlice)
1737            NbProcess=Param.IndexRange.NbSlice;% the parameter NbSlice sets the nbre of run processes
1738        end
[902]1739end
[867]1740
1741%% record nbre of output files and starting time for computation for status
1742StatusData=get(handles.status,'UserData');
1743if isfield(StatusData,'OutputFileMode')
1744    switch StatusData.OutputFileMode
1745        case 'NbInput'
1746            StatusData.NbOutputFile=numel(ref_i)*nbfield_j;
1747        case 'NbInput_i'
1748            StatusData.NbOutputFile=numel(ref_i);
[932]1749        case 'NbSlice'
[867]1750            StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
1751    end
1752end
1753StatusData.TimeStart=now;
1754set(handles.status,'UserData',StatusData)
1755
[897]1756%% case of a function in Python
[867]1757if strcmp(ActionExt, '.py (in dev.)')
1758    fprintf([
1759        '\n' ...
1760        '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ...
1761        'The option .py is used. It is still in development.\n' ...
1762        'Do not use it unless you really know what you do!\n' ...
[942]1763        'To try it, first install Pyp and the most recent version of FluidImage.\n' ...
[867]1764        '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n'])
1765    RunMode = 'python';
1766end
1767
1768
[919]1769%% direct processing on the current Matlab session or creation of command files
1770filexml=cell(1,NbProcess);% initialisation of the names of the files containing the processing parameters
1771extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process
[918]1772for iprocess=1:NbProcess
[922]1773    extxml{iprocess}='.xml';
1774end
1775for iprocess=1:NbProcess
[918]1776    if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1777        disp('program stopped by user')
1778        return
1779    end
1780    if isempty(Param.IndexRange.NbSlice)
1781        Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1782        if Param.IndexRange.first_i>last_i
1783            NbProcess=iprocess-1;% leave the loop, we are at the end of the calculation
1784            break
[917]1785        end
[918]1786        Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
1787    else %multislices (then incr_i is not empty)
1788        Param.IndexRange.first_i= first_i+iprocess-1;
1789        Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;
1790    end
1791    for ilist=1:size(Param.InputTable,1)
1792        Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/');%correct path name for PCWIN system
1793    end
1794   
1795    if isfield(Param,'OutputSubDir')
1796        t=struct2xml(Param);
1797        t=set(t,1,'name','Series');
1798        extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,...
1799            Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
[919]1800        filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess});
1801        try
1802            save(t, filexml{iprocess});% save the xml file containing the processing parameters
1803        catch ME
1804            if ~strcmp (RunMode,'local')
1805                errormsg=['error writting ' filexml{iprocess} ': ' ME.message];
1806                return
1807            end
1808        end
[918]1809    end
1810    if strcmp (RunMode,'local')
[867]1811        switch ActionExt
1812            case '.m'
[918]1813                h_fun(Param);% direct launching
[932]1814               
[867]1815            case '.sh'
1816                switch computer
1817                    case {'PCWIN','PCWIN64'} %Windows system
1818                        filexml=regexprep(filexml,'\\','\\\\');% add '\' so that '\' are left as characters
[922]1819                        system([ActionFullName ' ' RunTime ' ' filexml]);% TODO: adapt to DOS system
[867]1820                    case {'GLNX86','GLNXA64','MACI64'}%Linux  system
[922]1821                        system([ActionFullName ' ' RunTime ' ' filexml]);
[867]1822                end
1823        end
1824    end
[918]1825end
[934]1826
[918]1827if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python')
[867]1828    %% processing on a different session of the same computer (background) or cluster, create executable files
1829    batch_file_list=cell(NbProcess,1);% initiate the list of executable files
[905]1830    DirExe=fullfile(OutputDir,'0_EXE');%directory name for executable files
[867]1831    switch computer
1832        case {'PCWIN','PCWIN64'} %Windows system
1833            ExeExt='.bat';
1834        case {'GLNX86','GLNXA64','MACI64'}%Linux  system
[917]1835            ExeExt='.sh';
[867]1836    end
1837    %create subdirectory for executable files
[905]1838    if ~exist(DirExe,'dir')
1839        [tild,msg1]=mkdir(DirExe);
[867]1840        if ~strcmp(msg1,'')
[905]1841            errormsg=['cannot create ' DirExe ': ' msg1];%error message for directory creation
[867]1842            return
1843        end
1844    end
1845    %create subdirectory for log files
1846    DirLog=fullfile(OutputDir,'0_LOG');
1847    if ~exist(DirLog,'dir')
1848        [tild,msg1]=mkdir(DirLog);
1849        if ~strcmp(msg1,'')
1850            errormsg=['cannot create ' DirLog ': ' msg1];%error message for directory creation
1851            return
1852        end
1853    end
[932]1854   
[918]1855    %create the executable file
1856    file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,...
1857        first_i,last_i,first_j,last_j);
1858    file_exe_global=fullfile(OutputDir,'0_EXE',file_exe_global);
1859    filelog_global=fullfile_uvmat('','',Param.InputTable{1,3},'.log',OutputNomType,...
1860        first_i,last_i,first_j,last_j);
1861    filelog_global=fullfile(OutputDir,'0_LOG',filelog_global);
[934]1862
[867]1863    for iprocess=1:NbProcess
1864       
[918]1865        %create the executable file
[917]1866       
[918]1867        batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt));
1868       
[917]1869        % set the log file name
[918]1870        filelog{iprocess}=fullfile(OutputDir,'0_LOG',regexprep(extxml{iprocess},'.xml$','.log'));
1871       
[917]1872    end
1873end
1874
1875%% launch the executable files for background or cluster processing
[918]1876
[917]1877switch RunMode
[918]1878   
[917]1879    case 'background'
[918]1880        [fid,message]=fopen(file_exe_global,'w');
[867]1881        if isequal(fid,-1)
[918]1882            errormsg=['creation of ' file_exe_global ':' message];
[867]1883            return
1884        end
1885        switch ActionExt
1886            case '.m'% Matlab function
1887                switch computer
1888                    case {'GLNX86','GLNXA64','MACI64'}
1889                        cmd=[...
1890                            '#!/bin/bash \n'...
1891                            '. /etc/sysprofile \n'...
[918]1892                            'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog_global ''' <<END_MATLAB \n'...
[867]1893                            'addpath(''' path_series '''); \n'...
[917]1894                            'addpath(''' Param.Action.ActionPath '''); \n'];
1895                        for iprocess=1:NbProcess
1896                            cmd=[cmd '' Param.Action.ActionName  '( ''' filexml{iprocess} '''); \n'];
1897                        end
1898                        cmd=[cmd  'exit \n' 'END_MATLAB \n'];
[867]1899                        fprintf(fid,cmd);%fill the executable file with the  char string cmd
1900                        fclose(fid);% close the executable file
[918]1901                        system(['chmod +x ' file_exe_global]);% set the file to executable
[867]1902                    case {'PCWIN','PCWIN64'}
[917]1903                        cmd=['matlab -automation -logfile ' regexprep(filelog{iprocess},'\\','\\\\')...
[867]1904                            ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
[917]1905                            'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');'];
1906                        for iprocess=1:NbProcess
[918]1907                            cmd=[cmd '' Param.Action.ActionName  '( ''' regexprep(filexml{iprocess},'\\','\\\\') ''');']
[917]1908                        end
1909                        cmd=[cmd ';exit"'];
1910                        fprintf(fid,cmd);%fill the executable file with the  char string cmd
[867]1911                        fclose(fid);% close the executable file
1912                end
[918]1913                system([file_exe_global ' &'])% directly execute the command file
[867]1914            case '.sh' % compiled Matlab function
[918]1915                for iprocess=1:NbProcess
1916                    switch computer
1917                        case {'GLNX86','GLNXA64','MACI64'}
1918                            [fid,message]=fopen(batch_file_list{iprocess},'w');% create the executable file
1919                            if isequal(fid,-1)
1920                                errormsg=['creation of .bat file: ' message];
1921                                return
1922                            end
1923                            cmd=['#!/bin/bash \n '...
1924                                '#$ -cwd \n '...
1925                                'hostname && date \n '...
1926                                'umask 002 \n'...
[934]1927                                ActionFullName ' ' RunTime ' ' filexml{iprocess}];%allow writting access to created files for user group
[918]1928                            fprintf(fid,cmd);%fill the executable file with the  char string cmd
1929                            fclose(fid);% close the executable file
1930                            system(['chmod +x ' batch_file_list{iprocess}]);% set the file to executable
1931                            system([batch_file_list{iprocess} ' &'])% directly execute the command file
1932                        case {'PCWIN','PCWIN64'}
1933                            msgbox_uvmat('ERROR','option for compiled Matlab functions not implemented for Windows system')
1934                            return
1935                    end
[867]1936                end
[922]1937                msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched in background: press STATUS to see results'])
[867]1938        end
[918]1939       
1940    case 'cluster_oar' % option 'oar-parexec' used
1941        %create subdirectory for oar commands
[932]1942        for iprocess=1:NbProcess
[918]1943            [fid,message]=fopen(batch_file_list{iprocess},'w');% create the executable file
1944            if isequal(fid,-1)
1945                errormsg=['creation of .bat file: ' message];
1946                return
1947            end
1948            if  strcmp(ActionExt,'.sh')
[932]1949                cmd=['#!/bin/bash \n '...
1950                    '#$ -cwd \n '...
1951                    'hostname && date \n '...
1952                    'umask 002 \n'...
1953                    ActionFullName ' ' RunTime ' ' filexml{iprocess}];%allow writting access to created files for user group
[918]1954            else
1955                cmd=[...
[932]1956                    '#!/bin/bash \n'...
1957                    '. /etc/sysprofile \n'...
[937]1958                    'module load matlab/8.6 \n'...% CHOICE OF MATLAB VERSION
[932]1959                    'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog{iprocess} ''' <<END_MATLAB \n'...
1960                    'addpath(''' path_series '''); \n'...
1961                    'addpath(''' Param.Action.ActionPath '''); \n'...
1962                    '' Param.Action.ActionName  '( ''' filexml{iprocess} '''); \n'...
1963                    'exit \n'...
1964                    'END_MATLAB \n'];
[918]1965            end
1966            fprintf(fid,cmd);%fill the executable file with the  char string cmd
1967            fclose(fid);% close the executable file
1968            system(['chmod +x ' batch_file_list{iprocess}]);% set the file to executable
1969        end
1970        DirOAR=fullfile(OutputDir,'0_OAR');
1971        if exist(DirOAR,'dir')% delete the content of the dir 0_LOG to allow new input
1972            curdir=pwd;
1973            cd(DirOAR)
1974            delete('*')
1975            cd(curdir)
1976        else
1977            [tild,msg1]=mkdir(DirOAR);
1978            if ~strcmp(msg1,'')
1979                errormsg=['cannot create ' DirOAR ': ' msg1];%error message for directory creation
1980                return
1981            end
1982        end
1983        % create file containing the list of jobs
[932]1984        filename_joblist=fullfile(DirOAR,'job_list.txt');% name of the file containing the list of executables
[918]1985        fid=fopen(filename_joblist,'w');%open it for writting
1986        for iprocess=1:length(batch_file_list)
1987            fprintf(fid,[batch_file_list{iprocess} '\n']);% write list of exe files
1988        end
1989        fclose(fid);
1990        system(['chmod +x ' filename_joblist]);% set the file to executable
1991       
1992        filename_log=fullfile(DirLog,'job_list.stdout');%file for output messages of the master oar process
1993        filename_errors=fullfile(DirLog,'job_list.stderr');%file for error messages of the master oar process
1994        % the command job_list.txt contains the list of NbProcess independent individual jobs
1995        % in which the total calculation has been split. Those are written as executable files .sh in the folder /O_EXE.
1996        %  These individual jobs are grouped by the system as oar jobs on the NbCore processors.
1997        %  For each processor, the oar job must stop after the walltime which has been set, which is limited to 24 h.
1998        %  However, the oar job is automatically restarted (option 'idempotent') provided the individual jobs are
1999        % shorter than the wall time: in the time interval 'checkpoint' (WallTimeOneJob) before the end of the allowed duration,
2000        %  the oar job restarts when an individual job ends.
2001        JobTime=CPUTime*BlockLength*nbfield_j;% estimated time for one individual job (in minutes)
2002        % wall time (in hours ) for each oar job, allowing 10 individual jobs, but limited to 23 h:
2003        WallTimeTotal=min(23,4*JobTime/60);
2004        %disp(['WallTimeTotal: ' num2str(WallTimeTotal) ' hours'])
2005        % estimated time of an individual job (in min), with a margin of error
2006        WallTimeOneJob=min(4*JobTime+10,WallTimeTotal*60/2);% estimated max time of an individual job for checkpoint
2007        disp(['WallTimeOneJob: ' num2str(WallTimeOneJob) ' minutes'])
[922]2008        oar_command=['oarsub -n UVmat_' ActionFullName ' '...
[918]2009            '-t idempotent --checkpoint ' num2str(WallTimeOneJob*60) ' '...
2010            '-l /core=' num2str(NbCore) ','...
2011            'walltime=' datestr(WallTimeTotal/24,13) ' '...
2012            '-E ' filename_errors ' '...
2013            '-O ' filename_log ' '...
2014            extra_oar ' '...
[932]2015            '"oar-parexec -s -f ' filename_joblist ' '...
[918]2016            '-l ' filename_joblist '.log"'];
[922]2017       
[918]2018        fprintf(oar_command);% display  system command on the Matlab command window
2019        [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window
2020        filename_oarcommand=fullfile(DirOAR,'0_oar_command');% keep track of the command in file '0-OAR/0_oar_command'
2021        fid=fopen(filename_oarcommand,'w');
2022        fprintf(fid,oar_command); % store the command
2023        fprintf(fid,result);% store the result (job ID number)
2024        fclose(fid);
[922]2025        msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched as  ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
[918]2026       
2027    case 'cluster_pbs' % for LMFA Kepler machine
2028        %create subdirectory for pbs command and log files
2029        DirPBS=fullfile(OutputDir,'0_PBS'); %todo : common name OAR/PBS
2030        if exist(DirPBS,'dir')% delete the content of the dir 0_LOG to allow new input
2031            curdir=pwd;
2032            cd(DirPBS)
2033            delete('*')
2034            cd(curdir)
2035        else
2036            [tild,msg1]=mkdir(DirPBS);
2037            if ~strcmp(msg1,'')
2038                errormsg=['cannot create ' DirPBS ': ' msg1];%error message for directory creation
2039                return
2040            end
2041        end
2042        max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h)
2043        walltime_onejob=1800; % seconds, max estimated time for asingle file index value
2044        filename_joblist=fullfile(DirPBS,'job_list.txt');%create name of the global executable file
2045        fid=fopen(filename_joblist,'w');
2046        for iprocess=1:length(batch_file_list)
2047            fprintf(fid,[batch_file_list{iprocess} '\n']);% list of exe files
2048        end
2049        fclose(fid);
2050        system(['chmod +x ' filename_joblist]);% set the file to executable
2051        pbs_command=['qstat -n CIVX '...
2052            '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
2053            '-l /core=' num2str(NbCore) ','...
2054            'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
2055            '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
2056            '-O ' regexprep(filename_joblist,'\.txt\>','.log') ' '...
2057            extra_oar ' '...
2058            '"oar-parexec -s -f ' filename_joblist ' '...
2059            '-l ' filename_joblist '.log"'];
2060        filename_oarcommand=fullfile(DirPBS,'pbs_command');
2061        fid=fopen(filename_oarcommand,'w');
2062        fprintf(fid,pbs_command);
2063        fclose(fid);
2064        fprintf(pbs_command);% display in command line
2065        %system(pbs_command);
[922]2066        msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster'])
[918]2067    case 'python'
2068        command = [
2069            'LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "p.split('':'') | [s for s in p if ''matlab'' not in s] | '':''.join(p)") ' ...
[942]2070            'python -m fluidimage.run_from_xml ' filexml{iprocess}];
[918]2071        % fprintf(['command:\n' command '\n\n'])
2072        system(command, '-echo');
[867]2073end
[932]2074if exist(OutputDir,'dir')
[935]2075    [SUCCESS,MESSAGE,MESSAGEID] = fileattrib (OutputDir)
2076    if MESSAGE.GroupWrite~=1
[932]2077    [success,msg] = fileattrib(OutputDir,'+w','g','s');% allow writing access for the group of users, recursively in the folder
2078    if success==0
[935]2079        msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg});%error message for directory creation
[932]2080    end
[935]2081    end
[932]2082end
[934]2083
[867]2084%------------------------------------------------------------------------
2085function STOP_Callback(hObject, eventdata, handles)
2086%------------------------------------------------------------------------
2087set(handles.RUN, 'BusyAction','cancel')
2088set(handles.RUN,'BackgroundColor',[1 0 0])
2089set(handles.RUN,'enable','on')
2090set(handles.RUN, 'Value',0)
2091
2092%------------------------------------------------------------------------
2093% --- read parameters from the GUI series
2094%------------------------------------------------------------------------
2095function Param=read_GUI_series(handles)
2096
2097%% read raw parameters from the GUI series
2098Param=read_GUI(handles.series);
2099
2100%% clean the output structure by removing unused information
2101if isfield(Param,'Pairs')
2102    Param=rmfield(Param,'Pairs'); %info Pairs not needed for output
2103end
2104if isfield(Param,'InputLine')
2105    Param=rmfield(Param,'InputLine');
2106end
2107if isfield(Param,'EditObject')
2108    Param=rmfield(Param,'EditObject');
2109end
2110Param.IndexRange.TimeSource=Param.IndexRange.TimeTable{end,1};
2111Param.IndexRange=rmfield(Param.IndexRange,'TimeTable');
2112empty_line=false(size(Param.InputTable,1),1);
2113for iline=1:size(Param.InputTable,1)
2114    empty_line(iline)=isempty(cell2mat(Param.InputTable(iline,1:3)));
2115end
2116Param.InputTable(empty_line,:)=[];
2117
2118%------------------------------------------------------------------------
2119% --- Executes on selection change in ActionName.
2120function ActionName_Callback(hObject, eventdata, handles)
2121%------------------------------------------------------------------------
2122
2123%% stop any ongoing series processing
2124if isequal(get(handles.RUN,'Value'),1)
2125    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
2126    if strcmp(answer,'Yes')
2127        STOP_Callback(hObject, eventdata, handles)
2128    else
2129        return
2130    end
2131end
2132set(handles.ActionName,'BackgroundColor',[1 1 0])
2133huigetfile=findobj(allchild(0),'tag','status_display');
2134if ~isempty(huigetfile)
2135    delete(huigetfile)
2136end
2137drawnow
2138
2139%% get Action name and path
2140NbBuiltinAction=get(handles.Action,'UserData'); %nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
2141ActionList=get(handles.ActionName,'String');% list menu fields
2142ActionIndex=get(handles.ActionName,'Value');
2143if ~isequal(ActionIndex,1)% if we are not just opening series
2144    InputTable=get(handles.InputTable,'Data');
2145    if isempty(InputTable{1,4})
2146        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
2147        return
2148    end
2149end
2150ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2151ActionPathList=get(handles.ActionName,'UserData');%list of recorded paths to functions of the list ActionName
2152
2153%% add a new function to the menu if 'more...' has been selected in the menu ActionName
2154if isequal(ActionName,'more...')
2155    [FileName, PathName] = uigetfile( ...
2156        {'*.m', ' (*.m)';
2157        '*.m',  '.m files '; ...
2158        '*.*', 'All Files (*.*)'}, ...
2159        'Pick a series processing function ',get(handles.ActionPath,'String'));
2160    if length(FileName)<2
2161        return
2162    end
2163    [tild,ActionName,ActionExt]=fileparts(FileName);
2164   
2165    % insert the choice in the menu ActionName
2166    ActionIndex=find(strcmp(ActionName,ActionList),1);% look for the selected function in the menu Action
2167    PathName=regexprep(PathName,'/$','');
2168    if ~isempty(ActionIndex) && ~strcmp(ActionPathList{ActionIndex},PathName)%compare the path to the existing fct
2169        ActionIndex=[]; % the selected path is different than the recorded one
2170    end
2171    if isempty(ActionIndex)%the qselected fct (with selected path) does not exist in the menu
2172        ActionIndex= length(ActionList);
2173        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)];% the selected function is appended in the menu, before the last item 'more...'
2174         ActionPathList=[ActionPathList; PathName];
2175    end
2176   
2177    % record the file extension and extend the path list if it is a new extension
[886]2178    ActionExtList=get(handles.ActionExt,'String');
2179    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
2180    if isempty(ActionExtIndex)
2181        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
2182    end
[867]2183
2184    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
2185    if length(ActionList)>NbBuiltinAction+5; %nb_builtin_ACTION=nbre of functions always remaining in the initial menu
2186        nbremove=length(ActionList)-NbBuiltinAction-5;
2187        ActionList(NbBuiltinAction+1:end-5)=[];
2188        ActionPathList(NbBuiltinAction+1:end-4,:)=[];
2189        ActionIndex=ActionIndex-nbremove;
2190    end
2191   
2192    % record action menu, choice and path
2193    set(handles.ActionName,'Value',ActionIndex)
2194    set(handles.ActionName,'String',ActionList)
2195       set(handles.ActionName,'UserData',ActionPathList);
2196    set(handles.ActionExt,'Value',ActionExtIndex)
2197       
2198    %record the user defined menu additions in personal file profil_perso
2199    dir_perso=prefdir;
2200    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2201    if NbBuiltinAction+1<=numel(ActionList)-1
2202        ActionListUser=ActionList(NbBuiltinAction+1:numel(ActionList)-1);
2203        ActionPathListUser=ActionPathList(NbBuiltinAction+1:numel(ActionList)-1);
[886]2204        ActionExtListUser={};
2205        if numel(ActionExtList)>2
2206            ActionExtListUser=ActionExtList(3:end);
2207        end
[867]2208        if exist(profil_perso,'file')
2209            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
2210        else
2211            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
2212        end
2213    end
2214end
2215
2216%% check the current ActionPath to the selected function
2217ActionPath=ActionPathList{ActionIndex};%current recorded path
2218set(handles.ActionPath,'String',ActionPath); %show the path to the senlected function
2219
2220%% reinitialise the waitbar
2221update_waitbar(handles.Waitbar,0)
2222
2223%% create the function handle for Action
[897]2224if ~exist(ActionPath,'dir')
2225    msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']);
2226    return
[867]2227end
[897]2228current_dir=pwd;%current working dir
2229cd(ActionPath)
2230h_fun=str2func(ActionName);
2231cd(current_dir)
[867]2232
[897]2233%
2234% checkaddpath=0;
2235% path_series=which('series');
2236% %eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
2237% spath=fileparts(which(ActionName)); %spath = current path of the selected function ACTION
2238% if ~exist(ActionPath,'dir')
2239%     msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']);
2240%     return
2241% end
2242% if ~strcmp(spath,ActionPath)
2243%     if strcmp(pwd,spath)
2244%         msgbox_uvmat('ERROR',[ 'a function called ' ActionName ' on your working space oversets the selected one']);
2245%         return
2246%     else
2247%         addpath(ActionPath)% add the prescribed path if not the current one
2248%         checkaddpath=1;
2249%     end
2250% end
2251% eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
2252% if checkaddpath && ~isequal(ActionPath,path_series)
2253%     rmpath(ActionPath)% add the prescribed path if not the current one
2254% end
2255
[867]2256%% Activate the Action fct to adapt the configuration of the GUI series and bring specific parameters in SeriesData
2257Param=read_GUI_series(handles);% read the parameters from the GUI series
2258ParamOut=h_fun(Param);%run the selected Action function to get the relevant input
2259
2260%% Put the first line of the selected Action fct as tooltip help
2261try
2262    [fid,errormsg] =fopen([ActionName '.m']);
2263    InputText=textscan(fid,'%s',1,'delimiter','\n');
2264    fclose(fid);
2265    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
2266end
2267
2268
2269%% Visibility of VelType and VelType_1 menus asked by ActionName
2270VelTypeRequest=1;%VelType requested by default
2271VelTypeRequest_1=1;%VelType requested by default
2272if isfield(ParamOut,'VelType')
2273    VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'});
2274    VelTypeRequest_1=strcmp( ParamOut.VelType,'two');
2275end
2276FieldNameRequest=0;  %hidden by default
2277FieldNameRequest_1=0;  %hidden by default
2278if isfield(ParamOut,'FieldName')
2279    FieldNameRequest=ismember(ParamOut.FieldName,{'on','one','two'});
2280    FieldNameRequest_1=strcmp( ParamOut.FieldName,'two');
2281end
2282
2283%% Detect the types of input files and set menus and default options in 'VelType'
2284SeriesData=get(handles.series,'UserData');% info on the input file series
2285iview_civ=find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));
2286iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));% all nc files, icluding civ
2287FieldList=get(handles.FieldName,'String');% previous list as default
2288if ~iscell(FieldList),FieldList={FieldList};end
2289FieldList_1=get(handles.FieldName_1,'String');% previous list as default
2290if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
[897]2291%CheckList=0;% indicate whether FieldName has been updated
[867]2292CheckList_1=1;% indicate whether FieldName_1 has been updated
2293handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title];
2294if VelTypeRequest && numel(iview_civ)>=1
2295    menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)});
2296    set(handles.VelType,'Value',1)% set first choice by default
2297    set(handles.VelType,'String',[{'*'};menu])
2298    set(handles.VelType,'Visible','on')
2299    set(handles.VelType_title,'Visible','on')
2300    FieldList=[set_field_list('U','V');{'C'};{'get_field...'}];%standard menu for civx data
[897]2301    %CheckList=1;
[867]2302    set(handles.FieldName,'Value',1); %velocity vector choice by default
2303    if  VelTypeRequest_1 && numel(iview_civ)>=2
2304        menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});
2305        set(handles.VelType_1,'Value',1)% set first choice by default
2306        set(handles.VelType_1,'String',[{'*'};menu])
2307        set(handles.VelType_1,'Visible','on')
2308        set(handles.VelType_title_1,'Visible','on')
2309        FieldList_1=[set_field_list('U','V');{'C'};{'get_field...'}];%standard menu for civx data
2310        CheckList_1=1;
2311        set(handles.FieldName_1,'Value',1); %velocity vector choice by default
2312    else
2313        set(handles.VelType_1,'Visible','off')
2314        set(handles.VelType_title_1,'Visible','off')
2315    end
2316else
2317    set(handles.VelType,'Visible','off')
2318    set(handles.VelType_title,'Visible','off')
2319end   
2320
2321%% Detect the types of input files and set menus and default options in 'FieldName'
[940]2322if (FieldNameRequest || VelTypeRequest) && numel(iview_netcdf)>=1
2323    set(handles.InputFields,'Visible','on')   
2324    if FieldNameRequest && isfield(SeriesData.FileInfo{iview_netcdf(1)},'ListVarName')
2325        set(handles.FieldName,'Visible','on')
[867]2326        ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName;
2327        ind_var=get(handles.FieldName,'Value');%indices of previously selected variables
2328        for ilist=1:numel(ind_var)
2329            if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2330                FieldList={};% previous choice not consistent with new input field
2331                set(handles.FieldName,'Value',1)
2332                break
2333            end
2334        end
2335        if ~isempty(FieldList)
2336            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2337                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2338                FieldList={};
2339                set(handles.Coord_x,'String','')
2340                set(handles.Coord_y,'String','')
2341            end
2342            Coord_z=get(handles.Coord_z,'String');
2343            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2344                FieldList={};
2345                set(handles.Coord_z,'String','')
2346            end
2347        end
2348        set(handles_coord,'Visible','on')
2349        FieldList=[FieldList;{'get_field...'}];
2350        if FieldNameRequest_1 && numel(iview_netcdf)>=2
2351            set(handles.FieldName_1,'Visible','on')
2352            if CheckList_1==0        % not civ input made
2353                ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName;
2354                ind_var=get(handles.FieldName,'Value');%indices of previously selected variables
2355                for ilist=1:numel(ind_var)
2356                    if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2357                        FieldList_1={};% previous choice not consistent with new input field
2358                        set(handles.FieldName_1,'Value',1)
2359                        break
2360                    end
2361                end
2362                warn_coord=0;
2363                if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2364                        isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2365                    warn_coord=1;
2366                end
2367                if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2368                    FieldList_1={};
2369                    warn_coord=1;
2370                end
2371                if warn_coord
2372                    msgbox_uvmat('WARNING','coordiante names do not exist in the second netcdf input file')
2373                end
2374                set(handles.FieldName,'String',[FieldList;{'get_field...'}])
2375                set(handles.FieldName_1,'Visible','on')
2376                set(handles.FieldName_1,'Value',1)
2377                set(handles.FieldName_1,'String',FieldList_1)
2378            end
2379        else
2380            set(handles.FieldName_1,'Visible','off')
2381        end
[940]2382    else
2383        set(handles.FieldName,'Visible','off')
2384    end
[867]2385    set(handles.FieldName,'String',FieldList)
2386else
2387    set(handles.InputFields,'Visible','off')
2388end
2389
[904]2390%% Introduce visibility of file overwrite option
2391if isfield(ParamOut,'CheckOverwriteVisible')&& strcmp(ParamOut.CheckOverwriteVisible,'on')
2392    set(handles.CheckOverwrite,'Visible','on')
2393else
2394    set(handles.CheckOverwrite,'Visible','off')
2395end
[867]2396
2397%% Check whether alphabetical sorting of input Subdir is allowed by the Action fct  (for multiples series entries)
2398if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Param.InputTable,1)>1
2399    [tild,iview]=sort(InputTable(:,2)); %subdirectories sorted in alphabetical order
2400    set(handles.InputTable,'Data',InputTable(iview,:));
2401    MinIndex_i=get(handles.MinIndex_i,'Data');
2402    MinIndex_j=get(handles.MinIndex_j,'Data');
2403    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2404    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2405    set(handles.MinIndex_i,'Data',MinIndex_i(iview,:));
2406    set(handles.MinIndex_j,'Data',MinIndex_j(iview,:));
2407    set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:));
2408    set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));
2409    TimeTable=get(handles.TimeTable,'Data');
2410    set(handles.TimeTable,'Data',TimeTable(iview,:));
2411    PairString=get(handles.PairString,'Data');
2412    set(handles.PairString,'Data',PairString(iview,:));
2413end
2414
2415%% Impose the whole input file index range if requested
2416if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on')
2417    MinIndex_i=get(handles.MinIndex_i,'Data');
2418    MinIndex_j=get(handles.MinIndex_j,'Data');
2419    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2420    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2421    set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line)
2422    set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line)
2423    set(handles.num_incr_i,'String','1')
2424    set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line)
2425    set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line)
2426    set(handles.num_incr_j,'String','1')
2427else  % check index ranges
2428    first_i=1;last_i=1;first_j=1;last_j=1;
2429    if isfield(Param.IndexRange,'first_i')
2430        first_i=Param.IndexRange.first_i;
2431        last_i=Param.IndexRange.last_i;
2432    end
2433    if isfield(Param.IndexRange,'first_j')
2434        first_j=Param.IndexRange.first_j;
2435        last_j=Param.IndexRange.last_j;
2436    end
2437    if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
2438            set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
2439end
2440
2441%% enable or desable j index visibility
2442status_j='on';%default
2443if isfield(ParamOut,'Desable_j_index')&&isequal(ParamOut.Desable_j_index,'on')
2444    status_j='off';
2445end
2446if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices
2447    status_j='off'; % no j index needed
2448elseif strcmp(get(handles.PairString,'Visible'),'on')
2449    check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j'));%=0 for burst case, 1 otherwise
2450    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
2451        status_j='off'; % no j index needed for bust case
2452    end
2453end
2454enable_j(handles,status_j) % no j index needed
2455
2456
2457%% NbSlice visibility
[897]2458%NbSliceVisible='off';%default
2459if isfield(ParamOut,'NbSlice') && (strcmp(ParamOut.NbSlice,'on')||isnumeric(ParamOut.NbSlice))
2460    set(handles.num_NbSlice,'Visible','on')
2461    set(handles.NbSlice_title,'Visible','on')
[867]2462else
[897]2463    set(handles.num_NbSlice,'Visible','off')
2464    set(handles.NbSlice_title,'Visible','off')
2465    %     set(handles.num_NbProcess,'String',get(handles.num_NbSlice,'String'))% the nbre of processes is imposed as the nbre of slices
2466    % else
2467    %     set(handles.num_NbProcess,'String','')% free nbre of processes
[867]2468end
[897]2469if isnumeric(ParamOut.NbSlice)
2470    set(handles.num_NbSlice,'String',num2str(ParamOut.NbSlice))
2471    set(handles.num_NbSlice,'Enable','off'); % NbSlice set by the activation of the Action function
2472else
2473    set(handles.num_NbSlice,'Enable','on'); % NbSlice can be modified on the GUI series
2474end
2475% set(handles.num_NbSlice,'Visible',NbSliceVisible)
2476% set(handles.NbSlice_title,'Visible',NbSliceVisible)
[867]2477
2478
2479
2480%% Visibility of FieldTransform menu
2481FieldTransformVisible='off';  %hidden by default
2482if isfield(ParamOut,'FieldTransform')
2483    FieldTransformVisible=ParamOut.FieldTransform; 
2484    TransformName_Callback([],[], handles)
2485end
2486set(handles.FieldTransform,'Visible',FieldTransformVisible)
2487if isfield(ParamOut,'TransformPath')
2488    set(handles.ActionExt,'UserData',ParamOut.TransformPath)
2489else
2490    set(handles.ActionExt,'UserData',[])
2491end
2492
2493%% Visibility of projection object
2494ProjObjectVisible='off';  %hidden by default
2495if isfield(ParamOut,'ProjObject')
2496    ProjObjectVisible=ParamOut.ProjObject;
2497end
2498set(handles.CheckObject,'Visible',ProjObjectVisible)
2499if ~get(handles.CheckObject,'Value')
2500    ProjObjectVisible='off';
2501end
2502set(handles.ProjObject,'Visible',ProjObjectVisible)
2503set(handles.DeleteObject,'Visible',ProjObjectVisible)
2504set(handles.ViewObject,'Visible',ProjObjectVisible)
2505set(handles.EditObject,'Visible',ProjObjectVisible)
2506
2507%% Visibility of mask input
2508MaskVisible='off';  %hidden by default
2509if isfield(ParamOut,'Mask')
2510    MaskVisible=ParamOut.Mask;
2511end
2512set(handles.CheckMask,'Visible',MaskVisible);
2513
2514%% definition of the directory containing the output files
2515if  ~(isfield(SeriesData,'ActionName') && strcmp(ActionName,SeriesData.ActionName))
2516    OutputDirExt='.series'; %default
2517    if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
2518        OutputDirExt=ParamOut.OutputDirExt;
2519    end
2520    set(handles.OutputDirExt,'String',OutputDirExt)
2521end
2522OutputDirVisible='off';
2523OutputSubDirMode='auto';%default
2524SubDirOut='';
2525if isfield(ParamOut,'OutputSubDirMode')
2526    OutputSubDirMode=ParamOut.OutputSubDirMode;
2527end
2528switch OutputSubDirMode
2529    case 'auto';%default
2530        OutputDirVisible='on';
2531        SubDir=InputTable(1:end,2); %set of subdirectories
2532        SubDirOut=SubDir{1};
2533        if numel(SubDir)>1
2534            for ilist=2:numel(SubDir)
2535                SubDirOut=[SubDirOut '-' regexprep(SubDir{ilist},'^/','')];
2536            end
2537        end
2538    case 'one'
2539        OutputDirVisible='on';
2540        SubDirOut=InputTable{1,2}; %use the first subdir name (+OutputDirExt) as output  subdirectory
2541    case 'two'
2542        OutputDirVisible='on';   
2543        SubDir=InputTable(1:2,2); %set of subdirectories
2544        SubDirOut=SubDir{1};
2545        if numel(SubDir)>1
2546                SubDirOut=[SubDirOut '-' regexprep(SubDir{2},'^/','')];
2547        end
2548    case 'last'
2549        OutputDirVisible='on';
2550        SubDirOut=InputTable{end,2}; %use the last subdir name (+OutputDirExt) as output  subdirectory
2551end
2552set(handles.OutputSubDir,'String',SubDirOut)
[883]2553set(handles.OutputSubDir,'BackgroundColor',[1 1 1])% set edit box to white color to indicate refreshment
[867]2554set(handles.OutputDirExt,'Visible',OutputDirVisible)
2555set(handles.OutputSubDir,'Visible',OutputDirVisible)
[904]2556%set(handles.CheckOverwrite,'Visible',OutputDirVisible)
[867]2557set(handles.OutputDir_title,'Visible',OutputDirVisible)
2558SeriesData.ActionName=ActionName;%record ActionName for next use
2559
2560
2561%% visibility of the run mode (local or background or cluster)
2562if strcmp(OutputSubDirMode,'none')
2563    RunModeVisible='off';% only local mode available if no output file is produced
2564else
2565    RunModeVisible='on';
2566end
2567set(handles.RunMode,'Visible',RunModeVisible)
2568set(handles.ActionExt,'Visible',RunModeVisible)
2569set(handles.RunMode_title,'Visible',RunModeVisible)
2570set(handles.ActionExt_title,'Visible',RunModeVisible)
2571
2572
2573%% Expected nbre of output files
2574if isfield(ParamOut,'OutputFileMode')
2575    StatusData.OutputFileMode=ParamOut.OutputFileMode;
2576    set(handles.status,'UserData',StatusData)
2577end
2578
2579%% definition of an additional parameter set, determined by an ancillary GUI
2580if isfield(ParamOut,'ActionInput')
2581    set(handles.ActionInput,'Visible','on')
2582    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
2583    SeriesData.ActionInput=ParamOut.ActionInput;
2584else
2585    set(handles.ActionInput,'Visible','off')
2586    if isfield(SeriesData,'ActionInput')
2587        SeriesData=rmfield(SeriesData,'ActionInput');
2588    end
2589end
2590set(handles.series,'UserData',SeriesData)
2591set(handles.ActionName,'BackgroundColor',[1 1 1])
2592
2593%------------------------------------------------------------------------
2594% --- Executes on selection change in FieldName.
2595function FieldName_Callback(hObject, eventdata, handles)
2596%------------------------------------------------------------------------
2597field_str=get(handles.FieldName,'String');
2598field_index=get(handles.FieldName,'Value');
2599field=field_str{field_index(1)};
2600if isequal(field,'get_field...')
2601    SeriesData=get(handles.series,'UserData');
2602    % input line for which the field choice is relevant
2603    iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'}));% all nc files, icluding civ
2604    hget_field=findobj(allchild(0),'name','get_field');
2605    if ~isempty(hget_field)
2606        delete(hget_field)%delete opened versions of get_field
2607    end
2608    Param=read_GUI(handles.series);
2609    InputTable=Param.InputTable(iview,:);
2610    % check the existence of the first file in the series
2611    first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1;%default setting for index j
2612    if isfield(Param.IndexRange,'first_j');% if index j is used     
2613        first_j=Param.IndexRange.first_j;
2614        last_j=Param.IndexRange.last_j;
2615        MinIndex_j=Param.IndexRange.MinIndex_j(iview);
2616        MaxIndex_j=Param.IndexRange.MaxIndex_j(iview);
2617    end
2618    PairString='';
2619    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end
2620    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2621    LineIndex=iview(1);
2622    if numel(iview)>1     
2623        answer=msgbox_uvmat('INPUT_TXT',['select the line of the input table:' num2str(iview)] ,num2str(iview(1)));
2624        LineIndex=str2num(answer);
2625%         InputLine=str2num(get(handles.InputLine,'String'));
2626%         if ismember(InputLine,iview)
2627%             LineIndex=InputLine;
2628%         end
2629    end
2630    FirstFileName=fullfile_uvmat(InputTable{LineIndex,1},InputTable{LineIndex,2},InputTable{LineIndex,3},...
2631        InputTable{LineIndex,5},InputTable{LineIndex,4},i1,i2,j1,j2);
2632    if exist(FirstFileName,'file')
2633        ParamIn.Title='get_field: pick input variables and coordinates for series processing';
2634        ParamIn.SeriesInput=1;
2635        GetFieldData=get_field(FirstFileName,ParamIn);
2636        FieldList={};
[876]2637        if isfield(GetFieldData,'FieldOption')% if a field has been selected
[867]2638        switch GetFieldData.FieldOption
2639            case 'vectors'
2640                UName=GetFieldData.PanelVectors.vector_x;
2641                VName=GetFieldData.PanelVectors.vector_y;
2642                YName={GetFieldData.Coordinates.Coord_y};
2643                FieldList={['vec(' UName ',' VName ')'];...
2644                    ['norm(' UName ',' VName ')'];...
2645                    UName;VName};
2646            case {'scalar'}
2647                FieldList=GetFieldData.PanelScalar.scalar;
2648                YName={GetFieldData.Coordinates.Coord_y};
2649                if ischar(FieldList)
2650                    FieldList={FieldList};
2651                end
2652            case 'civdata...'
2653                FieldList=[set_field_list('U','V') ;{'C'}];
2654                set(handles.FieldName,'Value',1) % set menu to 'velocity
2655                XName='X';
2656                YName='y';
2657        end
2658        set(handles.FieldName,'Value',1)
2659        set(handles.FieldName,'String',[FieldList; {'get_field...'}]);
2660        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2661           if ~isempty(regexp(FieldList{1},'^vec'))
2662                set(handles.FieldName,'Value',1)
2663           else
2664                set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
2665           end
2666            XName=GetFieldData.Coordinates.Coord_x;
2667            YName=GetFieldData.Coordinates.Coord_y;
2668            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2669            % get the time info                     
2670            TimeTable=get(handles.TimeTable,'Data');
2671            switch TimeNameStr
2672                case 'file index'
2673                    TimeName='';
2674                case 'attribute'
2675                    TimeName=['att:' GetFieldData.Time.TimeName];
2676                    % update the time table
2677                    TimeTable{LineIndex,2}=get_time(Param.IndexRange.MinIndex_i(LineIndex),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Min time     
2678                    TimeTable{LineIndex,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % first time             
2679                    TimeTable{LineIndex,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % last time                     
2680                    TimeTable{LineIndex,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Max time
2681                case 'variable'
2682                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2683                    set(handles.NomType,'String','*')
2684                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2685                    set(handles.FileIndex,'String','')
2686                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2687                case 'matrix_index'
2688                    TimeName=['dim:' GetFieldData.Time.TimeName];
2689                    set(handles.NomType,'String','*')
2690                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2691                    set(handles.FileIndex,'String','')
2692                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2693            end
2694            TimeTable{LineIndex,1}=TimeName;
2695            set(handles.TimeTable,'Data',TimeTable);
2696        end
2697        set(handles.Coord_x,'String',XName)
2698        set(handles.Coord_y,'String',YName)
2699        set(handles.Coord_x,'Visible','on')
2700        set(handles.Coord_y,'Visible','on')
[876]2701        end
[867]2702    else
2703        msgbox_uvmat('ERROR',[FirstFileName ' does not exist'])
2704    end
2705end
2706
2707function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
2708[i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
2709FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2);
2710Data=nc2struct(FileName,[]);
2711TimeValue=[];
2712DtValue=[];
2713if isequal(FileInfo.FileType,'civdata')
2714    if ismember(TimeName,{'civ1','filter1'})
2715        TimeValue=Data.Civ1_Time;
2716        DtValue=Data.Civ1_Dt;
2717    else
2718        TimeValue=Data.Civ2_Time;
2719        DtValue=Data.Civ2_Dt;
2720    end
2721else
2722    if ~isempty(TimeName)&& isfield(Data,TimeName)
2723        TimeValue=Data.(TimeName);
2724    end
2725    if exist('DtName','var') && isfield(Data,DtName)
2726        DtValue=Data.(DtName);
2727    end
2728end
2729
2730%------------------------------------------------------------------------
2731% --- Executes on selection change in FieldName_1.
2732function FieldName_1_Callback(hObject, eventdata, handles)
2733%------------------------------------------------------------------------
2734field_str=get(handles.FieldName_1,'String');
2735field_index=get(handles.FieldName_1,'Value');
2736field=field_str{field_index(1)};
2737if isequal(field,'get_field...')
2738    hget_field=findobj(allchild(0),'name','get_field');
2739    if ~isempty(hget_field)
2740        delete(hget_field)%delete opened versions of get_field
2741    end
2742    Param=read_GUI(handles.series);
2743    Param.InputTable=Param.InputTable(1,:);
2744    % check the existence of the first file in the series
2745    first_j=[];
2746    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
2747    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
2748    PairString='';
2749    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
2750    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2751    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
2752        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
2753    if exist(FirstFileName,'file')
2754        ParamIn.SeriesInput=1;
2755        GetFieldData=get_field(FirstFileName,ParamIn);
2756        FieldList={};
2757        switch GetFieldData.FieldOption
2758            case 'vectors'
2759                UName=GetFieldData.PanelVectors.vector_x;
2760                VName=GetFieldData.PanelVectors.vector_y;
2761                FieldList={['vec(' UName ',' VName ')'];...
2762                    ['norm(' UName ',' VName ')'];...
2763                    UName;VName};
2764            case {'scalar','pick variables'}
2765                FieldList=GetFieldData.PanelScalar.scalar;
2766                if ischar(FieldList)
2767                    FieldList={FieldList};
2768                end
2769            case '1D plot'
2770
2771            case 'civdata...'
2772                FieldList=set_field_list('U','V','C');
2773                set(handles.FieldName,'Value',2) % set menu to 'velocity
2774        end
2775        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2776            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2777            switch TimeNameStr
2778                case 'file index'
2779                    set(handles.TimeName,'String','');
2780                case 'attribute'
2781                    set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
2782                case 'variable'
2783                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2784                    set(handles.NomType,'String','*')
2785                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2786                    set(handles.FileIndex,'String','')
2787                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2788                case 'matrix_index'
2789                    set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]);
2790                    set(handles.NomType,'String','*')
2791                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2792                    set(handles.FileIndex,'String','')
2793                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2794            end
2795        end
2796        set(handles.FieldName_1,'Value',1)
2797        set(handles.FieldName_1,'String',[FieldList; {'get_field...'}]);
2798    end
2799end   
2800
2801
2802%%%%%%%%%%%%%
2803function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
2804indsel=ind_i;
2805indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
2806indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds
2807if ~isempty(indiff)
2808    indiff2=diff(indiff);
2809    indiffp=[indiff2 1];
2810    indiffm=[1 indiff2];
2811    ind_multi_m=find((indiff==0)&(indiffm<0))-1;%indices of first members of multiplets
2812    ind_multi_p=find((indiff==0)&(indiffp>0));%indices of last members of multiplets
2813    %for each multiplet, select the most recent file
2814    ind_remove=[];
2815    for i=1:length(ind_multi_m)
2816        ind_pairs=ind_multi_m(i):ind_multi_p(i);
2817        for imulti=1:length(ind_pairs)
2818            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date);%dates of creation
2819        end
2820        [datenew,indsort2]=sort(datepair); %sort the multiplet by creation date
2821        ind_s=indsort2(1:end-1);%
2822        ind_remove=[ind_remove ind_pairs(ind_s)];%remove these indices, leave the last one
2823    end
2824end
2825
2826%------------------------------------------------------------------------
2827% --- determine the list of index pairstring of processing file
2828function [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)
2829%------------------------------------------------------------------------
2830num_i1=num_i;% set of first image numbers by default
2831num_i2=num_i;
2832num_j1=num_j;
2833num_j2=num_j;
2834num_i_out=num_i;
2835num_j_out=num_j;
2836% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
2837if isequal(mode,'series(Di)')
2838    num_i1_line=num_i+ind_shift(3);% set of first image numbers
2839    num_i2_line=num_i+ind_shift(4);
2840    % adjust the first and last field number
2841        indsel=find(num_i1_line >= 1);
2842    num_i_out=num_i(indsel);
2843    num_i1_line=num_i1_line(indsel);
2844    num_i2_line=num_i2_line(indsel);
2845    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
2846    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
2847    [xx,num_i1]=meshgrid(num_j,num_i1_line);
2848    [xx,num_i2]=meshgrid(num_j,num_i2_line);
2849elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
2850    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
2851        num_j1=ind_shift(1)*ones(size(num_i));
2852        num_j2=ind_shift(2)*ones(size(num_i));
2853    else
2854        num_j1_col=num_j+ind_shift(1);% set of first image numbers
2855        num_j2_col=num_j+ind_shift(2);
2856        % adjust the first field number
2857        indsel=find((num_j1_col >= 1));   
2858        num_j_out=num_j(indsel);
2859        num_j1_col=num_j1_col(indsel);
2860        num_j2_col=num_j2_col(indsel);
2861        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
2862        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
2863    end   
2864end
2865
2866%------------------------------------------------------------------------
2867% --- Executes on button press in CheckObject.
2868function CheckObject_Callback(hObject, eventdata, handles)
2869%------------------------------------------------------------------------
2870hset_object=findobj(allchild(0),'tag','set_object');%find the set_object interface handle
2871if get(handles.CheckObject,'Value')
2872    SeriesData=get(handles.series,'UserData');
2873    if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject)
2874        set(handles.ViewObject,'Value',1)
2875        ViewObject_Callback(hObject, eventdata, handles)
2876    else
2877        if ishandle(hset_object)
2878            uistack(hset_object,'top')% show the GUI set_object if opened
2879        else
2880            %get the object file
2881            InputTable=get(handles.InputTable,'Data');
2882            defaultname=InputTable{1,1};
2883            if isempty(defaultname)
2884                defaultname={''};
2885            end
2886            fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml');
2887            if isempty(fileinput)% exit if no object file is selected
2888                set(handles.CheckObject,'Value',0)
2889                return
2890            end
2891            %read the file
2892            data=xml2struct(fileinput);
2893            if ~isfield(data,'Type')
2894                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
2895                set(handles.CheckObject,'Value',0)
2896                return
2897            end
2898            if ~isfield(data,'ProjMode')
2899                data.ProjMode='none';
2900            end
2901            hset_object=set_object(data);% call the set_object interface
2902            set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat
2903        end
2904        ProjObject=read_GUI(hset_object);
2905        set(handles.ProjObject,'String',ProjObject.Name);%display the object name
2906        SeriesData=get(handles.series,'UserData');
2907        SeriesData.ProjObject=ProjObject;
2908        set(handles.series,'UserData',SeriesData);
2909    end
2910    set(handles.EditObject,'Visible','on');
2911    set(handles.DeleteObject,'Visible','on');
2912    set(handles.ViewObject,'Visible','on');
2913    set(handles.ProjObject,'Visible','on');
2914else
2915    set(handles.EditObject,'Visible','off');
2916    set(handles.DeleteObject,'Visible','off');
2917    set(handles.ViewObject,'Visible','off');
2918    if ~ishandle(hset_object)
2919        set(handles.ViewObject,'Value',0);
2920    end
2921    set(handles.ProjObject,'Visible','off');
2922end
2923
2924%------------------------------------------------------------------------
2925% --- Executes on button press in ViewObject.
2926%------------------------------------------------------------------------
2927function ViewObject_Callback(hObject, eventdata, handles)
2928
2929UserData=get(handles.series,'UserData');
2930hset_object=findobj(allchild(0),'Tag','set_object');
2931if ~isempty(hset_object)
2932    delete(hset_object)% refresh set_object if already opened
2933end
2934hset_object=set_object(UserData.ProjObject);
2935set(hset_object,'Name','view_object_series')
2936
2937
2938%------------------------------------------------------------------------
2939% --- Executes on button press in EditObject.
2940function EditObject_Callback(hObject, eventdata, handles)
2941%------------------------------------------------------------------------
2942if get(handles.EditObject,'Value')
2943    set(handles.ViewObject,'Value',0)
2944        UserData=get(handles.series,'UserData');
2945    hset_object=set_object(UserData.ProjObject);
2946    set(hset_object,'Name','edit_object_series')
2947    set(get(hset_object,'Children'),'Enable','on')
2948else
2949    hset_object=findobj(allchild(0),'Tag','set_object');
2950    if ~isempty(hset_object)
2951        set(get(hset_object,'Children'),'Enable','off')
2952    end
2953end
2954
2955%------------------------------------------------------------------------
2956% --- Executes on button press in DeleteObject.
2957function DeleteObject_Callback(hObject, eventdata, handles)
2958%------------------------------------------------------------------------
2959SeriesData=get(handles.series,'UserData');
2960SeriesData.ProjObject=[];
2961set(handles.series,'UserData',SeriesData)
2962set(handles.ProjObject,'String','')
2963set(handles.ProjObject,'Visible','off')
2964set(handles.CheckObject,'Value',0)
2965set(handles.ViewObject,'Visible','off')
2966set(handles.EditObject,'Visible','off')
2967hset_object=findobj(allchild(0),'name','set_object_series');
2968if ~isempty(hset_object)
2969    delete(hset_object)
2970end
2971set(handles.DeleteObject,'Visible','off')
2972
2973%------------------------------------------------------------------------
2974% --- Executed when CheckMask is activated
2975%------------------------------------------------------------------------
2976function CheckMask_Callback(hObject, eventdata, handles)
2977
2978if get(handles.CheckMask,'Value')
2979    InputTable=get(handles.InputTable,'Data');
2980    nbview=size(InputTable,1);
2981    MaskTable=cell(nbview,1);%default
2982    ListMask=cell(nbview,1);%default
2983    MaskData=get(handles.MaskTable,'Data');
2984    MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1);%complement if undefined lines
2985    for iview=1:nbview
2986        ListMask{iview,1}=num2str(iview);
2987        RootPath=InputTable{iview,1};
2988        if ~isempty(RootPath)
2989            if isempty(MaskData{iview})
2990                SubDir=InputTable{iview,2};
2991                MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']);%take the root part of SubDir, before the first dot '.'
2992                if exist(MaskPath,'dir')
2993                    ListStruct=dir(MaskPath);%look for a mask file
2994                    ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray
2995                    check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files
2996                    ListFiles=ListCells(1,:);%list of file and dri names
2997                    ListFiles=ListFiles(~check_dir);%list of file names (excluding dir)
2998                    mdetect=0;
2999                    if ~isempty(ListFiles)
3000                        for ifile=1:numel(ListFiles)
3001                            [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0);
3002                            if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series)
3003                                mdetect=1;
3004                                MaskName=ListFiles{ifile};
3005                            end
3006                            if ~strcmp(MaskFile{ifile},MaskFile{1})
3007                                mdetect=0;% cancel detection test in case of multiple masks, use the brower for selection
3008                                break
3009                            end
3010                        end
3011                    end
3012                    if mdetect==1
3013                        MaskName=fullfile(MaskPath,'mask_1.png');
3014                    else
3015                        MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image');
3016                    end
3017                else
3018                    MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3019                end
3020                MaskTable{iview,1}=MaskName ;
3021                ListMask{iview,1}=num2str(iview);
3022            end
3023        end
3024    end
3025    set(handles.MaskTable,'Data',MaskTable)
3026    set(handles.MaskTable,'Visible','on')
3027    set(handles.MaskBrowse,'Visible','on')
3028    set(handles.ListMask,'Visible','on')
3029    set(handles.ListMask,'String',ListMask)
3030    set(handles.ListMask,'Value',1)
3031else
3032    set(handles.MaskTable,'Visible','off')
3033    set(handles.MaskBrowse,'Visible','off')
3034    set(handles.ListMask,'Visible','off')
3035end
3036
3037%------------------------------------------------------------------------
3038% --- Executes on button press in MaskBrowse.
3039%------------------------------------------------------------------------
3040function MaskBrowse_Callback(hObject, eventdata, handles)
3041
3042InputTable=get(handles.InputTable,'Data');
3043iview=get(handles.ListMask,'Value');
3044RootPath=InputTable{iview,1};
3045MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3046if ~isempty(MaskName)
3047    MaskTable=get(handles.MaskTable,'Data');
3048    MaskTable{iview,1}=MaskName ;
3049    set(handles.MaskTable,'Data',MaskTable)
3050end
3051
3052%------------------------------------------------------------------------
3053% --- Executes when selected cell(s) is changed in MaskTable.
3054%------------------------------------------------------------------------
3055function MaskTable_CellSelectionCallback(hObject, eventdata, handles)
3056
3057if numel(eventdata.Indices)>=1
3058set(handles.ListMask,'Value',eventdata.Indices(1))
3059end
3060
3061%-------------------------------------------------------------------
3062function MenuHelp_Callback(hObject, eventdata, handles)
3063%-------------------------------------------------------------------
3064
3065
3066% path_to_uvmat=which ('uvmat');% check the path of uvmat
3067% pathelp=fileparts(path_to_uvmat);
3068% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
3069% 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')
3070% else
3071%     addpath (fullfile(pathelp,'uvmat_doc'))
3072%     web([helpfile '#series'])
3073% end
3074
3075%-------------------------------------------------------------------
3076% --- Executes on selection change in TransformName.
3077function TransformName_Callback(hObject, eventdata, handles)
3078%----------------------------------------------------------------------
3079TransformList=get(handles.TransformName,'String');
3080TransformIndex=get(handles.TransformName,'Value');
3081TransformName=TransformList{TransformIndex};
3082TransformPathList=get(handles.TransformName,'UserData');
3083nb_builtin_transform=4;
3084if isequal(TransformName,'more...');     
3085    FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
3086    if isempty(FileName)
3087        return     %browser closed without choice
3088    end
3089    [TransformPath,TransformName,TransformExt]=fileparts(FileName);% removes extension .m
3090    if ~strcmp(TransformExt,'.m')
3091        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3092        return
3093    end
3094     % insert the choice in the menu
3095    TransformIndex=find(strcmp(TransformName,TransformList),1);% look for the selected function in the menu Action
3096    if isempty(TransformIndex)%the input string does not exist in the menu
3097        TransformIndex= length(TransformList);
3098        TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)];% the selected function is appended in the menu, before the last item 'more...'
3099        set(handles.TransformName,'String',TransformList)
3100        TransformPathList=[TransformPathList;{TransformPath}];
3101    else% the input function already exist, we update its path (possibly new)
3102        TransformPathList{TransformIndex}=TransformPath;%
3103        set(handles.TransformName,'Value',TransformIndex)
3104    end
3105   % save the new menu in the personal file 'uvmat_perso.mat'
3106   dir_perso=prefdir;%personal Matalb directory
3107   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3108   if exist(profil_perso,'file')
3109       for ilist=nb_builtin_transform+1:numel(TransformPathList)
3110           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
3111           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
3112       end
3113       TransformPathListUser=TransformPathListUser';
3114       TransformListUser=TransformListUser';
3115       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); %store the root name for future opening of uvmat
3116   end
3117end
3118
3119%display the current function path
3120set(handles.TransformPath,'String',TransformPathList{TransformIndex}); %show the path to the senlected function
3121set(handles.TransformName,'UserData',TransformPathList);
3122
[883]3123%% create the function handle of the selected fct
3124if ~isempty(TransformName)
[897]3125    if ~exist(TransformPathList{TransformIndex},'dir')
3126        msgbox_uvmat('ERROR',['The prescribed transform function path ' TransformPathList{TransformIndex} ' does not exist']);
3127        return
3128    end
[883]3129    current_dir=pwd;%current working dir
3130    cd(TransformPathList{TransformIndex})
3131    transform_handle=str2func(TransformName);
3132    cd(current_dir)
3133    Field.Action.RUN=0;% indicate that the transform fct is called only to get input param
3134    DataOut=feval(transform_handle,Field,[]);% execute the transform fct to get the required conditions
3135    if isfield(DataOut,'TransformInput')%  used to add transform parameters at selection of the transform fct
3136        SeriesData=get(handles.series,'UserData');
3137        SeriesData.TransformInput=DataOut.TransformInput;
3138        set(handles.series,'UserData',SeriesData)
3139    end
3140end
3141
[867]3142%------------------------------------------------------------------------
3143% --- fct activated by the upper bar menu ExportConfig
3144%------------------------------------------------------------------------
3145function MenuDisplayConfig_Callback(hObject, eventdata, handles)
3146
3147global Param
3148Param=read_GUI_series(handles);
3149evalin('base','global Param')%make CurData global in the workspace
3150display('current series config :')
3151evalin('base','Param') %display CurData in the workspace
3152commandwindow; %brings the Matlab command window to the front
3153
3154%------------------------------------------------------------------------
3155% --- fct activated by the upper bar menu InportConfig: import
3156%     menu settings from an xml file (stored in /0_XML for each run)
3157%------------------------------------------------------------------------
3158function MenuImportConfig_Callback(hObject, eventdata, handles)
3159
3160%% use a browser to choose the xml file containing the processing config
3161InputTable=get(handles.InputTable,'Data');
3162oldfile=InputTable{1,1};%current path in InputTable
3163if isempty(oldfile)
3164    % use a file name stored in prefdir
3165    dir_perso=prefdir;
3166    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3167    if exist(profil_perso,'file')
3168        h=load (profil_perso);
3169        if isfield(h,'RootPath') && ischar(h.RootPath)
3170            oldfile=h.RootPath;
3171        end
3172    end
3173end
3174filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml');% get the xml file containing processing parameters
3175if isempty(filexml), return, end % quit function if an xml file has not been opened
3176
3177%% fill the GUI series with the content of the xml file
3178Param=xml2struct(filexml);% read the input xml file as a Matlab structure
3179
3180% ask to stop current Action if button RUN is in action (another process is already running)
3181if isequal(get(handles.RUN,'Value'),1)
3182    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
3183    if strcmp(answer,'Yes')
3184        STOP_Callback(hObject, eventdata, handles)
3185    else
3186        return
3187    end
3188end
3189Param.Action.RUN=0; %desactivate the input RUN=1
3190
3191fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
3192SeriesData=get(handles.series,'UserData');
3193if isfield(Param,'InputFields')
3194    ListField=Param.InputFields.FieldName;
3195    if ischar(ListField),ListField={ListField}; end
3196    set(handles.FieldName,'String',[ListField;{'get-field...'}])
3197     set(handles.FieldName,'Value',1:numel(ListField))
3198     set(handles.FieldName,'Visible','on')
3199end       
3200if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
3201    set(handles.ActionInput,'Visible','on')
3202    set(handles.ActionInput,'Value',0)
3203    Param.ActionInput.ConfigSource=filexml;% record the source of config for future info
3204    SeriesData.ActionInput=Param.ActionInput;
3205end
[883]3206if isfield(Param,'TransformInput')%  introduce  parameters specific to a transform fct
3207    SeriesData.TransformInput=Param.TransformInput;
3208end
[867]3209if isfield(Param,'ProjObject') %introduce projection object if relevant
3210    SeriesData.ProjObject=Param.ProjObject;
3211end
3212set(handles.series,'UserData',SeriesData)
3213if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
3214    set(handles.ProjObject,'String',Param.ProjObject.Name)
3215    set(handles.ViewObject,'Visible','on')
3216    set(handles.EditObject,'Visible','on')
3217    set(handles.DeleteObject,'Visible','on')
3218else     
3219    set(handles.ProjObject,'String','')
3220    set(handles.ProjObject,'Visible','off')
3221    set(handles.ViewObject,'Visible','off')
3222    set(handles.EditObject,'Visible','off')
3223    set(handles.DeleteObject,'Visible','off')     
3224end     
3225set(handles.REFRESH,'BackgroundColor',[1 0 1]); %paint REFRESH button in magenta to indicate that it should be activated
3226
3227
3228%------------------------------------------------------------------------
3229% --- Executes when the GUI series is resized.
3230%------------------------------------------------------------------------
3231function series_ResizeFcn(hObject, eventdata, handles)
3232
3233%% input table
3234set(handles.InputTable,'Unit','pixel')
3235Pos=get(handles.InputTable,'Position');
3236set(handles.InputTable,'Unit','normalized')
3237ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
3238ColumnWidth=num2cell(ColumnWidth);
3239set(handles.InputTable,'ColumnWidth',ColumnWidth)
3240
3241%% MinIndex_j and MaxIndex_i
3242unit=get(handles.MinIndex_i,'Unit');
3243set(handles.MinIndex_i,'Unit','pixel')
3244Pos=get(handles.MinIndex_i,'Position');
3245set(handles.MinIndex_i,'Unit',unit)
3246set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18})
3247set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18})
3248set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18})
3249set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18})
3250
3251%% TimeTable
3252set(handles.TimeTable,'Unit','pixel')
3253Pos=get(handles.TimeTable,'Position');
3254set(handles.TimeTable,'Unit','normalized')
3255% ColumnWidth=get(handles.TimeTable,'ColumnWidth');
3256ColumnWidth=num2cell(floor([0.2 0.2 0.2 0.2 0.2]*(Pos(3)-20)));
3257set(handles.TimeTable,'ColumnWidth',ColumnWidth)
3258
3259
3260%% PairString
3261set(handles.PairString,'Unit','pixel')
3262Pos=get(handles.PairString,'Position');
3263set(handles.PairString,'Unit','normalized')
3264set(handles.PairString,'ColumnWidth',{Pos(3)-5})
3265
3266%% MaskTable
3267set(handles.MaskTable,'Unit','pixel')
3268Pos=get(handles.MaskTable,'Position');
3269set(handles.MaskTable,'Unit','normalized')
3270set(handles.MaskTable,'ColumnWidth',{Pos(3)-5})
3271
3272%------------------------------------------------------------------------
3273% --- Executes on button press in status.
3274%------------------------------------------------------------------------
3275function status_Callback(hObject, eventdata, handles)
3276
3277if get(handles.status,'Value')
3278    set(handles.status,'BackgroundColor',[1 1 0])
3279    drawnow
3280    Param=read_GUI(handles.series);
3281    RootPath=Param.InputTable{1,1};
3282    if ~isfield(Param,'OutputSubDir')   
3283        msgbox_uvmat('ERROR','no standard sub-directory definition for output files, use a browser to check the output')
3284        set(handles.status,'BackgroundColor',[0 1 0])
3285        return
3286    end
3287    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
3288    OutputDir=fullfile(RootPath,OutputSubDir);
3289    if exist(OutputDir,'dir')
3290        uigetfile_uvmat('status_display',OutputDir)
3291    else
3292        msgbox_uvmat('ERROR','output folder not created yet: calculation did not start')
3293        set(handles.status,'BackgroundColor',[0 1 0])
3294    end
3295else
3296    %% delete current display fig if selection is off
3297    set(handles.status,'BackgroundColor',[0 1 0])
3298    hfig=findobj(allchild(0),'name','status_display');
3299    if ~isempty(hfig)
3300        delete(hfig)
3301    end
3302    return
3303end
3304
3305
3306%------------------------------------------------------------------------   
3307% launched by selecting a file on the list
3308%------------------------------------------------------------------------
3309function view_file(hObject, eventdata)
3310
3311list=get(hObject,'String');
3312index=get(hObject,'Value');
3313rootroot=get(hObject,'UserData');
3314selectname=list{index};
3315ind_dot=regexp(selectname,'\.\.\.');
3316if ~isempty(ind_dot)
3317    selectname=selectname(1:ind_dot-1);
3318end
3319FullSelectName=fullfile(rootroot,selectname);
3320if exist(FullSelectName,'dir')% a directory has been selected
3321    ListFiles=dir(FullSelectName);
3322    ListDisplay=cell(numel(ListFiles),1);
3323    for ilist=2:numel(ListDisplay)% suppress the first line '.'
3324        ListDisplay{ilist-1}=ListFiles(ilist).name;
3325    end
3326    set(hObject,'Value',1)
3327    set(hObject,'String',ListDisplay)
3328    if strcmp(selectname,'..')
3329        FullSelectName=fileparts(fileparts(FullSelectName));
3330    end
3331    set(hObject,'UserData',FullSelectName)
3332    hfig=get(hObject,'parent');
3333    htitlebox=findobj(hfig,'tag','titlebox');   
3334    set(htitlebox,'String',FullSelectName)
3335elseif exist(FullSelectName,'file')%visualise the vel field if it exists
3336    FileInfo=get_file_info(FullSelectName);   
3337    if strcmp(FileInfo.FileType,'txt')
3338        edit(FullSelectName)
3339    elseif strcmp(FileInfo.FileType,'xml')
3340        editxml(FullSelectName)
3341    else
3342        uvmat(FullSelectName)
3343    end
3344    set(gcbo,'Value',1)
3345end
3346
3347
3348%------------------------------------------------------------------------   
3349% launched by refreshing the status figure
3350%------------------------------------------------------------------------
3351function refresh_GUI(hfig)
3352
3353htitlebox=findobj(hfig,'tag','titlebox');
3354hlist=findobj(hfig,'tag','list');
3355hseries=findobj(allchild(0),'tag','series');
3356hstatus=findobj(hseries,'tag','status');
3357StatusData=get(hstatus,'UserData');
3358OutputDir=get(htitlebox,'String');
3359if ischar(OutputDir),OutputDir={OutputDir};end
3360ListFiles=dir(OutputDir{1});
3361if numel(ListFiles)<1
3362    return
3363end
3364ListFiles(1)=[];%removes the first line ='.'
3365ListDisplay=cell(numel(ListFiles),1);
3366testrecent=0;
3367datnum=zeros(numel(ListDisplay),1);
3368for ilist=1:numel(ListDisplay)
3369    ListDisplay{ilist}=ListFiles(ilist).name;
3370      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
3371            datnum(ilist)=ListFiles(ilist).datenum;%only available in recent matlab versions
3372            testrecent=1;
3373       end
3374end
3375set(hlist,'String',ListDisplay)
3376
3377%% Look at date of creation
3378ListDisplay=ListDisplay(datnum~=0);
3379datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
3380NbOutputFile=[];
3381if isempty(datnum)
3382    if testrecent
3383        message='no civ result created yet';
3384    else
3385        message='';
3386    end
3387else
3388    [first,indfirst]=min(datnum);
3389    [last,indlast]=max(datnum);
3390    NbOutputFile_str='?';
3391    NbOutputFile=[];
3392    if isfield(StatusData,'NbOutputFile')
3393        NbOutputFile=StatusData.NbOutputFile;
3394        NbOutputFile_str=num2str(NbOutputFile);
3395    end
3396    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
3397        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
3398end
3399set(htitlebox,'String', [OutputDir{1};message])
3400
3401%% update the waitbar
3402hwaitbar=findobj(hfig,'tag','waitbar');
3403if ~isempty(NbOutputFile)
3404    BarPosition=get(hwaitbar,'Position');
3405    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
3406    set(hwaitbar,'Position',BarPosition)
3407end
3408
3409%------------------------------------------------------------------------
3410% --- Executes on selection change in ActionExt.
3411%------------------------------------------------------------------------
3412function ActionExt_Callback(hObject, eventdata, handles)
3413
3414ActionExtList=get(handles.ActionExt,'String');
3415ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
3416if strcmp(ActionExt,'.py (in dev.)')
3417    set(handles.RunMode,'Value',2)
3418end
3419
[897]3420%function num_NbProcess_Callback(hObject, eventdata, handles)
[867]3421
3422
3423function num_NbSlice_Callback(hObject, eventdata, handles)
3424NbSlice=str2num(get(handles.num_NbSlice,'String'));
[897]3425%set(handles.num_NbProcess,'String',num2str(NbSlice))
[867]3426
3427%------------------------------------------------------------------------
3428% --- set the visibility of relevant velocity type menus:
3429function menu=set_veltype_display(Civ,FileType)
3430%------------------------------------------------------------------------
3431if ~exist('FileType','var')
3432    FileType='civx';
3433end
3434switch FileType
3435    case 'civx'
3436        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3437        if isequal(Civ,0)
3438            imax=0;
3439        elseif isequal(Civ,1) || isequal(Civ,2)
3440            imax=1;
3441        elseif isequal(Civ,3)
3442            imax=3;
3443        elseif isequal(Civ,4) || isequal(Civ,5)
3444            imax=4;
3445        elseif isequal(Civ,6) %patch2
3446            imax=6;
3447        end
3448    case 'civdata'
3449        menu={'civ1';'filter1';'civ2';'filter2'};
3450        if isequal(Civ,0)
3451            imax=0;
3452        elseif isequal(Civ,1) || isequal(Civ,2)
3453            imax=1;
3454        elseif isequal(Civ,3)
3455            imax=2;
3456        elseif isequal(Civ,4) || isequal(Civ,5)
3457            imax=3;
[912]3458        else%if isequal(Civ,6) %patch2
[867]3459            imax=4;
3460        end
3461end
3462menu=menu(1:imax);
3463
3464
3465% --- Executes on mouse motion over figure - except title and menu.
3466function series_WindowButtonMotionFcn(hObject, eventdata, handles)
3467set(hObject,'Pointer','arrow');
3468
3469
3470% --- Executes on button press in SetPairs.
3471function SetPairs_Callback(hObject, iview, handles)
3472
3473%% delete previous occurrence of 'set_pairs'
3474hfig=findobj(allchild(0),'Tag','set_pairs');
3475if ~isempty(hfig)
3476delete(hfig)
3477end
3478
3479%% create the GUI set_pairs
3480set(0,'Unit','points')
3481ScreenSize=get(0,'ScreenSize');% get the size of the screen, to put the fig on the upper right
3482Width=220;% fig width in points (1/72 inch)
3483Height=min(0.8*ScreenSize(4),300);
3484Left=ScreenSize(3)- Width-40; %right edge close to the right, with margin=40
3485Bottom=ScreenSize(4)-Height-40; %put fig at top right
3486hfig=findobj(allchild(0),'Tag','set_slice');
3487if ~isempty(hfig),delete(hfig), end; %delete existing version of the GUI
3488hfig=figure('name','set_pairs','tag','set_pairs','MenuBar','none','NumberTitle','off','Unit','points','Position',[Left,Bottom,Width,Height]);
3489BackgroundColor=get(hfig,'Color');
3490SeriesData=get(handles.series,'UserData');
3491TimeUnit=get(handles.TimeUnit,'String');
3492PairString=get(handles.PairString,'Data');
3493ListViewLines=find(cellfun('isempty',PairString)==0);%find list of non empty pairs
3494ListViewMenu=cell(numel(ListViewLines),1);
3495for ilist=1:numel(ListViewLines)
3496    ListViewMenu{ilist}=num2str(ListViewLines(ilist));
3497end
3498if isempty(iview)
3499    ListViewValue=numel(ListViewLines);% we work by default on the pair option for the last line which requires pairs
3500    iview=ListViewLines(end);
3501else
3502    ListViewValue=find(ListViewLines==iview);
3503end
3504ref_i=str2num(get(handles.num_first_i,'String'));
3505ref_j=1;%default
3506if strcmp(get(handles.num_first_j,'String'),'Visible')
3507    ref_j=str2num(get(handles.num_first_j,'String'));
3508end
3509[ModeMenu,ModeValue]=update_mode(SeriesData.i1_series{iview},SeriesData.i2_series{iview},SeriesData.j2_series{iview});
3510displ_pair=update_listpair(SeriesData.i1_series{iview},SeriesData.i2_series{iview},SeriesData.j1_series{iview},SeriesData.j2_series{iview},ModeMenu{ModeValue},...
3511                                                     SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo{iview});
3512% first raw of the GUI
3513uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,...
3514    'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right');%title
3515uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.54 0.8 0.3 0.2],'BackgroundColor',[1 1 1],...
3516    'Callback',@(hObject,eventdata)ListView_Callback(hObject,eventdata),'String',ListViewMenu,'Value',ListViewValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3517    'Tag','ListView','TooltipString','''ListView'':choice of the file series w for pair display');
3518% second raw of the GUI
3519uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.79 0.7 0.1],'BackgroundColor',BackgroundColor,...
3520    'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left');%title
3521uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.05 0.62 0.9 0.2],'BackgroundColor',[1 1 1],...
3522    'Callback',@(hObject,eventdata)Mode_Callback(hObject,eventdata),'String',ModeMenu,'Value',ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3523    'Tag','Mode','TooltipString','''Mode'': choice of the image pair mode');
3524% third raw
3525uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.6 0.7 0.1],'BackgroundColor',BackgroundColor,...
3526    'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left');%title
3527uicontrol('Style','listbox','Units','normalized', 'Position', [0.05 0.42 0.9 0.2],'BackgroundColor',[1 1 1],...
3528    'Callback',@(hObject,eventdata)ListPair_Callback(hObject,eventdata),'String',displ_pair,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3529    'Tag','ListPair','TooltipString','''ListPair'': menu for selecting the image pair');
3530uicontrol('Style','text','Units','normalized', 'Position', [0.1 0.22 0.8 0.1],'BackgroundColor',BackgroundColor,...
3531    'String','ref_i           ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center');%title
3532uicontrol('Style','edit','Units','normalized', 'Position', [0.15 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3533    'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),'String',num2str(ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3534    'Tag','num_ref_i','TooltipString','''num_ref_i'': reference field index i used to display dt in ''list_pair_civ''');
3535uicontrol('Style','edit','Units','normalized', 'Position', [0.55 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3536    'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),'String',num2str(ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3537    'Tag','num_ref_j','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ''');
[880]3538uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.01 0.01 0.3 0.12],'BackgroundColor',[0 1 0],...
3539    'Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),'String','OK','FontUnits','points','FontSize',12,'FontWeight','bold',...
3540    'Tag','OK','TooltipString','''OK'': validate the choice');
[867]3541%  last raw  of the GUI: pushbuttons
3542% 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),...
3543%     'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''OK'': apply the output to the current field series in uvmat');
3544drawnow
3545
3546%------------------------------------------------------------------------
3547function ListView_Callback(hObject,eventdata)
3548Mode_Callback(hObject,eventdata)
3549
3550%------------------------------------------------------------------------   
3551function Mode_Callback(hObject,eventdata)
3552%% get input info
3553hseries=findobj(allchild(0),'tag','series');%handles of the GUI series
3554hhseries=guidata(hseries);%handles of the elements in the GUI series
3555TimeUnit=get(hhseries.TimeUnit,'String');
3556SeriesData=get(hseries,'UserData');
3557mode_list=get(hObject,'String');
3558mode=mode_list{get(hObject,'Value')};
3559hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3560iview=get(hListView,'Value');
3561i1_series=SeriesData.i1_series{iview};
3562i2_series=SeriesData.i2_series{iview};
3563j1_series=SeriesData.j1_series{iview};
3564j2_series=SeriesData.j2_series{iview};
3565
3566%% enable j index visibility after the new choice
3567status_j='on';%default
3568if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices
3569    status_j='off'; % no j index needed
3570elseif strcmp(get(handles.PairString,'Visible'),'on')
3571    check_burst=cellfun(@isempty,regexp(PairString,'^j'));%=0 for burst case, 1 otherwise
3572    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
3573        status_j='off'; % no j index needed for bust case
3574    end
3575end
3576enable_j(handles,status_j) % no j index needed
3577
3578%% get the reference indices for the time interval Dt
3579href_i=findobj(get(hObject,'parent'),'Tag','ref_i');
3580ref_i=[];ref_j=[];
3581if strcmp(get(href_i,'Visible'),'on')
3582    ref_i=str2num(get(href_i,'String'));
3583end
3584if isempty(ref_i)
3585    ref_i=1;
3586end
3587if isempty(ref_j)
3588    ref_j=1;
3589end
3590
3591%% update the menu ListPair
3592Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,SeriesData.Time{iview},TimeUnit,ref_i,ref_j,FileInfo);
3593hlist_pairs=findobj(get(hObject,'parent'),'Tag','ListPair');
3594set(hlist_pairs,'Value',1)% set the first choice by default in ListPair
3595set(hlist_pairs,'String',Menu)% set the menu in ListPair
3596ListPair_Callback(hlist_pairs,[])% apply the default choice in ListPair
3597
3598%-------------------------------------------------------------
3599% --- Executes on selection in ListPair.
3600function ListPair_Callback(hObject,eventdata)
3601%------------------------------------------------------------
3602list_pair=get(hObject,'String');%get the menu of image pairs
3603if isempty(list_pair)
3604    string='';
3605else
3606    string=list_pair{get(hObject,'Value')};
3607   % string=regexprep(string,',.*','');%removes time indication (after ',')
3608end
3609hseries=findobj(allchild(0),'tag','series');
3610hPairString=findobj(hseries,'tag','PairString');
3611PairString=get(hPairString,'Data');
3612hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3613iview=get(hListView,'Value');
3614PairString{iview,1}=string;
3615% report the selected pair string to the table PairString
3616set(hPairString,'Data',PairString)
3617
3618
3619%------------------------------------------------------------------------
3620function num_ref_i_Callback(hObject, eventdata)
3621%------------------------------------------------------------------------
3622Mode_Callback([],[])
3623
3624%------------------------------------------------------------------------
3625function num_ref_j_Callback(hObject, eventdata)
3626%------------------------------------------------------------------------
3627Mode_Callback([],[])
3628
3629%------------------------------------------------------------------------
[880]3630function OK_Callback(hObject, eventdata)
3631%------------------------------------------------------------------------
3632delete(get(hObject,'parent'))
3633
3634
3635%------------------------------------------------------------------------
[867]3636% --- Executes on button press in ClearLine.
3637%------------------------------------------------------------------------
3638function ClearLine_Callback(hObject, eventdata, handles)
3639InputTable=get(handles.InputTable,'Data');
3640iline=str2double(get(handles.InputLine,'String'));
3641if size(InputTable,1)>1
3642    InputTable(iline,:)=[];% suppress the current line if not the first
3643    set(handles.InputTable,'Data',InputTable);
3644end
[883]3645set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refr
[880]3646
3647
3648% --- Executes on button press in MonitorCluster.
3649function MonitorCluster_Callback(hObject, eventdata, handles)
3650web('https://www.legi.grenoble-inp.fr/servload/monika')
3651
3652
3653
3654function OutputSubDir_Callback(hObject, eventdata, handles)
3655set(handles.OutputSubDir,'BackgroundColor',[1 1 1])
[904]3656
3657
3658% --- Executes on button press in CheckOverwrite.
3659function CheckOverwrite_Callback(hObject, eventdata, handles)
[880]3660
[904]3661
3662
3663% --- Executes on button press in TestCPUTime.
3664function TestCPUTime_Callback(hObject, eventdata, handles)
3665% hObject    handle to TestCPUTime (see GCBO)
3666% eventdata  reserved - to be defined in a future version of MATLAB
3667% handles    structure with handles and user data (see GUIDATA)
3668
3669
3670
3671
3672
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