source: trunk/src/series.m @ 942

Last change on this file since 942 was 942, checked in by augier3pi, 8 years ago

Adapte pour fluidimage.

File size: 159.2 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';
992    end
993    if isfield(XmlData,'Camera')
[937]994        %         if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
995        %             if iview>1 && ~isempty(NbSlice) && ~strcmp(NbSlice,XmlData.Camera.NbSlice)
996        %                 msgbox_uvmat('WARNING','inconsistent number of slices with the first field series');
997        %             end
998        %             NbSlice=XmlData.Camera.NbSlice;% Nbre of slices from camera
999        %         end
[867]1000        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
1001            if iview>1 && ~isempty(TimeUnit) && ~strcmp(TimeUnit,XmlData.Camera.TimeUnit)
1002                msgbox_uvmat('WARNING','inconsistent time unit with the first field series');
1003            end
1004            TimeUnit=XmlData.Camera.TimeUnit;
1005        end
1006    end
1007    % number of slices
[937]1008    if isfield(XmlData,'TranslationMotor')&& isfield(XmlData.TranslationMotor,'NbSlice')
1009        NbSlice_motor=XmlData.TranslationMotor.NbSlice;
1010        if ~isempty(NbSlice) && ~isequal(NbSlice_motor,NbSlice)
1011                msgbox_uvmat('WARNING','inconsistent Z numbers of Z indices');
1012        else
1013            NbSlice=NbSlice_motor;
1014        end
1015    end
1016   
[867]1017    if isfield(XmlData,'GeometryCalib')
1018        check_calib=1;
1019        if isfield(XmlData.GeometryCalib,'SliceCoord')
1020            siz=size(XmlData.GeometryCalib.SliceCoord);
[937]1021            if ~isempty(NbSlice)&& ~isequal(size(1),NbSlice)
1022                msgbox_uvmat('WARNING','inconsistent numbers of Z indices between motor and calibration');
1023            else
[867]1024                NbSlice=siz(1);
1025            end
1026        end
1027    end
1028end
[937]1029if ~isempty(NbSlice)
1030set(handles.num_NbSlice,'String',num2str(NbSlice))
1031set(handles.num_NbSlice,'Visible','on')
1032end
[867]1033
1034%% read timing  from the current file (prioritary)
1035if ~isempty(VideoObject)% case of movies
1036    imainfo=get(VideoObject);
1037    if isempty(j1_series); %frame index along i
1038        Time=zeros(imainfo.NumberOfFrames+1,2);
1039        Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
1040    else
1041        Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
1042    end
1043    TimeName='video';
1044end
1045
1046
1047%% determine the min and max times: case of Netcdf files will be treated later in FieldName_Callback
1048if ~isempty(TimeName)
1049    TimeMin=Time(MinIndex_i+1,MinIndex_j+1);
1050    if size(Time)>=[first_i+1 first_j+1]
1051        TimeFirst=Time(first_i+1,first_j+1);
1052    end
1053    if size(Time)>=[last_i+1 last_j+1]
1054        TimeLast=Time(last_i+1,last_j+1);
1055    end
1056    if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1];
1057        TimeMax=Time(MaxIndex_i+1,MaxIndex_j+1);
1058    end
1059end
1060
1061%% update the time table
1062TimeTable=get(handles.TimeTable,'Data');
1063TimeTable{iview,1}=TimeName;
1064TimeTable{iview,2}=TimeMin;
1065TimeTable{iview,3}=TimeFirst;
1066TimeTable{iview,4}=TimeLast;
1067TimeTable{iview,5}=TimeMax;
1068set(handles.TimeTable,'Data',TimeTable)
1069
1070%% update the series info in 'UserData'
1071SeriesData.i1_series{iview}=i1_series;
1072SeriesData.i2_series{iview}=i2_series;
1073SeriesData.j1_series{iview}=j1_series;
1074SeriesData.j2_series{iview}=j2_series;
1075SeriesData.FileType{iview}=FileInfo.FileType;
1076SeriesData.FileInfo{iview}=FileInfo;
1077SeriesData.Time{iview}=Time;
1078% if ~isempty(TimeName)
1079%     SeriesData.TimeSource=TimeSource;
1080% end
1081if check_calib
1082    SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib;
1083end
1084set(handles.series,'UserData',SeriesData)
1085
1086%% update pair menus
1087hset_pair=findobj(allchild(0),'Tag','set_pairs');
1088if ~isempty(hset_pair), delete(hset_pair); end % delete the GUI set_pair if opened
1089CheckPair= ~isempty(i2_series)||~isempty(j2_series); % check whether index pairs need to be defined
1090PairString=get(handles.PairString,'Data');
1091if CheckPair% if pairs need to be display for line iview
1092    [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series);
1093    Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,ModeMenu{ModeValue},Time,TimeUnit,ref_i,ref_j,TimeName,InputTable(iview,:),FileInfo);
1094    PairString{iview,1}=Menu{1};
1095else
1096    PairString{iview,1}='';%no pair for #iview
1097end
1098set(handles.PairString,'Data',PairString)
1099if isempty(find(cellfun('isempty',get(handles.PairString,'Data'))==0, 1))% if all lines of pairs are empty
1100    set(handles.PairString,'Visible','off')
1101    set(handles.SetPairs,'Visible','off')
1102else
1103    set(handles.PairString,'Visible','on')
1104    set(handles.SetPairs,'Visible','on')
1105end
1106
1107
1108%% display the set of existing files as an image
1109set(handles.FileStatus,'Units','pixels')
1110Position=get(handles.FileStatus,'Position');
1111set(handles.FileStatus,'Units','normalized')
1112%xI=0.5:Position(3)-0.5;
1113nbview=numel(SeriesData.i1_series);
1114j_max=cell(1,nbview);
1115MaxIndex_i=ones(1,nbview);%default
1116MinIndex_i=ones(1,nbview);%default
1117for iline=1:nbview
1118    pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); %max on pair index
1119    j_max{iline}=max(pair_max,[],1);%max on j index
1120    if ~isempty(j_max{iline})
1121    MaxIndex_i(iline)=max(find(j_max{iline}))-1;% max ref index i
1122    MinIndex_i(iline)=min(find(j_max{iline}))-1;% min ref index i
1123    end
1124end
1125MinIndex_i=min(MinIndex_i);
1126MaxIndex_i=max(MaxIndex_i);
1127range_index=MaxIndex_i-MinIndex_i+1;
1128range_y=max(1,floor(Position(4)/nbview));
1129npx=floor(Position(3));
1130file_indices=MinIndex_i+floor(((0.5:npx-0.5)/npx)*range_index)+1;
1131CData=zeros(nbview*range_y,npx);% initiate the image representing the existing files
1132for iline=1:nbview
1133    ind_y=1+(iline-1)*range_y:iline*range_y;
1134    LineData=zeros(size(file_indices));
1135    file_select=file_indices(file_indices<=numel(j_max{iline}));
1136    ind_select=find(file_indices<=numel(j_max{iline}));
1137    LineData(ind_select)=j_max{iline}(file_select)~=0;
1138    CData(ind_y,:)=ones(size(ind_y'))*LineData;
1139end
1140CData=cat(3,zeros(size(CData)),CData,zeros(size(CData)));%make color images r=0,g,b=0
1141set(handles.FileStatus,'CData',CData);
1142
1143%-----------------------------------------------------------guide -------------
1144%------------------------------------------------------------------------
1145%  III - FUNCTIONS ASSOCIATED TO THE FRAME IndexRange
1146%------------------------------------------------------------------------
1147
1148
1149% ---- determine the menu to put in mode and advice a default choice
1150%------------------------------------------------------------------------
1151function [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series)
1152%------------------------------------------------------------------------   
1153ModeMenu={''};
1154if isempty(j2_series)% no j pair
1155    ModeValue=1;
1156    if ~isempty(i2_series)
1157        ModeMenu={'series(Di)'}; % pair menu with only option Di
1158    end
1159else %existence of j pairs
1160    pair_max=squeeze(max(i1_series,[],1)); %max on pair index
1161    j_max=max(pair_max,[],1);
1162    MaxIndex_i=find(j_max, 1, 'last' )-1;% max ref index i
1163    MinIndex_i=find(j_max, 1 )-1;% min ref index i
1164    i_max=max(pair_max,[],2);
1165    MaxIndex_j=find(i_max, 1, 'last' )-1;% max ref index i
1166    MinIndex_j=find(i_max, 1 )-1;% min ref index i
1167    if MaxIndex_j==MinIndex_j
1168        ModeValue=1;
1169        ModeMenu={'bursts'};
1170    elseif MaxIndex_i==MinIndex_i
1171        ModeValue=1;
1172        ModeMenu={'series(Dj)'};
1173    else
1174        ModeMenu={'bursts';'series(Dj)'};
1175        if (MaxIndex_j-MinIndex_j)>10
1176            ModeValue=2;%set mode to series(Dj) if more than 10 j values
1177        else
1178            ModeValue=1;
1179        end
1180    end
1181end
1182
1183
1184%------------------------------------------------------------------------
1185function displ_pair=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo)
1186%------------------------------------------------------------------------
1187displ_pair={};
1188if isempty(TimeUnit)
1189    dtunit='e-03';
1190else
1191    dtunit=['m' TimeUnit];
1192end
1193switch mode
1194    case 'series(Di)'
1195        diff_i=i2_series-i1_series;
1196        min_diff=min(diff_i(diff_i>0));
1197        max_diff=max(diff_i(diff_i>0));
1198        for ipair=min_diff:max_diff
1199            if numel(diff_i(diff_i==ipair))>0
1200                pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1201                if ~isempty(time)
1202                    if ref_i<=floor(ipair/2)
1203                        ref_i=floor(ipair/2)+1;% shift ref_i to get the first pair
1204                    end
1205                    Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1206                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1207                end
1208                displ_pair=[displ_pair;{pair_string}];
1209            end
1210        end
1211        if ~isempty(displ_pair)
1212            displ_pair=[displ_pair;{'Di=*|*'}];
1213        end
1214    case 'series(Dj)'
1215        if isempty(j2_series)
1216            msgbox_uvmat('ERROR','no j1-j2 pair available')
1217            return
1218        end
1219        diff_j=j2_series-j1_series;
1220        min_diff=min(diff_j(diff_j>0));
1221        max_diff=max(diff_j(diff_j>0));
1222        for ipair=min_diff:max_diff
1223            if numel(diff_j(diff_j==ipair))>0
1224                pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1225                if ~isempty(time)
1226                    if ref_j<=floor(ipair/2)
1227                        ref_j=floor(ipair/2)+1;% shift ref_i to get the first pair
1228                    end
1229                    Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1230                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1231                end
1232                displ_pair=[displ_pair;{pair_string}];
1233            end
1234        end
1235        if ~isempty(displ_pair)
1236            displ_pair=[displ_pair;{'Dj=*|*'}];
1237        end
1238    case 'bursts'
1239        if isempty(j2_series)
1240            msgbox_uvmat('ERROR','no j1-j2 pair available')
1241            return
1242        end
1243        %diff_j=j2_series-j1_series;
1244        min_j1=min(j1_series(j1_series>0));
1245        max_j1=max(j1_series(j1_series>0));
1246        min_j2=min(j2_series(j2_series>0));
1247        max_j2=max(j2_series(j2_series>0));
1248        for pair1=min_j1:min(max_j1,min_j1+20)
1249            for pair2=min_j2:min(max_j2,min_j2+20)
1250                if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1251                    pair_string=['j= ' num2str(pair1) '-' num2str(pair2)];
1252                    [TimeValue,DtValue]=get_time(ref_i,[],pair_string,InputTable,FileInfo,TimeName,'Dt');
1253                    %Dt=time(ref_i,pair2+1)-time(ref_i,pair1+1);
1254                    pair_string=[pair_string ', Dt=' num2str(DtValue) ' ' dtunit];
1255                    displ_pair=[displ_pair;{pair_string}];
1256                end
1257            end
1258        end
1259        if ~isempty(displ_pair)
1260            displ_pair=[displ_pair;{'j=*-*'}];
1261        end
1262end
1263
1264%------------------------------------------------------------------------
1265function num_first_i_Callback(hObject, eventdata, handles)
1266%------------------------------------------------------------------------
1267num_last_i_Callback(hObject, eventdata, handles)
1268
1269%------------------------------------------------------------------------
1270function num_last_i_Callback(hObject, eventdata, handles)
1271%------------------------------------------------------------------------
1272SeriesData=get(handles.series,'UserData');
1273if ~isfield(SeriesData,'Time')
1274    SeriesData.Time{1}=[];
1275end
1276displ_time(handles);
1277
1278%------------------------------------------------------------------------
1279function num_first_j_Callback(hObject, eventdata, handles)
1280%------------------------------------------------------------------------
1281 num_last_j_Callback(hObject, eventdata, handles)
1282
1283%------------------------------------------------------------------------
1284function num_last_j_Callback(hObject, eventdata, handles)
1285%------------------------------------------------------------------------
1286% first_j=str2num(get(handles.num_first_j,'String'));
1287% last_j=str2num(get(handles.num_last_j,'String'));
1288% ref_j=ceil((first_j+last_j)/2);
1289% set(handles.num_ref_j,'String', num2str(ref_j))
1290% num_ref_j_Callback(hObject, eventdata, handles)
1291SeriesData=get(handles.series,'UserData');
1292if ~isfield(SeriesData,'Time')
1293    SeriesData.Time{1}=[];
1294end
1295displ_time(handles);
1296
1297%------------------------------------------------------------------------
1298% ---- find the times corresponding to the first and last indices of a series
1299function displ_time(handles)
1300%------------------------------------------------------------------------
1301SeriesData=get(handles.series,'UserData');%
1302if ~isfield(SeriesData,'Time')
1303    return
1304end
1305PairString=get(handles.PairString,'Data');
1306ref_i_1=str2num(get(handles.num_first_i,'String'));%first reference index
1307ref_i_2=str2num(get(handles.num_last_i,'String'));%last reference index
1308ref_j_1=[];ref_j_2=[];
1309if strcmp(get(handles.num_first_j,'Visible'),'on')
1310ref_j_1=str2num(get(handles.num_first_j,'String'));
1311ref_j_2=str2num(get(handles.num_last_j,'String'));
1312end
1313[i1_1,i2_1,j1_1,j2_1] = get_file_index(ref_i_1,ref_j_1,PairString);
1314[i1_2,i2_2,j1_2,j2_2] = get_file_index(ref_i_2,ref_j_2,PairString);
1315TimeTable=get(handles.TimeTable,'Data');
1316%%%%%%
1317%TODO: read time in netcdf file, see ActionName_Callback
1318%%%%%%%
1319%Pairs=get(handles.PairString,'Data');
1320for iview=1:size(TimeTable,1)
1321    if size(SeriesData.Time,1)<iview
1322        break
1323    end
1324    TimeTable{iview,3}=[];
1325    TimeTable{iview,4}=[];
1326    if size(SeriesData.Time{iview},1)>=i2_2+1 && (isempty(ref_j_1)||size(SeriesData.Time{iview},2)>=j2_2+1)
1327        if isempty(ref_j_1)
1328            time_first=(SeriesData.Time{iview}(i1_1+1,2)+SeriesData.Time{iview}(i2_1+1,2))/2;
1329            time_last=(SeriesData.Time{iview}(i1_2+1,2)+SeriesData.Time{iview}(i2_2+1,2))/2;
1330        else
1331            time_first=(SeriesData.Time{iview}(i1_1+1,j1_1+1)+SeriesData.Time{iview}(i2_1+1,j2_1+1))/2;
1332            time_last=(SeriesData.Time{iview}(i1_2+1,j1_2+1)+SeriesData.Time{iview}(i2_2+1,j2_1+1))/2;
1333        end
1334        TimeTable{iview,3}=time_first; %TODO: take into account pairs
1335        TimeTable{iview,4}=time_last; %TODO: take into account pairs
1336    end
1337end
1338set(handles.TimeTable,'Data',TimeTable)
1339
1340%% set the waitbar position with respect to the min and max in the series
1341MinIndex_i=min(get(handles.MinIndex_i,'Data'));
1342MaxIndex_i=max(get(handles.MaxIndex_i,'Data'));
1343pos_first=(ref_i_1-MinIndex_i)/(MaxIndex_i-MinIndex_i+1);
1344pos_last=(ref_i_2-MinIndex_i+1)/(MaxIndex_i-MinIndex_i+1);
1345if isempty(pos_first), pos_first=0; end
1346if isempty(pos_last), pos_last=1; end
1347Position=get(handles.Waitbar,'Position');% position of the waitbar:= [ x,y, width, height]
1348Position_status=get(handles.FileStatus,'Position');
1349Position(1)=Position_status(1)+Position_status(3)*pos_first;
1350Position(3)=max(Position_status(3)*(pos_last-pos_first),0.001);% width must remain positive
1351set(handles.Waitbar,'Position',Position)
1352update_waitbar(handles.Waitbar,0)
1353
1354%------------------------------------------------------------------------
1355% --- Executes when selected cell(s) is changed in PairString.
1356function PairString_CellSelectionCallback(hObject, eventdata, handles)
1357%------------------------------------------------------------------------   
1358if numel(eventdata.Indices)>=1
1359    PairString=get(hObject,'Data');
1360    if ~isempty(PairString{eventdata.Indices(1)})
1361        SetPairs_Callback(hObject, eventdata.Indices(1), handles)
1362    end
1363end
1364
1365%-------------------------------------
1366function enable_i(handles,state)
1367set(handles.i_txt,'Visible',state)
1368set(handles.num_first_i,'Visible',state)
1369set(handles.num_last_i,'Visible',state)
1370set(handles.num_incr_i,'Visible',state)
1371
1372%-----------------------------------
1373function enable_j(handles,state)
1374set(handles.j_txt,'Visible',state)
1375set(handles.num_first_j,'Visible',state)
1376set(handles.num_last_j,'Visible',state)
1377set(handles.num_incr_j,'Visible',state)
1378set(handles.MinIndex_j,'Visible',state)
1379set(handles.MaxIndex_j,'Visible',state)
1380
1381
1382%%%%%%%%%%%%%%%%%%%%
1383%%  MAIN ActionName FUNCTIONS
1384%%%%%%%%%%%%%%%%%%%%
1385%------------------------------------------------------------------------
1386% --- Executes on button press in RUN.
1387%------------------------------------------------------------------------
1388function RUN_Callback(hObject, eventdata, handles)
1389
1390%% settings of the button RUN
1391set(handles.RUN,'BusyAction','queue');% activation of STOP button will set BusyAction to 'cancel'
1392set(handles.RUN, 'Enable','Off')% avoid further RUN action until the current one is finished
1393set(handles.RUN,'BackgroundColor',[1 1 0])%show activation of RUN by yellow color
1394drawnow
1395set(handles.status,'Value',0)% desable status display if relevant
1396status_Callback([], eventdata, handles)
1397
1398%% launch action
1399errormsg=launch_action(handles);
1400if ~isempty(errormsg)
1401     msgbox_uvmat('ERROR',errormsg)
1402end
1403
1404%% reset the GUI series
1405update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate launching is finished
1406set(handles.RUN, 'Enable','On')
1407set(handles.RUN,'BackgroundColor',[1 0 0])
1408set(handles.RUN, 'Value',0)
1409
1410%------------------------------------------------------------------------
1411% --- called by RUN_Callback
1412%------------------------------------------------------------------------
1413function errormsg=launch_action(handles)
1414errormsg='';%default
1415
1416%% read the data on the GUI series
1417Param=read_GUI_series(handles);%displayed parameters
1418SeriesData=get(handles.series,'UserData');%hidden parameters
[883]1419if isfield(SeriesData,'TransformInput')
1420    Param.TransformInput=SeriesData.TransformInput;
1421end
[867]1422if ~isfield(SeriesData,'i1_series')
1423    errormsg='The input field series needs to be refreshed: press REFRESH';
1424    return
1425end
[940]1426if isfield(Param,'InputFields')&& isfield(Param.InputFields,'FieldName')&& isequal(Param.InputFields.FieldName,'get_field...')
[867]1427    errormsg='input field name(s) not defined, select get_field...';
1428    return
1429end
1430
1431%% select the Action mode, 'local', 'background' or 'cluster' (if available)
1432RunMode='local';%default (needed for first opening of the GUI series)
1433if isfield(Param.Action,'RunMode')
1434    RunMode=Param.Action.RunMode;
1435    Param.Action=rmfield(Param.Action,'RunMode');%remove from the recorded xml file to avoid interference during ImportConfig
1436end
1437ActionExt='.m';%default
1438if isfield(Param.Action,'ActionExt')
1439    ActionExt=Param.Action.ActionExt;% '.m', '.sh' (compiled)  or '.py' (Python)
1440    Param.Action=rmfield(Param.Action,'ActionExt');%remove from the recorded xml file to avoid interference during ImportConfig
1441end
1442ActionName=Param.Action.ActionName;
1443ActionPath=Param.Action.ActionPath;
1444path_series=fileparts(which('series'));
1445
1446%% create the Action fct handle if RunMode option = 'local'
1447if strcmp(RunMode,'local')
1448    if ~isequal(ActionPath,path_series)
1449        eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1450        if ~exist(ActionPath,'dir')
1451            errormsg=['The prescribed function path ' ActionPath ' does not exist'];
1452            return
1453        end
1454        if ~isequal(spath,ActionPath)
1455            addpath(ActionPath)% add the prescribed path if not the current one
1456        end
1457    end
1458    eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1459    if ~isequal(ActionPath,path_series)
1460        rmpath(ActionPath)% add the prescribed path if not the current one
1461    end
1462end
1463
[918]1464%% Get  PARAM.xml (not used at this stage)
[867]1465errormsg='';%default error message
1466xmlfile=fullfile(path_series,'PARAM.xml');
1467if ~exist(xmlfile,'file')
1468    [success,message]=copyfile(fullfile(path_series,'PARAM.xml.default'),xmlfile);
1469end
1470if strcmp(ActionExt,'.sh')
1471    if exist(xmlfile,'file')
1472        s=xml2struct(xmlfile);
1473        if strcmp(RunMode,'cluster_oar') && isfield(s,'BatchParam')
1474            if isfield(s.BatchParam,'NbCore')
1475                NbCore=s.BatchParam.NbCore;
1476            end
1477        elseif (strcmp(RunMode,'background')||strcmp(RunMode,'local')) && isfield(s,'RunParam')
1478            if isfield(s.RunParam,'NbCore')
1479                NbCore=s.RunParam.NbCore;
1480            end
1481        end
1482    end
1483end
[928]1484ActionFullName=fullfile(get(handles.ActionPath,'String'),ActionName);
[934]1485
1486%% If a compiled version has been selected (ext .sh) check wether it needs to be recompiled
[867]1487if strcmp(ActionExt,'.sh')
1488    TransformPath='';
1489    if ~isempty(get(handles.ActionExt,'UserData'))
1490        TransformPath=get(handles.ActionExt,'UserData');
1491    end
1492    set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
1493    set(handles.ActionExt,'BackgroundColor',[1 1 0])
[923]1494    [mcrmajor, mcrminor] = mcrversion;   
1495    MCRROOT = ['MCRROOT',int2str(mcrmajor),int2str(mcrminor)];
[895]1496    RunTime = getenv(MCRROOT);
1497    ActionNameVersion=[ActionName '_' MCRROOT];
1498    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']);
[934]1499    % compile the .m file if the .sh file does not exist yet
[867]1500    if ~exist(ActionFullName,'file')
1501        answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
1502        if strcmp(answer,'Yes')
1503            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1504            path_uvmat=fileparts(which('series'));
1505            currentdir=pwd;
1506            cd(get(handles.ActionPath,'String'))% go to the directory of Action
1507            addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1508            compile(ActionName,TransformPath)
1509            cd(currentdir)
[880]1510        else
1511            errormsg='Action launch interrupted';
1512            return
[867]1513        end       
1514    else
[895]1515        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']));
[867]1516        m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
1517        if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
1518            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1519            drawnow
[895]1520            answer=msgbox_uvmat('INPUT_Y-N',[ActionNameVersion '.sh needs to be updated: recompile now?']);
[867]1521            if strcmp(answer,'Yes')
1522                path_uvmat=fileparts(which('series'));
1523                currentdir=pwd;
1524                cd(get(handles.ActionPath,'String'))% go to the directory of Action
1525                addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1526                addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile'
1527                compile(ActionName,TransformPath)
1528                cd(currentdir)
1529            end
1530        end
1531    end
[934]1532
[867]1533    set(handles.ActionExt,'BackgroundColor',[1 1 1])
1534     set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch
1535end
1536
[897]1537%% set nbre of cluster cores and processes:
1538% NbCore is the number of computer processors used
[917]1539% NbProcess is the number of independent processes in which the required calculation is split.
[867]1540switch RunMode
1541    case {'local','background'}
1542        NbCore=1;% no need to split the calculation
1543    case 'cluster_oar'
[935]1544        %%%%% TEST A REMETTRE%%%%%
1545 %       if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1546%             NbCore=1;% one core used only (limitation of Matlab licences)
1547%             answer=msgbox_uvmat('INPUT_Y-N','Number of cores =1: select the compiled version .sh for multi-core processing. Proceed with the .m version?');
1548%             if ~strcmp(answer,'Yes')
1549%                 errormsg='Action launch interrupted by user';
1550%                 return
1551%             end
1552%             extra_oar='';
1553 %       else
[867]1554            answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''});
[896]1555            if isempty(answer)
1556                                errormsg='Action launch interrupted by user';
1557                return
1558            end
[867]1559            NbCore=str2double(answer{1});
1560            extra_oar=answer{2};
[935]1561 %       end
[882]1562    case 'cluster_pbs'
1563        if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1564            NbCore=1;% one core used only (limitation of Matlab licences)
1565            answer=msgbox_uvmat('INPUT_Y-N','Number of cores =1: select the compiled version .sh for multi-core processing. Proceed with the .m version?');
1566            if ~strcmp(answer,'Yes')
1567                errormsg='Action launch interrupted';
1568                return
1569            end
1570            extra_oar='';
1571        else
1572            answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''});
1573            NbCore=str2double(answer{1});
1574            %extra_oar=answer{2};%TODO : fix this for LMFA cluster. Maybe
1575            %extrs_oar and extra_pbs are not the best names
1576        end
[867]1577end
1578if ~isfield(Param.IndexRange,'NbSlice')
1579    Param.IndexRange.NbSlice=[];
1580end
1581
1582%% create the output data directory if needed
1583OutputDir='';
1584if isfield(Param,'OutputSubDir')
1585    SubDirOut=[get(handles.OutputSubDir,'String') Param.OutputDirExt];
1586    SubDirOutNew=SubDirOut;
1587    detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exist
1588    check_create=1; %need to create the result directory by default
[905]1589    CheckOverwrite=1;
1590    if isfield(Param,'CheckOverwrite')
1591        CheckOverwrite=Param.CheckOverwrite;
1592    end
[867]1593    while detect
[905]1594        if CheckOverwrite
[904]1595            comment=', possibly overwrite previous data';
1596        else
1597            comment=', will complement existing result files (no overwriting)';
1598        end
1599        answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(Param.InputTable{1,1},SubDirOutNew) comment]);
[867]1600        if strcmp(answer,'Cancel')
1601            return
1602        elseif strcmp(answer,'Yes')
1603            detect=0;
1604            check_create=0;
1605        else
1606            r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names');%detect whether name ends by a number
1607            if isempty(r)
1608                r(1).root=[SubDirOutNew '_'];
1609                r(1).num1='0';
1610            end
1611            SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1
1612            detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exists
1613            check_create=1;
1614        end
1615    end
1616    Param.OutputDirExt=regexprep(SubDirOutNew,Param.OutputSubDir,'');
1617    Param.OutputRootFile=Param.InputTable{1,3};% the first sorted RootFile taken for output
1618    set(handles.OutputDirExt,'String',Param.OutputDirExt)
1619    OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]);% full name (with path) of output directory
1620    if check_create    % create output directory if it does not exist
1621        [tild,msg1]=mkdir(OutputDir);
1622        if ~strcmp(msg1,'')
1623            errormsg=['cannot create ' OutputDir ': ' msg1];%error message for directory creation
1624            return
1625        end
1626    end
1627   
1628elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir
1629    OutputDir=Param.ActionInput.LogPath;   
1630end
1631DirXml=fullfile(OutputDir,'0_XML');
1632if ~exist(DirXml,'dir')
[935]1633    [~,msg1]=mkdir(DirXml);
[867]1634    if ~strcmp(msg1,'')
1635        errormsg=['cannot create ' DirXml ': ' msg1];%error message for directory creation
1636        return
1637    end
1638end
1639OutputNomType=nomtype2pair(Param.InputTable{1,4});% nomenclature for output files
1640
[897]1641%% get the set of reference input field indices
1642first_i=1;% first i index to process
1643last_i=1;% last i index to process
1644incr_i=1;% increment step in i index
1645first_j=1;% first j index to process
1646last_j=1;% last j index to process
1647incr_j=1;% increment step in j index
[867]1648if isfield(Param.IndexRange,'first_i')
1649    first_i=Param.IndexRange.first_i;
1650    incr_i=Param.IndexRange.incr_i;
1651    last_i=Param.IndexRange.last_i;
1652end
1653if isfield(Param.IndexRange,'first_j')
1654    first_j=Param.IndexRange.first_j;
1655    last_j=Param.IndexRange.last_j;
1656    incr_j=Param.IndexRange.incr_j;
1657end
[932]1658if last_i < first_i || last_j < first_j
[867]1659    errormsg= 'series/Run_Callback:last field index must be larger or equal to the first one';
1660    return
1661end
1662%incr_i must be defined, =1 by default, if NbSlice is active
1663if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice)
1664    incr_i=1;
1665    set(handles.num_incr_i,'String','1')
1666end
[897]1667% case of no increment i defined: processing is done on the available files found in i1_series
[867]1668if isempty(incr_i)
1669    if isempty(incr_j)
1670        [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1671        ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1672        ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1673        ref_j=ref_j-1;
1674        ref_i=ref_i-1;
1675    else
1676        ref_j=first_j:incr_j:last_j;
1677        [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1678        ref_i=ref_i-1;
1679        ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1680    end
[932]1681    % increment i is defined: processing is done on first_i:incr_i:last_i;
[867]1682else
1683    ref_i=first_i:incr_i:last_i;
[904]1684    if isempty(incr_j)% automatic finding of the existing j indices
[867]1685        [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1686        ref_j=ref_j-1;
1687        ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1688    else
1689        ref_j=first_j:incr_j:last_j;
1690    end
1691end
[914]1692CPUTime=1;% job time estimated at 1 min per iteration (on index i and j) by default
[906]1693if isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime)
1694    CPUTime=Param.Action.CPUTime;%Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j
[904]1695end
1696nbfield_j=numel(ref_j); % number of j indices
[932]1697BlockLength=numel(ref_i);% by default, job involves the full set of i field indices
[910]1698NbProcess=1;
1699switch RunMode
1700    case {'cluster_oar','cluster_pbs'}
1701        if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined
[932]1702            BlockLength= ceil(20/(CPUTime*nbfield_j));% short iterations are grouped such that the minimum time of a process is 20 min.
1703            BlockLength=max(BlockLength,ceil(numel(ref_i)/500));% possibly increase the BlockLength to have less than 500 jobs
1704            NbProcess=ceil(numel(ref_i)/BlockLength) ; % nbre of processes sent to oar
[910]1705        else
1706            NbProcess=Param.IndexRange.NbSlice;% the parameter NbSlice sets the nbre of run processes
1707            NbCore=min(NbCore,NbProcess);% reduces the number of cores if it exceeds the number of processes
1708        end
[917]1709    otherwise
[932]1710        if ~isempty(Param.IndexRange.NbSlice)
1711            NbProcess=Param.IndexRange.NbSlice;% the parameter NbSlice sets the nbre of run processes
1712        end
[902]1713end
[867]1714
1715%% record nbre of output files and starting time for computation for status
1716StatusData=get(handles.status,'UserData');
1717if isfield(StatusData,'OutputFileMode')
1718    switch StatusData.OutputFileMode
1719        case 'NbInput'
1720            StatusData.NbOutputFile=numel(ref_i)*nbfield_j;
1721        case 'NbInput_i'
1722            StatusData.NbOutputFile=numel(ref_i);
[932]1723        case 'NbSlice'
[867]1724            StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
1725    end
1726end
1727StatusData.TimeStart=now;
1728set(handles.status,'UserData',StatusData)
1729
[897]1730%% case of a function in Python
[867]1731if strcmp(ActionExt, '.py (in dev.)')
1732    fprintf([
1733        '\n' ...
1734        '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ...
1735        'The option .py is used. It is still in development.\n' ...
1736        'Do not use it unless you really know what you do!\n' ...
[942]1737        'To try it, first install Pyp and the most recent version of FluidImage.\n' ...
[867]1738        '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n'])
1739    RunMode = 'python';
1740end
1741
1742
[919]1743%% direct processing on the current Matlab session or creation of command files
1744filexml=cell(1,NbProcess);% initialisation of the names of the files containing the processing parameters
1745extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process
[918]1746for iprocess=1:NbProcess
[922]1747    extxml{iprocess}='.xml';
1748end
1749for iprocess=1:NbProcess
[918]1750    if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1751        disp('program stopped by user')
1752        return
1753    end
1754    if isempty(Param.IndexRange.NbSlice)
1755        Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1756        if Param.IndexRange.first_i>last_i
1757            NbProcess=iprocess-1;% leave the loop, we are at the end of the calculation
1758            break
[917]1759        end
[918]1760        Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
1761    else %multislices (then incr_i is not empty)
1762        Param.IndexRange.first_i= first_i+iprocess-1;
1763        Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;
1764    end
1765    for ilist=1:size(Param.InputTable,1)
1766        Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/');%correct path name for PCWIN system
1767    end
1768   
1769    if isfield(Param,'OutputSubDir')
1770        t=struct2xml(Param);
1771        t=set(t,1,'name','Series');
1772        extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,...
1773            Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
[919]1774        filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess});
1775        try
1776            save(t, filexml{iprocess});% save the xml file containing the processing parameters
1777        catch ME
1778            if ~strcmp (RunMode,'local')
1779                errormsg=['error writting ' filexml{iprocess} ': ' ME.message];
1780                return
1781            end
1782        end
[918]1783    end
1784    if strcmp (RunMode,'local')
[867]1785        switch ActionExt
1786            case '.m'
[918]1787                h_fun(Param);% direct launching
[932]1788               
[867]1789            case '.sh'
1790                switch computer
1791                    case {'PCWIN','PCWIN64'} %Windows system
1792                        filexml=regexprep(filexml,'\\','\\\\');% add '\' so that '\' are left as characters
[922]1793                        system([ActionFullName ' ' RunTime ' ' filexml]);% TODO: adapt to DOS system
[867]1794                    case {'GLNX86','GLNXA64','MACI64'}%Linux  system
[922]1795                        system([ActionFullName ' ' RunTime ' ' filexml]);
[867]1796                end
1797        end
1798    end
[918]1799end
[934]1800
[918]1801if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python')
[867]1802    %% processing on a different session of the same computer (background) or cluster, create executable files
1803    batch_file_list=cell(NbProcess,1);% initiate the list of executable files
[905]1804    DirExe=fullfile(OutputDir,'0_EXE');%directory name for executable files
[867]1805    switch computer
1806        case {'PCWIN','PCWIN64'} %Windows system
1807            ExeExt='.bat';
1808        case {'GLNX86','GLNXA64','MACI64'}%Linux  system
[917]1809            ExeExt='.sh';
[867]1810    end
1811    %create subdirectory for executable files
[905]1812    if ~exist(DirExe,'dir')
1813        [tild,msg1]=mkdir(DirExe);
[867]1814        if ~strcmp(msg1,'')
[905]1815            errormsg=['cannot create ' DirExe ': ' msg1];%error message for directory creation
[867]1816            return
1817        end
1818    end
1819    %create subdirectory for log files
1820    DirLog=fullfile(OutputDir,'0_LOG');
1821    if ~exist(DirLog,'dir')
1822        [tild,msg1]=mkdir(DirLog);
1823        if ~strcmp(msg1,'')
1824            errormsg=['cannot create ' DirLog ': ' msg1];%error message for directory creation
1825            return
1826        end
1827    end
[932]1828   
[918]1829    %create the executable file
1830    file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,...
1831        first_i,last_i,first_j,last_j);
1832    file_exe_global=fullfile(OutputDir,'0_EXE',file_exe_global);
1833    filelog_global=fullfile_uvmat('','',Param.InputTable{1,3},'.log',OutputNomType,...
1834        first_i,last_i,first_j,last_j);
1835    filelog_global=fullfile(OutputDir,'0_LOG',filelog_global);
[934]1836
[867]1837    for iprocess=1:NbProcess
1838       
[918]1839        %create the executable file
[917]1840       
[918]1841        batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt));
1842       
[917]1843        % set the log file name
[918]1844        filelog{iprocess}=fullfile(OutputDir,'0_LOG',regexprep(extxml{iprocess},'.xml$','.log'));
1845       
[917]1846    end
1847end
1848
1849%% launch the executable files for background or cluster processing
[918]1850
[917]1851switch RunMode
[918]1852   
[917]1853    case 'background'
[918]1854        [fid,message]=fopen(file_exe_global,'w');
[867]1855        if isequal(fid,-1)
[918]1856            errormsg=['creation of ' file_exe_global ':' message];
[867]1857            return
1858        end
1859        switch ActionExt
1860            case '.m'% Matlab function
1861                switch computer
1862                    case {'GLNX86','GLNXA64','MACI64'}
1863                        cmd=[...
1864                            '#!/bin/bash \n'...
1865                            '. /etc/sysprofile \n'...
[918]1866                            'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog_global ''' <<END_MATLAB \n'...
[867]1867                            'addpath(''' path_series '''); \n'...
[917]1868                            'addpath(''' Param.Action.ActionPath '''); \n'];
1869                        for iprocess=1:NbProcess
1870                            cmd=[cmd '' Param.Action.ActionName  '( ''' filexml{iprocess} '''); \n'];
1871                        end
1872                        cmd=[cmd  'exit \n' 'END_MATLAB \n'];
[867]1873                        fprintf(fid,cmd);%fill the executable file with the  char string cmd
1874                        fclose(fid);% close the executable file
[918]1875                        system(['chmod +x ' file_exe_global]);% set the file to executable
[867]1876                    case {'PCWIN','PCWIN64'}
[917]1877                        cmd=['matlab -automation -logfile ' regexprep(filelog{iprocess},'\\','\\\\')...
[867]1878                            ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
[917]1879                            'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');'];
1880                        for iprocess=1:NbProcess
[918]1881                            cmd=[cmd '' Param.Action.ActionName  '( ''' regexprep(filexml{iprocess},'\\','\\\\') ''');']
[917]1882                        end
1883                        cmd=[cmd ';exit"'];
1884                        fprintf(fid,cmd);%fill the executable file with the  char string cmd
[867]1885                        fclose(fid);% close the executable file
1886                end
[918]1887                system([file_exe_global ' &'])% directly execute the command file
[867]1888            case '.sh' % compiled Matlab function
[918]1889                for iprocess=1:NbProcess
1890                    switch computer
1891                        case {'GLNX86','GLNXA64','MACI64'}
1892                            [fid,message]=fopen(batch_file_list{iprocess},'w');% create the executable file
1893                            if isequal(fid,-1)
1894                                errormsg=['creation of .bat file: ' message];
1895                                return
1896                            end
1897                            cmd=['#!/bin/bash \n '...
1898                                '#$ -cwd \n '...
1899                                'hostname && date \n '...
1900                                'umask 002 \n'...
[934]1901                                ActionFullName ' ' RunTime ' ' filexml{iprocess}];%allow writting access to created files for user group
[918]1902                            fprintf(fid,cmd);%fill the executable file with the  char string cmd
1903                            fclose(fid);% close the executable file
1904                            system(['chmod +x ' batch_file_list{iprocess}]);% set the file to executable
1905                            system([batch_file_list{iprocess} ' &'])% directly execute the command file
1906                        case {'PCWIN','PCWIN64'}
1907                            msgbox_uvmat('ERROR','option for compiled Matlab functions not implemented for Windows system')
1908                            return
1909                    end
[867]1910                end
[922]1911                msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched in background: press STATUS to see results'])
[867]1912        end
[918]1913       
1914    case 'cluster_oar' % option 'oar-parexec' used
1915        %create subdirectory for oar commands
[932]1916        for iprocess=1:NbProcess
[918]1917            [fid,message]=fopen(batch_file_list{iprocess},'w');% create the executable file
1918            if isequal(fid,-1)
1919                errormsg=['creation of .bat file: ' message];
1920                return
1921            end
1922            if  strcmp(ActionExt,'.sh')
[932]1923                cmd=['#!/bin/bash \n '...
1924                    '#$ -cwd \n '...
1925                    'hostname && date \n '...
1926                    'umask 002 \n'...
1927                    ActionFullName ' ' RunTime ' ' filexml{iprocess}];%allow writting access to created files for user group
[918]1928            else
1929                cmd=[...
[932]1930                    '#!/bin/bash \n'...
1931                    '. /etc/sysprofile \n'...
[937]1932                    'module load matlab/8.6 \n'...% CHOICE OF MATLAB VERSION
[932]1933                    'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog{iprocess} ''' <<END_MATLAB \n'...
1934                    'addpath(''' path_series '''); \n'...
1935                    'addpath(''' Param.Action.ActionPath '''); \n'...
1936                    '' Param.Action.ActionName  '( ''' filexml{iprocess} '''); \n'...
1937                    'exit \n'...
1938                    'END_MATLAB \n'];
[918]1939            end
1940            fprintf(fid,cmd);%fill the executable file with the  char string cmd
1941            fclose(fid);% close the executable file
1942            system(['chmod +x ' batch_file_list{iprocess}]);% set the file to executable
1943        end
1944        DirOAR=fullfile(OutputDir,'0_OAR');
1945        if exist(DirOAR,'dir')% delete the content of the dir 0_LOG to allow new input
1946            curdir=pwd;
1947            cd(DirOAR)
1948            delete('*')
1949            cd(curdir)
1950        else
1951            [tild,msg1]=mkdir(DirOAR);
1952            if ~strcmp(msg1,'')
1953                errormsg=['cannot create ' DirOAR ': ' msg1];%error message for directory creation
1954                return
1955            end
1956        end
1957        % create file containing the list of jobs
[932]1958        filename_joblist=fullfile(DirOAR,'job_list.txt');% name of the file containing the list of executables
[918]1959        fid=fopen(filename_joblist,'w');%open it for writting
1960        for iprocess=1:length(batch_file_list)
1961            fprintf(fid,[batch_file_list{iprocess} '\n']);% write list of exe files
1962        end
1963        fclose(fid);
1964        system(['chmod +x ' filename_joblist]);% set the file to executable
1965       
1966        filename_log=fullfile(DirLog,'job_list.stdout');%file for output messages of the master oar process
1967        filename_errors=fullfile(DirLog,'job_list.stderr');%file for error messages of the master oar process
1968        % the command job_list.txt contains the list of NbProcess independent individual jobs
1969        % in which the total calculation has been split. Those are written as executable files .sh in the folder /O_EXE.
1970        %  These individual jobs are grouped by the system as oar jobs on the NbCore processors.
1971        %  For each processor, the oar job must stop after the walltime which has been set, which is limited to 24 h.
1972        %  However, the oar job is automatically restarted (option 'idempotent') provided the individual jobs are
1973        % shorter than the wall time: in the time interval 'checkpoint' (WallTimeOneJob) before the end of the allowed duration,
1974        %  the oar job restarts when an individual job ends.
1975        JobTime=CPUTime*BlockLength*nbfield_j;% estimated time for one individual job (in minutes)
1976        % wall time (in hours ) for each oar job, allowing 10 individual jobs, but limited to 23 h:
1977        WallTimeTotal=min(23,4*JobTime/60);
1978        %disp(['WallTimeTotal: ' num2str(WallTimeTotal) ' hours'])
1979        % estimated time of an individual job (in min), with a margin of error
1980        WallTimeOneJob=min(4*JobTime+10,WallTimeTotal*60/2);% estimated max time of an individual job for checkpoint
1981        disp(['WallTimeOneJob: ' num2str(WallTimeOneJob) ' minutes'])
[922]1982        oar_command=['oarsub -n UVmat_' ActionFullName ' '...
[918]1983            '-t idempotent --checkpoint ' num2str(WallTimeOneJob*60) ' '...
1984            '-l /core=' num2str(NbCore) ','...
1985            'walltime=' datestr(WallTimeTotal/24,13) ' '...
1986            '-E ' filename_errors ' '...
1987            '-O ' filename_log ' '...
1988            extra_oar ' '...
[932]1989            '"oar-parexec -s -f ' filename_joblist ' '...
[918]1990            '-l ' filename_joblist '.log"'];
[922]1991       
[918]1992        fprintf(oar_command);% display  system command on the Matlab command window
1993        [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window
1994        filename_oarcommand=fullfile(DirOAR,'0_oar_command');% keep track of the command in file '0-OAR/0_oar_command'
1995        fid=fopen(filename_oarcommand,'w');
1996        fprintf(fid,oar_command); % store the command
1997        fprintf(fid,result);% store the result (job ID number)
1998        fclose(fid);
[922]1999        msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched as  ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
[918]2000       
2001    case 'cluster_pbs' % for LMFA Kepler machine
2002        %create subdirectory for pbs command and log files
2003        DirPBS=fullfile(OutputDir,'0_PBS'); %todo : common name OAR/PBS
2004        if exist(DirPBS,'dir')% delete the content of the dir 0_LOG to allow new input
2005            curdir=pwd;
2006            cd(DirPBS)
2007            delete('*')
2008            cd(curdir)
2009        else
2010            [tild,msg1]=mkdir(DirPBS);
2011            if ~strcmp(msg1,'')
2012                errormsg=['cannot create ' DirPBS ': ' msg1];%error message for directory creation
2013                return
2014            end
2015        end
2016        max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h)
2017        walltime_onejob=1800; % seconds, max estimated time for asingle file index value
2018        filename_joblist=fullfile(DirPBS,'job_list.txt');%create name of the global executable file
2019        fid=fopen(filename_joblist,'w');
2020        for iprocess=1:length(batch_file_list)
2021            fprintf(fid,[batch_file_list{iprocess} '\n']);% list of exe files
2022        end
2023        fclose(fid);
2024        system(['chmod +x ' filename_joblist]);% set the file to executable
2025        pbs_command=['qstat -n CIVX '...
2026            '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
2027            '-l /core=' num2str(NbCore) ','...
2028            'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
2029            '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
2030            '-O ' regexprep(filename_joblist,'\.txt\>','.log') ' '...
2031            extra_oar ' '...
2032            '"oar-parexec -s -f ' filename_joblist ' '...
2033            '-l ' filename_joblist '.log"'];
2034        filename_oarcommand=fullfile(DirPBS,'pbs_command');
2035        fid=fopen(filename_oarcommand,'w');
2036        fprintf(fid,pbs_command);
2037        fclose(fid);
2038        fprintf(pbs_command);% display in command line
2039        %system(pbs_command);
[922]2040        msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster'])
[918]2041    case 'python'
2042        command = [
2043            'LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "p.split('':'') | [s for s in p if ''matlab'' not in s] | '':''.join(p)") ' ...
[942]2044            'python -m fluidimage.run_from_xml ' filexml{iprocess}];
[918]2045        % fprintf(['command:\n' command '\n\n'])
2046        system(command, '-echo');
[867]2047end
[932]2048if exist(OutputDir,'dir')
[935]2049    [SUCCESS,MESSAGE,MESSAGEID] = fileattrib (OutputDir)
2050    if MESSAGE.GroupWrite~=1
[932]2051    [success,msg] = fileattrib(OutputDir,'+w','g','s');% allow writing access for the group of users, recursively in the folder
2052    if success==0
[935]2053        msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg});%error message for directory creation
[932]2054    end
[935]2055    end
[932]2056end
[934]2057
[867]2058%------------------------------------------------------------------------
2059function STOP_Callback(hObject, eventdata, handles)
2060%------------------------------------------------------------------------
2061set(handles.RUN, 'BusyAction','cancel')
2062set(handles.RUN,'BackgroundColor',[1 0 0])
2063set(handles.RUN,'enable','on')
2064set(handles.RUN, 'Value',0)
2065
2066%------------------------------------------------------------------------
2067% --- read parameters from the GUI series
2068%------------------------------------------------------------------------
2069function Param=read_GUI_series(handles)
2070
2071%% read raw parameters from the GUI series
2072Param=read_GUI(handles.series);
2073
2074%% clean the output structure by removing unused information
2075if isfield(Param,'Pairs')
2076    Param=rmfield(Param,'Pairs'); %info Pairs not needed for output
2077end
2078if isfield(Param,'InputLine')
2079    Param=rmfield(Param,'InputLine');
2080end
2081if isfield(Param,'EditObject')
2082    Param=rmfield(Param,'EditObject');
2083end
2084Param.IndexRange.TimeSource=Param.IndexRange.TimeTable{end,1};
2085Param.IndexRange=rmfield(Param.IndexRange,'TimeTable');
2086empty_line=false(size(Param.InputTable,1),1);
2087for iline=1:size(Param.InputTable,1)
2088    empty_line(iline)=isempty(cell2mat(Param.InputTable(iline,1:3)));
2089end
2090Param.InputTable(empty_line,:)=[];
2091
2092%------------------------------------------------------------------------
2093% --- Executes on selection change in ActionName.
2094function ActionName_Callback(hObject, eventdata, handles)
2095%------------------------------------------------------------------------
2096
2097%% stop any ongoing series processing
2098if isequal(get(handles.RUN,'Value'),1)
2099    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
2100    if strcmp(answer,'Yes')
2101        STOP_Callback(hObject, eventdata, handles)
2102    else
2103        return
2104    end
2105end
2106set(handles.ActionName,'BackgroundColor',[1 1 0])
2107huigetfile=findobj(allchild(0),'tag','status_display');
2108if ~isempty(huigetfile)
2109    delete(huigetfile)
2110end
2111drawnow
2112
2113%% get Action name and path
2114NbBuiltinAction=get(handles.Action,'UserData'); %nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
2115ActionList=get(handles.ActionName,'String');% list menu fields
2116ActionIndex=get(handles.ActionName,'Value');
2117if ~isequal(ActionIndex,1)% if we are not just opening series
2118    InputTable=get(handles.InputTable,'Data');
2119    if isempty(InputTable{1,4})
2120        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
2121        return
2122    end
2123end
2124ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2125ActionPathList=get(handles.ActionName,'UserData');%list of recorded paths to functions of the list ActionName
2126
2127%% add a new function to the menu if 'more...' has been selected in the menu ActionName
2128if isequal(ActionName,'more...')
2129    [FileName, PathName] = uigetfile( ...
2130        {'*.m', ' (*.m)';
2131        '*.m',  '.m files '; ...
2132        '*.*', 'All Files (*.*)'}, ...
2133        'Pick a series processing function ',get(handles.ActionPath,'String'));
2134    if length(FileName)<2
2135        return
2136    end
2137    [tild,ActionName,ActionExt]=fileparts(FileName);
2138   
2139    % insert the choice in the menu ActionName
2140    ActionIndex=find(strcmp(ActionName,ActionList),1);% look for the selected function in the menu Action
2141    PathName=regexprep(PathName,'/$','');
2142    if ~isempty(ActionIndex) && ~strcmp(ActionPathList{ActionIndex},PathName)%compare the path to the existing fct
2143        ActionIndex=[]; % the selected path is different than the recorded one
2144    end
2145    if isempty(ActionIndex)%the qselected fct (with selected path) does not exist in the menu
2146        ActionIndex= length(ActionList);
2147        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)];% the selected function is appended in the menu, before the last item 'more...'
2148         ActionPathList=[ActionPathList; PathName];
2149    end
2150   
2151    % record the file extension and extend the path list if it is a new extension
[886]2152    ActionExtList=get(handles.ActionExt,'String');
2153    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
2154    if isempty(ActionExtIndex)
2155        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
2156    end
[867]2157
2158    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
2159    if length(ActionList)>NbBuiltinAction+5; %nb_builtin_ACTION=nbre of functions always remaining in the initial menu
2160        nbremove=length(ActionList)-NbBuiltinAction-5;
2161        ActionList(NbBuiltinAction+1:end-5)=[];
2162        ActionPathList(NbBuiltinAction+1:end-4,:)=[];
2163        ActionIndex=ActionIndex-nbremove;
2164    end
2165   
2166    % record action menu, choice and path
2167    set(handles.ActionName,'Value',ActionIndex)
2168    set(handles.ActionName,'String',ActionList)
2169       set(handles.ActionName,'UserData',ActionPathList);
2170    set(handles.ActionExt,'Value',ActionExtIndex)
2171       
2172    %record the user defined menu additions in personal file profil_perso
2173    dir_perso=prefdir;
2174    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2175    if NbBuiltinAction+1<=numel(ActionList)-1
2176        ActionListUser=ActionList(NbBuiltinAction+1:numel(ActionList)-1);
2177        ActionPathListUser=ActionPathList(NbBuiltinAction+1:numel(ActionList)-1);
[886]2178        ActionExtListUser={};
2179        if numel(ActionExtList)>2
2180            ActionExtListUser=ActionExtList(3:end);
2181        end
[867]2182        if exist(profil_perso,'file')
2183            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
2184        else
2185            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
2186        end
2187    end
2188end
2189
2190%% check the current ActionPath to the selected function
2191ActionPath=ActionPathList{ActionIndex};%current recorded path
2192set(handles.ActionPath,'String',ActionPath); %show the path to the senlected function
2193
2194%% reinitialise the waitbar
2195update_waitbar(handles.Waitbar,0)
2196
2197%% create the function handle for Action
[897]2198if ~exist(ActionPath,'dir')
2199    msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']);
2200    return
[867]2201end
[897]2202current_dir=pwd;%current working dir
2203cd(ActionPath)
2204h_fun=str2func(ActionName);
2205cd(current_dir)
[867]2206
[897]2207%
2208% checkaddpath=0;
2209% path_series=which('series');
2210% %eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
2211% spath=fileparts(which(ActionName)); %spath = current path of the selected function ACTION
2212% if ~exist(ActionPath,'dir')
2213%     msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']);
2214%     return
2215% end
2216% if ~strcmp(spath,ActionPath)
2217%     if strcmp(pwd,spath)
2218%         msgbox_uvmat('ERROR',[ 'a function called ' ActionName ' on your working space oversets the selected one']);
2219%         return
2220%     else
2221%         addpath(ActionPath)% add the prescribed path if not the current one
2222%         checkaddpath=1;
2223%     end
2224% end
2225% eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
2226% if checkaddpath && ~isequal(ActionPath,path_series)
2227%     rmpath(ActionPath)% add the prescribed path if not the current one
2228% end
2229
[867]2230%% Activate the Action fct to adapt the configuration of the GUI series and bring specific parameters in SeriesData
2231Param=read_GUI_series(handles);% read the parameters from the GUI series
2232ParamOut=h_fun(Param);%run the selected Action function to get the relevant input
2233
2234%% Put the first line of the selected Action fct as tooltip help
2235try
2236    [fid,errormsg] =fopen([ActionName '.m']);
2237    InputText=textscan(fid,'%s',1,'delimiter','\n');
2238    fclose(fid);
2239    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
2240end
2241
2242
2243%% Visibility of VelType and VelType_1 menus asked by ActionName
2244VelTypeRequest=1;%VelType requested by default
2245VelTypeRequest_1=1;%VelType requested by default
2246if isfield(ParamOut,'VelType')
2247    VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'});
2248    VelTypeRequest_1=strcmp( ParamOut.VelType,'two');
2249end
2250FieldNameRequest=0;  %hidden by default
2251FieldNameRequest_1=0;  %hidden by default
2252if isfield(ParamOut,'FieldName')
2253    FieldNameRequest=ismember(ParamOut.FieldName,{'on','one','two'});
2254    FieldNameRequest_1=strcmp( ParamOut.FieldName,'two');
2255end
2256
2257%% Detect the types of input files and set menus and default options in 'VelType'
2258SeriesData=get(handles.series,'UserData');% info on the input file series
2259iview_civ=find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));
2260iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));% all nc files, icluding civ
2261FieldList=get(handles.FieldName,'String');% previous list as default
2262if ~iscell(FieldList),FieldList={FieldList};end
2263FieldList_1=get(handles.FieldName_1,'String');% previous list as default
2264if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
[897]2265%CheckList=0;% indicate whether FieldName has been updated
[867]2266CheckList_1=1;% indicate whether FieldName_1 has been updated
2267handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title];
2268if VelTypeRequest && numel(iview_civ)>=1
2269    menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)});
2270    set(handles.VelType,'Value',1)% set first choice by default
2271    set(handles.VelType,'String',[{'*'};menu])
2272    set(handles.VelType,'Visible','on')
2273    set(handles.VelType_title,'Visible','on')
2274    FieldList=[set_field_list('U','V');{'C'};{'get_field...'}];%standard menu for civx data
[897]2275    %CheckList=1;
[867]2276    set(handles.FieldName,'Value',1); %velocity vector choice by default
2277    if  VelTypeRequest_1 && numel(iview_civ)>=2
2278        menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});
2279        set(handles.VelType_1,'Value',1)% set first choice by default
2280        set(handles.VelType_1,'String',[{'*'};menu])
2281        set(handles.VelType_1,'Visible','on')
2282        set(handles.VelType_title_1,'Visible','on')
2283        FieldList_1=[set_field_list('U','V');{'C'};{'get_field...'}];%standard menu for civx data
2284        CheckList_1=1;
2285        set(handles.FieldName_1,'Value',1); %velocity vector choice by default
2286    else
2287        set(handles.VelType_1,'Visible','off')
2288        set(handles.VelType_title_1,'Visible','off')
2289    end
2290else
2291    set(handles.VelType,'Visible','off')
2292    set(handles.VelType_title,'Visible','off')
2293end   
2294
2295%% Detect the types of input files and set menus and default options in 'FieldName'
[940]2296if (FieldNameRequest || VelTypeRequest) && numel(iview_netcdf)>=1
2297    set(handles.InputFields,'Visible','on')   
2298    if FieldNameRequest && isfield(SeriesData.FileInfo{iview_netcdf(1)},'ListVarName')
2299        set(handles.FieldName,'Visible','on')
[867]2300        ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName;
2301        ind_var=get(handles.FieldName,'Value');%indices of previously selected variables
2302        for ilist=1:numel(ind_var)
2303            if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2304                FieldList={};% previous choice not consistent with new input field
2305                set(handles.FieldName,'Value',1)
2306                break
2307            end
2308        end
2309        if ~isempty(FieldList)
2310            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2311                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2312                FieldList={};
2313                set(handles.Coord_x,'String','')
2314                set(handles.Coord_y,'String','')
2315            end
2316            Coord_z=get(handles.Coord_z,'String');
2317            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2318                FieldList={};
2319                set(handles.Coord_z,'String','')
2320            end
2321        end
2322        set(handles_coord,'Visible','on')
2323        FieldList=[FieldList;{'get_field...'}];
2324        if FieldNameRequest_1 && numel(iview_netcdf)>=2
2325            set(handles.FieldName_1,'Visible','on')
2326            if CheckList_1==0        % not civ input made
2327                ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName;
2328                ind_var=get(handles.FieldName,'Value');%indices of previously selected variables
2329                for ilist=1:numel(ind_var)
2330                    if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2331                        FieldList_1={};% previous choice not consistent with new input field
2332                        set(handles.FieldName_1,'Value',1)
2333                        break
2334                    end
2335                end
2336                warn_coord=0;
2337                if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2338                        isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2339                    warn_coord=1;
2340                end
2341                if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2342                    FieldList_1={};
2343                    warn_coord=1;
2344                end
2345                if warn_coord
2346                    msgbox_uvmat('WARNING','coordiante names do not exist in the second netcdf input file')
2347                end
2348                set(handles.FieldName,'String',[FieldList;{'get_field...'}])
2349                set(handles.FieldName_1,'Visible','on')
2350                set(handles.FieldName_1,'Value',1)
2351                set(handles.FieldName_1,'String',FieldList_1)
2352            end
2353        else
2354            set(handles.FieldName_1,'Visible','off')
2355        end
[940]2356    else
2357        set(handles.FieldName,'Visible','off')
2358    end
[867]2359    set(handles.FieldName,'String',FieldList)
2360else
2361    set(handles.InputFields,'Visible','off')
2362end
2363
[904]2364%% Introduce visibility of file overwrite option
2365if isfield(ParamOut,'CheckOverwriteVisible')&& strcmp(ParamOut.CheckOverwriteVisible,'on')
2366    set(handles.CheckOverwrite,'Visible','on')
2367else
2368    set(handles.CheckOverwrite,'Visible','off')
2369end
[867]2370
2371%% Check whether alphabetical sorting of input Subdir is allowed by the Action fct  (for multiples series entries)
2372if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Param.InputTable,1)>1
2373    [tild,iview]=sort(InputTable(:,2)); %subdirectories sorted in alphabetical order
2374    set(handles.InputTable,'Data',InputTable(iview,:));
2375    MinIndex_i=get(handles.MinIndex_i,'Data');
2376    MinIndex_j=get(handles.MinIndex_j,'Data');
2377    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2378    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2379    set(handles.MinIndex_i,'Data',MinIndex_i(iview,:));
2380    set(handles.MinIndex_j,'Data',MinIndex_j(iview,:));
2381    set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:));
2382    set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));
2383    TimeTable=get(handles.TimeTable,'Data');
2384    set(handles.TimeTable,'Data',TimeTable(iview,:));
2385    PairString=get(handles.PairString,'Data');
2386    set(handles.PairString,'Data',PairString(iview,:));
2387end
2388
2389%% Impose the whole input file index range if requested
2390if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on')
2391    MinIndex_i=get(handles.MinIndex_i,'Data');
2392    MinIndex_j=get(handles.MinIndex_j,'Data');
2393    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2394    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2395    set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line)
2396    set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line)
2397    set(handles.num_incr_i,'String','1')
2398    set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line)
2399    set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line)
2400    set(handles.num_incr_j,'String','1')
2401else  % check index ranges
2402    first_i=1;last_i=1;first_j=1;last_j=1;
2403    if isfield(Param.IndexRange,'first_i')
2404        first_i=Param.IndexRange.first_i;
2405        last_i=Param.IndexRange.last_i;
2406    end
2407    if isfield(Param.IndexRange,'first_j')
2408        first_j=Param.IndexRange.first_j;
2409        last_j=Param.IndexRange.last_j;
2410    end
2411    if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
2412            set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
2413end
2414
2415%% enable or desable j index visibility
2416status_j='on';%default
2417if isfield(ParamOut,'Desable_j_index')&&isequal(ParamOut.Desable_j_index,'on')
2418    status_j='off';
2419end
2420if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices
2421    status_j='off'; % no j index needed
2422elseif strcmp(get(handles.PairString,'Visible'),'on')
2423    check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j'));%=0 for burst case, 1 otherwise
2424    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
2425        status_j='off'; % no j index needed for bust case
2426    end
2427end
2428enable_j(handles,status_j) % no j index needed
2429
2430
2431%% NbSlice visibility
[897]2432%NbSliceVisible='off';%default
2433if isfield(ParamOut,'NbSlice') && (strcmp(ParamOut.NbSlice,'on')||isnumeric(ParamOut.NbSlice))
2434    set(handles.num_NbSlice,'Visible','on')
2435    set(handles.NbSlice_title,'Visible','on')
[867]2436else
[897]2437    set(handles.num_NbSlice,'Visible','off')
2438    set(handles.NbSlice_title,'Visible','off')
2439    %     set(handles.num_NbProcess,'String',get(handles.num_NbSlice,'String'))% the nbre of processes is imposed as the nbre of slices
2440    % else
2441    %     set(handles.num_NbProcess,'String','')% free nbre of processes
[867]2442end
[897]2443if isnumeric(ParamOut.NbSlice)
2444    set(handles.num_NbSlice,'String',num2str(ParamOut.NbSlice))
2445    set(handles.num_NbSlice,'Enable','off'); % NbSlice set by the activation of the Action function
2446else
2447    set(handles.num_NbSlice,'Enable','on'); % NbSlice can be modified on the GUI series
2448end
2449% set(handles.num_NbSlice,'Visible',NbSliceVisible)
2450% set(handles.NbSlice_title,'Visible',NbSliceVisible)
[867]2451
2452
2453
2454%% Visibility of FieldTransform menu
2455FieldTransformVisible='off';  %hidden by default
2456if isfield(ParamOut,'FieldTransform')
2457    FieldTransformVisible=ParamOut.FieldTransform; 
2458    TransformName_Callback([],[], handles)
2459end
2460set(handles.FieldTransform,'Visible',FieldTransformVisible)
2461if isfield(ParamOut,'TransformPath')
2462    set(handles.ActionExt,'UserData',ParamOut.TransformPath)
2463else
2464    set(handles.ActionExt,'UserData',[])
2465end
2466
2467%% Visibility of projection object
2468ProjObjectVisible='off';  %hidden by default
2469if isfield(ParamOut,'ProjObject')
2470    ProjObjectVisible=ParamOut.ProjObject;
2471end
2472set(handles.CheckObject,'Visible',ProjObjectVisible)
2473if ~get(handles.CheckObject,'Value')
2474    ProjObjectVisible='off';
2475end
2476set(handles.ProjObject,'Visible',ProjObjectVisible)
2477set(handles.DeleteObject,'Visible',ProjObjectVisible)
2478set(handles.ViewObject,'Visible',ProjObjectVisible)
2479set(handles.EditObject,'Visible',ProjObjectVisible)
2480
2481%% Visibility of mask input
2482MaskVisible='off';  %hidden by default
2483if isfield(ParamOut,'Mask')
2484    MaskVisible=ParamOut.Mask;
2485end
2486set(handles.CheckMask,'Visible',MaskVisible);
2487
2488%% definition of the directory containing the output files
2489if  ~(isfield(SeriesData,'ActionName') && strcmp(ActionName,SeriesData.ActionName))
2490    OutputDirExt='.series'; %default
2491    if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
2492        OutputDirExt=ParamOut.OutputDirExt;
2493    end
2494    set(handles.OutputDirExt,'String',OutputDirExt)
2495end
2496OutputDirVisible='off';
2497OutputSubDirMode='auto';%default
2498SubDirOut='';
2499if isfield(ParamOut,'OutputSubDirMode')
2500    OutputSubDirMode=ParamOut.OutputSubDirMode;
2501end
2502switch OutputSubDirMode
2503    case 'auto';%default
2504        OutputDirVisible='on';
2505        SubDir=InputTable(1:end,2); %set of subdirectories
2506        SubDirOut=SubDir{1};
2507        if numel(SubDir)>1
2508            for ilist=2:numel(SubDir)
2509                SubDirOut=[SubDirOut '-' regexprep(SubDir{ilist},'^/','')];
2510            end
2511        end
2512    case 'one'
2513        OutputDirVisible='on';
2514        SubDirOut=InputTable{1,2}; %use the first subdir name (+OutputDirExt) as output  subdirectory
2515    case 'two'
2516        OutputDirVisible='on';   
2517        SubDir=InputTable(1:2,2); %set of subdirectories
2518        SubDirOut=SubDir{1};
2519        if numel(SubDir)>1
2520                SubDirOut=[SubDirOut '-' regexprep(SubDir{2},'^/','')];
2521        end
2522    case 'last'
2523        OutputDirVisible='on';
2524        SubDirOut=InputTable{end,2}; %use the last subdir name (+OutputDirExt) as output  subdirectory
2525end
2526set(handles.OutputSubDir,'String',SubDirOut)
[883]2527set(handles.OutputSubDir,'BackgroundColor',[1 1 1])% set edit box to white color to indicate refreshment
[867]2528set(handles.OutputDirExt,'Visible',OutputDirVisible)
2529set(handles.OutputSubDir,'Visible',OutputDirVisible)
[904]2530%set(handles.CheckOverwrite,'Visible',OutputDirVisible)
[867]2531set(handles.OutputDir_title,'Visible',OutputDirVisible)
2532SeriesData.ActionName=ActionName;%record ActionName for next use
2533
2534
2535%% visibility of the run mode (local or background or cluster)
2536if strcmp(OutputSubDirMode,'none')
2537    RunModeVisible='off';% only local mode available if no output file is produced
2538else
2539    RunModeVisible='on';
2540end
2541set(handles.RunMode,'Visible',RunModeVisible)
2542set(handles.ActionExt,'Visible',RunModeVisible)
2543set(handles.RunMode_title,'Visible',RunModeVisible)
2544set(handles.ActionExt_title,'Visible',RunModeVisible)
2545
2546
2547%% Expected nbre of output files
2548if isfield(ParamOut,'OutputFileMode')
2549    StatusData.OutputFileMode=ParamOut.OutputFileMode;
2550    set(handles.status,'UserData',StatusData)
2551end
2552
2553%% definition of an additional parameter set, determined by an ancillary GUI
2554if isfield(ParamOut,'ActionInput')
2555    set(handles.ActionInput,'Visible','on')
2556    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
2557    SeriesData.ActionInput=ParamOut.ActionInput;
2558else
2559    set(handles.ActionInput,'Visible','off')
2560    if isfield(SeriesData,'ActionInput')
2561        SeriesData=rmfield(SeriesData,'ActionInput');
2562    end
2563end
2564set(handles.series,'UserData',SeriesData)
2565set(handles.ActionName,'BackgroundColor',[1 1 1])
2566
2567%------------------------------------------------------------------------
2568% --- Executes on selection change in FieldName.
2569function FieldName_Callback(hObject, eventdata, handles)
2570%------------------------------------------------------------------------
2571field_str=get(handles.FieldName,'String');
2572field_index=get(handles.FieldName,'Value');
2573field=field_str{field_index(1)};
2574if isequal(field,'get_field...')
2575    SeriesData=get(handles.series,'UserData');
2576    % input line for which the field choice is relevant
2577    iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'}));% all nc files, icluding civ
2578    hget_field=findobj(allchild(0),'name','get_field');
2579    if ~isempty(hget_field)
2580        delete(hget_field)%delete opened versions of get_field
2581    end
2582    Param=read_GUI(handles.series);
2583    InputTable=Param.InputTable(iview,:);
2584    % check the existence of the first file in the series
2585    first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1;%default setting for index j
2586    if isfield(Param.IndexRange,'first_j');% if index j is used     
2587        first_j=Param.IndexRange.first_j;
2588        last_j=Param.IndexRange.last_j;
2589        MinIndex_j=Param.IndexRange.MinIndex_j(iview);
2590        MaxIndex_j=Param.IndexRange.MaxIndex_j(iview);
2591    end
2592    PairString='';
2593    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end
2594    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2595    LineIndex=iview(1);
2596    if numel(iview)>1     
2597        answer=msgbox_uvmat('INPUT_TXT',['select the line of the input table:' num2str(iview)] ,num2str(iview(1)));
2598        LineIndex=str2num(answer);
2599%         InputLine=str2num(get(handles.InputLine,'String'));
2600%         if ismember(InputLine,iview)
2601%             LineIndex=InputLine;
2602%         end
2603    end
2604    FirstFileName=fullfile_uvmat(InputTable{LineIndex,1},InputTable{LineIndex,2},InputTable{LineIndex,3},...
2605        InputTable{LineIndex,5},InputTable{LineIndex,4},i1,i2,j1,j2);
2606    if exist(FirstFileName,'file')
2607        ParamIn.Title='get_field: pick input variables and coordinates for series processing';
2608        ParamIn.SeriesInput=1;
2609        GetFieldData=get_field(FirstFileName,ParamIn);
2610        FieldList={};
[876]2611        if isfield(GetFieldData,'FieldOption')% if a field has been selected
[867]2612        switch GetFieldData.FieldOption
2613            case 'vectors'
2614                UName=GetFieldData.PanelVectors.vector_x;
2615                VName=GetFieldData.PanelVectors.vector_y;
2616                YName={GetFieldData.Coordinates.Coord_y};
2617                FieldList={['vec(' UName ',' VName ')'];...
2618                    ['norm(' UName ',' VName ')'];...
2619                    UName;VName};
2620            case {'scalar'}
2621                FieldList=GetFieldData.PanelScalar.scalar;
2622                YName={GetFieldData.Coordinates.Coord_y};
2623                if ischar(FieldList)
2624                    FieldList={FieldList};
2625                end
2626            case 'civdata...'
2627                FieldList=[set_field_list('U','V') ;{'C'}];
2628                set(handles.FieldName,'Value',1) % set menu to 'velocity
2629                XName='X';
2630                YName='y';
2631        end
2632        set(handles.FieldName,'Value',1)
2633        set(handles.FieldName,'String',[FieldList; {'get_field...'}]);
2634        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2635           if ~isempty(regexp(FieldList{1},'^vec'))
2636                set(handles.FieldName,'Value',1)
2637           else
2638                set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
2639           end
2640            XName=GetFieldData.Coordinates.Coord_x;
2641            YName=GetFieldData.Coordinates.Coord_y;
2642            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2643            % get the time info                     
2644            TimeTable=get(handles.TimeTable,'Data');
2645            switch TimeNameStr
2646                case 'file index'
2647                    TimeName='';
2648                case 'attribute'
2649                    TimeName=['att:' GetFieldData.Time.TimeName];
2650                    % update the time table
2651                    TimeTable{LineIndex,2}=get_time(Param.IndexRange.MinIndex_i(LineIndex),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Min time     
2652                    TimeTable{LineIndex,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % first time             
2653                    TimeTable{LineIndex,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % last time                     
2654                    TimeTable{LineIndex,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Max time
2655                case 'variable'
2656                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2657                    set(handles.NomType,'String','*')
2658                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2659                    set(handles.FileIndex,'String','')
2660                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2661                case 'matrix_index'
2662                    TimeName=['dim:' GetFieldData.Time.TimeName];
2663                    set(handles.NomType,'String','*')
2664                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2665                    set(handles.FileIndex,'String','')
2666                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2667            end
2668            TimeTable{LineIndex,1}=TimeName;
2669            set(handles.TimeTable,'Data',TimeTable);
2670        end
2671        set(handles.Coord_x,'String',XName)
2672        set(handles.Coord_y,'String',YName)
2673        set(handles.Coord_x,'Visible','on')
2674        set(handles.Coord_y,'Visible','on')
[876]2675        end
[867]2676    else
2677        msgbox_uvmat('ERROR',[FirstFileName ' does not exist'])
2678    end
2679end
2680
2681function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
2682[i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
2683FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2);
2684Data=nc2struct(FileName,[]);
2685TimeValue=[];
2686DtValue=[];
2687if isequal(FileInfo.FileType,'civdata')
2688    if ismember(TimeName,{'civ1','filter1'})
2689        TimeValue=Data.Civ1_Time;
2690        DtValue=Data.Civ1_Dt;
2691    else
2692        TimeValue=Data.Civ2_Time;
2693        DtValue=Data.Civ2_Dt;
2694    end
2695else
2696    if ~isempty(TimeName)&& isfield(Data,TimeName)
2697        TimeValue=Data.(TimeName);
2698    end
2699    if exist('DtName','var') && isfield(Data,DtName)
2700        DtValue=Data.(DtName);
2701    end
2702end
2703
2704%------------------------------------------------------------------------
2705% --- Executes on selection change in FieldName_1.
2706function FieldName_1_Callback(hObject, eventdata, handles)
2707%------------------------------------------------------------------------
2708field_str=get(handles.FieldName_1,'String');
2709field_index=get(handles.FieldName_1,'Value');
2710field=field_str{field_index(1)};
2711if isequal(field,'get_field...')
2712    hget_field=findobj(allchild(0),'name','get_field');
2713    if ~isempty(hget_field)
2714        delete(hget_field)%delete opened versions of get_field
2715    end
2716    Param=read_GUI(handles.series);
2717    Param.InputTable=Param.InputTable(1,:);
2718    % check the existence of the first file in the series
2719    first_j=[];
2720    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
2721    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
2722    PairString='';
2723    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
2724    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2725    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
2726        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
2727    if exist(FirstFileName,'file')
2728        ParamIn.SeriesInput=1;
2729        GetFieldData=get_field(FirstFileName,ParamIn);
2730        FieldList={};
2731        switch GetFieldData.FieldOption
2732            case 'vectors'
2733                UName=GetFieldData.PanelVectors.vector_x;
2734                VName=GetFieldData.PanelVectors.vector_y;
2735                FieldList={['vec(' UName ',' VName ')'];...
2736                    ['norm(' UName ',' VName ')'];...
2737                    UName;VName};
2738            case {'scalar','pick variables'}
2739                FieldList=GetFieldData.PanelScalar.scalar;
2740                if ischar(FieldList)
2741                    FieldList={FieldList};
2742                end
2743            case '1D plot'
2744
2745            case 'civdata...'
2746                FieldList=set_field_list('U','V','C');
2747                set(handles.FieldName,'Value',2) % set menu to 'velocity
2748        end
2749        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2750            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2751            switch TimeNameStr
2752                case 'file index'
2753                    set(handles.TimeName,'String','');
2754                case 'attribute'
2755                    set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
2756                case 'variable'
2757                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2758                    set(handles.NomType,'String','*')
2759                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2760                    set(handles.FileIndex,'String','')
2761                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2762                case 'matrix_index'
2763                    set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]);
2764                    set(handles.NomType,'String','*')
2765                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2766                    set(handles.FileIndex,'String','')
2767                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2768            end
2769        end
2770        set(handles.FieldName_1,'Value',1)
2771        set(handles.FieldName_1,'String',[FieldList; {'get_field...'}]);
2772    end
2773end   
2774
2775
2776%%%%%%%%%%%%%
2777function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
2778indsel=ind_i;
2779indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
2780indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds
2781if ~isempty(indiff)
2782    indiff2=diff(indiff);
2783    indiffp=[indiff2 1];
2784    indiffm=[1 indiff2];
2785    ind_multi_m=find((indiff==0)&(indiffm<0))-1;%indices of first members of multiplets
2786    ind_multi_p=find((indiff==0)&(indiffp>0));%indices of last members of multiplets
2787    %for each multiplet, select the most recent file
2788    ind_remove=[];
2789    for i=1:length(ind_multi_m)
2790        ind_pairs=ind_multi_m(i):ind_multi_p(i);
2791        for imulti=1:length(ind_pairs)
2792            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date);%dates of creation
2793        end
2794        [datenew,indsort2]=sort(datepair); %sort the multiplet by creation date
2795        ind_s=indsort2(1:end-1);%
2796        ind_remove=[ind_remove ind_pairs(ind_s)];%remove these indices, leave the last one
2797    end
2798end
2799
2800%------------------------------------------------------------------------
2801% --- determine the list of index pairstring of processing file
2802function [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)
2803%------------------------------------------------------------------------
2804num_i1=num_i;% set of first image numbers by default
2805num_i2=num_i;
2806num_j1=num_j;
2807num_j2=num_j;
2808num_i_out=num_i;
2809num_j_out=num_j;
2810% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
2811if isequal(mode,'series(Di)')
2812    num_i1_line=num_i+ind_shift(3);% set of first image numbers
2813    num_i2_line=num_i+ind_shift(4);
2814    % adjust the first and last field number
2815        indsel=find(num_i1_line >= 1);
2816    num_i_out=num_i(indsel);
2817    num_i1_line=num_i1_line(indsel);
2818    num_i2_line=num_i2_line(indsel);
2819    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
2820    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
2821    [xx,num_i1]=meshgrid(num_j,num_i1_line);
2822    [xx,num_i2]=meshgrid(num_j,num_i2_line);
2823elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
2824    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
2825        num_j1=ind_shift(1)*ones(size(num_i));
2826        num_j2=ind_shift(2)*ones(size(num_i));
2827    else
2828        num_j1_col=num_j+ind_shift(1);% set of first image numbers
2829        num_j2_col=num_j+ind_shift(2);
2830        % adjust the first field number
2831        indsel=find((num_j1_col >= 1));   
2832        num_j_out=num_j(indsel);
2833        num_j1_col=num_j1_col(indsel);
2834        num_j2_col=num_j2_col(indsel);
2835        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
2836        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
2837    end   
2838end
2839
2840%------------------------------------------------------------------------
2841% --- Executes on button press in CheckObject.
2842function CheckObject_Callback(hObject, eventdata, handles)
2843%------------------------------------------------------------------------
2844hset_object=findobj(allchild(0),'tag','set_object');%find the set_object interface handle
2845if get(handles.CheckObject,'Value')
2846    SeriesData=get(handles.series,'UserData');
2847    if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject)
2848        set(handles.ViewObject,'Value',1)
2849        ViewObject_Callback(hObject, eventdata, handles)
2850    else
2851        if ishandle(hset_object)
2852            uistack(hset_object,'top')% show the GUI set_object if opened
2853        else
2854            %get the object file
2855            InputTable=get(handles.InputTable,'Data');
2856            defaultname=InputTable{1,1};
2857            if isempty(defaultname)
2858                defaultname={''};
2859            end
2860            fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml');
2861            if isempty(fileinput)% exit if no object file is selected
2862                set(handles.CheckObject,'Value',0)
2863                return
2864            end
2865            %read the file
2866            data=xml2struct(fileinput);
2867            if ~isfield(data,'Type')
2868                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
2869                set(handles.CheckObject,'Value',0)
2870                return
2871            end
2872            if ~isfield(data,'ProjMode')
2873                data.ProjMode='none';
2874            end
2875            hset_object=set_object(data);% call the set_object interface
2876            set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat
2877        end
2878        ProjObject=read_GUI(hset_object);
2879        set(handles.ProjObject,'String',ProjObject.Name);%display the object name
2880        SeriesData=get(handles.series,'UserData');
2881        SeriesData.ProjObject=ProjObject;
2882        set(handles.series,'UserData',SeriesData);
2883    end
2884    set(handles.EditObject,'Visible','on');
2885    set(handles.DeleteObject,'Visible','on');
2886    set(handles.ViewObject,'Visible','on');
2887    set(handles.ProjObject,'Visible','on');
2888else
2889    set(handles.EditObject,'Visible','off');
2890    set(handles.DeleteObject,'Visible','off');
2891    set(handles.ViewObject,'Visible','off');
2892    if ~ishandle(hset_object)
2893        set(handles.ViewObject,'Value',0);
2894    end
2895    set(handles.ProjObject,'Visible','off');
2896end
2897
2898%------------------------------------------------------------------------
2899% --- Executes on button press in ViewObject.
2900%------------------------------------------------------------------------
2901function ViewObject_Callback(hObject, eventdata, handles)
2902
2903UserData=get(handles.series,'UserData');
2904hset_object=findobj(allchild(0),'Tag','set_object');
2905if ~isempty(hset_object)
2906    delete(hset_object)% refresh set_object if already opened
2907end
2908hset_object=set_object(UserData.ProjObject);
2909set(hset_object,'Name','view_object_series')
2910
2911
2912%------------------------------------------------------------------------
2913% --- Executes on button press in EditObject.
2914function EditObject_Callback(hObject, eventdata, handles)
2915%------------------------------------------------------------------------
2916if get(handles.EditObject,'Value')
2917    set(handles.ViewObject,'Value',0)
2918        UserData=get(handles.series,'UserData');
2919    hset_object=set_object(UserData.ProjObject);
2920    set(hset_object,'Name','edit_object_series')
2921    set(get(hset_object,'Children'),'Enable','on')
2922else
2923    hset_object=findobj(allchild(0),'Tag','set_object');
2924    if ~isempty(hset_object)
2925        set(get(hset_object,'Children'),'Enable','off')
2926    end
2927end
2928
2929%------------------------------------------------------------------------
2930% --- Executes on button press in DeleteObject.
2931function DeleteObject_Callback(hObject, eventdata, handles)
2932%------------------------------------------------------------------------
2933SeriesData=get(handles.series,'UserData');
2934SeriesData.ProjObject=[];
2935set(handles.series,'UserData',SeriesData)
2936set(handles.ProjObject,'String','')
2937set(handles.ProjObject,'Visible','off')
2938set(handles.CheckObject,'Value',0)
2939set(handles.ViewObject,'Visible','off')
2940set(handles.EditObject,'Visible','off')
2941hset_object=findobj(allchild(0),'name','set_object_series');
2942if ~isempty(hset_object)
2943    delete(hset_object)
2944end
2945set(handles.DeleteObject,'Visible','off')
2946
2947%------------------------------------------------------------------------
2948% --- Executed when CheckMask is activated
2949%------------------------------------------------------------------------
2950function CheckMask_Callback(hObject, eventdata, handles)
2951
2952if get(handles.CheckMask,'Value')
2953    InputTable=get(handles.InputTable,'Data');
2954    nbview=size(InputTable,1);
2955    MaskTable=cell(nbview,1);%default
2956    ListMask=cell(nbview,1);%default
2957    MaskData=get(handles.MaskTable,'Data');
2958    MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1);%complement if undefined lines
2959    for iview=1:nbview
2960        ListMask{iview,1}=num2str(iview);
2961        RootPath=InputTable{iview,1};
2962        if ~isempty(RootPath)
2963            if isempty(MaskData{iview})
2964                SubDir=InputTable{iview,2};
2965                MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']);%take the root part of SubDir, before the first dot '.'
2966                if exist(MaskPath,'dir')
2967                    ListStruct=dir(MaskPath);%look for a mask file
2968                    ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray
2969                    check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files
2970                    ListFiles=ListCells(1,:);%list of file and dri names
2971                    ListFiles=ListFiles(~check_dir);%list of file names (excluding dir)
2972                    mdetect=0;
2973                    if ~isempty(ListFiles)
2974                        for ifile=1:numel(ListFiles)
2975                            [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0);
2976                            if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series)
2977                                mdetect=1;
2978                                MaskName=ListFiles{ifile};
2979                            end
2980                            if ~strcmp(MaskFile{ifile},MaskFile{1})
2981                                mdetect=0;% cancel detection test in case of multiple masks, use the brower for selection
2982                                break
2983                            end
2984                        end
2985                    end
2986                    if mdetect==1
2987                        MaskName=fullfile(MaskPath,'mask_1.png');
2988                    else
2989                        MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image');
2990                    end
2991                else
2992                    MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
2993                end
2994                MaskTable{iview,1}=MaskName ;
2995                ListMask{iview,1}=num2str(iview);
2996            end
2997        end
2998    end
2999    set(handles.MaskTable,'Data',MaskTable)
3000    set(handles.MaskTable,'Visible','on')
3001    set(handles.MaskBrowse,'Visible','on')
3002    set(handles.ListMask,'Visible','on')
3003    set(handles.ListMask,'String',ListMask)
3004    set(handles.ListMask,'Value',1)
3005else
3006    set(handles.MaskTable,'Visible','off')
3007    set(handles.MaskBrowse,'Visible','off')
3008    set(handles.ListMask,'Visible','off')
3009end
3010
3011%------------------------------------------------------------------------
3012% --- Executes on button press in MaskBrowse.
3013%------------------------------------------------------------------------
3014function MaskBrowse_Callback(hObject, eventdata, handles)
3015
3016InputTable=get(handles.InputTable,'Data');
3017iview=get(handles.ListMask,'Value');
3018RootPath=InputTable{iview,1};
3019MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3020if ~isempty(MaskName)
3021    MaskTable=get(handles.MaskTable,'Data');
3022    MaskTable{iview,1}=MaskName ;
3023    set(handles.MaskTable,'Data',MaskTable)
3024end
3025
3026%------------------------------------------------------------------------
3027% --- Executes when selected cell(s) is changed in MaskTable.
3028%------------------------------------------------------------------------
3029function MaskTable_CellSelectionCallback(hObject, eventdata, handles)
3030
3031if numel(eventdata.Indices)>=1
3032set(handles.ListMask,'Value',eventdata.Indices(1))
3033end
3034
3035%-------------------------------------------------------------------
3036function MenuHelp_Callback(hObject, eventdata, handles)
3037%-------------------------------------------------------------------
3038
3039
3040% path_to_uvmat=which ('uvmat');% check the path of uvmat
3041% pathelp=fileparts(path_to_uvmat);
3042% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
3043% 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')
3044% else
3045%     addpath (fullfile(pathelp,'uvmat_doc'))
3046%     web([helpfile '#series'])
3047% end
3048
3049%-------------------------------------------------------------------
3050% --- Executes on selection change in TransformName.
3051function TransformName_Callback(hObject, eventdata, handles)
3052%----------------------------------------------------------------------
3053TransformList=get(handles.TransformName,'String');
3054TransformIndex=get(handles.TransformName,'Value');
3055TransformName=TransformList{TransformIndex};
3056TransformPathList=get(handles.TransformName,'UserData');
3057nb_builtin_transform=4;
3058if isequal(TransformName,'more...');     
3059    FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
3060    if isempty(FileName)
3061        return     %browser closed without choice
3062    end
3063    [TransformPath,TransformName,TransformExt]=fileparts(FileName);% removes extension .m
3064    if ~strcmp(TransformExt,'.m')
3065        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3066        return
3067    end
3068     % insert the choice in the menu
3069    TransformIndex=find(strcmp(TransformName,TransformList),1);% look for the selected function in the menu Action
3070    if isempty(TransformIndex)%the input string does not exist in the menu
3071        TransformIndex= length(TransformList);
3072        TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)];% the selected function is appended in the menu, before the last item 'more...'
3073        set(handles.TransformName,'String',TransformList)
3074        TransformPathList=[TransformPathList;{TransformPath}];
3075    else% the input function already exist, we update its path (possibly new)
3076        TransformPathList{TransformIndex}=TransformPath;%
3077        set(handles.TransformName,'Value',TransformIndex)
3078    end
3079   % save the new menu in the personal file 'uvmat_perso.mat'
3080   dir_perso=prefdir;%personal Matalb directory
3081   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3082   if exist(profil_perso,'file')
3083       for ilist=nb_builtin_transform+1:numel(TransformPathList)
3084           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
3085           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
3086       end
3087       TransformPathListUser=TransformPathListUser';
3088       TransformListUser=TransformListUser';
3089       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); %store the root name for future opening of uvmat
3090   end
3091end
3092
3093%display the current function path
3094set(handles.TransformPath,'String',TransformPathList{TransformIndex}); %show the path to the senlected function
3095set(handles.TransformName,'UserData',TransformPathList);
3096
[883]3097%% create the function handle of the selected fct
3098if ~isempty(TransformName)
[897]3099    if ~exist(TransformPathList{TransformIndex},'dir')
3100        msgbox_uvmat('ERROR',['The prescribed transform function path ' TransformPathList{TransformIndex} ' does not exist']);
3101        return
3102    end
[883]3103    current_dir=pwd;%current working dir
3104    cd(TransformPathList{TransformIndex})
3105    transform_handle=str2func(TransformName);
3106    cd(current_dir)
3107    Field.Action.RUN=0;% indicate that the transform fct is called only to get input param
3108    DataOut=feval(transform_handle,Field,[]);% execute the transform fct to get the required conditions
3109    if isfield(DataOut,'TransformInput')%  used to add transform parameters at selection of the transform fct
3110        SeriesData=get(handles.series,'UserData');
3111        SeriesData.TransformInput=DataOut.TransformInput;
3112        set(handles.series,'UserData',SeriesData)
3113    end
3114end
3115
[867]3116%------------------------------------------------------------------------
3117% --- fct activated by the upper bar menu ExportConfig
3118%------------------------------------------------------------------------
3119function MenuDisplayConfig_Callback(hObject, eventdata, handles)
3120
3121global Param
3122Param=read_GUI_series(handles);
3123evalin('base','global Param')%make CurData global in the workspace
3124display('current series config :')
3125evalin('base','Param') %display CurData in the workspace
3126commandwindow; %brings the Matlab command window to the front
3127
3128%------------------------------------------------------------------------
3129% --- fct activated by the upper bar menu InportConfig: import
3130%     menu settings from an xml file (stored in /0_XML for each run)
3131%------------------------------------------------------------------------
3132function MenuImportConfig_Callback(hObject, eventdata, handles)
3133
3134%% use a browser to choose the xml file containing the processing config
3135InputTable=get(handles.InputTable,'Data');
3136oldfile=InputTable{1,1};%current path in InputTable
3137if isempty(oldfile)
3138    % use a file name stored in prefdir
3139    dir_perso=prefdir;
3140    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3141    if exist(profil_perso,'file')
3142        h=load (profil_perso);
3143        if isfield(h,'RootPath') && ischar(h.RootPath)
3144            oldfile=h.RootPath;
3145        end
3146    end
3147end
3148filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml');% get the xml file containing processing parameters
3149if isempty(filexml), return, end % quit function if an xml file has not been opened
3150
3151%% fill the GUI series with the content of the xml file
3152Param=xml2struct(filexml);% read the input xml file as a Matlab structure
3153
3154% ask to stop current Action if button RUN is in action (another process is already running)
3155if isequal(get(handles.RUN,'Value'),1)
3156    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
3157    if strcmp(answer,'Yes')
3158        STOP_Callback(hObject, eventdata, handles)
3159    else
3160        return
3161    end
3162end
3163Param.Action.RUN=0; %desactivate the input RUN=1
3164
3165fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
3166SeriesData=get(handles.series,'UserData');
3167if isfield(Param,'InputFields')
3168    ListField=Param.InputFields.FieldName;
3169    if ischar(ListField),ListField={ListField}; end
3170    set(handles.FieldName,'String',[ListField;{'get-field...'}])
3171     set(handles.FieldName,'Value',1:numel(ListField))
3172     set(handles.FieldName,'Visible','on')
3173end       
3174if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
3175    set(handles.ActionInput,'Visible','on')
3176    set(handles.ActionInput,'Value',0)
3177    Param.ActionInput.ConfigSource=filexml;% record the source of config for future info
3178    SeriesData.ActionInput=Param.ActionInput;
3179end
[883]3180if isfield(Param,'TransformInput')%  introduce  parameters specific to a transform fct
3181    SeriesData.TransformInput=Param.TransformInput;
3182end
[867]3183if isfield(Param,'ProjObject') %introduce projection object if relevant
3184    SeriesData.ProjObject=Param.ProjObject;
3185end
3186set(handles.series,'UserData',SeriesData)
3187if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
3188    set(handles.ProjObject,'String',Param.ProjObject.Name)
3189    set(handles.ViewObject,'Visible','on')
3190    set(handles.EditObject,'Visible','on')
3191    set(handles.DeleteObject,'Visible','on')
3192else     
3193    set(handles.ProjObject,'String','')
3194    set(handles.ProjObject,'Visible','off')
3195    set(handles.ViewObject,'Visible','off')
3196    set(handles.EditObject,'Visible','off')
3197    set(handles.DeleteObject,'Visible','off')     
3198end     
3199set(handles.REFRESH,'BackgroundColor',[1 0 1]); %paint REFRESH button in magenta to indicate that it should be activated
3200
3201
3202%------------------------------------------------------------------------
3203% --- Executes when the GUI series is resized.
3204%------------------------------------------------------------------------
3205function series_ResizeFcn(hObject, eventdata, handles)
3206
3207%% input table
3208set(handles.InputTable,'Unit','pixel')
3209Pos=get(handles.InputTable,'Position');
3210set(handles.InputTable,'Unit','normalized')
3211ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
3212ColumnWidth=num2cell(ColumnWidth);
3213set(handles.InputTable,'ColumnWidth',ColumnWidth)
3214
3215%% MinIndex_j and MaxIndex_i
3216unit=get(handles.MinIndex_i,'Unit');
3217set(handles.MinIndex_i,'Unit','pixel')
3218Pos=get(handles.MinIndex_i,'Position');
3219set(handles.MinIndex_i,'Unit',unit)
3220set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18})
3221set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18})
3222set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18})
3223set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18})
3224
3225%% TimeTable
3226set(handles.TimeTable,'Unit','pixel')
3227Pos=get(handles.TimeTable,'Position');
3228set(handles.TimeTable,'Unit','normalized')
3229% ColumnWidth=get(handles.TimeTable,'ColumnWidth');
3230ColumnWidth=num2cell(floor([0.2 0.2 0.2 0.2 0.2]*(Pos(3)-20)));
3231set(handles.TimeTable,'ColumnWidth',ColumnWidth)
3232
3233
3234%% PairString
3235set(handles.PairString,'Unit','pixel')
3236Pos=get(handles.PairString,'Position');
3237set(handles.PairString,'Unit','normalized')
3238set(handles.PairString,'ColumnWidth',{Pos(3)-5})
3239
3240%% MaskTable
3241set(handles.MaskTable,'Unit','pixel')
3242Pos=get(handles.MaskTable,'Position');
3243set(handles.MaskTable,'Unit','normalized')
3244set(handles.MaskTable,'ColumnWidth',{Pos(3)-5})
3245
3246%------------------------------------------------------------------------
3247% --- Executes on button press in status.
3248%------------------------------------------------------------------------
3249function status_Callback(hObject, eventdata, handles)
3250
3251if get(handles.status,'Value')
3252    set(handles.status,'BackgroundColor',[1 1 0])
3253    drawnow
3254    Param=read_GUI(handles.series);
3255    RootPath=Param.InputTable{1,1};
3256    if ~isfield(Param,'OutputSubDir')   
3257        msgbox_uvmat('ERROR','no standard sub-directory definition for output files, use a browser to check the output')
3258        set(handles.status,'BackgroundColor',[0 1 0])
3259        return
3260    end
3261    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
3262    OutputDir=fullfile(RootPath,OutputSubDir);
3263    if exist(OutputDir,'dir')
3264        uigetfile_uvmat('status_display',OutputDir)
3265    else
3266        msgbox_uvmat('ERROR','output folder not created yet: calculation did not start')
3267        set(handles.status,'BackgroundColor',[0 1 0])
3268    end
3269else
3270    %% delete current display fig if selection is off
3271    set(handles.status,'BackgroundColor',[0 1 0])
3272    hfig=findobj(allchild(0),'name','status_display');
3273    if ~isempty(hfig)
3274        delete(hfig)
3275    end
3276    return
3277end
3278
3279
3280%------------------------------------------------------------------------   
3281% launched by selecting a file on the list
3282%------------------------------------------------------------------------
3283function view_file(hObject, eventdata)
3284
3285list=get(hObject,'String');
3286index=get(hObject,'Value');
3287rootroot=get(hObject,'UserData');
3288selectname=list{index};
3289ind_dot=regexp(selectname,'\.\.\.');
3290if ~isempty(ind_dot)
3291    selectname=selectname(1:ind_dot-1);
3292end
3293FullSelectName=fullfile(rootroot,selectname);
3294if exist(FullSelectName,'dir')% a directory has been selected
3295    ListFiles=dir(FullSelectName);
3296    ListDisplay=cell(numel(ListFiles),1);
3297    for ilist=2:numel(ListDisplay)% suppress the first line '.'
3298        ListDisplay{ilist-1}=ListFiles(ilist).name;
3299    end
3300    set(hObject,'Value',1)
3301    set(hObject,'String',ListDisplay)
3302    if strcmp(selectname,'..')
3303        FullSelectName=fileparts(fileparts(FullSelectName));
3304    end
3305    set(hObject,'UserData',FullSelectName)
3306    hfig=get(hObject,'parent');
3307    htitlebox=findobj(hfig,'tag','titlebox');   
3308    set(htitlebox,'String',FullSelectName)
3309elseif exist(FullSelectName,'file')%visualise the vel field if it exists
3310    FileInfo=get_file_info(FullSelectName);   
3311    if strcmp(FileInfo.FileType,'txt')
3312        edit(FullSelectName)
3313    elseif strcmp(FileInfo.FileType,'xml')
3314        editxml(FullSelectName)
3315    else
3316        uvmat(FullSelectName)
3317    end
3318    set(gcbo,'Value',1)
3319end
3320
3321
3322%------------------------------------------------------------------------   
3323% launched by refreshing the status figure
3324%------------------------------------------------------------------------
3325function refresh_GUI(hfig)
3326
3327htitlebox=findobj(hfig,'tag','titlebox');
3328hlist=findobj(hfig,'tag','list');
3329hseries=findobj(allchild(0),'tag','series');
3330hstatus=findobj(hseries,'tag','status');
3331StatusData=get(hstatus,'UserData');
3332OutputDir=get(htitlebox,'String');
3333if ischar(OutputDir),OutputDir={OutputDir};end
3334ListFiles=dir(OutputDir{1});
3335if numel(ListFiles)<1
3336    return
3337end
3338ListFiles(1)=[];%removes the first line ='.'
3339ListDisplay=cell(numel(ListFiles),1);
3340testrecent=0;
3341datnum=zeros(numel(ListDisplay),1);
3342for ilist=1:numel(ListDisplay)
3343    ListDisplay{ilist}=ListFiles(ilist).name;
3344      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
3345            datnum(ilist)=ListFiles(ilist).datenum;%only available in recent matlab versions
3346            testrecent=1;
3347       end
3348end
3349set(hlist,'String',ListDisplay)
3350
3351%% Look at date of creation
3352ListDisplay=ListDisplay(datnum~=0);
3353datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
3354NbOutputFile=[];
3355if isempty(datnum)
3356    if testrecent
3357        message='no civ result created yet';
3358    else
3359        message='';
3360    end
3361else
3362    [first,indfirst]=min(datnum);
3363    [last,indlast]=max(datnum);
3364    NbOutputFile_str='?';
3365    NbOutputFile=[];
3366    if isfield(StatusData,'NbOutputFile')
3367        NbOutputFile=StatusData.NbOutputFile;
3368        NbOutputFile_str=num2str(NbOutputFile);
3369    end
3370    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
3371        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
3372end
3373set(htitlebox,'String', [OutputDir{1};message])
3374
3375%% update the waitbar
3376hwaitbar=findobj(hfig,'tag','waitbar');
3377if ~isempty(NbOutputFile)
3378    BarPosition=get(hwaitbar,'Position');
3379    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
3380    set(hwaitbar,'Position',BarPosition)
3381end
3382
3383%------------------------------------------------------------------------
3384% --- Executes on selection change in ActionExt.
3385%------------------------------------------------------------------------
3386function ActionExt_Callback(hObject, eventdata, handles)
3387
3388ActionExtList=get(handles.ActionExt,'String');
3389ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
3390if strcmp(ActionExt,'.py (in dev.)')
3391    set(handles.RunMode,'Value',2)
3392end
3393
[897]3394%function num_NbProcess_Callback(hObject, eventdata, handles)
[867]3395
3396
3397function num_NbSlice_Callback(hObject, eventdata, handles)
3398NbSlice=str2num(get(handles.num_NbSlice,'String'));
[897]3399%set(handles.num_NbProcess,'String',num2str(NbSlice))
[867]3400
3401%------------------------------------------------------------------------
3402% --- set the visibility of relevant velocity type menus:
3403function menu=set_veltype_display(Civ,FileType)
3404%------------------------------------------------------------------------
3405if ~exist('FileType','var')
3406    FileType='civx';
3407end
3408switch FileType
3409    case 'civx'
3410        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3411        if isequal(Civ,0)
3412            imax=0;
3413        elseif isequal(Civ,1) || isequal(Civ,2)
3414            imax=1;
3415        elseif isequal(Civ,3)
3416            imax=3;
3417        elseif isequal(Civ,4) || isequal(Civ,5)
3418            imax=4;
3419        elseif isequal(Civ,6) %patch2
3420            imax=6;
3421        end
3422    case 'civdata'
3423        menu={'civ1';'filter1';'civ2';'filter2'};
3424        if isequal(Civ,0)
3425            imax=0;
3426        elseif isequal(Civ,1) || isequal(Civ,2)
3427            imax=1;
3428        elseif isequal(Civ,3)
3429            imax=2;
3430        elseif isequal(Civ,4) || isequal(Civ,5)
3431            imax=3;
[912]3432        else%if isequal(Civ,6) %patch2
[867]3433            imax=4;
3434        end
3435end
3436menu=menu(1:imax);
3437
3438
3439% --- Executes on mouse motion over figure - except title and menu.
3440function series_WindowButtonMotionFcn(hObject, eventdata, handles)
3441set(hObject,'Pointer','arrow');
3442
3443
3444% --- Executes on button press in SetPairs.
3445function SetPairs_Callback(hObject, iview, handles)
3446
3447%% delete previous occurrence of 'set_pairs'
3448hfig=findobj(allchild(0),'Tag','set_pairs');
3449if ~isempty(hfig)
3450delete(hfig)
3451end
3452
3453%% create the GUI set_pairs
3454set(0,'Unit','points')
3455ScreenSize=get(0,'ScreenSize');% get the size of the screen, to put the fig on the upper right
3456Width=220;% fig width in points (1/72 inch)
3457Height=min(0.8*ScreenSize(4),300);
3458Left=ScreenSize(3)- Width-40; %right edge close to the right, with margin=40
3459Bottom=ScreenSize(4)-Height-40; %put fig at top right
3460hfig=findobj(allchild(0),'Tag','set_slice');
3461if ~isempty(hfig),delete(hfig), end; %delete existing version of the GUI
3462hfig=figure('name','set_pairs','tag','set_pairs','MenuBar','none','NumberTitle','off','Unit','points','Position',[Left,Bottom,Width,Height]);
3463BackgroundColor=get(hfig,'Color');
3464SeriesData=get(handles.series,'UserData');
3465TimeUnit=get(handles.TimeUnit,'String');
3466PairString=get(handles.PairString,'Data');
3467ListViewLines=find(cellfun('isempty',PairString)==0);%find list of non empty pairs
3468ListViewMenu=cell(numel(ListViewLines),1);
3469for ilist=1:numel(ListViewLines)
3470    ListViewMenu{ilist}=num2str(ListViewLines(ilist));
3471end
3472if isempty(iview)
3473    ListViewValue=numel(ListViewLines);% we work by default on the pair option for the last line which requires pairs
3474    iview=ListViewLines(end);
3475else
3476    ListViewValue=find(ListViewLines==iview);
3477end
3478ref_i=str2num(get(handles.num_first_i,'String'));
3479ref_j=1;%default
3480if strcmp(get(handles.num_first_j,'String'),'Visible')
3481    ref_j=str2num(get(handles.num_first_j,'String'));
3482end
3483[ModeMenu,ModeValue]=update_mode(SeriesData.i1_series{iview},SeriesData.i2_series{iview},SeriesData.j2_series{iview});
3484displ_pair=update_listpair(SeriesData.i1_series{iview},SeriesData.i2_series{iview},SeriesData.j1_series{iview},SeriesData.j2_series{iview},ModeMenu{ModeValue},...
3485                                                     SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo{iview});
3486% first raw of the GUI
3487uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,...
3488    'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right');%title
3489uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.54 0.8 0.3 0.2],'BackgroundColor',[1 1 1],...
3490    'Callback',@(hObject,eventdata)ListView_Callback(hObject,eventdata),'String',ListViewMenu,'Value',ListViewValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3491    'Tag','ListView','TooltipString','''ListView'':choice of the file series w for pair display');
3492% second raw of the GUI
3493uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.79 0.7 0.1],'BackgroundColor',BackgroundColor,...
3494    'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left');%title
3495uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.05 0.62 0.9 0.2],'BackgroundColor',[1 1 1],...
3496    'Callback',@(hObject,eventdata)Mode_Callback(hObject,eventdata),'String',ModeMenu,'Value',ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3497    'Tag','Mode','TooltipString','''Mode'': choice of the image pair mode');
3498% third raw
3499uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.6 0.7 0.1],'BackgroundColor',BackgroundColor,...
3500    'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left');%title
3501uicontrol('Style','listbox','Units','normalized', 'Position', [0.05 0.42 0.9 0.2],'BackgroundColor',[1 1 1],...
3502    'Callback',@(hObject,eventdata)ListPair_Callback(hObject,eventdata),'String',displ_pair,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3503    'Tag','ListPair','TooltipString','''ListPair'': menu for selecting the image pair');
3504uicontrol('Style','text','Units','normalized', 'Position', [0.1 0.22 0.8 0.1],'BackgroundColor',BackgroundColor,...
3505    'String','ref_i           ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center');%title
3506uicontrol('Style','edit','Units','normalized', 'Position', [0.15 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3507    'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),'String',num2str(ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3508    'Tag','num_ref_i','TooltipString','''num_ref_i'': reference field index i used to display dt in ''list_pair_civ''');
3509uicontrol('Style','edit','Units','normalized', 'Position', [0.55 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3510    'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),'String',num2str(ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3511    'Tag','num_ref_j','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ''');
[880]3512uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.01 0.01 0.3 0.12],'BackgroundColor',[0 1 0],...
3513    'Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),'String','OK','FontUnits','points','FontSize',12,'FontWeight','bold',...
3514    'Tag','OK','TooltipString','''OK'': validate the choice');
[867]3515%  last raw  of the GUI: pushbuttons
3516% 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),...
3517%     'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''OK'': apply the output to the current field series in uvmat');
3518drawnow
3519
3520%------------------------------------------------------------------------
3521function ListView_Callback(hObject,eventdata)
3522Mode_Callback(hObject,eventdata)
3523
3524%------------------------------------------------------------------------   
3525function Mode_Callback(hObject,eventdata)
3526%% get input info
3527hseries=findobj(allchild(0),'tag','series');%handles of the GUI series
3528hhseries=guidata(hseries);%handles of the elements in the GUI series
3529TimeUnit=get(hhseries.TimeUnit,'String');
3530SeriesData=get(hseries,'UserData');
3531mode_list=get(hObject,'String');
3532mode=mode_list{get(hObject,'Value')};
3533hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3534iview=get(hListView,'Value');
3535i1_series=SeriesData.i1_series{iview};
3536i2_series=SeriesData.i2_series{iview};
3537j1_series=SeriesData.j1_series{iview};
3538j2_series=SeriesData.j2_series{iview};
3539
3540%% enable j index visibility after the new choice
3541status_j='on';%default
3542if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices
3543    status_j='off'; % no j index needed
3544elseif strcmp(get(handles.PairString,'Visible'),'on')
3545    check_burst=cellfun(@isempty,regexp(PairString,'^j'));%=0 for burst case, 1 otherwise
3546    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
3547        status_j='off'; % no j index needed for bust case
3548    end
3549end
3550enable_j(handles,status_j) % no j index needed
3551
3552%% get the reference indices for the time interval Dt
3553href_i=findobj(get(hObject,'parent'),'Tag','ref_i');
3554ref_i=[];ref_j=[];
3555if strcmp(get(href_i,'Visible'),'on')
3556    ref_i=str2num(get(href_i,'String'));
3557end
3558if isempty(ref_i)
3559    ref_i=1;
3560end
3561if isempty(ref_j)
3562    ref_j=1;
3563end
3564
3565%% update the menu ListPair
3566Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,SeriesData.Time{iview},TimeUnit,ref_i,ref_j,FileInfo);
3567hlist_pairs=findobj(get(hObject,'parent'),'Tag','ListPair');
3568set(hlist_pairs,'Value',1)% set the first choice by default in ListPair
3569set(hlist_pairs,'String',Menu)% set the menu in ListPair
3570ListPair_Callback(hlist_pairs,[])% apply the default choice in ListPair
3571
3572%-------------------------------------------------------------
3573% --- Executes on selection in ListPair.
3574function ListPair_Callback(hObject,eventdata)
3575%------------------------------------------------------------
3576list_pair=get(hObject,'String');%get the menu of image pairs
3577if isempty(list_pair)
3578    string='';
3579else
3580    string=list_pair{get(hObject,'Value')};
3581   % string=regexprep(string,',.*','');%removes time indication (after ',')
3582end
3583hseries=findobj(allchild(0),'tag','series');
3584hPairString=findobj(hseries,'tag','PairString');
3585PairString=get(hPairString,'Data');
3586hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3587iview=get(hListView,'Value');
3588PairString{iview,1}=string;
3589% report the selected pair string to the table PairString
3590set(hPairString,'Data',PairString)
3591
3592
3593%------------------------------------------------------------------------
3594function num_ref_i_Callback(hObject, eventdata)
3595%------------------------------------------------------------------------
3596Mode_Callback([],[])
3597
3598%------------------------------------------------------------------------
3599function num_ref_j_Callback(hObject, eventdata)
3600%------------------------------------------------------------------------
3601Mode_Callback([],[])
3602
3603%------------------------------------------------------------------------
[880]3604function OK_Callback(hObject, eventdata)
3605%------------------------------------------------------------------------
3606delete(get(hObject,'parent'))
3607
3608
3609%------------------------------------------------------------------------
[867]3610% --- Executes on button press in ClearLine.
3611%------------------------------------------------------------------------
3612function ClearLine_Callback(hObject, eventdata, handles)
3613InputTable=get(handles.InputTable,'Data');
3614iline=str2double(get(handles.InputLine,'String'));
3615if size(InputTable,1)>1
3616    InputTable(iline,:)=[];% suppress the current line if not the first
3617    set(handles.InputTable,'Data',InputTable);
3618end
[883]3619set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refr
[880]3620
3621
3622% --- Executes on button press in MonitorCluster.
3623function MonitorCluster_Callback(hObject, eventdata, handles)
3624web('https://www.legi.grenoble-inp.fr/servload/monika')
3625
3626
3627
3628function OutputSubDir_Callback(hObject, eventdata, handles)
3629set(handles.OutputSubDir,'BackgroundColor',[1 1 1])
[904]3630
3631
3632% --- Executes on button press in CheckOverwrite.
3633function CheckOverwrite_Callback(hObject, eventdata, handles)
[880]3634
[904]3635
3636
3637% --- Executes on button press in TestCPUTime.
3638function TestCPUTime_Callback(hObject, eventdata, handles)
3639% hObject    handle to TestCPUTime (see GCBO)
3640% eventdata  reserved - to be defined in a future version of MATLAB
3641% handles    structure with handles and user data (see GUIDATA)
3642
3643
3644
3645
3646
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