source: trunk/src/series.m @ 1011

Last change on this file since 1011 was 1011, checked in by sommeria, 5 years ago

series REFRESH improved

File size: 168.1 KB
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4%'series': master function associated to the GUI series.m for analysis field series 
5%------------------------------------------------------------------------
6% function varargout = series(varargin)
7% associated with the GUI series.fig
8%
9%INPUT
10% param: structure with input parameters (link with the GUI uvmat)
11%      .menu_coord_str: string for the TransformName (menu for coordinate transforms)
12%      .menu_coord_val: value for TransformName (menu for coordinate transforms)
13%      .FileName: input file name
14%      .FileName_1: second input file name
15%      .list_field: menu of input fields
16%      .index_fields: chosen index
17%      .civ1=0 or 1, .interp1,  ... : input civ field type
18%
19
20%=======================================================================
21% Copyright 2008-2017, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
22%   http://www.legi.grenoble-inp.fr
23%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
24%
25%     This file is part of the toolbox UVMAT.
26%
27%     UVMAT is free software; you can redistribute it and/or modify
28%     it under the terms of the GNU General Public License as published
29%     by the Free Software Foundation; either version 2 of the license,
30%     or (at your option) any later version.
31%
32%     UVMAT is distributed in the hope that it will be useful,
33%     but WITHOUT ANY WARRANTY; without even the implied warranty of
34%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
35%     GNU General Public License (see LICENSE.txt) for more details.
36%=======================================================================
37
38%------------------------------------------------------------------------
39%------------------------------------------------------------------------
40%  I - MAIN FUNCTION series
41%------------------------------------------------------------------------
42%------------------------------------------------------------------------
43function varargout = series(varargin)
44
45% Begin initialization code - DO NOT EDIT
46gui_Singleton = 1;
47gui_State = struct('gui_Name',       mfilename, ...
48                   'gui_Singleton',  gui_Singleton, ...
49                   'gui_OpeningFcn', @series_OpeningFcn, ...
50                   'gui_OutputFcn',  @series_OutputFcn, ...
51                   'gui_LayoutFcn',  [] , ...
52                   'gui_Callback',   []);
53if nargin && ischar(varargin{1})
54    gui_State.gui_Callback = str2func(varargin{1});
55end
56
57if nargout
58    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
59else
60    gui_mainfcn(gui_State, varargin{:});
61end
62% End initialization code - DO NOT EDIT
63
64%--------------------------------------------------------------------------
65% --- Executes just before series is made visible.
66%--------------------------------------------------------------------------
67function series_OpeningFcn(hObject, eventdata, handles,Param)
68
69% Choose default command line output for series
70handles.output = hObject;
71% Update handles structure
72guidata(hObject, handles);
73
74%% initial settings
75% position and  size of the GUI at opening
76set(0,'Unit','points')
77ScreenSize=get(0,'ScreenSize'); % size of the current screen, in points (1/72 inch)
78Width=900; % prefered width of the GUI in points (1/72 inch)
79Height=624; % prefered height of the GUI in points (1/72 inch)
80%adjust to screen size (reduced by a min margin)
81RescaleFactor=min((ScreenSize(3)-80)/Width,(ScreenSize(4)-80)/Height);
82if RescaleFactor>1
83    RescaleFactor=min(RescaleFactor,1);
84end
85Width=Width*RescaleFactor;
86Height=Height*RescaleFactor;
87LeftX=80*RescaleFactor; % position of the left fig side, in pixels (put to the left side, with some margin)
88LowY=round(ScreenSize(4)/2-Height/2); % put at the middle height on the screen
89set(hObject,'Units','points')
90set(hObject,'Position',[LeftX LowY Width Height])% position and size of the GUI at opening
91
92% settings of table MinIndex_j
93set(handles.MinIndex_i,'ColumnFormat',{'numeric'})
94set(handles.MinIndex_i,'ColumnEditable',false)
95set(handles.MinIndex_i,'ColumnName',{'i min'})
96set(handles.MinIndex_i,'Data',[])% initiate Data to double (not cell)
97
98% settings of table MinIndex_j
99set(handles.MinIndex_j,'ColumnFormat',{'numeric'})
100set(handles.MinIndex_j,'ColumnEditable',false)
101set(handles.MinIndex_j,'ColumnName',{'j min'})
102set(handles.MinIndex_j,'Data',[])% initiate Data to double (not cell)
103
104% settings of table MaxIndex_i
105set(handles.MaxIndex_i,'ColumnFormat',{'numeric'})
106set(handles.MaxIndex_i,'ColumnEditable',false)
107set(handles.MaxIndex_i,'ColumnName',{'i max'})
108set(handles.MaxIndex_i,'Data',[])% initiate Data to double (not cell)
109
110% settings of table MaxIndex_j
111set(handles.MaxIndex_j,'ColumnFormat',{'numeric'})
112set(handles.MaxIndex_j,'ColumnEditable',false)
113set(handles.MaxIndex_j,'ColumnName',{'j max'})
114set(handles.MaxIndex_j,'Data',[])% initiate Data to double (not cell)
115
116% settings of table PairString
117set(handles.PairString,'ColumnName',{'pairs'})
118set(handles.PairString,'ColumnEditable',false)
119set(handles.PairString,'ColumnFormat',{'char'})
120set(handles.PairString,'Data',{''})
121
122% settings of table MaskTable
123set(handles.MaskTable,'ColumnName',{'mask name'})
124set(handles.PairString,'ColumnEditable',false)
125set(handles.PairString,'ColumnFormat',{'char'})
126set(handles.PairString,'Data',{''})
127
128series_ResizeFcn(hObject, eventdata, handles)%resize table according to series GUI size
129set(hObject,'WindowButtonDownFcn',{'mouse_down'})%allows mouse action with right button (zoom for uicontrol display)
130set(hObject,'DeleteFcn',{@closefcn})%
131
132% check default input data
133if ~exist('Param','var')
134    Param=[]; % default
135end
136
137%% Read the parameter file series.xml, or created from series.xml.default if it does not exist
138SeriesData=[];
139[path_series,name,ext]=fileparts(which('series'));% path to the GUI series
140xmlfile=fullfile(path_series,'series.xml');
141if ~exist(xmlfile,'file')
142    [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);
143end
144if exist(xmlfile,'file')
145    SeriesData.SeriesParam=xml2struct(xmlfile);
146end
147
148%% list of builtin functions in the menu ActionName
149ActionList={'check_data_files';'aver_stat';'time_series';'civ_series';'merge_proj'}; % WARNING: fits with nb_builtin_ACTION=4 in ActionName_callback
150NbBuiltinAction=numel(ActionList);
151set(handles.Action,'UserData',NbBuiltinAction)
152path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series'
153[path_series,name,ext]=fileparts(which('series')); % path to the GUI series
154path_series_fct=fullfile(path_series,'series'); % path of the functions in subdirectroy 'series'
155command = ['LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "l = x.split('':''); l = [s for s in l if ''matlab'' not in s]; print('':''.join(l))") ' ...
156            'python -c "import fluidimage"'];
157[code, ~] = system(command);
158if code==0
159    ActionExtList={'.m';'.sh';'.py (in dev.)'}; % default choice of extensions (Matlab fct .m or compiled version .sh
160else
161    ActionExtList={'.m';'.sh'};  % python options not installed
162end
163ActionPathList=cell(NbBuiltinAction,1); % initiate the cell matrix of Action fct paths
164ActionPathList(:)={path_series_fct}; % set the default path to series fcts to all list members
165RunModeList={'local';'background'}; % default choice of extensions (Matlab fct .m or compiled version .sh)
166[s,w]=system('oarstat'); % look for cluster system 'oar'
167if isequal(s,0)
168    RunModeList=[RunModeList;{'cluster_oar'}];
169    set(handles.MonitorCluster,'Visible','on'); % make visible button for access to Monika
170    set(handles.num_CPUTime,'Visible','on'); % make visible button for access to Monika
171    set(handles.CPUTime_txt,'Visible','on'); % make visible button for access to Monika
172end
173[s,w]=system('qstat -help'); % look for cluster system 'sge'
174if isequal(s,0)
175    if regexp(w,'^pbs')
176        RunModeList=[RunModeList;{'cluster_pbs'}];
177    elseif regexp(w,'^SGE')
178        RunModeList=[RunModeList;{'cluster_sge'}];
179    else
180        RunModeList=[RunModeList;{'cluster_qstat_unknown'}];
181    end
182end
183set(handles.RunMode,'String',RunModeList)% display the menu of available run modes, local, background or cluster manager
184
185%% list of builtin transform functions in the menu TransformName
186TransformList={'';'sub_field';'phys';'phys_polar'}; % WARNING: must fit with the corresponding menu in uvmat and nb_builtin_transform=4 in  TransformName_callback
187NbBuiltinTransform=numel(TransformList);
188path_transform_fct=fullfile(path_series,'transform_field');
189TransformPathList=cell(NbBuiltinTransform,1); % initiate the cell matrix of Action fct paths
190TransformPathList(:)={path_transform_fct}; % set the default path to series fcts to all list members
191SeriesData.TransformPath=path_transform_fct;% store the standard path for trqnsform functions (needed for compilation)
192
193%% get the user defined functions stored in the personal file uvmat_perso.mat
194dir_perso=prefdir;
195profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
196if exist(profil_perso,'file')
197    h=load (profil_perso);
198    %get the list of previous input files in the upper bar menu Open
199    if isfield(h,'MenuFile')
200        for ifile=1:min(length(h.MenuFile),5)
201            set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile});
202            set(handles.(['MenuFile_' num2str(ifile+5)]),'Label',h.MenuFile{ifile});
203        end
204    end
205    %get the list of previous campaigns in the upper bar menu Open campaign
206    if isfield(h,'MenuCampaign')
207        for ifile=1:min(length(h.MenuCampaign),5)
208            set(handles.(['MenuCampaign_' num2str(ifile)]),'Label',h.MenuCampaign{ifile});
209        end
210    end
211    %get the menu of actions
212%     if isfield(h,'ActionExtListUser') && iscell(h.ActionExtListUser)
213%         ActionExtList=[ActionExtList; h.ActionExtListUser];
214%     end
215    if isfield(h,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser)
216        ActionList=[ActionList;h.ActionListUser];
217        ActionPathList=[ActionPathList;h.ActionPathListUser(:,1)];
218    end
219    %get the menu of transform fct
220    if isfield(h,'TransformListUser') && iscell(h.TransformListUser) && isfield(h,'TransformPathListUser') && iscell(h.TransformPathListUser)
221        TransformList=[TransformList;h.TransformListUser];
222        TransformPathList=[TransformPathList;h.TransformPathListUser];
223    end
224end
225
226%% selection of the input Action fct
227ActionCheckExist=true(size(ActionList)); % initiate the check of the path to the listed action fct
228for ilist=NbBuiltinAction+1:numel(ActionList)%check  the validity of the path of the user defined Action fct
229    ActionCheckExist(ilist)=exist(fullfile(ActionPathList{ilist},[ActionList{ilist} '.m']),'file');
230end
231ActionPathList=ActionPathList(ActionCheckExist,:); % suppress the menu options which are not valid anymore
232ActionList=ActionList(ActionCheckExist);
233set(handles.ActionName,'String',[ActionList;{'more...'}])
234set(handles.ActionName,'UserData',ActionPathList)
235ActionIndex=[];
236if isfield(Param,'ActionName')% copy the selected menu index transferred in Param from uvmat
237    ActionIndex=find(strcmp(Param.ActionName,ActionList),1);
238end
239if isempty(ActionIndex)
240    ActionIndex=1;
241end
242set(handles.ActionName,'Value',ActionIndex)
243set(handles.ActionPath,'String',ActionPathList{ActionIndex})
244set(handles.ActionExt,'Value',1)
245set(handles.ActionExt,'String',ActionExtList)
246
247%% selection of the input transform fct
248TransformCheckExist=true(size(TransformList));
249for ilist=NbBuiltinTransform+1:numel(TransformList)
250    TransformCheckExist(ilist)=exist(fullfile(TransformPathList{ilist},[TransformList{ilist} '.m']),'file');
251end
252TransformPathList=TransformPathList(TransformCheckExist);
253TransformList=TransformList(TransformCheckExist);
254set(handles.TransformName,'String',[TransformList;{'more...'}])
255set(handles.TransformName,'UserData',TransformPathList)
256TransformIndex=[];
257if isfield(Param,'TransformName')% copy the selected menu index transferred in Param from uvmat
258    TransformIndex=find(strcmp(Param.TransformName,TransformList),1);
259end
260if isempty(TransformIndex)
261    TransformIndex=1;
262end
263set(handles.TransformName,'Value',TransformIndex)
264set(handles.TransformPath,'String',TransformPathList{TransformIndex})
265   
266%% fields input initialisation
267if isfield(Param,'list_fields')&& isfield(Param,'index_fields') &&~isempty(Param.list_fields) &&~isempty(Param.index_fields)
268    set(handles.FieldName,'String',Param.list_fields); % list menu fields
269    set(handles.FieldName,'Value',Param.index_fields); % selected string index
270end
271if isfield(Param,'Coordinates')
272    if isfield(Param.Coordinates,'Coord_x')
273        set(handles.Coord_x,'String',Param.Coordinates.Coord_x)
274    end
275    if isfield(Param.Coordinates,'Coord_y')
276        set(handles.Coord_y,'String',Param.Coordinates.Coord_y)
277    end
278    if isfield(Param.Coordinates,'Coord_z')
279        set(handles.Coord_z,'String',Param.Coordinates.Coord_z)
280    end
281end
282% if isfield(Param,'Coord_x_str') && ischar(Param.Coord_x_str)
283%         set(handles.Coord_x,'String',Param.Coord_x_str); % list menu fields
284% end
285% if isfield(Param,'Coord_y_str')&& ischar(Param.Coord_y_str)
286%         set(handles.Coord_y,'String',Param.Coord_y_str); % list menu fields
287% end
288
289%% introduce the input file name(s) if defined from input Param,
290set(handles.series,'UserData',SeriesData)% initiate Userdata
291if isfield(Param,'InputFile')
292   
293    %% fill the list of file series
294    InputTable=[{Param.InputFile.RootPath},{Param.InputFile.SubDir},{Param.InputFile.RootFile},{Param.InputFile.NomType},{Param.InputFile.FileExt}];
295    if isempty(find(cellfun('isempty',InputTable)==0)); % if there is no input file, do not introduce input info
296        set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
297        return
298    end
299    TimeTable=[{Param.InputFile.TimeName},{[]},{[]},{[]},{[]}];
300    if isfield(Param.InputFile,'RootPath_1')
301        InputTable=[InputTable;[{Param.InputFile.RootPath_1},{Param.InputFile.SubDir_1},{Param.InputFile.RootFile_1},{Param.InputFile.NomType_1},{Param.InputFile.FileExt_1}]];
302        TimeTable=[TimeTable; [{Param.InputFile.TimeName_1},{[]},{[]},{[]},{[]}]];
303    end
304    set(handles.InputTable,'Data',InputTable)
305    %% determine the selected reference field indices for pair display
306   
307    [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(Param.InputFile.FileIndex);
308    if isempty(i1)
309        i1=1;
310    end
311    if isempty(i2)
312        i2=i1;
313    end
314    ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
315    % set(handles.num_ref_i,'String',num2str(ref_i));
316    if isempty(j1)
317        j1=1;
318    end
319    if isempty(j2)
320        j2=j1;
321    end
322    ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
323    SeriesData.ref_i=ref_i;
324    SeriesData.ref_j=ref_j;
325    set(handles.series,'UserData',SeriesData)
326    update_rootinfo(handles,Param.HiddenData.i1_series{1},Param.HiddenData.i2_series{1},Param.HiddenData.j1_series{1},Param.HiddenData.j2_series{1},...
327        Param.HiddenData.FileInfo{1},Param.HiddenData.MovieObject{1},1)
328    if isfield(Param,'FileName_1')
329        %         display_file_name(handles,Param,2)
330        update_rootinfo(handles,Param.HiddenData.i1_series{2},Param.HiddenData.i2_series{2},Param.HiddenData.j1_series{2},Param.HiddenData.j2_series{2},...
331            Param.HiddenData.FileInfo{2},Param.HiddenData.MovieObject{2},2)
332    end
333    %% enable field and veltype menus, in accordance with the current action
334    ActionName_Callback([],[], handles)
335   
336    %% set length of waitbar
337    displ_time(handles)
338   
339else
340    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
341end
342if isfield(Param,'incr_i')
343    set(handles.num_incr_i,'String',num2str(Param.incr_i))
344else
345    set(handles.num_incr_i,'String','1')
346end
347if isfield(Param,'incr_j')
348    set(handles.num_incr_j,'String',num2str(Param.incr_j))
349else
350    set(handles.num_incr_j,'String','1')
351end
352
353%------------------------------------------------------------------------
354% --- Outputs from this function are returned to the command line.
355function varargout = series_OutputFcn(hObject, eventdata, handles)
356%------------------------------------------------------------------------
357varargout{1} = handles.output;
358
359%------------------------------------------------------------------------
360% --- executed when closing uvmat: delete or desactivate the associated figures if exist
361function closefcn(gcbo,eventdata)
362%------------------------------------------------------------------------
363
364% delete set_object_series if detected
365hh=findobj(allchild(0),'name','view_object_series');
366if ~isempty(hh)
367    delete(hh)
368end
369hh=findobj(allchild(0),'name','edit_object_series');
370if ~isempty(hh)
371    delete(hh)
372end
373
374%delete the bowser if detected
375hh=findobj(allchild(0),'tag','browser');
376if ~isempty(hh)
377    delete(hh)
378end
379
380
381%------------------------------------------------------------------------
382%------------------------------------------------------------------------
383%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
384% automatically sets the global properties when the rootfile name is introduced
385% then activate the view-field actionname if selected
386% it is activated either by clicking on the RootPath window or by the
387% browser
388%------------------------------------------------------------------------
389%------------------------------------------------------------------------
390% --- fct activated by the browser under 'Open'
391%------------------------------------------------------------------------ 
392function MenuBrowse_Callback(hObject, eventdata, handles)
393%% look for the previously opened file 'oldfile'
394InputTable=get(handles.InputTable,'Data');
395oldfile=InputTable{1,1};
396if isempty(oldfile)
397    % use a file name stored in prefdir
398    dir_perso=prefdir;
399    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
400    if exist(profil_perso,'file')
401        h=load (profil_perso);
402        if isfield(h,'RootPath') && ischar(h.RootPath)
403            oldfile=h.RootPath;
404        end
405    end
406end
407%% launch the browser
408fileinput=uigetfile_uvmat('pick an input file in the series',oldfile);
409hh=dir(fileinput);
410if numel(hh)>1
411    msgbox_uvmat('ERROR','invalid input, probably a broken link');
412else
413    if ~isempty(fileinput)
414        display_file_name(handles,fileinput,'one')
415    end
416end
417
418% --------------------------------------------------------------------
419function MenuBrowseAppend_Callback(hObject, eventdata, handles)
420
421%% look for the previously opened file 'oldfile'
422InputTable=get(handles.InputTable,'Data');
423RootPathCell=InputTable(:,1);
424if isempty(RootPathCell{1})% no input file in the table
425     MenuBrowse_Callback(hObject, eventdata, handles)%refresh the input table, not append
426     return
427end
428SubDirCell=InputTable(:,2);
429oldfile=fullfile(RootPathCell{1},SubDirCell{1});
430
431%% use a file name stored in prefdir
432dir_perso=prefdir;
433profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
434if exist(profil_perso,'file')
435    h=load (profil_perso);
436    if isfield(h,'RootPath') && ischar(h.RootPath)
437        oldfile=h.RootPath;
438    end
439end
440
441%% launch the browser
442fileinput=uigetfile_uvmat('pick a file to append in the input table',oldfile);
443hh=dir(fileinput);
444if numel(hh)>1
445    msgbox_uvmat('ERROR','invalid input, probably a broken link');
446else
447    if ~isempty(fileinput)
448        display_file_name(handles,fileinput,'append')
449    end
450end
451
452%------------------------------------------------------------------------
453% --- fct activated by selecting a previous file under the menu Open
454%------------------------------------------------------------------------
455function MenuFile_Callback(hObject, eventdata, handles)
456
457errormsg=display_file_name(handles,get(hObject,'Label'),'one');
458if ~isempty(errormsg)
459    set(hObject,'Label','')
460    MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
461        {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
462    str_find=strcmp(get(hObject,'Label'),MenuFile);
463    MenuFile(str_find)=[]; % suppress the input file to the list
464    for ifile=1:numel(MenuFile)
465        set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile});
466    end
467end
468
469%------------------------------------------------------------------------
470% --- fct activated by selecting a previous file under the menu Open/append
471%------------------------------------------------------------------------
472function MenuFile_append_Callback(hObject, eventdata, handles)
473
474InputTable=get(handles.InputTable,'Data');
475if isempty(InputTable{1,1})% no input file in the table
476    display_file_name(handles,get(hObject,'Label'),'one') %refresh the input table, not append
477else
478    display_file_name(handles,get(hObject,'Label'),'append')% append the selected file to the current list of InputTable
479end
480
481%------------------------------------------------------------------------
482% --- fct activated by the browser under 'Open campaign/Browse...'
483%------------------------------------------------------------------------
484function MenuBrowseCampaign_Callback(hObject, eventdata, handles)
485
486%% look for the previously opened file 'oldfile'
487InputTable=get(handles.InputTable,'Data');
488if ~isempty(InputTable)
489oldfile=fullfile(InputTable{1,1},InputTable{1,2});
490else
491    % use a file name stored in prefdir
492    dir_perso=prefdir;
493    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
494    if exist(profil_perso,'file')
495        h=load (profil_perso);
496        if isfield(h,'MenuCampaign') && ~isempty(h.MenuCampaign)&& ischar(h.MenuCampaign{1})
497            oldfile=h.MenuCampaign{1};
498        end
499    end
500end
501
502OutPut=browse_data(oldfile,'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
503NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
504icount=0;
505for iexp=1:numel(OutPut.Experiment)
506    for idevice=1:numel(OutPut.DataSeries)
507        icount=icount+1;
508        InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp});
509        InputTable{icount,2}=OutPut.DataSeries{idevice};
510        if isempty(InputTable{icount,3})
511            if icount>1
512            InputTable{icount,3}=InputTable{icount-1,3};
513            else
514                InputTable{icount,3}='';
515            end
516        end
517        if isempty(InputTable{icount,4})
518            if icount>1
519            InputTable{icount,4}=InputTable{icount-1,4};
520            else
521                InputTable{icount,4}='';
522            end
523        end
524                if isempty(InputTable{icount,5})
525            if icount>1
526            InputTable{icount,5}=InputTable{icount-1,5};
527            else
528                InputTable{icount,5}='';
529            end
530        end
531    end
532end
533if size(InputTable,1)>icount
534    InputTable(icount+1:size(InputTable,1),:)=[];
535end
536set(handles.InputTable,'Data',InputTable)
537REFRESH_Callback(hObject, eventdata, handles)
538
539% --------------------------------------------------------------------
540function MenuCampaign_Callback(hObject, eventdata, handles)
541% --------------------------------------------------------------------
542
543OutPut=browse_data(get(hObject,'Label'),'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
544if ~isfield(OutPut,'Campaign')
545    return
546end
547NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
548icount=0;
549InputTable=get(handles.InputTable,'Data');
550for iexp=1:numel(OutPut.Experiment)
551    for idevice=1:numel(OutPut.DataSeries)
552        icount=icount+1;
553        InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp});
554        InputTable{icount,2}=OutPut.DataSeries{idevice};
555        if isempty(InputTable{icount,3})
556            if icount>1
557                InputTable{icount,3}=InputTable{icount-1,3};
558            else
559                InputTable{icount,3}='';
560            end
561        end
562        if isempty(InputTable{icount,4})
563            if icount>1
564                InputTable{icount,4}=InputTable{icount-1,4};
565            else
566                InputTable{icount,4}='';
567            end
568        end
569        if isempty(InputTable{icount,5})
570            if icount>1
571                InputTable{icount,5}=InputTable{icount-1,5};
572            else
573                InputTable{icount,5}='';
574            end
575        end
576    end
577end
578if size(InputTable,1)>icount
579    InputTable(icount+1:size(InputTable,1),:)=[];
580end
581set(handles.InputTable,'Data',InputTable)
582REFRESH_Callback(hObject, eventdata, handles)
583
584
585% --- Executes when selected cell(s) is changed in InputTable.
586function InputTable_CellSelectionCallback(hObject, eventdata, handles)
587iline=[];
588if ~isempty(eventdata.Indices)
589    iline=eventdata.Indices(1);
590end
591set(handles.InputLine,'String',num2str(iline));
592
593%------------------------------------------------------------------------
594% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
595%------------------------------------------------------------------------
596function InputTable_KeyPressFcn(hObject, eventdata, handles)
597set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
598set(handles.OutputSubDir,'BackgroundColor',[1 0 1])% set edit box OutputSubDir to magenta color to indicate that refresh may be needed
599xx=double(get(handles.series,'CurrentCharacter')); % get the keyboard character
600if ~isempty(xx)
601    switch xx
602        case 31 %downward arrow
603            InputTable=get(handles.InputTable,'Data');
604            iline=str2double(get(handles.InputLine,'String'));
605            if isequal(iline,size(InputTable,1))% arrow downward
606                InputTable=[InputTable;InputTable(iline,:)]; % create a new line as a copy of the last one
607                set(handles.InputTable,'Data',InputTable);
608            end
609        case 127  %key 'Suppress'
610            ClearLine_Callback(hObject, eventdata, handles)
611    end
612end
613
614%------------------------------------------------------------------------
615% --- Executes on button press in REFRESH.
616function REFRESH_Callback(hObject, eventdata, handles)
617%------------------------------------------------------------------------
618InputTable=get(handles.InputTable,'Data');
619set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
620set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
621drawnow
622empty_line=false(size(InputTable,1),1);
623for iline=1:size(InputTable,1)
624    empty_line(iline)= isempty(cell2mat(InputTable(iline,1:3)));
625end
626if ~isempty(find(empty_line));
627    InputTable(empty_line,:)=[]; % remove empty lines
628    set(handles.InputTable,'Data',InputTable)
629    ListTable={'MinIndex_i','MaxIndex_i','MinIndex_j','MaxIndex_j','PairString','TimeTable'};
630    for ilist=1:numel(ListTable)
631        Table=get(handles.(ListTable{ilist}),'Data');
632        Table(empty_line,:)=[]; % remove empty lines
633        set(handles.(ListTable{ilist}),'Data',Table);
634    end
635    set(handles.series,'UserData',[])%refresh the stored info
636end
637nbview=size(InputTable,1);
638for iview=1:nbview
639    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
640    if ~exist(RootPath,'dir')
641        i1_series=[];
642        RootFile='';
643    else %scan the input folder
644        InputTable{iview,3}=regexprep(InputTable{iview,3},'^/','');
645            [RootPath,~,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=...
646                find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]);
647    end
648    % if no file is found, open a browser
649    if isempty(RootFile)&& isempty(i1_series)
650        fileinput=uigetfile_uvmat(['wrong input at line ' num2str(iview) ':pick a new input file'],RootPath);
651        if isempty(fileinput)
652            set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  back to red color
653            return
654        else
655            display_file_name(handles,fileinput,iview)
656        end
657    else
658       update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview)
659    end
660end
661
662%% update MinIndex_i and MaxIndex_i if the input table content has been reduced in line nbre
663MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
664set(handles.MinIndex_i,'Data',MinIndex_i_table(1:nbview,:));
665MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
666set(handles.MinIndex_j,'Data',MinIndex_j_table(1:nbview,:));
667MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
668
669set(handles.MaxIndex_i,'Data',MaxIndex_i_table(1:nbview,:));
670MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
671set(handles.MaxIndex_j,'Data',MaxIndex_j_table(1:nbview,:));
672PairString=get(handles.PairString,'Data'); % retrieve the min indices in the table MinIndex
673set(handles.PairString,'Data',PairString(1:nbview,:));
674TimeTable=get(handles.TimeTable,'Data'); % retrieve the min indices in the table MinIndex
675set(handles.TimeTable,'Data',TimeTable(1:nbview,:));
676
677%% set length of waitbar
678displ_time(handles)
679set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (indicate activation finished)
680set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch'
681
682%% enable field and veltype menus, in accordance with the current action
683ActionInput_Callback([],[], handles)
684
685
686%------------------------------------------------------------------------
687% --- Function called when a new file is opened, either by series_OpeningFcn or by the browser
688%------------------------------------------------------------------------
689% INPUT:
690% handles: handles of elements in the GUI
691% Param: structure of input parameters, including  input file name and path
692% iview: line index in the input table
693%       or 'one': refresh the list
694%         'append': add a new line to the input table
695function errormsg=display_file_name(handles,Param,iview)
696 
697set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
698drawnow
699errormsg=''; % default
700if ischar(Param)
701    fileinput=Param;
702else% input set when series is opened (called by the GUI uvmat)
703    fileinput=Param.FileName;
704end
705   
706%% get the input root name, indices, file extension and nomenclature NomType
707if ~exist(fileinput,'file')
708    errormsg=['input file ' fileinput  ' does not exist'];
709    msgbox_uvmat('ERROR',errormsg)
710    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (refresh still needed)
711    return
712end
713
714%% detect root name, nomenclature and indices in the input file name:
715[FilePath,FileName,FileExt]=fileparts(fileinput);
716%%%%%%%%%%%%%%%%%%
717%TODO: case of input by uvmat: do not check agai the input seies %%%%%%%
718%%%%%%%%%%%%%%%%%%%
719% detect the file type, get the movie object if relevant, and look for the corresponding file series:
720% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
721[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
722FileType=FileInfo.FileType;
723if isempty(RootFile)&&isempty(i1_series)
724    errormsg='no input file in the series';
725    msgbox_uvmat('ERROR',errormsg)
726    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (end of activation)
727    return
728end
729if strcmp(FileType,'txt')
730    edit(fileinput)
731    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to  magenta color (end of activation)
732    return
733elseif strcmp(FileType,'xml')
734    editxml(fileinput)
735    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
736     return
737elseif strcmp(FileType,'figure')
738    open(fileinput)
739    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
740     return
741end
742
743%% enable other menus and uicontrols
744% set(handles.MenuOpenCampaign,'Enable','on')
745set(handles.MenuCampaign_1,'Enable','on')
746set(handles.MenuCampaign_2,'Enable','on')
747set(handles.MenuCampaign_3,'Enable','on')
748set(handles.MenuCampaign_4,'Enable','on')
749set(handles.MenuCampaign_5,'Enable','on')
750set(handles.RUN, 'Enable','On')
751set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
752set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
753drawnow
754
755
756%% fill the list of file series
757InputTable=get(handles.InputTable,'Data');
758SeriesData=get(handles.series,'UserData');
759if strcmp(iview,'append') % display the input data as a new line in the table
760    iview=size(InputTable,1)+1; % the next line in InputTable becomes the current line
761%     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
762elseif strcmp(iview,'one') % refresh the list of  input  file series
763    iview=1; % the first line in InputTable becomes the current line
764    InputTable={'','','','',''};
765%     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
766    set(handles.TimeTable,'Data',[{''},{[]},{[]},{[]},{[]}])
767    set(handles.MinIndex_i,'Data',[])
768    set(handles.MaxIndex_i,'Data',[])
769    set(handles.MinIndex_j,'Data',[])
770    set(handles.MaxIndex_j,'Data',[])
771    set(handles.PairString,'Data',{''})
772    SeriesData.CheckPair=0; % reset the list of input lines with pairs
773    SeriesData.i1_series={};
774    SeriesData.i2_series={};
775    SeriesData.j1_series={};
776    SeriesData.j2_series={};
777    SeriesData.FileType={};
778    SeriesData.FileInfo={};
779    SeriesData.Time={};
780end
781if isfield(SeriesData,'i1_series')
782    SeriesData.i1_series(iview+1:end)=[];
783    SeriesData.i2_series(iview+1:end)=[];
784    SeriesData.j1_series(iview+1:end)=[];
785    SeriesData.j2_series(iview+1:end)=[];
786    SeriesData.FileType(iview+1:end)=[];
787    SeriesData.FileInfo(iview+1:end)=[];
788    SeriesData.Time(iview+1:end)=[];
789end
790InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
791if iview >1
792    set(handles.InputLine,'String',num2str(iview))
793end
794set(handles.InputTable,'Data',InputTable)
795
796%% determine the selected reference field indices for pair display
797if isempty(i1)
798    i1=1;
799end
800if isempty(i2)
801    i2=i1;
802end
803ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
804% set(handles.num_ref_i,'String',num2str(ref_i));
805if isempty(j1)
806    j1=1;
807end
808if isempty(j2)
809    j2=j1;
810end
811ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
812SeriesData.ref_i=ref_i;
813SeriesData.ref_j=ref_j;
814
815%% update first and last indices if they do not exist
816Param=read_GUI(handles.series);
817first_j=[];
818if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
819last_j=[];
820if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
821PairString='';
822if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
823[i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
824FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
825    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
826if ~exist(FirstFileName,'file')
827    set(handles.num_first_i,'String',num2str(ref_i))
828    set(handles.num_first_j,'String',num2str(ref_j))
829end
830[i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
831LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
832    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
833if ~exist(LastFileName,'file')
834    set(handles.num_last_i,'String',num2str(ref_i))
835    set(handles.num_last_j,'String',num2str(ref_j))
836end
837
838%% update the list of recent files in the menubar and save it for future opening
839MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
840    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
841str_find=strcmp(fileinput,MenuFile);
842if isempty(find(str_find,1))
843    MenuFile=[{fileinput};MenuFile]; % insert the current file if not already in the list
844end
845for ifile=1:min(length(MenuFile),5)
846    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
847end
848dir_perso=prefdir;
849profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
850if exist(profil_perso,'file')
851    save (profil_perso,'MenuFile','-append'); % store the file names for future opening of uvmat
852else
853    save (profil_perso,'MenuFile','-V6'); % store the file names for future opening of uvmat
854end
855% save the opened file to initiate future opening
856SeriesData.RefFile{iview}=fileinput; % reference opening file for line iview
857SeriesData.Ref_i1=i1;
858SeriesData.Ref_i2=i2;
859SeriesData.Ref_j1=j1;
860SeriesData.Ref_j2=j2;
861set(handles.series,'UserData',SeriesData)
862
863set(handles.InputTable,'BackgroundColor',[1 1 1])
864
865%% initiate input file series and refresh the current field view:     
866update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview);
867%% enable field and veltype menus, in accordance with the current action
868ActionName_Callback([],[], handles)
869
870%% set length of waitbar
871displ_time(handles)
872
873set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (end of activation)
874
875%------------------------------------------------------------------------
876% --- Update information about a new field series (indices to scan, timing,
877%     calibration from an xml file
878function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,VideoObject,iview)
879%------------------------------------------------------------------------
880InputTable=get(handles.InputTable,'Data');
881
882%% display the min and max indices for the whole file series
883if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
884    MinIndex_j=1; % index j set to 1 by default
885    MaxIndex_j=1;
886    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)
887    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)
888else
889    ref_i=squeeze(max(i1_series(1,:,:),[],2)); % select ref_j index for each ref_i
890    ref_j=squeeze(max(j1_series(1,:,:),[],3)); % select ref_i index for each ref_j
891     MinIndex_i=min(find(ref_i))-1;
892     MaxIndex_i=max(find(ref_i))-1;
893     MaxIndex_j=max(find(ref_j))-1;
894     MinIndex_j=min(find(ref_j))-1;
895    diff_j_max=diff(ref_j);
896    diff_i_max=diff(ref_i);
897    if ~isempty(diff_i_max) && isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max)))
898        set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to dispaly by default
899    end
900    if ~isempty(diff_j_max) && isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max)))
901        set(handles.num_incr_j,'String',num2str(diff_j_max(1)))
902    end
903end
904if isequal(MinIndex_i,-1)
905    MinIndex_i=0;
906end
907if isequal(MinIndex_j,-1)
908    MinIndex_j=0;
909end
910MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
911MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
912MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
913MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
914if ~isempty(MinIndex_i)&&~isempty(MaxIndex_i)
915    MinIndex_i_table(iview,1)=MinIndex_i;
916    MaxIndex_i_table(iview,1)=MaxIndex_i;
917end
918if ~isempty(MinIndex_j)&&~isempty(MaxIndex_j)
919    MinIndex_j_table(iview,1)=MinIndex_j;
920    MaxIndex_j_table(iview,1)=MaxIndex_j;
921end
922set(handles.MinIndex_i,'Data',MinIndex_i_table)%display the min indices in the table MinIndex
923set(handles.MinIndex_j,'Data',MinIndex_j_table)%display the max indices in the table MaxIndex
924set(handles.MaxIndex_i,'Data',MaxIndex_i_table)%display the min indices in the table MinIndex
925set(handles.MaxIndex_j,'Data',MaxIndex_j_table)%display the max indices in the table MaxIndex
926SeriesData=get(handles.series,'UserData');
927
928%% adjust the first and last indices for the selected series, only if requested by the bounds
929% i index, compare input to min index i
930first_i=str2num(get(handles.num_first_i,'String')); % retrieve previous first i
931% ref_i=str2num(get(handles.num_ref_i,'String')); % index i given by the input field
932ref_i=1;
933if isfield(SeriesData,'ref_i')
934    ref_i=SeriesData.ref_i;
935end
936if isempty(first_i)
937    first_i=ref_i; % first_i updated by the input value
938elseif first_i < MinIndex_i
939    first_i=MinIndex_i; % first_i set to the min i index (restricted by oter input lines)
940elseif first_i >MaxIndex_i
941    first_i=MaxIndex_i; % first_i set to the max i index (restricted by oter input lines)
942end
943% j index,  compare input to min index j
944first_j=str2num(get(handles.num_first_j,'String'));
945ref_j=1;
946if isfield(SeriesData,'ref_j')
947    ref_j=SeriesData.ref_j;
948end
949if isempty(first_j)
950    first_j=ref_j; % first_j updated by the input value
951elseif first_j<MinIndex_j
952    first_j=MinIndex_j; % first_j set to the min j index (restricted by oter input lines)
953elseif first_j >MaxIndex_j
954    first_j=MaxIndex_j; % first_j set to the max j index (restricted by oter input lines)
955end
956% i index, compare input to max index i
957last_i=str2num(get(handles.num_last_i,'String'));
958if isempty(last_i)
959    last_i=ref_i;
960elseif last_i > MaxIndex_i
961    last_i=MaxIndex_i;
962elseif last_i<first_i
963    last_i=first_i;
964end
965% j index, compare input to max index j
966last_j=str2num(get(handles.num_last_j,'String'));
967if isempty(last_j)
968    last_j=ref_j;
969elseif last_j>MaxIndex_j
970    last_j=MaxIndex_j;
971elseif last_j<first_j
972    last_j=first_j;
973end
974set(handles.num_first_i,'String',num2str(first_i));
975set(handles.num_first_j,'String',num2str(first_j));
976set(handles.num_last_i,'String',num2str(last_i));
977set(handles.num_last_j,'String',num2str(last_j));
978
979%% number of slices set by default
980NbSlice=[]; % default
981% read  value set by the first series for the append mode (iwiew >1)
982if iview>1 && strcmp(get(handles.num_NbSlice,'Visible'),'on')
983    NbSlice=str2double(get(handles.num_NbSlice,'String'));
984end
985
986%% default time settings
987TimeUnit='';
988% read  value set by the first series for the append mode (iwiew >1)
989if iview>1
990    TimeUnit=get(handles.TimeUnit,'String');
991end
992TimeName='';
993Time=[]; % default
994TimeMin=[];
995TimeFirst=[];
996TimeLast=[];
997TimeMax=[];
998
999%%  read image documentation file if found
1000XmlData=[];
1001check_calib=0;
1002XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
1003if ~isempty(XmlFileName)
1004    [XmlData,errormsg]=imadoc2struct(XmlFileName);
1005    if ~isempty(errormsg)
1006        msgbox_uvmat('WARNING',['error in reading ' XmlFileName ': ' errormsg]);
1007    end
1008    % read time if available
1009    if isfield(XmlData,'Time')
1010        Time=XmlData.Time;
1011        TimeName='xml';
1012%                         if XmlData.Time(1,:)==XmlData.Time(2,:)% case starting with index 1
1013%                     sizDti=size(XmlData.Time,1)-1; % size of the time vector explicitly defined in the xml file
1014%                     ind_start=1;
1015%                 else
1016%                     sizDti=size(XmlData.Time,1); % case starting with index 0
1017%                     ind_start=0;
1018%                 end
1019%         % complement the input if the whole time series is not defined
1020%             if size(i1_series,3)>size(XmlData.Time,1)-ind_start %only the first time interval is defined, extrapolate to the whole series
1021%                 Dti_total=XmlData.Time(end)-XmlData.Time(1); % total time interval covered by the time vector
1022%                 missing_indices=sizDti+1+ind_start:size(i1_series,3)+1; % remaining set of frame indices for which time needs to be found
1023%                 repeat_nbre=1+floor((missing_indices-sizDti-ind_start)/(sizDti-1)); % number of repetitions of Dti
1024%                 time_indices=1+mod(missing_indices-sizDti-1,sizDti-1);
1025%                 for j=1:size(XmlData.Time,2)
1026%                 Time(missing_indices,j)=XmlData.Time(time_indices,j)+repeat_nbre'*Dti_total;
1027%                 end
1028%                 % update the xml file with NbDti
1029%                 t=xmltree(XmlFileName);
1030%                 uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti')
1031%                 if isempty(uid_NbDti)
1032%                     uid_BurstTiming=find(t,'ImaDoc/Camera/BurstTiming')
1033%                     [t,uid_NbDti]=add(t,uid_BurstTiming,'element','NbDti');
1034%                 end
1035%                 [t,uid_NbDti]=add(t,uid_NbDti,'chardata',num2str(repeat_nbre(end)-1));
1036%                 save(t,XmlFileName)
1037%             end
1038    end
1039    if isfield(XmlData,'Camera')
1040        %         if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
1041        %             if iview>1 && ~isempty(NbSlice) && ~strcmp(NbSlice,XmlData.Camera.NbSlice)
1042        %                 msgbox_uvmat('WARNING','inconsistent number of slices with the first field series');
1043        %             end
1044        %             NbSlice=XmlData.Camera.NbSlice; % Nbre of slices from camera
1045        %         end
1046        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
1047            if iview>1 && ~isempty(TimeUnit) && ~strcmp(TimeUnit,XmlData.Camera.TimeUnit)
1048                msgbox_uvmat('WARNING','inconsistent time unit with the first field series');
1049            end
1050            TimeUnit=XmlData.Camera.TimeUnit;
1051        end
1052    end
1053    % number of slices
1054    if isfield(XmlData,'TranslationMotor')&& isfield(XmlData.TranslationMotor,'NbSlice')
1055        NbSlice_motor=XmlData.TranslationMotor.NbSlice;
1056        if ~isempty(NbSlice) && ~isequal(NbSlice_motor,NbSlice)
1057                msgbox_uvmat('WARNING','inconsistent Z numbers of Z indices');
1058        else
1059            NbSlice=NbSlice_motor;
1060        end
1061    end
1062   
1063    if isfield(XmlData,'GeometryCalib')
1064        check_calib=1;
1065        if isfield(XmlData.GeometryCalib,'SliceCoord')
1066            siz=size(XmlData.GeometryCalib.SliceCoord);
1067            if ~isempty(NbSlice)&& ~isequal(size(1),NbSlice)
1068                msgbox_uvmat('WARNING','inconsistent numbers of Z indices between motor and calibration');
1069            else
1070                NbSlice=siz(1);
1071            end
1072        end
1073    end
1074end
1075if ~isempty(NbSlice)
1076set(handles.num_NbSlice,'String',num2str(NbSlice))
1077set(handles.num_NbSlice,'Visible','on')
1078end
1079
1080%% read timing  from the current file (prioritary)
1081if ~isempty(VideoObject)% case of movies
1082    imainfo=get(VideoObject);
1083    if isempty(j1_series); % frame index along i
1084        Time=zeros(imainfo.NumberOfFrames+1,2);
1085        Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
1086    else
1087        Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
1088    end
1089    TimeName='video';
1090end
1091
1092
1093%% determine the min and max times: case of Netcdf files will be treated later in FieldName_Callback
1094if ~isempty(TimeName)
1095    TimeMin=Time(MinIndex_i+1,MinIndex_j+1);
1096    if size(Time)>=[first_i+1 first_j+1]
1097        TimeFirst=Time(first_i+1,first_j+1);
1098    end
1099    if size(Time)>=[last_i+1 last_j+1]
1100        TimeLast=Time(last_i+1,last_j+1);
1101    end
1102    if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1];
1103        TimeMax=Time(MaxIndex_i+1,MaxIndex_j+1);
1104    end
1105end
1106
1107%% update the time table
1108TimeTable=get(handles.TimeTable,'Data');
1109TimeTable{iview,1}=TimeName;
1110TimeTable{iview,2}=TimeMin;
1111TimeTable{iview,3}=TimeFirst;
1112TimeTable{iview,4}=TimeLast;
1113TimeTable{iview,5}=TimeMax;
1114set(handles.TimeTable,'Data',TimeTable)
1115
1116%% update the series info in 'UserData'
1117SeriesData.i1_series{iview}=i1_series;
1118SeriesData.i2_series{iview}=i2_series;
1119SeriesData.j1_series{iview}=j1_series;
1120SeriesData.j2_series{iview}=j2_series;
1121SeriesData.FileType{iview}=FileInfo.FileType;
1122SeriesData.FileInfo{iview}=FileInfo;
1123SeriesData.Time{iview}=Time;
1124% if ~isempty(TimeName)
1125%     SeriesData.TimeSource=TimeSource;
1126% end
1127if check_calib
1128    SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib;
1129end
1130set(handles.series,'UserData',SeriesData)
1131
1132%% update pair menus
1133hset_pair=findobj(allchild(0),'Tag','set_pairs');
1134if ~isempty(hset_pair), delete(hset_pair); end % delete the GUI set_pair if opened
1135CheckPair= ~isempty(i2_series)||~isempty(j2_series); % check whether index pairs need to be defined
1136PairString=get(handles.PairString,'Data');
1137if CheckPair% if pairs need to be display for line iview
1138    [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series);
1139    Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,ModeMenu{ModeValue},Time,TimeUnit,ref_i,ref_j,TimeName,InputTable(iview,:),FileInfo);
1140    PairString{iview,1}=Menu{1};
1141else
1142    PairString{iview,1}=''; % no pair for #iview
1143end
1144set(handles.PairString,'Data',PairString)
1145if isempty(find(cellfun('isempty',get(handles.PairString,'Data'))==0, 1))% if all lines of pairs are empty
1146    set(handles.PairString,'Visible','off')
1147    set(handles.SetPairs,'Visible','off')
1148else
1149    set(handles.PairString,'Visible','on')
1150    set(handles.SetPairs,'Visible','on')
1151end
1152
1153
1154%% display the set of existing files as an image
1155set(handles.FileStatus,'Units','pixels')
1156Position=get(handles.FileStatus,'Position');
1157set(handles.FileStatus,'Units','normalized')
1158%xI=0.5:Position(3)-0.5;
1159nbview=numel(SeriesData.i1_series);
1160j_max=cell(1,nbview);
1161MaxIndex_i=ones(1,nbview); % default
1162MinIndex_i=ones(1,nbview); % default
1163for iline=1:nbview
1164    pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); % max on pair index
1165    j_max{iline}=max(pair_max,[],1); % max on j index
1166    if ~isempty(j_max{iline})
1167    MaxIndex_i(iline)=max(find(j_max{iline}))-1; % max ref index i
1168    MinIndex_i(iline)=min(find(j_max{iline}))-1; % min ref index i
1169    end
1170end
1171MinIndex_i=min(MinIndex_i);
1172MaxIndex_i=max(MaxIndex_i);
1173range_index=MaxIndex_i-MinIndex_i+1;
1174range_y=max(1,floor(Position(4)/nbview));
1175npx=floor(Position(3));
1176file_indices=MinIndex_i+floor(((0.5:npx-0.5)/npx)*range_index)+1;
1177CData=zeros(nbview*range_y,npx); % initiate the image representing the existing files
1178for iline=1:nbview
1179    ind_y=1+(iline-1)*range_y:iline*range_y;
1180    LineData=zeros(size(file_indices));
1181    file_select=file_indices(file_indices<=numel(j_max{iline}));
1182    ind_select=find(file_indices<=numel(j_max{iline}));
1183    LineData(ind_select)=j_max{iline}(file_select)~=0;
1184    CData(ind_y,:)=ones(size(ind_y'))*LineData;
1185end
1186CData=cat(3,zeros(size(CData)),CData,zeros(size(CData))); % make color images r=0,g,b=0
1187set(handles.FileStatus,'CData',CData);
1188
1189%-----------------------------------------------------------guide -------------
1190%------------------------------------------------------------------------
1191%  III - FUNCTIONS ASSOCIATED TO THE FRAME IndexRange
1192%------------------------------------------------------------------------
1193
1194
1195% ---- determine the menu to put in mode and advice a default choice
1196%------------------------------------------------------------------------
1197function [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series)
1198%------------------------------------------------------------------------   
1199ModeMenu={''};
1200if isempty(j2_series)% no j pair
1201    ModeValue=1;
1202    if ~isempty(i2_series)
1203        ModeMenu={'series(Di)'}; % pair menu with only option Di
1204    end
1205else %existence of j pairs
1206    pair_max=squeeze(max(i1_series,[],1)); % max on pair index
1207    j_max=max(pair_max,[],1);
1208    MaxIndex_i=find(j_max, 1, 'last' )-1; % max ref index i
1209    MinIndex_i=find(j_max, 1 )-1; % min ref index i
1210    i_max=max(pair_max,[],2);
1211    MaxIndex_j=find(i_max, 1, 'last' )-1; % max ref index i
1212    MinIndex_j=find(i_max, 1 )-1; % min ref index i
1213    if MaxIndex_j==MinIndex_j
1214        ModeValue=1;
1215        ModeMenu={'bursts'};
1216    elseif MaxIndex_i==MinIndex_i
1217        ModeValue=1;
1218        ModeMenu={'series(Dj)'};
1219    else
1220        ModeMenu={'bursts';'series(Dj)'};
1221        if (MaxIndex_j-MinIndex_j)>10
1222            ModeValue=2; % set mode to series(Dj) if more than 10 j values
1223        else
1224            ModeValue=1;
1225        end
1226    end
1227end
1228
1229
1230%------------------------------------------------------------------------
1231function displ_pair=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo)
1232%------------------------------------------------------------------------
1233displ_pair={};
1234if isempty(TimeUnit)
1235    dtunit='e-03';
1236else
1237    dtunit=['m' TimeUnit];
1238end
1239switch mode
1240    case 'series(Di)'
1241        diff_i=i2_series-i1_series;
1242        min_diff=min(diff_i(diff_i>0));
1243        max_diff=max(diff_i(diff_i>0));
1244        for ipair=min_diff:max_diff
1245            if numel(diff_i(diff_i==ipair))>0
1246                pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1247                if ~isempty(time)
1248                    if ref_i<=floor(ipair/2)
1249                        ref_i=floor(ipair/2)+1; % shift ref_i to get the first pair
1250                    end
1251                    Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1252                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1253                end
1254                displ_pair=[displ_pair;{pair_string}];
1255            end
1256        end
1257        if ~isempty(displ_pair)
1258            displ_pair=[displ_pair;{'Di=*|*'}];
1259        end
1260    case 'series(Dj)'
1261        if isempty(j2_series)
1262            msgbox_uvmat('ERROR','no j1-j2 pair available')
1263            return
1264        end
1265        diff_j=j2_series-j1_series;
1266        min_diff=min(diff_j(diff_j>0));
1267        max_diff=max(diff_j(diff_j>0));
1268        for ipair=min_diff:max_diff
1269            if numel(diff_j(diff_j==ipair))>0
1270                pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1271                if ~isempty(time)
1272                    if ref_j<=floor(ipair/2)
1273                        ref_j=floor(ipair/2)+1; % shift ref_i to get the first pair
1274                    end
1275                    Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1276                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1277                end
1278                displ_pair=[displ_pair;{pair_string}];
1279            end
1280        end
1281        if ~isempty(displ_pair)
1282            displ_pair=[displ_pair;{'Dj=*|*'}];
1283        end
1284    case 'bursts'
1285        if isempty(j2_series)
1286            msgbox_uvmat('ERROR','no j1-j2 pair available')
1287            return
1288        end
1289        %diff_j=j2_series-j1_series;
1290        min_j1=min(j1_series(j1_series>0));
1291        max_j1=max(j1_series(j1_series>0));
1292        min_j2=min(j2_series(j2_series>0));
1293        max_j2=max(j2_series(j2_series>0));
1294        for pair1=min_j1:min(max_j1,min_j1+20)
1295            for pair2=min_j2:min(max_j2,min_j2+20)
1296                if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1297                    pair_string=['j= ' num2str(pair1) '-' num2str(pair2)];
1298                    [TimeValue,DtValue]=get_time(ref_i,[],pair_string,InputTable,FileInfo,TimeName,'Dt');
1299                    %Dt=time(ref_i,pair2+1)-time(ref_i,pair1+1);
1300                    pair_string=[pair_string ', Dt=' num2str(DtValue) ' ' dtunit];
1301                    displ_pair=[displ_pair;{pair_string}];
1302                end
1303            end
1304        end
1305        if ~isempty(displ_pair)
1306            displ_pair=[displ_pair;{'j=*-*'}];
1307        end
1308end
1309
1310%------------------------------------------------------------------------
1311function num_first_i_Callback(hObject, eventdata, handles)
1312%------------------------------------------------------------------------
1313num_last_i_Callback(hObject, eventdata, handles)
1314
1315%------------------------------------------------------------------------
1316function num_last_i_Callback(hObject, eventdata, handles)
1317%------------------------------------------------------------------------
1318SeriesData=get(handles.series,'UserData');
1319if ~isfield(SeriesData,'Time')
1320    SeriesData.Time{1}=[];
1321end
1322displ_time(handles);
1323
1324%------------------------------------------------------------------------
1325function num_first_j_Callback(hObject, eventdata, handles)
1326%------------------------------------------------------------------------
1327 num_last_j_Callback(hObject, eventdata, handles)
1328
1329%------------------------------------------------------------------------
1330function num_last_j_Callback(hObject, eventdata, handles)
1331%------------------------------------------------------------------------
1332% first_j=str2num(get(handles.num_first_j,'String'));
1333% last_j=str2num(get(handles.num_last_j,'String'));
1334% ref_j=ceil((first_j+last_j)/2);
1335% set(handles.num_ref_j,'String', num2str(ref_j))
1336% num_ref_j_Callback(hObject, eventdata, handles)
1337SeriesData=get(handles.series,'UserData');
1338if ~isfield(SeriesData,'Time')
1339    SeriesData.Time{1}=[];
1340end
1341displ_time(handles);
1342
1343%------------------------------------------------------------------------
1344% ---- find the times corresponding to the first and last indices of a series
1345function displ_time(handles)
1346%------------------------------------------------------------------------
1347SeriesData=get(handles.series,'UserData'); %
1348if ~isfield(SeriesData,'Time')
1349    return
1350end
1351PairString=get(handles.PairString,'Data');
1352ref_i_1=str2num(get(handles.num_first_i,'String')); % first reference index
1353ref_i_2=str2num(get(handles.num_last_i,'String')); % last reference index
1354ref_j_1=[];ref_j_2=[];
1355if strcmp(get(handles.num_first_j,'Visible'),'on')
1356ref_j_1=str2num(get(handles.num_first_j,'String'));
1357ref_j_2=str2num(get(handles.num_last_j,'String'));
1358end
1359[i1_1,i2_1,j1_1,j2_1] = get_file_index(ref_i_1,ref_j_1,PairString);
1360[i1_2,i2_2,j1_2,j2_2] = get_file_index(ref_i_2,ref_j_2,PairString);
1361TimeTable=get(handles.TimeTable,'Data');
1362%%%%%%
1363%TODO: read time in netcdf file, see ActionName_Callback
1364%%%%%%%
1365%Pairs=get(handles.PairString,'Data');
1366for iview=1:size(TimeTable,1)
1367    if size(SeriesData.Time,1)<iview
1368        break
1369    end
1370    TimeTable{iview,3}=[];
1371    TimeTable{iview,4}=[];
1372    if size(SeriesData.Time{iview},1)>=i2_2+1 && (isempty(ref_j_1)||size(SeriesData.Time{iview},2)>=j2_2+1)
1373        if isempty(ref_j_1)
1374            time_first=(SeriesData.Time{iview}(i1_1+1,2)+SeriesData.Time{iview}(i2_1+1,2))/2;
1375            time_last=(SeriesData.Time{iview}(i1_2+1,2)+SeriesData.Time{iview}(i2_2+1,2))/2;
1376        else
1377            time_first=(SeriesData.Time{iview}(i1_1+1,j1_1+1)+SeriesData.Time{iview}(i2_1+1,j2_1+1))/2;
1378            time_last=(SeriesData.Time{iview}(i1_2+1,j1_2+1)+SeriesData.Time{iview}(i2_2+1,j2_1+1))/2;
1379        end
1380        TimeTable{iview,3}=time_first; % TODO: take into account pairs
1381        TimeTable{iview,4}=time_last; % TODO: take into account pairs
1382    end
1383end
1384set(handles.TimeTable,'Data',TimeTable)
1385
1386%% set the waitbar position with respect to the min and max in the series
1387MinIndex_i=min(get(handles.MinIndex_i,'Data'));
1388MaxIndex_i=max(get(handles.MaxIndex_i,'Data'));
1389pos_first=(ref_i_1-MinIndex_i)/(MaxIndex_i-MinIndex_i+1);
1390pos_last=(ref_i_2-MinIndex_i+1)/(MaxIndex_i-MinIndex_i+1);
1391if isempty(pos_first), pos_first=0; end
1392if isempty(pos_last), pos_last=1; end
1393Position=get(handles.Waitbar,'Position'); % position of the waitbar:= [ x,y, width, height]
1394Position_status=get(handles.FileStatus,'Position');
1395Position(1)=Position_status(1)+Position_status(3)*pos_first;
1396Position(3)=max(Position_status(3)*(pos_last-pos_first),0.001); % width must remain positive
1397set(handles.Waitbar,'Position',Position)
1398update_waitbar(handles.Waitbar,0)
1399
1400%------------------------------------------------------------------------
1401% --- Executes when selected cell(s) is changed in PairString.
1402function PairString_CellSelectionCallback(hObject, eventdata, handles)
1403%------------------------------------------------------------------------   
1404if numel(eventdata.Indices)>=1
1405    PairString=get(hObject,'Data');
1406    if ~isempty(PairString{eventdata.Indices(1)})
1407        SetPairs_Callback(hObject, eventdata.Indices(1), handles)
1408    end
1409end
1410
1411%-------------------------------------
1412function enable_i(handles,state)
1413set(handles.i_txt,'Visible',state)
1414set(handles.num_first_i,'Visible',state)
1415set(handles.num_last_i,'Visible',state)
1416set(handles.num_incr_i,'Visible',state)
1417
1418%-----------------------------------
1419function enable_j(handles,state)
1420set(handles.j_txt,'Visible',state)
1421set(handles.num_first_j,'Visible',state)
1422set(handles.num_last_j,'Visible',state)
1423set(handles.num_incr_j,'Visible',state)
1424set(handles.MinIndex_j,'Visible',state)
1425set(handles.MaxIndex_j,'Visible',state)
1426
1427
1428%%%%%%%%%%%%%%%%%%%%
1429%%  MAIN ActionName FUNCTIONS
1430%%%%%%%%%%%%%%%%%%%%
1431%------------------------------------------------------------------------
1432% --- Executes on button press in RUN.
1433%------------------------------------------------------------------------
1434function RUN_Callback(hObject, eventdata, handles)
1435
1436%% settings of the button RUN
1437if ~isequal(get(handles.ActionInput,'BackgroundColor'),[1 0 0])
1438    msgbox_uvmat('ERROR','first activate the button ActionInput')
1439    return
1440end
1441set(handles.RUN,'BusyAction','queue'); % activation of STOP button will set BusyAction to 'cancel'
1442set(handles.RUN, 'Enable','Off')% avoid further RUN action until the current one is finished
1443set(handles.RUN,'BackgroundColor',[1 1 0])%show activation of RUN by yellow color
1444drawnow
1445set(handles.status,'Value',0)% desable status display if relevant
1446status_Callback([], eventdata, handles)
1447
1448%% launch action
1449errormsg=launch_action(handles);
1450if ~isempty(errormsg)
1451     msgbox_uvmat('ERROR',errormsg)
1452end
1453
1454%% reset the GUI series
1455update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate launching is finished
1456set(handles.RUN, 'Enable','On')
1457set(handles.RUN,'BackgroundColor',[1 0 0])
1458set(handles.RUN, 'Value',0)
1459
1460%------------------------------------------------------------------------
1461% --- called by RUN_Callback
1462%------------------------------------------------------------------------
1463% The calculations are launched in three different ways:
1464% RunMode='local': calculation on the local Matlab session, will prevent other actions during that time.
1465% RunMode='background': calculation on the local computer, but in a new Matlab session (with no graphic output).
1466% RunMode='cluster': calculations dispatched in a cluster, using a managing system, 'oar, 'sge, or 'sgb'.
1467% In the latter case, the calculation is split in 'packets' of i index (all j indices are contained in a single packet).
1468% This splitting is possible only if the different calculations in the series are independent. Otherwise the action
1469% function imposes a number of processes NbSlice in input, for instance NbSlice=1 for a time series.
1470% If NbSlice is not imposed, the splitting in packets (jobs) is determined
1471% so that a job is optimum length AdvisedJobCPUTime), and the total job number in any case smaller
1472% than MaxJobNumber (these parameters are defined in the file series.xml in
1473% accordance with the management strategy for the cluster). The jobs are
1474% dispatched in parallel into NbCore processors by the cluster managing system.
1475
1476function errormsg=launch_action(handles)
1477errormsg=''; % default
1478
1479%% read the data on the GUI series
1480Param=read_GUI_series(handles); % displayed parameters
1481SeriesData=get(handles.series,'UserData'); % hidden parameters
1482if isfield(SeriesData,'TransformInput')
1483    Param.TransformInput=SeriesData.TransformInput;
1484end
1485if ~isfield(SeriesData,'i1_series')
1486    errormsg='The input field series needs to be refreshed: press REFRESH';
1487    return
1488end
1489if isfield(Param,'InputFields')&& isfield(Param.InputFields,'FieldName')&& isequal(Param.InputFields.FieldName,'get_field...')
1490    errormsg='input field name(s) not defined, select get_field...';
1491    return
1492end
1493
1494%% select the Action mode, 'local', 'background' or 'cluster' (if available)
1495RunMode='local'; % default (needed for first opening of the GUI series)
1496if isfield(Param.Action,'RunMode')
1497    RunMode=Param.Action.RunMode;
1498    Param.Action=rmfield(Param.Action,'RunMode'); % remove from the recorded xml file to avoid interference during ImportConfig
1499end
1500ActionExt='.m'; % default
1501if isfield(Param.Action,'ActionExt')
1502    ActionExt=Param.Action.ActionExt; % '.m', '.sh' (compiled)  or '.py' (Python)
1503    Param.Action=rmfield(Param.Action,'ActionExt'); % remove from the recorded xml file to avoid interference during ImportConfig
1504end
1505ActionName=Param.Action.ActionName;
1506ActionPath=Param.Action.ActionPath;
1507path_series=fileparts(which('series'));
1508
1509%% create the Action fct handle if RunMode option = 'local'
1510if strcmp(RunMode,'local')
1511    if ~isequal(ActionPath,path_series)
1512        eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1513        if ~exist(ActionPath,'dir')
1514            errormsg=['The prescribed function path ' ActionPath ' does not exist'];
1515            return
1516        end
1517        if ~isequal(spath,ActionPath)
1518            addpath(ActionPath)% add the prescribed path if not the current one
1519        end
1520    end
1521    eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1522    if ~isequal(ActionPath,path_series)
1523        rmpath(ActionPath)% add the prescribed path if not the current one
1524    end
1525end
1526
1527%% Get  parameters from series.xml
1528errormsg=''; % default error message
1529ActionFullName=fullfile(get(handles.ActionPath,'String'),ActionName);
1530
1531%% If a compiled version has been selected (ext .sh) check wether it needs to be recompiled
1532if strcmp(ActionExt,'.sh')
1533    TransformPath='';
1534    if isfield(SeriesData,'TransformPath')
1535        TransformPath=SeriesData.TransformPath;
1536        if isfield(SeriesData,'TransformList')
1537            TransformList=get(handles.TransformName,'String');
1538            TransformIndex=get(handles.TransformName,'Value');
1539            TransformName=TransformList{TransformIndex};
1540            if ~ismember(TransformName,SeriesData.TransformList)
1541                TransformPath='';
1542            end
1543        end
1544    end
1545    if ~isempty(TransformPath)&&...
1546          ~strcmp(TransformPath,get(handles.TransformPath,'String'))% if the transform is not in paths set for compilation
1547        msgbox_uvmat('ERROR', 'compilation not available for this transform function, select .m')
1548        return
1549    end
1550    set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
1551    set(handles.ActionExt,'BackgroundColor',[1 1 0])
1552    [mcrmajor, mcrminor] = mcrversion;   
1553    MCRROOT = ['MCRROOT',int2str(mcrmajor),int2str(mcrminor)];
1554    RunTime = getenv(MCRROOT);
1555    ActionNameVersion=[ActionName '_' MCRROOT];
1556    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']);
1557    % compile the .m file if the .sh file does not exist yet
1558    if ~exist(ActionFullName,'file')
1559        answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
1560        if strcmp(answer,'Yes')
1561            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1562            path_uvmat=fileparts(which('series'));
1563            currentdir=pwd;
1564            cd(get(handles.ActionPath,'String'))% go to the directory of Action
1565            addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1566            compile(ActionName,TransformPath)
1567            cd(currentdir)
1568        else
1569            errormsg='Action launch interrupted';
1570            return
1571        end       
1572    else
1573        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']));
1574        m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
1575        if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
1576            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1577            drawnow
1578            answer=msgbox_uvmat('INPUT_Y-N',[ActionNameVersion '.sh needs to be updated: recompile now?']);
1579            if strcmp(answer,'Yes')
1580                path_uvmat=fileparts(which('series'));
1581                currentdir=pwd;
1582                cd(get(handles.ActionPath,'String'))% go to the directory of Action
1583                addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1584                addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile'
1585                compile(ActionName,TransformPath)
1586                cd(currentdir)
1587            end
1588        end
1589    end
1590
1591    set(handles.ActionExt,'BackgroundColor',[1 1 1])
1592     set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch
1593end
1594
1595%% set nbre of cluster cores and processes:
1596% NbCore is the number of computer processors used
1597% NbProcess is the number of independent processes in which the required calculation is split.
1598switch RunMode
1599    case {'local','background'}
1600        NbCore=1; % no need to split the calculation
1601    case 'cluster_oar'
1602        %proposed number of cores to reserve in the cluster
1603        NbCoreAdvised=SeriesData.SeriesParam.OarParam.NbCoreAdvised;
1604        NbCoreMax=SeriesData.SeriesParam.OarParam.NbCoreMax;
1605        if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1606            warning_string=', preferably use .sh option to save Matlab licences';
1607        else
1608            warning_string=')';
1609        end
1610        answer=inputdlg({['Number of cores (max ' num2str(NbCoreMax) warning_string],'extra oar options'},'oarsub parameter',1,{num2str(NbCoreAdvised),''});
1611        if isempty(answer)
1612            errormsg='Action launch interrupted by user';
1613            return
1614        end
1615        NbCore=str2double(answer{1});
1616        extra_oar=answer{2};
1617    case {'cluster_pbs', 'cluster_sge', 'cluster_qstat_unknown'}
1618        if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1619            NbCore=1; % one core used only (limitation of Matlab licences)
1620            answer=msgbox_uvmat('INPUT_Y-N','Number of cores =1: select the compiled version .sh for multi-core processing. Proceed with the .m version?');
1621            if ~strcmp(answer,'Yes')
1622                errormsg='Action launch interrupted';
1623                return
1624            end
1625            extra_oar='';
1626        else
1627            answer=inputdlg({'Number of jobs (max 1000)','Queue'},'qsub parameters',1,{'100','piv_debian'});
1628            NbCore=str2double(answer{1});
1629            qstat_Queue=answer{2};
1630            %extra_oar=answer{2}; % TODO : fix this for LMFA cluster. Maybe
1631            %extrs_oar and extra_pbs are not the best names
1632        end
1633end
1634if ~isfield(Param.IndexRange,'NbSlice')
1635    Param.IndexRange.NbSlice=[];
1636end
1637
1638%% create the output data directory if needed
1639OutputDir='';
1640if isfield(Param,'OutputSubDir')
1641    SubDirOut=[get(handles.OutputSubDir,'String') Param.OutputDirExt];
1642    SubDirOutNew=SubDirOut;
1643    detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir'); % test if  the dir  already exist
1644    check_create=1; % need to create the result directory by default
1645    CheckOverwrite=1;
1646    if isfield(Param,'CheckOverwrite')
1647        CheckOverwrite=Param.CheckOverwrite;
1648    end
1649    while detect
1650        if CheckOverwrite
1651            comment=', possibly overwrite previous data';
1652        else
1653            comment=', will complement existing result files (no overwriting)';
1654        end
1655        answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(Param.InputTable{1,1},SubDirOutNew) comment]);
1656        if strcmp(answer,'Cancel')
1657            return
1658        elseif strcmp(answer,'Yes')
1659            detect=0;
1660            check_create=0;
1661        else
1662            r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names'); % detect whether name ends by a number
1663            if isempty(r)
1664                r(1).root=[SubDirOutNew '_'];
1665                r(1).num1='0';
1666            end
1667            SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)]; % increment the index by 1 or put 1
1668            detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir'); % test if  the dir  already exists
1669            check_create=1;
1670        end
1671    end
1672    Param.OutputDirExt=regexprep(SubDirOutNew,Param.OutputSubDir,'');
1673    Param.OutputRootFile=Param.InputTable{1,3}; % the first sorted RootFile taken for output
1674    set(handles.OutputDirExt,'String',Param.OutputDirExt)
1675    OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]); % full name (with path) of output directory
1676    if check_create    % create output directory if it does not exist
1677        [tild,msg1]=mkdir(OutputDir);
1678        if ~strcmp(msg1,'')
1679            errormsg=['cannot create ' OutputDir ': ' msg1]; % error message for directory creation
1680            return
1681        end
1682    end
1683   
1684elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir
1685    OutputDir=Param.ActionInput.LogPath;   
1686end
1687DirXml=fullfile(OutputDir,'0_XML');
1688if ~exist(DirXml,'dir')
1689    [~,msg1]=mkdir(DirXml);
1690    if ~strcmp(msg1,'')
1691        errormsg=['cannot create ' DirXml ': ' msg1]; % error message for directory creation
1692        return
1693    end
1694end
1695OutputNomType=nomtype2pair(Param.InputTable{1,4}); % nomenclature for output files
1696
1697%% get the set of reference input field indices
1698first_i=1; % first i index to process
1699last_i=1; % last i index to process
1700incr_i=1; % increment step in i index
1701first_j=1; % first j index to process
1702last_j=1; % last j index to process
1703incr_j=1; % increment step in j index
1704if isfield(Param.IndexRange,'first_i')
1705    first_i=Param.IndexRange.first_i;
1706    incr_i=Param.IndexRange.incr_i;
1707    last_i=Param.IndexRange.last_i;
1708end
1709if isfield(Param.IndexRange,'incr_j')
1710    first_j=Param.IndexRange.first_j;
1711    last_j=Param.IndexRange.last_j;
1712    incr_j=Param.IndexRange.incr_j;
1713end
1714if last_i < first_i || last_j < first_j
1715    errormsg= 'series/Run_Callback:last field index must be larger or equal to the first one';
1716    return
1717end
1718%incr_i must be defined, =1 by default, if NbSlice is active
1719if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice)
1720    incr_i=1;
1721    set(handles.num_incr_i,'String','1')
1722end
1723% case of no increment i defined: processing is done on the available files found in i1_series
1724if isempty(incr_i)
1725    if isempty(incr_j)
1726        [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1727        ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1728        ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1729        ref_j=ref_j-1;
1730        ref_i=ref_i-1;
1731    else
1732        ref_j=first_j:incr_j:last_j;
1733        [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1734        ref_i=ref_i-1;
1735        ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1736    end
1737    % increment i is defined: processing is done on first_i:incr_i:last_i;
1738else
1739    ref_i=first_i:incr_i:last_i;
1740    if isempty(incr_j)% automatic finding of the existing j indices
1741        [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1742        ref_j=ref_j-1;
1743        ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1744    else
1745        ref_j=first_j:incr_j:last_j;
1746    end
1747end
1748CPUTime=1; % job time estimated at 1 min per iteration (on index i and j) by default
1749if isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime)
1750    CPUTime=Param.Action.CPUTime; % Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j
1751end
1752nbfield_j=numel(ref_j); % number of j indices
1753BlockLength=numel(ref_i); % by default, job involves the full set of i field indices
1754NbProcess=1;
1755switch RunMode
1756    case {'cluster_oar','cluster_pbs','cluster_sge','cluster_qstat_unknown'}
1757        JobNumberMax=SeriesData.SeriesParam.OarParam.JobNumberMax;
1758        JobCPUTimeAdvised=SeriesData.SeriesParam.OarParam.JobCPUTimeAdvised;
1759        if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined
1760            BlockLength= ceil(JobCPUTimeAdvised/(CPUTime*nbfield_j)); % iterations are grouped in sets with length BlockLength  such that the typical CPU time of a job is MinJobNumber.
1761            BlockLength=max(BlockLength,ceil(numel(ref_i)/JobNumberMax)); % possibly increase the BlockLength to have less than MaxJobNumber jobs
1762            NbProcess=ceil(numel(ref_i)/BlockLength) ; % nbre of processes sent to oar
1763        else
1764            NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1765        end
1766        NbCore=min(NbCore,NbProcess); % reduces the number of cores if it exceeds the number of processes
1767    otherwise
1768        if ~isempty(Param.IndexRange.NbSlice)
1769            NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1770        end
1771end
1772
1773%% record nbre of output files and starting time for computation for status
1774StatusData=get(handles.status,'UserData');
1775if isfield(StatusData,'OutputFileMode')
1776    switch StatusData.OutputFileMode
1777        case 'NbInput'
1778            StatusData.NbOutputFile=numel(ref_i)*nbfield_j;
1779        case 'NbInput_i'
1780            StatusData.NbOutputFile=numel(ref_i);
1781        case 'NbSlice'
1782            StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
1783    end
1784end
1785StatusData.TimeStart=now;
1786set(handles.status,'UserData',StatusData)
1787
1788%% case of a function in Python
1789if strcmp(ActionExt, '.py (in dev.)')
1790    fprintf([
1791        '\n' ...
1792        '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ...
1793        'The option .py is used. It is still in development.\n' ...
1794        'To try it, first install pyper and the most recent version of fluidimage\n' ...
1795        '(see https://bitbucket.org/fluiddyn/fluidimage).\n' ...
1796        'Warning: there is no direct correspondance between UVMAT and fluidimage parameters\n' ...
1797        '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n'])
1798    RunMode = 'python';
1799end
1800
1801
1802%% direct processing on the current Matlab session or creation of command files
1803filexml=cell(1,NbProcess); % initialisation of the names of the files containing the processing parameters
1804extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process
1805for iprocess=1:NbProcess
1806    extxml{iprocess}='.xml';
1807end
1808for iprocess=1:NbProcess
1809    if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1810        disp('program stopped by user')
1811        return
1812    end
1813    if isempty(Param.IndexRange.NbSlice)
1814        Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1815        if Param.IndexRange.first_i>last_i
1816            NbProcess=iprocess-1; % leave the loop, we are at the end of the calculation
1817            break
1818        end
1819        Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
1820    else %multislices (then incr_i is not empty)
1821        Param.IndexRange.first_i= first_i+iprocess-1;
1822        Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;
1823    end
1824    for ilist=1:size(Param.InputTable,1)
1825        Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/'); % correct path name for PCWIN system
1826    end
1827   
1828    if isfield(Param,'OutputSubDir')
1829        t=struct2xml(Param);
1830        t=set(t,1,'name','Series');
1831        extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,...
1832            Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1833        filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess});
1834        try
1835            save(t, filexml{iprocess}); % save the xml file containing the processing parameters
1836        catch ME
1837            if ~strcmp (RunMode,'local')
1838                errormsg=['error writting ' filexml{iprocess} ': ' ME.message];
1839                return
1840            end
1841        end
1842    end
1843    if strcmp (RunMode,'local')
1844        switch ActionExt
1845            case '.m'
1846                h_fun(Param); % direct launching
1847               
1848            case '.sh'
1849                switch computer
1850                    case {'PCWIN','PCWIN64'} %Windows system
1851                        filexml=regexprep(filexml,'\\','\\\\'); % add '\' so that '\' are left as characters
1852                        system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); % TODO: adapt to DOS system
1853                    case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1854                        system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]);
1855                end
1856        end
1857    end
1858end
1859
1860if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python')
1861    %% processing on a different session of the same computer (background) or cluster, create executable files
1862    batch_file_list=cell(NbProcess,1); % initiate the list of executable files
1863    DirExe=fullfile(OutputDir,'0_EXE'); % directory name for executable files
1864    switch computer
1865        case {'PCWIN','PCWIN64'} %Windows system
1866            ExeExt='.bat';
1867        case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1868            ExeExt='.sh';
1869    end
1870    %create subdirectory for executable files
1871    if ~exist(DirExe,'dir')
1872        [tild,msg1]=mkdir(DirExe);
1873        if ~strcmp(msg1,'')
1874            errormsg=['cannot create ' DirExe ': ' msg1]; % error message for directory creation
1875            return
1876        end
1877    end
1878    %create subdirectory for log files
1879    DirLog=fullfile(OutputDir,'0_LOG');
1880    if ~exist(DirLog,'dir')
1881        [tild,msg1]=mkdir(DirLog);
1882        if ~strcmp(msg1,'')
1883            errormsg=['cannot create ' DirLog ': ' msg1]; % error message for directory creation
1884            return
1885        end
1886    end
1887   
1888    %create the executable file
1889    file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,...
1890        first_i,last_i,first_j,last_j);
1891    file_exe_global=fullfile(OutputDir,'0_EXE',file_exe_global);
1892    filelog_global=fullfile_uvmat('','',Param.InputTable{1,3},'.log',OutputNomType,...
1893        first_i,last_i,first_j,last_j);
1894    filelog_global=fullfile(OutputDir,'0_LOG',filelog_global);
1895
1896    for iprocess=1:NbProcess   
1897        %create the executable file       
1898        batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt));
1899       
1900        % set the log file name
1901        filelog{iprocess}=fullfile(OutputDir,'0_LOG',regexprep(extxml{iprocess},'.xml$','.log'));     
1902    end
1903end
1904
1905%% launch the executable files for background or cluster processing
1906
1907switch RunMode
1908   
1909    case 'background'
1910        [fid,message]=fopen(file_exe_global,'w');
1911        if isequal(fid,-1)
1912            errormsg=['creation of ' file_exe_global ':' message];
1913            return
1914        end
1915        switch ActionExt
1916            case '.m'% Matlab function
1917                switch computer
1918                    case {'GLNX86','GLNXA64','MACI64'}
1919                        matlab_ver = ver('MATLAB');
1920                        matlab_version = matlab_ver.Version;
1921                        cmd=[...
1922                            '#!/bin/bash \n'...
1923                            'source /etc/profile \n'...
1924                            'module load matlab/''' matlab_version ''' \n'...% CHOICE OF MATLAB VERSION
1925                            'time_start=$(date +%%s)\n'...
1926                            'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog_global ''' <<END_MATLAB\n'...
1927                            'addpath(''' path_series '''); \n'...
1928                            'addpath(''' Param.Action.ActionPath '''); \n'];
1929                        for iprocess=1:NbProcess
1930                            cmd=[cmd '' Param.Action.ActionName  '( ''' filexml{iprocess} '''); \n'];
1931                        end
1932                        cmd=[cmd  'exit \n' 'END_MATLAB\n'...
1933                            'time_end=$(date +%%s)\n'...
1934                            'echo "global time = " $(($time_end - $time_start)) >> ''' filelog_global '''\n'];
1935                        fprintf(fid,cmd); % fill the executable file with the  char string cmd
1936                        fclose(fid); % close the executable filefilelog_global
1937                        system(['chmod +x ' file_exe_global]); % set the file to executable
1938                    case {'PCWIN','PCWIN64'}
1939                        cmd=['matlab -automation -logfile ' regexprep(filelog{iprocess},'\\','\\\\')...
1940                            ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
1941                            'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');'];
1942                        for iprocess=1:NbProcess
1943                            cmd=[cmd '' Param.Action.ActionName  '( ''' regexprep(filexml{iprocess},'\\','\\\\') ''');']
1944                        end
1945                        cmd=[cmd ';exit"'];
1946                        fprintf(fid,cmd); % fill the executable file with the  char string cmd
1947                        fclose(fid); % close the executable file
1948                end
1949                system([file_exe_global ' &'])% directly execute the command file
1950            case '.sh' % compiled Matlab function
1951                for iprocess=1:NbProcess
1952                    switch computer
1953                        case {'GLNX86','GLNXA64','MACI64'}
1954                            [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
1955                            if isequal(fid,-1)
1956                                errormsg=['creation of .bat file: ' message];
1957                                return
1958                            end
1959                            cmd=['#!/bin/bash \n '...
1960                                '#$ -cwd \n '...
1961                                'hostname && date \n '...
1962                                'umask 002 \n'...
1963                                ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
1964                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
1965                            fclose(fid); % close the executable file
1966                            system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
1967                            system([batch_file_list{iprocess} ' &'])% directly execute the command file
1968                        case {'PCWIN','PCWIN64'}
1969                            msgbox_uvmat('ERROR','option for compiled Matlab functions not implemented for Windows system')
1970                            return
1971                    end
1972                end
1973                msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched in background: press STATUS to see results'])
1974        end
1975       
1976    case 'cluster_oar' % option 'oar-parexec' used
1977        %create subdirectory for oar commands
1978        for iprocess=1:NbProcess
1979            [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
1980            if isequal(fid,-1)
1981                errormsg=['creation of .bat file: ' message];
1982                return
1983            end
1984            if  strcmp(ActionExt,'.sh')
1985                cmd=['#!/bin/bash \n '...
1986                    '#$ -cwd \n '...
1987                    'hostname && date \n '...
1988                    'umask 002 \n'...
1989                    ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
1990            else
1991                matlab_ver = ver('MATLAB');
1992                matlab_version = matlab_ver.Version;
1993                cmd=[...
1994                    '#!/bin/bash \n'...
1995                    'source /etc/profile \n'...
1996                    'module load matlab/''' matlab_version ''' \n'...% CHOICE OF MATLAB VERSION
1997                    'matlab -nodisplay -nosplash -nojvm -singleCompThread -logfile ''' filelog{iprocess} ''' <<END_MATLAB\n'...
1998                    'addpath(''' path_series '''); \n'...
1999                    'addpath(''' Param.Action.ActionPath '''); \n'...
2000                    '' Param.Action.ActionName  '( ''' filexml{iprocess} '''); \n'...
2001                    'exit' '\n'...
2002                    'END_MATLAB\n'];
2003            end
2004            fprintf(fid,cmd); % fill the executable file with the  char string cmd
2005            fclose(fid); % close the executable file
2006            system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
2007        end
2008        DirOAR=fullfile(OutputDir,'0_OAR');
2009        if exist(DirOAR,'dir')% delete the content of the dir 0_LOG to allow new input
2010            curdir=pwd;
2011            cd(DirOAR)
2012            delete('*')
2013            cd(curdir)
2014        else
2015            [tild,msg1]=mkdir(DirOAR);
2016            if ~strcmp(msg1,'')
2017                errormsg=['cannot create ' DirOAR ': ' msg1]; % error message for directory creation
2018                return
2019            end
2020        end
2021        % create file containing the list of jobs
2022        filename_joblist=fullfile(DirOAR,'job_list.txt'); % name of the file containing the list of executables
2023        fid=fopen(filename_joblist,'w'); % open it for writting
2024        for iprocess=1:length(batch_file_list)
2025            fprintf(fid,[batch_file_list{iprocess} '\n']); % write list of exe files
2026        end
2027        fclose(fid);
2028        system(['chmod +x ' filename_joblist]); % set the file to executable
2029       
2030        filename_log=fullfile(DirLog,'job_list.stdout'); % file for output messages of the master oar process
2031        filename_errors=fullfile(DirLog,'job_list.stderr'); % file for error messages of the master oar process
2032        % the command job_list.txt contains the list of NbProcess independent individual jobs
2033        % in which the total calculation has been split. Those are written as executable files .sh in the folder /O_EXE.
2034        %  These individual jobs are grouped by the system as oar jobs on the NbCore processors.
2035        %  For each processor, the oar job must stop after the walltime which has been set, which is limited to 24 h.
2036        %  However, the oar job is automatically restarted (option 'idempotent') provided the individual jobs are
2037        % shorter than the wall time: in the time interval 'checkpoint' (WallTimeOneJob) before the end of the allowed duration,
2038        %  the oar job restarts when an individual job ends.
2039        WallTimeMax=SeriesData.SeriesParam.OarParam.WallTimeMax;
2040        JobTime=CPUTime*BlockLength*nbfield_j; % estimated CPU time for one individual job (in minutes)
2041        % wall time (in hours ) for each oar job, allowing 10 individual jobs, but limited to 23 h:
2042        WallTimeTotal=min(WallTimeMax,4*JobTime/60);
2043        %disp(['WallTimeTotal: ' num2str(WallTimeTotal) ' hours'])
2044        % estimated time of an individual job (in min), with a margin of error
2045        WallTimeOneJob=min(4*JobTime+10,WallTimeTotal*60/2); % estimated max time of an individual job for checkpoint
2046        disp(['WallTimeOneJob: ' num2str(WallTimeOneJob) ' minutes'])
2047        if NbProcess>=8
2048            bigiojob_string=['+{type = ' char(39) 'bigiojob' char(39) '}/licence=1'];% char(39) is quote - bigiojob limit UVmat parallel launch on cluster to avoid saturation of disk access to data
2049        else
2050            bigiojob_string='';
2051        end
2052        oar_command=['oarsub -n UVmat_' ActionFullName ' '...
2053            '-t idempotent --checkpoint ' num2str(WallTimeOneJob*60) ' '...
2054            '-l "/core=' num2str(NbCore)...
2055            bigiojob_string... % char(39) is quote - bigiojob limit UVmat parallel launch on cluster
2056            ',walltime=' datestr(WallTimeTotal/24,13) '" '...
2057            '-E ' filename_errors ' '...
2058            '-O ' filename_log ' '...
2059            extra_oar ' '...
2060            '"oar-parexec -s -f ' filename_joblist ' '...
2061            '-l ' filename_joblist '.log"'];
2062       
2063        fprintf(oar_command); % display  system command on the Matlab command window
2064        [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window
2065        filename_oarcommand=fullfile(DirOAR,'0_oar_command'); % keep track of the command in file '0-OAR/0_oar_command'
2066        fid=fopen(filename_oarcommand,'w');
2067        fprintf(fid,oar_command); % store the command
2068        fprintf(fid,result); % store the result (job ID number)
2069        fclose(fid);
2070        msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched as  ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
2071       
2072    case 'cluster_pbs' % for LMFA Kepler machine
2073        %create subdirectory for pbs command and log files
2074        DirPBS=fullfile(OutputDir,'0_PBS'); % todo : common name OAR/PBS
2075        if exist(DirPBS,'dir')% delete the content of the dir 0_LOG to allow new input
2076            curdir=pwd;
2077            cd(DirPBS)
2078            delete('*')
2079            cd(curdir)
2080        else
2081            [tild,msg1]=mkdir(DirPBS);
2082            if ~strcmp(msg1,'')
2083                errormsg=['cannot create ' DirPBS ': ' msg1]; % error message for directory creation
2084                return
2085            end
2086        end
2087        max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h)
2088        walltime_onejob=1800; % seconds, max estimated time for asingle file index value
2089        filename_joblist=fullfile(DirPBS,'job_list.txt'); % create name of the global executable file
2090        fid=fopen(filename_joblist,'w');
2091        for iprocess=1:length(batch_file_list)
2092            fprintf(fid,[batch_file_list{iprocess} '\n']); % list of exe files
2093        end
2094        fclose(fid);
2095        system(['chmod +x ' filename_joblist]); % set the file to executable
2096        pbs_command=['qsub -n CIVX '...
2097            '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
2098            '-l /core=' num2str(NbCore) ','...
2099            'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
2100            '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
2101            '-O ' regexprep(filename_joblist,'\.txt\>','.log') ' '...
2102            extra_qstat ' '...
2103            '"oar-parexec -s -f ' filename_joblist ' '...
2104            '-l ' filename_joblist '.log"'];
2105        filename_oarcommand=fullfile(DirPBS,'pbs_command');
2106        fid=fopen(filename_oarcommand,'w');
2107        fprintf(fid,pbs_command);
2108        fclose(fid);
2109        fprintf(pbs_command); % display in command line
2110        %system(pbs_command);
2111        msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster'])
2112
2113     case 'cluster_sge' % for PSMN
2114        % Au PSMN, on ne cr??e pas 1 job avec plusieurs c??urs, mais N jobs de 1 c??urs
2115        % o?? N < 1000.
2116        %create subdirectory for pbs command and log files
2117
2118        DirSGE=fullfile(OutputDir,'0_SGE');
2119        if exist(DirSGE,'dir')% delete the content of the dir 0_LOG to allow new input
2120            curdir=pwd;
2121            cd(DirSGE)
2122            delete('*')
2123            cd(curdir)
2124        else
2125            [tild,msg1]=mkdir(DirSGE);
2126            if ~strcmp(msg1,'')
2127                errormsg=['cannot create ' DirSGE ': ' msg1]; % error message for directory creation
2128                return
2129            end
2130        end
2131        maxImgsPerJob = ceil(length(batch_file_list)/NbCore);
2132        disp(['Max number of jobs: ' num2str(NbCore)])
2133        disp(['Images per job: ' num2str(maxImgsPerJob)])
2134       
2135        iprocess = 1;
2136        imgsInJob = [];
2137        currJobIndex = 1;
2138        done = 0;
2139        while(~done)
2140            if(iprocess <= length(batch_file_list))
2141                imgsInJob = [imgsInJob, iprocess];
2142            end
2143            if((numel(imgsInJob) >= maxImgsPerJob) || (iprocess == length(batch_file_list)))
2144                cmd=['#!/bin/sh \n'...
2145                     '#$ -cwd \n'...
2146                     'hostname && date\n']
2147                for ii=1:numel(imgsInJob)
2148                    cmd=[cmd ActionFullName ' /softs/matlab ' filexml{imgsInJob(ii)} '\n'];
2149                end
2150                [fid, message] = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w');
2151                fprintf(fid, cmd);
2152                fclose(fid);
2153                system(['chmod +x ' DirSGE '/job' num2str(currJobIndex) '.sh'])
2154                sge_command=['qsub -N civ_' num2str(currJobIndex) ' '...
2155                    '-q ' qstat_Queue ' '...
2156                    '-e ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2157                    '-o ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2158                    fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])];
2159                fprintf(sge_command); % display in command line
2160                [status, result] = system(sge_command);
2161                fprintf(result);
2162                currJobIndex = currJobIndex + 1;
2163                imgsInJob = [];
2164            end
2165            if(iprocess == length(batch_file_list))
2166                done = 1;
2167            end
2168            iprocess = iprocess + 1;
2169        end
2170        msgbox_uvmat('CONFIRMATION',[num2str(currJobIndex-1) ' jobs launched on queue ' qstat_Queue '.'])
2171    case 'python'
2172        command = ['LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "l = x.split('':''); l = [s for s in l if ''matlab'' not in s]; print('':''.join(l))") ' ...
2173            'python -m fluidimage.run_from_xml ' filexml{iprocess}];
2174        fprintf(['command:\n' command '\n\n'])
2175        system(command, '-echo');
2176end
2177if exist(OutputDir,'dir')
2178    [SUCCESS,MESSAGE,MESSAGEID] = fileattrib (OutputDir);
2179    if MESSAGE.GroupWrite~=1
2180    [success,msg] = fileattrib(OutputDir,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2181    if success==0
2182        msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg}); % error message for directory creation
2183    end
2184    end
2185end
2186
2187%------------------------------------------------------------------------
2188function STOP_Callback(hObject, eventdata, handles)
2189%------------------------------------------------------------------------
2190set(handles.RUN, 'BusyAction','cancel')
2191set(handles.RUN,'BackgroundColor',[1 0 0])
2192set(handles.RUN,'enable','on')
2193set(handles.RUN, 'Value',0)
2194
2195%------------------------------------------------------------------------
2196% --- read parameters from the GUI series
2197%------------------------------------------------------------------------
2198function Param=read_GUI_series(handles)
2199
2200%% read raw parameters from the GUI series
2201Param=read_GUI(handles.series);
2202
2203%% clean the output structure by removing unused information
2204if isfield(Param,'Pairs')
2205    Param=rmfield(Param,'Pairs'); % info Pairs not needed for output
2206end
2207if isfield(Param,'InputLine')
2208    Param=rmfield(Param,'InputLine');
2209end
2210if isfield(Param,'EditObject')
2211    Param=rmfield(Param,'EditObject');
2212end
2213Param.IndexRange.TimeSource=Param.IndexRange.TimeTable{end,1};
2214Param.IndexRange=rmfield(Param.IndexRange,'TimeTable');
2215empty_line=false(size(Param.InputTable,1),1);
2216for iline=1:size(Param.InputTable,1)
2217    empty_line(iline)=isempty(cell2mat(Param.InputTable(iline,1:3)));
2218end
2219Param.InputTable(empty_line,:)=[];
2220
2221%------------------------------------------------------------------------
2222% --- Executes on selection change in ActionName.
2223function ActionName_Callback(hObject, eventdata, handles)
2224%------------------------------------------------------------------------
2225
2226%% stop any ongoing series processing
2227if isequal(get(handles.RUN,'Value'),1)
2228    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
2229    if strcmp(answer,'Yes')
2230        STOP_Callback(hObject, eventdata, handles)
2231    else
2232        return
2233    end
2234end
2235set(handles.ActionName,'BackgroundColor',[1 1 0])
2236huigetfile=findobj(allchild(0),'tag','status_display');
2237if ~isempty(huigetfile)
2238    delete(huigetfile)
2239end
2240drawnow
2241
2242%% get Action name and path
2243NbBuiltinAction=get(handles.Action,'UserData'); % nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
2244ActionList=get(handles.ActionName,'String'); % list menu fields
2245ActionIndex=get(handles.ActionName,'Value');
2246if ~isequal(ActionIndex,1)% if we are not just opening series
2247    InputTable=get(handles.InputTable,'Data');
2248    if isempty(InputTable{1,4})
2249        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
2250        return
2251    end
2252end
2253ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2254ActionPathList=get(handles.ActionName,'UserData'); % list of recorded paths to functions of the list ActionName
2255
2256%% add a new function to the menu if 'more...' has been selected in the menu ActionName
2257if isequal(ActionName,'more...')
2258    [FileName, PathName] = uigetfile( ...
2259        {'*.m', ' (*.m)';
2260        '*.m',  '.m files '; ...
2261        '*.*', 'All Files (*.*)'}, ...
2262        'Pick a series processing function ',get(handles.ActionPath,'String'));
2263    if length(FileName)<2
2264        return
2265    end
2266    [tild,ActionName,ActionExt]=fileparts(FileName);
2267   
2268    % insert the choice in the menu ActionName
2269    ActionIndex=find(strcmp(ActionName,ActionList),1); % look for the selected function in the menu Action
2270    PathName=regexprep(PathName,'/$','');
2271    if ~isempty(ActionIndex) && ~strcmp(ActionPathList{ActionIndex},PathName)%compare the path to the existing fct
2272        ActionIndex=[]; % the selected path is different than the recorded one
2273    end
2274    if isempty(ActionIndex)%the qselected fct (with selected path) does not exist in the menu
2275        ActionIndex= length(ActionList);
2276        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)]; % the selected function is appended in the menu, before the last item 'more...'
2277         ActionPathList=[ActionPathList; PathName];
2278    end
2279   
2280    % record the file extension and extend the path list if it is a new extension
2281    ActionExtList=get(handles.ActionExt,'String');
2282    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
2283    if isempty(ActionExtIndex)
2284        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
2285    end
2286
2287    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
2288    if length(ActionList)>NbBuiltinAction+5; % nb_builtin_ACTION=nbre of functions always remaining in the initial menu
2289        nbremove=length(ActionList)-NbBuiltinAction-5;
2290        ActionList(NbBuiltinAction+1:end-5)=[];
2291        ActionPathList(NbBuiltinAction+1:end-4,:)=[];
2292        ActionIndex=ActionIndex-nbremove;
2293    end
2294   
2295    % record action menu, choice and path
2296    set(handles.ActionName,'Value',ActionIndex)
2297    set(handles.ActionName,'String',ActionList)
2298       set(handles.ActionName,'UserData',ActionPathList);
2299    set(handles.ActionExt,'Value',ActionExtIndex)
2300       
2301    %record the user defined menu additions in personal file profil_perso
2302    dir_perso=prefdir;
2303    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2304    if NbBuiltinAction+1<=numel(ActionList)-1
2305        ActionListUser=ActionList(NbBuiltinAction+1:numel(ActionList)-1);
2306        ActionPathListUser=ActionPathList(NbBuiltinAction+1:numel(ActionList)-1);
2307        ActionExtListUser={};
2308        if numel(ActionExtList)>2
2309            ActionExtListUser=ActionExtList(3:end);
2310        end
2311        if exist(profil_perso,'file')
2312            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
2313        else
2314            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
2315        end
2316    end
2317end
2318
2319%% check the current ActionPath to the selected function
2320ActionPath=ActionPathList{ActionIndex}; % current recorded path
2321set(handles.ActionPath,'String',ActionPath); % show the path to the senlected function
2322
2323%% reinitialise the waitbar
2324update_waitbar(handles.Waitbar,0)
2325
2326%% Put the first line of the selected Action fct as tooltip help
2327try
2328    [fid,errormsg] =fopen([ActionName '.m']);
2329    InputText=textscan(fid,'%s',1,'delimiter','\n');
2330    fclose(fid);
2331    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
2332end
2333set(handles.ActionName,'BackgroundColor',[1 1 1])
2334set(handles.ActionInput,'BackgroundColor',[1 0 1])% set ActionInput button to magenta color to indicate that input refr
2335
2336
2337% --- Executes on button press in ActionInput.
2338function ActionInput_Callback(hObject, eventdata, handles)
2339
2340set(handles.ActionInput,'BackgroundColor',[1 1 0])
2341
2342%% create the function handle for Action
2343ActionPath=get(handles.ActionPath,'String');
2344ActionList=get(handles.ActionName,'String');
2345ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2346if ~exist(ActionPath,'dir')
2347    msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']);
2348    return
2349end
2350current_dir=pwd; % current working dir
2351cd(ActionPath)
2352h_fun=str2func(ActionName);
2353cd(current_dir)
2354
2355%% Activate the Action fct to adapt the configuration of the GUI series and bring specific parameters in SeriesData
2356Param=read_GUI_series(handles); % read the parameters from the GUI series
2357Param.Action.RUN=0;
2358ParamOut=h_fun(Param); % run the selected Action function to get the relevant input
2359
2360
2361%% Visibility of VelType and VelType_1 menus asked by ActionName
2362VelTypeRequest=1; % VelType requested by default
2363VelTypeRequest_1=1; % VelType requested by default
2364if isfield(ParamOut,'VelType')
2365    VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'});
2366    VelTypeRequest_1=strcmp( ParamOut.VelType,'two');
2367end
2368FieldNameRequest=0;  %hidden by default
2369FieldNameRequest_1=0;  %hidden by default
2370if isfield(ParamOut,'FieldName')
2371    FieldNameRequest=ismember(ParamOut.FieldName,{'on','one','two'});
2372    FieldNameRequest_1=strcmp( ParamOut.FieldName,'two');
2373end
2374
2375%% Detect the types of input files and set menus and default options in 'VelType'
2376SeriesData=get(handles.series,'UserData'); % info on the input file series
2377iview_civ=find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));
2378iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)); % all nc files, icluding civ
2379FieldList=get(handles.FieldName,'String'); % previous list as default
2380if ~iscell(FieldList),FieldList={FieldList};end
2381FieldList_1=get(handles.FieldName_1,'String'); % previous list as default
2382if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
2383%CheckList=0; % indicate whether FieldName has been updated
2384CheckList_1=1; % indicate whether FieldName_1 has been updated
2385handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title];
2386if VelTypeRequest && numel(iview_civ)>=1
2387    menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)});
2388    set(handles.VelType,'Value',1)% set first choice by default
2389    set(handles.VelType,'String',[{'*'};menu])
2390    set(handles.VelType,'Visible','on')
2391    set(handles.VelType_title,'Visible','on')
2392    FieldList=[set_field_list('U','V');{'C'};{'get_field...'}]; % standard menu for civx data
2393    %CheckList=1;
2394    set(handles.FieldName,'Value',1); % velocity vector choice by default
2395    if  VelTypeRequest_1 && numel(iview_civ)>=2
2396        menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});
2397        set(handles.VelType_1,'Value',1)% set first choice by default
2398        set(handles.VelType_1,'String',[{'*'};menu])
2399        set(handles.VelType_1,'Visible','on')
2400        set(handles.VelType_title_1,'Visible','on')
2401        FieldList_1=[set_field_list('U','V');{'C'};{'get_field...'}]; % standard menu for civx data
2402        CheckList_1=1;
2403        set(handles.FieldName_1,'Value',1); % velocity vector choice by default
2404    else
2405        set(handles.VelType_1,'Visible','off')
2406        set(handles.VelType_title_1,'Visible','off')
2407    end
2408else
2409    set(handles.VelType,'Visible','off')
2410    set(handles.VelType_title,'Visible','off')
2411end
2412
2413%% Detect the types of input files and set menus and default options in 'FieldName'
2414if (FieldNameRequest || VelTypeRequest) && numel(iview_netcdf)>=1
2415    set(handles.InputFields,'Visible','on')% set the frame InputFields visible
2416    if FieldNameRequest && isfield(SeriesData.FileInfo{iview_netcdf(1)},'ListVarName')
2417        set(handles.FieldName,'Visible','on')
2418        ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName;
2419        ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2420        for ilist=1:numel(ind_var)
2421            if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2422                FieldList={}; % previous choice not consistent with new input field
2423                set(handles.FieldName,'Value',1)
2424                break
2425            end
2426        end
2427        if ~isempty(FieldList)
2428            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2429                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2430                FieldList={};
2431                set(handles.Coord_x,'String','')
2432                set(handles.Coord_y,'String','')
2433            end
2434            Coord_z=get(handles.Coord_z,'String');
2435            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2436                FieldList={};
2437                set(handles.Coord_z,'String','')
2438            end
2439        end
2440    else
2441        set(handles.FieldName,'Visible','off')
2442    end
2443   
2444    set(handles_coord,'Visible','on')
2445    FieldList=[FieldList;{'get_field...'}];
2446    if FieldNameRequest_1 && numel(iview_netcdf)>=2
2447        set(handles.FieldName_1,'Visible','on')
2448        if CheckList_1==0        % not civ input made
2449            ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName;
2450            ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2451            for ilist=1:numel(ind_var)
2452                if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2453                    FieldList_1={}; % previous choice not consistent with new input field
2454                    set(handles.FieldName_1,'Value',1)
2455                    break
2456                end
2457            end
2458            warn_coord=0;
2459            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2460                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2461                warn_coord=1;
2462            end
2463            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2464                FieldList_1={};
2465                warn_coord=1;
2466            end
2467            if warn_coord
2468                msgbox_uvmat('WARNING','coordinate names do not exist in the second netcdf input file')
2469            end
2470           
2471            set(handles.FieldName_1,'Visible','on')
2472            set(handles.FieldName_1,'Value',1)
2473            set(handles.FieldName_1,'String',FieldList_1)
2474        end
2475    else
2476        set(handles.FieldName_1,'Visible','off')
2477    end
2478    if isempty(FieldList)
2479        set(handles.FieldName,'Visible','off')
2480    else
2481        set(handles.FieldName,'Visible','on')
2482        set(handles.FieldName,'String',FieldList)
2483    end
2484else
2485    set(handles.InputFields,'Visible','off')
2486end
2487
2488%% Introduce visibility of file overwrite option
2489if isfield(ParamOut,'CheckOverwriteVisible')&& strcmp(ParamOut.CheckOverwriteVisible,'on')
2490    set(handles.CheckOverwrite,'Visible','on')
2491else
2492    set(handles.CheckOverwrite,'Visible','off')
2493end
2494
2495%% Check whether alphabetical sorting of input Subdir is allowed by the Action fct  (for multiples series entries)
2496if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Param.InputTable,1)>1
2497    [tild,iview]=sort(Param.InputTable(:,2)); % subdirectories sorted in alphabetical order
2498    set(handles.InputTable,'Data',Param.InputTable(iview,:));
2499    MinIndex_i=get(handles.MinIndex_i,'Data');
2500    MinIndex_j=get(handles.MinIndex_j,'Data');
2501    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2502    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2503    set(handles.MinIndex_i,'Data',MinIndex_i(iview,:));
2504    set(handles.MinIndex_j,'Data',MinIndex_j(iview,:));
2505    set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:));
2506    set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));
2507    TimeTable=get(handles.TimeTable,'Data');
2508    set(handles.TimeTable,'Data',TimeTable(iview,:));
2509    PairString=get(handles.PairString,'Data');
2510    set(handles.PairString,'Data',PairString(iview,:));
2511end
2512
2513%% Impose the whole input file index range if requested
2514if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on')
2515    MinIndex_i=get(handles.MinIndex_i,'Data');
2516    MinIndex_j=get(handles.MinIndex_j,'Data');
2517    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2518    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2519    set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line)
2520    set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line)
2521    set(handles.num_incr_i,'String','1')
2522    set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line)
2523    set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line)
2524    set(handles.num_incr_j,'String','1')
2525else  % check index ranges
2526    first_i=1;last_i=1;first_j=1;last_j=1;
2527    if isfield(Param.IndexRange,'first_i')
2528        first_i=Param.IndexRange.first_i;
2529        last_i=Param.IndexRange.last_i;
2530    end
2531    if isfield(Param.IndexRange,'first_j')
2532        first_j=Param.IndexRange.first_j;
2533        last_j=Param.IndexRange.last_j;
2534    end
2535    if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
2536            set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
2537end
2538
2539%% enable or desable j index visibility
2540status_j='on'; % default
2541if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices
2542    status_j='off'; % no j index needed
2543elseif strcmp(get(handles.PairString,'Visible'),'on')
2544    check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j')); % =0 for burst case, 1 otherwise
2545    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
2546        status_j='off'; % no j index needed for bust case
2547    end
2548end
2549enable_j(handles,status_j) % no j index needed
2550if isfield(ParamOut,'j_index_1')&& isfield(ParamOut,'j_index_2')%strcmp(ParamOut.Desable_j_index,'on')
2551    %status_j='off';
2552    set(handles.num_first_j,'String',num2str(ParamOut.j_index_1))
2553    set(handles.num_last_j,'String',num2str(ParamOut.j_index_2))
2554    set(handles.num_first_j,'enable','off')
2555    set(handles.num_last_j,'enable','off')
2556    set(handles.num_incr_j,'visible','off')
2557else
2558    set(handles.num_first_j,'enable','on')
2559    set(handles.num_last_j,'enable','on')
2560    set(handles.num_incr_j,'visible',status_j)
2561end
2562
2563%% NbSlice visibility
2564if isfield(ParamOut,'NbSlice') && (strcmp(ParamOut.NbSlice,'on')||isnumeric(ParamOut.NbSlice))
2565    set(handles.num_NbSlice,'Visible','on')
2566    set(handles.NbSlice_title,'Visible','on')
2567else
2568    set(handles.num_NbSlice,'Visible','off')
2569    set(handles.NbSlice_title,'Visible','off')
2570end
2571if isfield(ParamOut,'NbSlice') && isnumeric(ParamOut.NbSlice)
2572    set(handles.num_NbSlice,'String',num2str(ParamOut.NbSlice))
2573    set(handles.num_NbSlice,'Enable','off'); % NbSlice set by the activation of the Action function
2574else
2575    set(handles.num_NbSlice,'Enable','on'); % NbSlice can be modified on the GUI series
2576end
2577
2578%% Visibility of FieldTransform menu
2579FieldTransformVisible='off';  %hidden by default
2580if isfield(ParamOut,'FieldTransform')
2581    if ~strcmp(ParamOut.FieldTransform,'off')
2582    FieldTransformVisible='on'; 
2583    end
2584    if iscell(ParamOut.FieldTransform)
2585        SeriesData.TransformList=ParamOut.FieldTransform;
2586    end
2587    TransformName_Callback([],[], handles)
2588end
2589set(handles.FieldTransform,'Visible',FieldTransformVisible)
2590if isfield(ParamOut,'TransformPath');% record the path of transform function requested for compilation
2591    set(handles.TransformPath,'UserData',ParamOut.TransformPath)
2592else
2593    set(handles.TransformPath,'UserData',[])
2594end
2595
2596%% Visibility of projection object
2597ProjObjectVisible='off';  %hidden by default
2598if isfield(ParamOut,'ProjObject')
2599    ProjObjectVisible=ParamOut.ProjObject;
2600end
2601set(handles.CheckObject,'Visible',ProjObjectVisible)
2602if ~get(handles.CheckObject,'Value')
2603    ProjObjectVisible='off';
2604end
2605set(handles.ProjObject,'Visible',ProjObjectVisible)
2606set(handles.DeleteObject,'Visible',ProjObjectVisible)
2607set(handles.ViewObject,'Visible',ProjObjectVisible)
2608set(handles.EditObject,'Visible',ProjObjectVisible)
2609
2610%% Visibility of mask input
2611MaskVisible='off';  %hidden by default
2612if isfield(ParamOut,'Mask')
2613    MaskVisible=ParamOut.Mask;
2614end
2615set(handles.CheckMask,'Visible',MaskVisible);
2616
2617%% definition of the directory containing the output files
2618if  ~(isfield(SeriesData,'ActionName') && strcmp(ActionName,SeriesData.ActionName))
2619    OutputDirExt='.series'; % default
2620    if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
2621        OutputDirExt=ParamOut.OutputDirExt;
2622    end
2623    set(handles.OutputDirExt,'String',OutputDirExt)
2624end
2625OutputDirVisible='off';
2626OutputSubDirMode='auto'; % default
2627SubDirOut='';
2628if isfield(ParamOut,'OutputSubDirMode')
2629    OutputSubDirMode=ParamOut.OutputSubDirMode;
2630end
2631InputTable=get(handles.InputTable,'Data');
2632switch OutputSubDirMode
2633    case 'auto'; % default
2634        OutputDirVisible='on';
2635        SubDir=InputTable(1:end,2); % set of subdirectories
2636        SubDirOut=SubDir{1};
2637        if numel(SubDir)>1
2638            for ilist=2:numel(SubDir)
2639                SubDirOut=[SubDirOut '-' regexprep(SubDir{ilist},'^/','')];
2640            end
2641        end
2642    case 'one'
2643        OutputDirVisible='on';
2644        SubDirOut=InputTable{1,2}; % use the first subdir name (+OutputDirExt) as output  subdirectory
2645    case 'two'
2646        OutputDirVisible='on';   
2647        SubDir=InputTable(1:2,2); % set of subdirectories
2648        SubDirOut=SubDir{1};
2649        if numel(SubDir)>1
2650                SubDirOut=[SubDirOut '-' regexprep(SubDir{2},'^/','')];
2651        end
2652    case 'last'
2653        OutputDirVisible='on';
2654        SubDirOut=InputTable{end,2}; % use the last subdir name (+OutputDirExt) as output  subdirectory
2655end
2656set(handles.OutputSubDir,'String',SubDirOut)
2657set(handles.OutputSubDir,'BackgroundColor',[1 1 1])% set edit box to white color to indicate refreshment
2658set(handles.OutputDirExt,'Visible',OutputDirVisible)
2659set(handles.OutputSubDir,'Visible',OutputDirVisible)
2660%set(handles.CheckOverwrite,'Visible',OutputDirVisible)
2661set(handles.OutputDir_title,'Visible',OutputDirVisible)
2662SeriesData.ActionName=ActionName; % record ActionName for next use
2663
2664
2665%% visibility of the run mode (local or background or cluster)
2666if strcmp(OutputSubDirMode,'none')
2667    RunModeVisible='off'; % only local mode available if no output file is produced
2668else
2669    RunModeVisible='on';
2670end
2671set(handles.RunMode,'Visible',RunModeVisible)
2672set(handles.ActionExt,'Visible',RunModeVisible)
2673set(handles.RunMode_title,'Visible',RunModeVisible)
2674set(handles.ActionExt_title,'Visible',RunModeVisible)
2675
2676
2677%% Expected nbre of output files
2678if isfield(ParamOut,'OutputFileMode')
2679    StatusData.OutputFileMode=ParamOut.OutputFileMode;
2680    set(handles.status,'UserData',StatusData)
2681end
2682
2683%% definition of an additional parameter set, determined by an ancillary GUI
2684if isfield(ParamOut,'ActionInput')
2685%     set(handles.ActionInput,'Visible','on')
2686    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
2687    SeriesData.ActionInput=ParamOut.ActionInput;
2688else
2689%     set(handles.ActionInput,'Visible','off')
2690    if isfield(SeriesData,'ActionInput')
2691        SeriesData=rmfield(SeriesData,'ActionInput');
2692    end
2693end
2694set(handles.series,'UserData',SeriesData)
2695set(handles.ActionInput,'BackgroundColor',[1 0 0])
2696
2697%------------------------------------------------------------------------
2698% --- Executes on selection change in FieldName.
2699function FieldName_Callback(hObject, eventdata, handles)
2700%------------------------------------------------------------------------
2701field_str=get(handles.FieldName,'String');
2702field_index=get(handles.FieldName,'Value');
2703field=field_str{field_index(1)};
2704if isequal(field,'get_field...')
2705    SeriesData=get(handles.series,'UserData');
2706    % input line for which the field choice is relevant
2707    iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ
2708    hget_field=findobj(allchild(0),'name','get_field');
2709    if ~isempty(hget_field)
2710        delete(hget_field)%delete opened versions of get_field
2711    end
2712    Param=read_GUI(handles.series);
2713    InputTable=Param.InputTable(iview,:);
2714    % check the existence of the first file in the series
2715    first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1; % default setting for index j
2716    if isfield(Param.IndexRange,'first_j'); % if index j is used     
2717        first_j=Param.IndexRange.first_j;
2718        last_j=Param.IndexRange.last_j;
2719        MinIndex_j=Param.IndexRange.MinIndex_j(iview);
2720        MaxIndex_j=Param.IndexRange.MaxIndex_j(iview);
2721    end
2722    PairString='';
2723    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end
2724    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2725    LineIndex=iview(1);
2726    if numel(iview)>1     
2727        answer=msgbox_uvmat('INPUT_TXT',['select the line of the input table:' num2str(iview)] ,num2str(iview(1)));
2728        LineIndex=str2num(answer);
2729%         InputLine=str2num(get(handles.InputLine,'String'));
2730%         if ismember(InputLine,iview)
2731%             LineIndex=InputLine;
2732%         end
2733    end
2734    FirstFileName=fullfile_uvmat(InputTable{LineIndex,1},InputTable{LineIndex,2},InputTable{LineIndex,3},...
2735        InputTable{LineIndex,5},InputTable{LineIndex,4},i1,i2,j1,j2);
2736    if exist(FirstFileName,'file')
2737        ParamIn.Title='get_field: pick input variables and coordinates for series processing';
2738        ParamIn.SeriesInput=1;
2739        GetFieldData=get_field(FirstFileName,ParamIn);
2740        FieldList={};
2741        if isfield(GetFieldData,'FieldOption')% if a field has been selected
2742        switch GetFieldData.FieldOption
2743            case 'vectors'
2744                UName=GetFieldData.PanelVectors.vector_x;
2745                VName=GetFieldData.PanelVectors.vector_y;
2746                YName={GetFieldData.Coordinates.Coord_y};
2747                FieldList={['vec(' UName ',' VName ')'];...
2748                    ['norm(' UName ',' VName ')'];...
2749                    UName;VName};
2750            case {'scalar'}
2751                FieldList=GetFieldData.PanelScalar.scalar;
2752                YName={GetFieldData.Coordinates.Coord_y};
2753                if ischar(FieldList)
2754                    FieldList={FieldList};
2755                end
2756            case 'civdata...'
2757                FieldList=[set_field_list('U','V') ;{'C'}];
2758                set(handles.FieldName,'Value',1) % set menu to 'velocity
2759                XName='X';
2760                YName='y';
2761        end
2762        set(handles.FieldName,'Value',1)
2763        set(handles.FieldName,'String',[FieldList; {'get_field...'}]);
2764        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2765           if ~isempty(regexp(FieldList{1},'^vec'))
2766                set(handles.FieldName,'Value',1)
2767           else
2768                set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
2769           end
2770            XName=GetFieldData.Coordinates.Coord_x;
2771            YName=GetFieldData.Coordinates.Coord_y;
2772            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2773            % get the time info                     
2774            TimeTable=get(handles.TimeTable,'Data');
2775            switch TimeNameStr
2776                case 'file index'
2777                    TimeName='';
2778                case 'attribute'
2779                    TimeName=['att:' GetFieldData.Time.TimeName];
2780                    % update the time table
2781                    TimeTable{LineIndex,2}=get_time(Param.IndexRange.MinIndex_i(LineIndex),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Min time     
2782                    TimeTable{LineIndex,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % first time             
2783                    TimeTable{LineIndex,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % last time                     
2784                    TimeTable{LineIndex,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Max time
2785                case 'variable'
2786                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2787                    set(handles.NomType,'String','*')
2788                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2789                    set(handles.FileIndex,'String','')
2790                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2791                case 'matrix_index'
2792                    TimeName=['dim:' GetFieldData.Time.TimeName];
2793                    set(handles.NomType,'String','*')
2794                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2795                    set(handles.FileIndex,'String','')
2796                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2797            end
2798            TimeTable{LineIndex,1}=TimeName;
2799            set(handles.TimeTable,'Data',TimeTable);
2800        end
2801        set(handles.Coord_x,'String',XName)
2802        set(handles.Coord_y,'String',YName)
2803        set(handles.Coord_x,'Visible','on')
2804        set(handles.Coord_y,'Visible','on')
2805        end
2806    else
2807        msgbox_uvmat('ERROR',[FirstFileName ' does not exist'])
2808    end
2809end
2810
2811
2812function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
2813[i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
2814FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2);
2815Data=nc2struct(FileName,[]);
2816TimeValue=[];
2817DtValue=[];
2818if isequal(FileInfo.FileType,'civdata')
2819    if ismember(TimeName,{'civ1','filter1'})
2820        if isfield(Data,'Civ1_Time')
2821        TimeValue=Data.Civ1_Time;
2822        end
2823        if isfield(Data,'Civ1_Dt')
2824        DtValue=Data.Civ1_Dt;
2825        end
2826    else
2827        if isfield(Data,'Civ2_Time')
2828        TimeValue=Data.Civ2_Time;
2829        end
2830        if isfield(Data,'Civ2_Dt')
2831        DtValue=Data.Civ2_Dt;
2832        end
2833    end
2834else
2835    if ~isempty(TimeName)&& isfield(Data,TimeName)
2836        TimeValue=Data.(TimeName);
2837    end
2838    if exist('DtName','var') && isfield(Data,DtName)
2839        DtValue=Data.(DtName);
2840    end
2841end
2842
2843%------------------------------------------------------------------------
2844% --- Executes on selection change in FieldName_1.
2845function FieldName_1_Callback(hObject, eventdata, handles)
2846%------------------------------------------------------------------------
2847field_str=get(handles.FieldName_1,'String');
2848field_index=get(handles.FieldName_1,'Value');
2849field=field_str{field_index(1)};
2850if isequal(field,'get_field...')
2851    hget_field=findobj(allchild(0),'name','get_field');
2852    if ~isempty(hget_field)
2853        delete(hget_field)%delete opened versions of get_field
2854    end
2855    Param=read_GUI(handles.series);
2856    Param.InputTable=Param.InputTable(1,:);
2857    % check the existence of the first file in the series
2858    first_j=[];
2859    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
2860    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
2861    PairString='';
2862    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
2863    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2864    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
2865        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
2866    if exist(FirstFileName,'file')
2867        ParamIn.SeriesInput=1;
2868        GetFieldData=get_field(FirstFileName,ParamIn);
2869        FieldList={};
2870        switch GetFieldData.FieldOption
2871            case 'vectors'
2872                UName=GetFieldData.PanelVectors.vector_x;
2873                VName=GetFieldData.PanelVectors.vector_y;
2874                FieldList={['vec(' UName ',' VName ')'];...
2875                    ['norm(' UName ',' VName ')'];...
2876                    UName;VName};
2877            case {'scalar','pick variables'}
2878                FieldList=GetFieldData.PanelScalar.scalar;
2879                if ischar(FieldList)
2880                    FieldList={FieldList};
2881                end
2882            case '1D plot'
2883
2884            case 'civdata...'
2885                FieldList=set_field_list('U','V','C');
2886                set(handles.FieldName,'Value',2) % set menu to 'velocity
2887        end
2888        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2889            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2890            switch TimeNameStr
2891                case 'file index'
2892                    set(handles.TimeName,'String','');
2893                case 'attribute'
2894                    set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
2895                case 'variable'
2896                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2897                    set(handles.NomType,'String','*')
2898                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2899                    set(handles.FileIndex,'String','')
2900                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2901                case 'matrix_index'
2902                    set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]);
2903                    set(handles.NomType,'String','*')
2904                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2905                    set(handles.FileIndex,'String','')
2906                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2907            end
2908        end
2909        set(handles.FieldName_1,'Value',1)
2910        set(handles.FieldName_1,'String',[FieldList; {'get_field...'}]);
2911    end
2912end   
2913
2914
2915%%%%%%%%%%%%%
2916function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
2917indsel=ind_i;
2918indiff=diff(ind_i); % test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
2919indiff=[1 indiff last_i-ind_i(end)+1]; % for testing gaps with the imposed bounds
2920if ~isempty(indiff)
2921    indiff2=diff(indiff);
2922    indiffp=[indiff2 1];
2923    indiffm=[1 indiff2];
2924    ind_multi_m=find((indiff==0)&(indiffm<0))-1; % indices of first members of multiplets
2925    ind_multi_p=find((indiff==0)&(indiffp>0)); % indices of last members of multiplets
2926    %for each multiplet, select the most recent file
2927    ind_remove=[];
2928    for i=1:length(ind_multi_m)
2929        ind_pairs=ind_multi_m(i):ind_multi_p(i);
2930        for imulti=1:length(ind_pairs)
2931            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date); % dates of creation
2932        end
2933        [datenew,indsort2]=sort(datepair); % sort the multiplet by creation date
2934        ind_s=indsort2(1:end-1); %
2935        ind_remove=[ind_remove ind_pairs(ind_s)]; % remove these indices, leave the last one
2936    end
2937end
2938
2939%------------------------------------------------------------------------
2940% --- determine the list of index pairstring of processing file
2941function [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)
2942%------------------------------------------------------------------------
2943num_i1=num_i; % set of first image numbers by default
2944num_i2=num_i;
2945num_j1=num_j;
2946num_j2=num_j;
2947num_i_out=num_i;
2948num_j_out=num_j;
2949% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
2950if isequal(mode,'series(Di)')
2951    num_i1_line=num_i+ind_shift(3); % set of first image numbers
2952    num_i2_line=num_i+ind_shift(4);
2953    % adjust the first and last field number
2954        indsel=find(num_i1_line >= 1);
2955    num_i_out=num_i(indsel);
2956    num_i1_line=num_i1_line(indsel);
2957    num_i2_line=num_i2_line(indsel);
2958    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
2959    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
2960    [xx,num_i1]=meshgrid(num_j,num_i1_line);
2961    [xx,num_i2]=meshgrid(num_j,num_i2_line);
2962elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
2963    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
2964        num_j1=ind_shift(1)*ones(size(num_i));
2965        num_j2=ind_shift(2)*ones(size(num_i));
2966    else
2967        num_j1_col=num_j+ind_shift(1); % set of first image numbers
2968        num_j2_col=num_j+ind_shift(2);
2969        % adjust the first field number
2970        indsel=find((num_j1_col >= 1));   
2971        num_j_out=num_j(indsel);
2972        num_j1_col=num_j1_col(indsel);
2973        num_j2_col=num_j2_col(indsel);
2974        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
2975        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
2976    end   
2977end
2978
2979%------------------------------------------------------------------------
2980% --- Executes on button press in CheckObject.
2981function CheckObject_Callback(hObject, eventdata, handles)
2982%------------------------------------------------------------------------
2983hset_object=findobj(allchild(0),'tag','set_object'); % find the set_object interface handle
2984if get(handles.CheckObject,'Value')
2985    SeriesData=get(handles.series,'UserData');
2986    if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject)
2987        set(handles.ViewObject,'Value',1)
2988        ViewObject_Callback(hObject, eventdata, handles)
2989    else
2990        if ishandle(hset_object)
2991            uistack(hset_object,'top')% show the GUI set_object if opened
2992        else
2993            %get the object file
2994            InputTable=get(handles.InputTable,'Data');
2995            defaultname=InputTable{1,1};
2996            if isempty(defaultname)
2997                defaultname={''};
2998            end
2999            fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml');
3000            if isempty(fileinput)% exit if no object file is selected
3001                set(handles.CheckObject,'Value',0)
3002                return
3003            end
3004            %read the file
3005            data=xml2struct(fileinput);
3006            if ~isfield(data,'Type')
3007                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
3008                set(handles.CheckObject,'Value',0)
3009                return
3010            end
3011            if ~isfield(data,'ProjMode')
3012                data.ProjMode='none';
3013            end
3014            hset_object=set_object(data); % call the set_object interface
3015            set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat
3016        end
3017        ProjObject=read_GUI(hset_object);
3018        set(handles.ProjObject,'String',ProjObject.Name); % display the object name
3019        SeriesData=get(handles.series,'UserData');
3020        SeriesData.ProjObject=ProjObject;
3021        set(handles.series,'UserData',SeriesData);
3022    end
3023    set(handles.EditObject,'Visible','on');
3024    set(handles.DeleteObject,'Visible','on');
3025    set(handles.ViewObject,'Visible','on');
3026    set(handles.ProjObject,'Visible','on');
3027else
3028    set(handles.EditObject,'Visible','off');
3029    set(handles.DeleteObject,'Visible','off');
3030    set(handles.ViewObject,'Visible','off');
3031    if ~ishandle(hset_object)
3032        set(handles.ViewObject,'Value',0);
3033    end
3034    set(handles.ProjObject,'Visible','off');
3035end
3036
3037%------------------------------------------------------------------------
3038% --- Executes on button press in ViewObject.
3039%------------------------------------------------------------------------
3040function ViewObject_Callback(hObject, eventdata, handles)
3041
3042UserData=get(handles.series,'UserData');
3043hset_object=findobj(allchild(0),'Tag','set_object');
3044if ~isempty(hset_object)
3045    delete(hset_object)% refresh set_object if already opened
3046end
3047hset_object=set_object(UserData.ProjObject);
3048set(hset_object,'Name','view_object_series')
3049
3050
3051%------------------------------------------------------------------------
3052% --- Executes on button press in EditObject.
3053function EditObject_Callback(hObject, eventdata, handles)
3054%------------------------------------------------------------------------
3055if get(handles.EditObject,'Value')
3056    set(handles.ViewObject,'Value',0)
3057    UserData=get(handles.series,'UserData');
3058    hset_object=set_object(UserData.ProjObject);
3059    set(hset_object,'Name','edit_object_series')
3060    set(get(hset_object,'Children'),'Enable','on')
3061else
3062    hset_object=findobj(allchild(0),'Tag','set_object');
3063    if ~isempty(hset_object)
3064        set(get(hset_object,'Children'),'Enable','off')
3065    end
3066end
3067
3068%------------------------------------------------------------------------
3069% --- Executes on button press in DeleteObject.
3070function DeleteObject_Callback(hObject, eventdata, handles)
3071%------------------------------------------------------------------------
3072SeriesData=get(handles.series,'UserData');
3073SeriesData.ProjObject=[];
3074set(handles.series,'UserData',SeriesData)
3075set(handles.ProjObject,'String','')
3076set(handles.ProjObject,'Visible','off')
3077set(handles.CheckObject,'Value',0)
3078set(handles.ViewObject,'Visible','off')
3079set(handles.EditObject,'Visible','off')
3080hset_object=findobj(allchild(0),'name','set_object_series');
3081if ~isempty(hset_object)
3082    delete(hset_object)
3083end
3084set(handles.DeleteObject,'Visible','off')
3085
3086%------------------------------------------------------------------------
3087% --- Executed when CheckMask is activated
3088%------------------------------------------------------------------------
3089function CheckMask_Callback(hObject, eventdata, handles)
3090
3091if get(handles.CheckMask,'Value')
3092    InputTable=get(handles.InputTable,'Data');
3093    nbview=size(InputTable,1);
3094    MaskTable=cell(nbview,1); % default
3095    ListMask=cell(nbview,1); % default
3096    MaskData=get(handles.MaskTable,'Data');
3097    MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1); % complement if undefined lines
3098    for iview=1:nbview
3099        ListMask{iview,1}=num2str(iview);
3100        RootPath=InputTable{iview,1};
3101        if ~isempty(RootPath)
3102            if isempty(MaskData{iview})
3103                SubDir=InputTable{iview,2};
3104                MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']); % take the root part of SubDir, before the first dot '.'
3105                if exist(MaskPath,'dir')
3106                    ListStruct=dir(MaskPath); % look for a mask file
3107                    ListCells=struct2cell(ListStruct); % transform dir struct to a cell arrray
3108                    check_dir=cell2mat(ListCells(4,:)); % =1 for directories, =0 for files
3109                    ListFiles=ListCells(1,:); % list of file and dri names
3110                    ListFiles=ListFiles(~check_dir); % list of file names (excluding dir)
3111                    mdetect=0;
3112                    if ~isempty(ListFiles)
3113                        for ifile=1:numel(ListFiles)
3114                            [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0);
3115                            if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series)
3116                                mdetect=1;
3117                                MaskName=ListFiles{ifile};
3118                            end
3119                            if ~strcmp(MaskFile{ifile},MaskFile{1})
3120                                mdetect=0; % cancel detection test in case of multiple masks, use the brower for selection
3121                                break
3122                            end
3123                        end
3124                    end
3125                    if mdetect==1
3126                        MaskName=fullfile(MaskPath,'mask_1.png');
3127                    else
3128                        MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image');
3129                    end
3130                else
3131                    MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3132                end
3133                MaskTable{iview,1}=MaskName ;
3134                ListMask{iview,1}=num2str(iview);
3135            end
3136        end
3137    end
3138    set(handles.MaskTable,'Data',MaskTable)
3139    set(handles.MaskTable,'Visible','on')
3140    set(handles.MaskBrowse,'Visible','on')
3141    set(handles.ListMask,'Visible','on')
3142    set(handles.ListMask,'String',ListMask)
3143    set(handles.ListMask,'Value',1)
3144else
3145    set(handles.MaskTable,'Visible','off')
3146    set(handles.MaskBrowse,'Visible','off')
3147    set(handles.ListMask,'Visible','off')
3148end
3149
3150%------------------------------------------------------------------------
3151% --- Executes on button press in MaskBrowse.
3152%------------------------------------------------------------------------
3153function MaskBrowse_Callback(hObject, eventdata, handles)
3154
3155InputTable=get(handles.InputTable,'Data');
3156iview=get(handles.ListMask,'Value');
3157RootPath=InputTable{iview,1};
3158MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3159if ~isempty(MaskName)
3160    MaskTable=get(handles.MaskTable,'Data');
3161    MaskTable{iview,1}=MaskName ;
3162    set(handles.MaskTable,'Data',MaskTable)
3163end
3164
3165%------------------------------------------------------------------------
3166% --- Executes when selected cell(s) is changed in MaskTable.
3167%------------------------------------------------------------------------
3168function MaskTable_CellSelectionCallback(hObject, eventdata, handles)
3169
3170if numel(eventdata.Indices)>=1
3171set(handles.ListMask,'Value',eventdata.Indices(1))
3172end
3173
3174%-------------------------------------------------------------------
3175function MenuHelp_Callback(hObject, eventdata, handles)
3176%-------------------------------------------------------------------
3177
3178
3179% path_to_uvmat=which ('uvmat'); % check the path of uvmat
3180% pathelp=fileparts(path_to_uvmat);
3181% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
3182% 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')
3183% else
3184%     addpath (fullfile(pathelp,'uvmat_doc'))
3185%     web([helpfile '#series'])
3186% end
3187
3188%-------------------------------------------------------------------
3189% --- Executes on selection change in TransformName.
3190function TransformName_Callback(hObject, eventdata, handles)
3191%----------------------------------------------------------------------
3192TransformList=get(handles.TransformName,'String');
3193TransformIndex=get(handles.TransformName,'Value');
3194TransformName=TransformList{TransformIndex};
3195TransformPathList=get(handles.TransformName,'UserData');
3196nb_builtin_transform=4;
3197if isequal(TransformName,'more...');     
3198    FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
3199    if isempty(FileName)
3200        return     %browser closed without choice
3201    end
3202    [TransformPath,TransformName,TransformExt]=fileparts(FileName); % removes extension .m
3203    if ~strcmp(TransformExt,'.m')
3204        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3205        return
3206    end
3207     % insert the choice in the menu
3208    TransformIndex=find(strcmp(TransformName,TransformList),1); % look for the selected function in the menu Action
3209    if isempty(TransformIndex)%the input string does not exist in the menu
3210        TransformIndex= length(TransformList);
3211        TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)]; % the selected function is appended in the menu, before the last item 'more...'
3212        set(handles.TransformName,'String',TransformList)
3213        TransformPathList=[TransformPathList;{TransformPath}];
3214    else% the input function already exist, we update its path (possibly new)
3215        TransformPathList{TransformIndex}=TransformPath; %
3216        set(handles.TransformName,'Value',TransformIndex)
3217    end
3218   % save the new menu in the personal file 'uvmat_perso.mat'
3219   dir_perso=prefdir; % personal Matalb directory
3220   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3221   if exist(profil_perso,'file')
3222       for ilist=nb_builtin_transform+1:numel(TransformPathList)
3223           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
3224           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
3225       end
3226       TransformPathListUser=TransformPathListUser';
3227       TransformListUser=TransformListUser';
3228       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); % store the root name for future opening of uvmat
3229   end
3230end
3231
3232%display the current function path
3233set(handles.TransformPath,'String',TransformPathList{TransformIndex}); % show the path to the senlected function
3234set(handles.TransformName,'UserData',TransformPathList);
3235
3236%% create the function handle of the selected fct
3237if ~isempty(TransformName)
3238    if ~exist(TransformPathList{TransformIndex},'dir')
3239        msgbox_uvmat('ERROR',['The prescribed transform function path ' TransformPathList{TransformIndex} ' does not exist']);
3240        return
3241    end
3242    current_dir=pwd; % current working dir
3243    cd(TransformPathList{TransformIndex})
3244    transform_handle=str2func(TransformName);
3245    cd(current_dir)
3246    Field.Action.RUN=0;% indicate that the transform fct is called only to get input param
3247    SeriesData=get(handles.series,'UserData');
3248    ParamIn=[];
3249    if isfield(SeriesData,'TransformInput')
3250        ParamIn.TransformInput=SeriesData.TransformInput;
3251    end
3252    DataOut=feval(transform_handle,Field,ParamIn);% execute the transform fct to get the required conditions
3253    Field.Action.RUN=0; % indicate that the transform fct is called only to get input param
3254    DataOut=feval(transform_handle,Field,[]); % execute the transform fct to get the required conditions
3255    if isfield(DataOut,'TransformInput')%  used to add transform parameters at selection of the transform fct
3256        SeriesData.TransformInput=DataOut.TransformInput;
3257        set(handles.series,'UserData',SeriesData)
3258    end
3259end
3260
3261%------------------------------------------------------------------------
3262% --- fct activated by the upper bar menu ExportConfig
3263%------------------------------------------------------------------------
3264function MenuDisplayConfig_Callback(hObject, eventdata, handles)
3265
3266global Param
3267Param=read_GUI_series(handles);
3268evalin('base','global Param')%make CurData global in the workspace
3269display('current series config :')
3270evalin('base','Param') %display CurData in the workspace
3271commandwindow; % brings the Matlab command window to the front
3272
3273%------------------------------------------------------------------------
3274% --- fct activated by the upper bar menu InportConfig: import
3275%     menu settings from an xml file (stored in /0_XML for each run)
3276%------------------------------------------------------------------------
3277function MenuImportConfig_Callback(hObject, eventdata, handles)
3278
3279%% use a browser to choose the xml file containing the processing config
3280InputTable=get(handles.InputTable,'Data');
3281oldfile=InputTable{1,1}; % current path in InputTable
3282if isempty(oldfile)
3283    % use a file name stored in prefdir
3284    dir_perso=prefdir;
3285    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3286    if exist(profil_perso,'file')
3287        h=load (profil_perso);
3288        if isfield(h,'RootPath') && ischar(h.RootPath)
3289            oldfile=h.RootPath;
3290        end
3291    end
3292end
3293filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml'); % get the xml file containing processing parameters
3294if isempty(filexml), return, end % quit function if an xml file has not been opened
3295
3296%% fill the GUI series with the content of the xml file
3297Param=xml2struct(filexml); % read the input xml file as a Matlab structure
3298
3299% ask to stop current Action if button RUN is in action (another process is already running)
3300if isequal(get(handles.RUN,'Value'),1)
3301    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
3302    if strcmp(answer,'Yes')
3303        STOP_Callback(hObject, eventdata, handles)
3304    else
3305        return
3306    end
3307end
3308Param.Action.RUN=0; % desactivate the input RUN=1
3309
3310fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
3311SeriesData=get(handles.series,'UserData');
3312if isfield(Param,'InputFields')
3313    ListField=Param.InputFields.FieldName;
3314    if ischar(ListField),ListField={ListField}; end
3315    set(handles.FieldName,'String',[ListField;{'get-field...'}])
3316     set(handles.FieldName,'Value',1:numel(ListField))
3317     set(handles.FieldName,'Visible','on')
3318end       
3319if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
3320%     set(handles.ActionInput,'Visible','on')
3321%     set(handles.ActionInput,'Value',0)
3322    Param.ActionInput.ConfigSource=filexml; % record the source of config for future info
3323    SeriesData.ActionInput=Param.ActionInput;
3324end
3325if isfield(Param,'TransformInput')%  introduce  parameters specific to a transform fct
3326    SeriesData.TransformInput=Param.TransformInput;
3327end
3328if isfield(Param,'ProjObject') %introduce projection object if relevant
3329    SeriesData.ProjObject=Param.ProjObject;
3330end
3331set(handles.series,'UserData',SeriesData)
3332if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
3333    set(handles.ProjObject,'String',Param.ProjObject.Name)
3334    set(handles.ViewObject,'Visible','on')
3335    set(handles.EditObject,'Visible','on')
3336    set(handles.DeleteObject,'Visible','on')
3337else     
3338    set(handles.ProjObject,'String','')
3339    set(handles.ProjObject,'Visible','off')
3340    set(handles.ViewObject,'Visible','off')
3341    set(handles.EditObject,'Visible','off')
3342    set(handles.DeleteObject,'Visible','off')     
3343end     
3344set(handles.REFRESH,'BackgroundColor',[1 0 1]); % paint REFRESH button in magenta to indicate that it should be activated
3345
3346
3347%------------------------------------------------------------------------
3348% --- Executes when the GUI series is resized.
3349%------------------------------------------------------------------------
3350function series_ResizeFcn(hObject, eventdata, handles)
3351
3352%% input table
3353set(handles.InputTable,'Unit','pixel')
3354Pos=get(handles.InputTable,'Position');
3355set(handles.InputTable,'Unit','normalized')
3356ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
3357ColumnWidth=num2cell(ColumnWidth);
3358set(handles.InputTable,'ColumnWidth',ColumnWidth)
3359
3360%% MinIndex_j and MaxIndex_i
3361unit=get(handles.MinIndex_i,'Unit');
3362set(handles.MinIndex_i,'Unit','pixel')
3363Pos=get(handles.MinIndex_i,'Position');
3364set(handles.MinIndex_i,'Unit',unit)
3365set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18})
3366set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18})
3367set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18})
3368set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18})
3369
3370%% TimeTable
3371set(handles.TimeTable,'Unit','pixel')
3372Pos=get(handles.TimeTable,'Position');
3373set(handles.TimeTable,'Unit','normalized')
3374% ColumnWidth=get(handles.TimeTable,'ColumnWidth');
3375ColumnWidth=num2cell(floor([0.2 0.2 0.2 0.2 0.2]*(Pos(3)-20)));
3376set(handles.TimeTable,'ColumnWidth',ColumnWidth)
3377
3378
3379%% PairString
3380set(handles.PairString,'Unit','pixel')
3381Pos=get(handles.PairString,'Position');
3382set(handles.PairString,'Unit','normalized')
3383set(handles.PairString,'ColumnWidth',{Pos(3)-5})
3384
3385%% MaskTable
3386set(handles.MaskTable,'Unit','pixel')
3387Pos=get(handles.MaskTable,'Position');
3388set(handles.MaskTable,'Unit','normalized')
3389set(handles.MaskTable,'ColumnWidth',{Pos(3)-5})
3390
3391%------------------------------------------------------------------------
3392% --- Executes on button press in status.
3393%------------------------------------------------------------------------
3394function status_Callback(hObject, eventdata, handles)
3395
3396if get(handles.status,'Value')
3397    set(handles.status,'BackgroundColor',[1 1 0])
3398    drawnow
3399    Param=read_GUI(handles.series);
3400    RootPath=Param.InputTable{1,1};
3401    if ~isfield(Param,'OutputSubDir')   
3402        msgbox_uvmat('ERROR','no standard sub-directory definition for output files, use a browser to check the output')
3403        set(handles.status,'BackgroundColor',[0 1 0])
3404        return
3405    end
3406    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt]; % subdirectory for output files
3407    OutputDir=fullfile(RootPath,OutputSubDir);
3408    if exist(OutputDir,'dir')
3409        uigetfile_uvmat('status_display',OutputDir)
3410    else
3411        msgbox_uvmat('ERROR','output folder not created yet: calculation did not start')
3412        set(handles.status,'BackgroundColor',[0 1 0])
3413    end
3414else
3415    %% delete current display fig if selection is off
3416    set(handles.status,'BackgroundColor',[0 1 0])
3417    hfig=findobj(allchild(0),'name','status_display');
3418    if ~isempty(hfig)
3419        delete(hfig)
3420    end
3421    return
3422end
3423
3424
3425%------------------------------------------------------------------------   
3426% launched by selecting a file on the list
3427%------------------------------------------------------------------------
3428function view_file(hObject, eventdata)
3429
3430list=get(hObject,'String');
3431index=get(hObject,'Value');
3432rootroot=get(hObject,'UserData');
3433selectname=list{index};
3434ind_dot=regexp(selectname,'\.\.\.');
3435if ~isempty(ind_dot)
3436    selectname=selectname(1:ind_dot-1);
3437end
3438FullSelectName=fullfile(rootroot,selectname);
3439if exist(FullSelectName,'dir')% a directory has been selected
3440    ListFiles=dir(FullSelectName);
3441    ListDisplay=cell(numel(ListFiles),1);
3442    for ilist=2:numel(ListDisplay)% suppress the first line '.'
3443        ListDisplay{ilist-1}=ListFiles(ilist).name;
3444    end
3445    set(hObject,'Value',1)
3446    set(hObject,'String',ListDisplay)
3447    if strcmp(selectname,'..')
3448        FullSelectName=fileparts(fileparts(FullSelectName));
3449    end
3450    set(hObject,'UserData',FullSelectName)
3451    hfig=get(hObject,'parent');
3452    htitlebox=findobj(hfig,'tag','titlebox');   
3453    set(htitlebox,'String',FullSelectName)
3454elseif exist(FullSelectName,'file')%visualise the vel field if it exists
3455    FileInfo=get_file_info(FullSelectName);   
3456    if strcmp(FileInfo.FileType,'txt')
3457        edit(FullSelectName)
3458    elseif strcmp(FileInfo.FileType,'xml')
3459        editxml(FullSelectName)
3460    else
3461        uvmat(FullSelectName)
3462    end
3463    set(gcbo,'Value',1)
3464end
3465
3466
3467%------------------------------------------------------------------------   
3468% launched by refreshing the status figure
3469%------------------------------------------------------------------------
3470function refresh_GUI(hfig)
3471
3472htitlebox=findobj(hfig,'tag','titlebox');
3473hlist=findobj(hfig,'tag','list');
3474hseries=findobj(allchild(0),'tag','series');
3475hstatus=findobj(hseries,'tag','status');
3476StatusData=get(hstatus,'UserData');
3477OutputDir=get(htitlebox,'String');
3478if ischar(OutputDir),OutputDir={OutputDir};end
3479ListFiles=dir(OutputDir{1});
3480if numel(ListFiles)<1
3481    return
3482end
3483ListFiles(1)=[]; % removes the first line ='.'
3484ListDisplay=cell(numel(ListFiles),1);
3485testrecent=0;
3486datnum=zeros(numel(ListDisplay),1);
3487for ilist=1:numel(ListDisplay)
3488    ListDisplay{ilist}=ListFiles(ilist).name;
3489      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
3490            datnum(ilist)=ListFiles(ilist).datenum; % only available in recent matlab versions
3491            testrecent=1;
3492       end
3493end
3494set(hlist,'String',ListDisplay)
3495
3496%% Look at date of creation
3497ListDisplay=ListDisplay(datnum~=0);
3498datnum=datnum(datnum~=0); % keep the non zero values corresponding to existing files
3499NbOutputFile=[];
3500if isempty(datnum)
3501    if testrecent
3502        message='no civ result created yet';
3503    else
3504        message='';
3505    end
3506else
3507    [first,indfirst]=min(datnum);
3508    [last,indlast]=max(datnum);
3509    NbOutputFile_str='?';
3510    NbOutputFile=[];
3511    if isfield(StatusData,'NbOutputFile')
3512        NbOutputFile=StatusData.NbOutputFile;
3513        NbOutputFile_str=num2str(NbOutputFile);
3514    end
3515    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
3516        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
3517end
3518set(htitlebox,'String', [OutputDir{1};message])
3519
3520%% update the waitbar
3521hwaitbar=findobj(hfig,'tag','waitbar');
3522if ~isempty(NbOutputFile)
3523    BarPosition=get(hwaitbar,'Position');
3524    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
3525    set(hwaitbar,'Position',BarPosition)
3526end
3527
3528%------------------------------------------------------------------------
3529% --- Executes on selection change in ActionExt.
3530%------------------------------------------------------------------------
3531function ActionExt_Callback(hObject, eventdata, handles)
3532
3533ActionExtList=get(handles.ActionExt,'String');
3534ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
3535if strcmp(ActionExt,'.py (in dev.)')
3536    set(handles.RunMode,'Value',2)
3537end
3538
3539%function num_NbProcess_Callback(hObject, eventdata, handles)
3540
3541
3542function num_NbSlice_Callback(hObject, eventdata, handles)
3543NbSlice=str2num(get(handles.num_NbSlice,'String'));
3544%set(handles.num_NbProcess,'String',num2str(NbSlice))
3545
3546%------------------------------------------------------------------------
3547% --- set the visibility of relevant velocity type menus:
3548function menu=set_veltype_display(Civ,FileType)
3549%------------------------------------------------------------------------
3550if ~exist('FileType','var')
3551    FileType='civx';
3552end
3553switch FileType
3554    case 'civx'
3555        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3556        if isequal(Civ,0)
3557            imax=0;
3558        elseif isequal(Civ,1) || isequal(Civ,2)
3559            imax=1;
3560        elseif isequal(Civ,3)
3561            imax=3;
3562        elseif isequal(Civ,4) || isequal(Civ,5)
3563            imax=4;
3564        elseif isequal(Civ,6) %patch2
3565            imax=6;
3566        end
3567    case 'civdata'
3568        menu={'civ1';'filter1';'civ2';'filter2'};
3569        if isequal(Civ,0)
3570            imax=0;
3571        elseif isequal(Civ,1) || isequal(Civ,2)
3572            imax=1;
3573        elseif isequal(Civ,3)
3574            imax=2;
3575        elseif isequal(Civ,4) || isequal(Civ,5)
3576            imax=3;
3577        else%if isequal(Civ,6) %patch2
3578            imax=4;
3579        end
3580end
3581menu=menu(1:imax);
3582
3583
3584% --- Executes on mouse motion over figure - except title and menu.
3585function series_WindowButtonMotionFcn(hObject, eventdata, handles)
3586set(hObject,'Pointer','arrow');
3587
3588
3589% --- Executes on button press in SetPairs.
3590function SetPairs_Callback(hObject, eventdata, handles)
3591
3592%% delete previous occurrence of 'set_pairs'
3593hfig=findobj(allchild(0),'Tag','set_pairs');
3594if ~isempty(hfig)
3595delete(hfig)
3596end
3597
3598%% create the GUI set_pairs
3599set(0,'Unit','points')
3600ScreenSize=get(0,'ScreenSize'); % get the size of the screen, to put the fig on the upper right
3601Width=220; % fig width in points (1/72 inch)
3602Height=min(0.8*ScreenSize(4),300);
3603Left=ScreenSize(3)- Width-40; % right edge close to the right, with margin=40
3604Bottom=ScreenSize(4)-Height-40; % put fig at top right
3605hfig=findobj(allchild(0),'Tag','set_slice');
3606if ~isempty(hfig),delete(hfig), end; % delete existing version of the GUI
3607hfig=figure('name','set_pairs','tag','set_pairs','MenuBar','none','NumberTitle','off','Unit','points','Position',[Left,Bottom,Width,Height]);
3608BackgroundColor=get(hfig,'Color');
3609SeriesData=get(handles.series,'UserData');
3610TimeUnit=get(handles.TimeUnit,'String');
3611PairString=get(handles.PairString,'Data');
3612ListViewLines=find(cellfun('isempty',PairString)==0); % find list of non empty pairs
3613ListViewMenu=cell(numel(ListViewLines),1);
3614%iview=get(handles.PairString,'Value');
3615iview=[];
3616for ilist=1:numel(ListViewLines)
3617    ListViewMenu{ilist}=num2str(ListViewLines(ilist));
3618end
3619if isempty(iview)
3620    ListViewValue=numel(ListViewLines); % we work by default on the pair option for the last line which requires pairs
3621    iview=ListViewLines(end);
3622else
3623    ListViewValue=find(ListViewLines==iview);
3624end
3625ref_i=str2num(get(handles.num_first_i,'String'));
3626ref_j=1; % default
3627if strcmp(get(handles.num_first_j,'String'),'Visible')
3628    ref_j=str2num(get(handles.num_first_j,'String'));
3629end
3630[ModeMenu,ModeValue]=update_mode(SeriesData.i1_series{iview},SeriesData.i2_series{iview},SeriesData.j2_series{iview});
3631displ_pair=update_listpair(SeriesData.i1_series{iview},SeriesData.i2_series{iview},SeriesData.j1_series{iview},SeriesData.j2_series{iview},ModeMenu{ModeValue},...
3632                                                     SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo{iview});
3633% first raw of the GUI
3634uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,...
3635    'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right'); % title
3636uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.54 0.8 0.3 0.2],'BackgroundColor',[1 1 1],...
3637    'Callback',@(hObject,eventdata)ListView_Callback(hObject,eventdata),'String',ListViewMenu,'Value',ListViewValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3638    'Tag','ListView','TooltipString','''ListView'':choice of the file series w for pair display');
3639% second raw of the GUI
3640uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.79 0.7 0.1],'BackgroundColor',BackgroundColor,...
3641    'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3642uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.05 0.62 0.9 0.2],'BackgroundColor',[1 1 1],...
3643    'Callback',@(hObject,eventdata)Mode_Callback(hObject,eventdata),'String',ModeMenu,'Value',ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3644    'Tag','Mode','TooltipString','''Mode'': choice of the image pair mode');
3645% third raw
3646uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.6 0.7 0.1],'BackgroundColor',BackgroundColor,...
3647    'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3648uicontrol('Style','listbox','Units','normalized', 'Position', [0.05 0.42 0.9 0.2],'BackgroundColor',[1 1 1],...
3649    'Callback',@(hObject,eventdata)ListPair_Callback(hObject,eventdata),'String',displ_pair,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3650    'Tag','ListPair','TooltipString','''ListPair'': menu for selecting the image pair');
3651uicontrol('Style','text','Units','normalized', 'Position', [0.1 0.22 0.8 0.1],'BackgroundColor',BackgroundColor,...
3652    'String','ref_i           ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center'); % title
3653uicontrol('Style','edit','Units','normalized', 'Position', [0.15 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3654    'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),'String',num2str(ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3655    'Tag','num_ref_i','TooltipString','''num_ref_i'': reference field index i used to display dt in ''list_pair_civ''');
3656uicontrol('Style','edit','Units','normalized', 'Position', [0.55 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3657    'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),'String',num2str(ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3658    'Tag','num_ref_j','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ''');
3659uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.01 0.01 0.3 0.12],'BackgroundColor',[0 1 0],...
3660    'Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),'String','OK','FontUnits','points','FontSize',12,'FontWeight','bold',...
3661    'Tag','OK','TooltipString','''OK'': validate the choice');
3662%  last raw  of the GUI: pushbuttons
3663% 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),...
3664%     'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''OK'': apply the output to the current field series in uvmat');
3665drawnow
3666
3667%------------------------------------------------------------------------
3668function ListView_Callback(hObject,eventdata)
3669Mode_Callback(hObject,eventdata)
3670
3671%------------------------------------------------------------------------   
3672function Mode_Callback(hObject,eventdata)
3673%% get input info
3674hseries=findobj(allchild(0),'tag','series'); % handles of the GUI series
3675hhseries=guidata(hseries); % handles of the elements in the GUI series
3676TimeUnit=get(hhseries.TimeUnit,'String');
3677SeriesData=get(hseries,'UserData');
3678mode_list=get(hObject,'String');
3679mode=mode_list{get(hObject,'Value')};
3680hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3681iview=get(hListView,'Value');
3682i1_series=SeriesData.i1_series{iview};
3683i2_series=SeriesData.i2_series{iview};
3684j1_series=SeriesData.j1_series{iview};
3685j2_series=SeriesData.j2_series{iview};
3686
3687%% enable j index visibility after the new choice
3688status_j='on'; % default
3689if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices
3690    status_j='off'; % no j index needed
3691elseif strcmp(get(handles.PairString,'Visible'),'on')
3692    check_burst=cellfun(@isempty,regexp(PairString,'^j')); % =0 for burst case, 1 otherwise
3693    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
3694        status_j='off'; % no j index needed for bust case
3695    end
3696end
3697enable_j(handles,status_j) % no j index needed
3698
3699%% get the reference indices for the time interval Dt
3700href_i=findobj(get(hObject,'parent'),'Tag','ref_i');
3701ref_i=[];ref_j=[];
3702if strcmp(get(href_i,'Visible'),'on')
3703    ref_i=str2num(get(href_i,'String'));
3704end
3705if isempty(ref_i)
3706    ref_i=1;
3707end
3708if isempty(ref_j)
3709    ref_j=1;
3710end
3711
3712%% update the menu ListPair
3713Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,SeriesData.Time{iview},TimeUnit,ref_i,ref_j,FileInfo);
3714hlist_pairs=findobj(get(hObject,'parent'),'Tag','ListPair');
3715set(hlist_pairs,'Value',1)% set the first choice by default in ListPair
3716set(hlist_pairs,'String',Menu)% set the menu in ListPair
3717ListPair_Callback(hlist_pairs,[])% apply the default choice in ListPair
3718
3719%-------------------------------------------------------------
3720% --- Executes on selection in ListPair.
3721function ListPair_Callback(hObject,eventdata)
3722%------------------------------------------------------------
3723list_pair=get(hObject,'String'); % get the menu of image pairs
3724if isempty(list_pair)
3725    string='';
3726else
3727    string=list_pair{get(hObject,'Value')};
3728   % string=regexprep(string,',.*',''); % removes time indication (after ',')
3729end
3730hseries=findobj(allchild(0),'tag','series');
3731hPairString=findobj(hseries,'tag','PairString');
3732PairString=get(hPairString,'Data');
3733hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3734iview=get(hListView,'Value');
3735PairString{iview,1}=string;
3736% report the selected pair string to the table PairString
3737set(hPairString,'Data',PairString)
3738
3739
3740%------------------------------------------------------------------------
3741function num_ref_i_Callback(hObject, eventdata)
3742%------------------------------------------------------------------------
3743Mode_Callback([],[])
3744
3745%------------------------------------------------------------------------
3746function num_ref_j_Callback(hObject, eventdata)
3747%------------------------------------------------------------------------
3748Mode_Callback([],[])
3749
3750%------------------------------------------------------------------------
3751function OK_Callback(hObject, eventdata)
3752%------------------------------------------------------------------------
3753delete(get(hObject,'parent'))
3754
3755
3756%------------------------------------------------------------------------
3757% --- Executes on button press in ClearLine.
3758%------------------------------------------------------------------------
3759function ClearLine_Callback(hObject, eventdata, handles)
3760InputTable=get(handles.InputTable,'Data');
3761iline=str2double(get(handles.InputLine,'String'));
3762if size(InputTable,1)>1
3763    InputTable(iline,:)=[]; % suppress the current line if not the first
3764    set(handles.InputTable,'Data',InputTable);
3765end
3766set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refr
3767
3768
3769% --- Executes on button press in MonitorCluster.
3770function MonitorCluster_Callback(hObject, eventdata, handles)
3771disp('format: R/W=run/wait, time lapsed, R=nbre of cores,W=walltime')
3772system('oarstat |grep N=UVmat')% check the list of jobs launched with uvmat
3773
3774
3775function OutputSubDir_Callback(hObject, eventdata, handles)
3776set(handles.OutputSubDir,'BackgroundColor',[1 1 1])
3777
3778
3779% --- Executes on button press in CheckOverwrite.
3780function CheckOverwrite_Callback(hObject, eventdata, handles)
3781
3782% --- Executes on button press in TestCPUTime.
3783function TestCPUTime_Callback(hObject, eventdata, handles)
3784% hObject    handle to TestCPUTime (see GCBO)
3785% eventdata  reserved - to be defined in a future version of MATLAB
3786% handles    structure with handles and user data (see GUIDATA)
3787
3788
3789% --- Executes on button press in DiskQuota.
3790function DiskQuota_Callback(hObject, eventdata, handles)
3791SeriesData=get(handles.series,'UserData');
3792system(SeriesData.SeriesParam.DiskQuotaCmd)
3793
3794
3795
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