source: trunk/src/series.m @ 1114

Last change on this file since 1114 was 1114, checked in by sommeria, 3 years ago

a few bugs repaired

File size: 179.9 KB
RevLine 
[867]1%'series': master function associated to the GUI series.m for analysis field series 
2%------------------------------------------------------------------------
3% function varargout = series(varargin)
4% associated with the GUI series.fig
5%
6%INPUT
7% param: structure with input parameters (link with the GUI uvmat)
8%      .menu_coord_str: string for the TransformName (menu for coordinate transforms)
9%      .menu_coord_val: value for TransformName (menu for coordinate transforms)
10%      .FileName: input file name
11%      .FileName_1: second input file name
12%      .list_field: menu of input fields
13%      .index_fields: chosen index
14%      .civ1=0 or 1, .interp1,  ... : input civ field type
15%
[924]16
17%=======================================================================
[1107]18% Copyright 2008-2022, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
[924]19%   http://www.legi.grenoble-inp.fr
20%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
21%
[867]22%     This file is part of the toolbox UVMAT.
[924]23%
[867]24%     UVMAT is free software; you can redistribute it and/or modify
[924]25%     it under the terms of the GNU General Public License as published
26%     by the Free Software Foundation; either version 2 of the license,
27%     or (at your option) any later version.
28%
[867]29%     UVMAT is distributed in the hope that it will be useful,
30%     but WITHOUT ANY WARRANTY; without even the implied warranty of
31%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
[924]32%     GNU General Public License (see LICENSE.txt) for more details.
33%=======================================================================
[867]34
35%------------------------------------------------------------------------
36%------------------------------------------------------------------------
37%  I - MAIN FUNCTION series
38%------------------------------------------------------------------------
39%------------------------------------------------------------------------
40function varargout = series(varargin)
41
42% Begin initialization code - DO NOT EDIT
43gui_Singleton = 1;
44gui_State = struct('gui_Name',       mfilename, ...
45                   'gui_Singleton',  gui_Singleton, ...
46                   'gui_OpeningFcn', @series_OpeningFcn, ...
47                   'gui_OutputFcn',  @series_OutputFcn, ...
48                   'gui_LayoutFcn',  [] , ...
49                   'gui_Callback',   []);
50if nargin && ischar(varargin{1})
51    gui_State.gui_Callback = str2func(varargin{1});
52end
53
54if nargout
55    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
56else
57    gui_mainfcn(gui_State, varargin{:});
58end
59% End initialization code - DO NOT EDIT
60
61%--------------------------------------------------------------------------
62% --- Executes just before series is made visible.
63%--------------------------------------------------------------------------
64function series_OpeningFcn(hObject, eventdata, handles,Param)
65
66% Choose default command line output for series
67handles.output = hObject;
68% Update handles structure
69guidata(hObject, handles);
70
71%% initial settings
72% position and  size of the GUI at opening
73set(0,'Unit','points')
[992]74ScreenSize=get(0,'ScreenSize'); % size of the current screen, in points (1/72 inch)
75Width=900; % prefered width of the GUI in points (1/72 inch)
76Height=624; % prefered height of the GUI in points (1/72 inch)
[867]77%adjust to screen size (reduced by a min margin)
78RescaleFactor=min((ScreenSize(3)-80)/Width,(ScreenSize(4)-80)/Height);
79if RescaleFactor>1
80    RescaleFactor=min(RescaleFactor,1);
81end
82Width=Width*RescaleFactor;
83Height=Height*RescaleFactor;
[992]84LeftX=80*RescaleFactor; % position of the left fig side, in pixels (put to the left side, with some margin)
[867]85LowY=round(ScreenSize(4)/2-Height/2); % put at the middle height on the screen
86set(hObject,'Units','points')
87set(hObject,'Position',[LeftX LowY Width Height])% position and size of the GUI at opening
88
89% settings of table MinIndex_j
90set(handles.MinIndex_i,'ColumnFormat',{'numeric'})
91set(handles.MinIndex_i,'ColumnEditable',false)
92set(handles.MinIndex_i,'ColumnName',{'i min'})
93set(handles.MinIndex_i,'Data',[])% initiate Data to double (not cell)
94
95% settings of table MinIndex_j
96set(handles.MinIndex_j,'ColumnFormat',{'numeric'})
97set(handles.MinIndex_j,'ColumnEditable',false)
98set(handles.MinIndex_j,'ColumnName',{'j min'})
99set(handles.MinIndex_j,'Data',[])% initiate Data to double (not cell)
100
101% settings of table MaxIndex_i
102set(handles.MaxIndex_i,'ColumnFormat',{'numeric'})
103set(handles.MaxIndex_i,'ColumnEditable',false)
104set(handles.MaxIndex_i,'ColumnName',{'i max'})
105set(handles.MaxIndex_i,'Data',[])% initiate Data to double (not cell)
106
107% settings of table MaxIndex_j
108set(handles.MaxIndex_j,'ColumnFormat',{'numeric'})
109set(handles.MaxIndex_j,'ColumnEditable',false)
110set(handles.MaxIndex_j,'ColumnName',{'j max'})
111set(handles.MaxIndex_j,'Data',[])% initiate Data to double (not cell)
112
113% settings of table PairString
114set(handles.PairString,'ColumnName',{'pairs'})
115set(handles.PairString,'ColumnEditable',false)
116set(handles.PairString,'ColumnFormat',{'char'})
117set(handles.PairString,'Data',{''})
118
119% settings of table MaskTable
120set(handles.MaskTable,'ColumnName',{'mask name'})
121set(handles.PairString,'ColumnEditable',false)
122set(handles.PairString,'ColumnFormat',{'char'})
123set(handles.PairString,'Data',{''})
124
125series_ResizeFcn(hObject, eventdata, handles)%resize table according to series GUI size
126set(hObject,'WindowButtonDownFcn',{'mouse_down'})%allows mouse action with right button (zoom for uicontrol display)
127set(hObject,'DeleteFcn',{@closefcn})%
128
129% check default input data
130if ~exist('Param','var')
[992]131    Param=[]; % default
[867]132end
133
[994]134%% Read the parameter file series.xml, or created from series.xml.default if it does not exist
[996]135SeriesData=[];
[994]136[path_series,name,ext]=fileparts(which('series'));% path to the GUI series
137xmlfile=fullfile(path_series,'series.xml');
138if ~exist(xmlfile,'file')
139    [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);
140end
141if exist(xmlfile,'file')
142    SeriesData.SeriesParam=xml2struct(xmlfile);
[1019]143    if ~(isfield(SeriesData.SeriesParam,'ClusterParam')&& isfield(SeriesData.SeriesParam.ClusterParam,'LaunchCmdFcn'))
144        [success,message]=copyfile(xmlfile,fullfile(path_series,'series_old.xml'));% update the file series.xml inot correctly documented
145        delete(xmlfile);
146        [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);
147    end 
148    SeriesData.SeriesParam=xml2struct(xmlfile);
[994]149end
150
151%% list of builtin functions in the menu ActionName
[992]152ActionList={'check_data_files';'aver_stat';'time_series';'civ_series';'merge_proj'}; % WARNING: fits with nb_builtin_ACTION=4 in ActionName_callback
[867]153NbBuiltinAction=numel(ActionList);
154set(handles.Action,'UserData',NbBuiltinAction)
[994]155path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series'
[992]156[path_series,name,ext]=fileparts(which('series')); % path to the GUI series
157path_series_fct=fullfile(path_series,'series'); % path of the functions in subdirectroy 'series'
[1003]158command = ['LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "l = x.split('':''); l = [s for s in l if ''matlab'' not in s]; print('':''.join(l))") ' ...
[1004]159            'python -c "import fluidimage"'];
[1003]160[code, ~] = system(command);
[872]161if code==0
[992]162    ActionExtList={'.m';'.sh';'.py (in dev.)'}; % default choice of extensions (Matlab fct .m or compiled version .sh
[872]163else
[880]164    ActionExtList={'.m';'.sh'};  % python options not installed
[872]165end
[992]166ActionPathList=cell(NbBuiltinAction,1); % initiate the cell matrix of Action fct paths
167ActionPathList(:)={path_series_fct}; % set the default path to series fcts to all list members
168RunModeList={'local';'background'}; % default choice of extensions (Matlab fct .m or compiled version .sh)
[1019]169[s,w]=system(SeriesData.SeriesParam.ClusterParam.ExistenceTest); % look for cluster system presence
[867]170if isequal(s,0)
[1019]171    RunModeList=[RunModeList;{'cluster'}];
[880]172    set(handles.MonitorCluster,'Visible','on'); % make visible button for access to Monika
[1033]173    set(handles.num_CPUTime,'Visible','on'); % make visible button for CPU time estimate for one ref index
[1097]174    set(handles.num_CPUTime,'String','')% default CPU time undefined
[1033]175    set(handles.CPUTime_txt,'Visible','on'); % make visible button for CPU time title
[867]176end
[984]177set(handles.RunMode,'String',RunModeList)% display the menu of available run modes, local, background or cluster manager
[867]178
179%% list of builtin transform functions in the menu TransformName
[992]180TransformList={'';'sub_field';'phys';'phys_polar'}; % WARNING: must fit with the corresponding menu in uvmat and nb_builtin_transform=4 in  TransformName_callback
[867]181NbBuiltinTransform=numel(TransformList);
182path_transform_fct=fullfile(path_series,'transform_field');
[992]183TransformPathList=cell(NbBuiltinTransform,1); % initiate the cell matrix of Action fct paths
184TransformPathList(:)={path_transform_fct}; % set the default path to series fcts to all list members
[1001]185SeriesData.TransformPath=path_transform_fct;% store the standard path for trqnsform functions (needed for compilation)
[867]186
187%% get the user defined functions stored in the personal file uvmat_perso.mat
188dir_perso=prefdir;
189profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
190if exist(profil_perso,'file')
191    h=load (profil_perso);
192    %get the list of previous input files in the upper bar menu Open
193    if isfield(h,'MenuFile')
194        for ifile=1:min(length(h.MenuFile),5)
195            set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile});
196            set(handles.(['MenuFile_' num2str(ifile+5)]),'Label',h.MenuFile{ifile});
197        end
198    end
199    %get the menu of actions
200    if isfield(h,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser)
201        ActionList=[ActionList;h.ActionListUser];
202        ActionPathList=[ActionPathList;h.ActionPathListUser(:,1)];
203    end
204    %get the menu of transform fct
205    if isfield(h,'TransformListUser') && iscell(h.TransformListUser) && isfield(h,'TransformPathListUser') && iscell(h.TransformPathListUser)
206        TransformList=[TransformList;h.TransformListUser];
207        TransformPathList=[TransformPathList;h.TransformPathListUser];
208    end
209end
210
211%% selection of the input Action fct
[992]212ActionCheckExist=true(size(ActionList)); % initiate the check of the path to the listed action fct
[867]213for ilist=NbBuiltinAction+1:numel(ActionList)%check  the validity of the path of the user defined Action fct
214    ActionCheckExist(ilist)=exist(fullfile(ActionPathList{ilist},[ActionList{ilist} '.m']),'file');
215end
[992]216ActionPathList=ActionPathList(ActionCheckExist,:); % suppress the menu options which are not valid anymore
[867]217ActionList=ActionList(ActionCheckExist);
218set(handles.ActionName,'String',[ActionList;{'more...'}])
219set(handles.ActionName,'UserData',ActionPathList)
220ActionIndex=[];
221if isfield(Param,'ActionName')% copy the selected menu index transferred in Param from uvmat
222    ActionIndex=find(strcmp(Param.ActionName,ActionList),1);
223end
224if isempty(ActionIndex)
225    ActionIndex=1;
226end
227set(handles.ActionName,'Value',ActionIndex)
228set(handles.ActionPath,'String',ActionPathList{ActionIndex})
229set(handles.ActionExt,'Value',1)
230set(handles.ActionExt,'String',ActionExtList)
231
232%% selection of the input transform fct
233TransformCheckExist=true(size(TransformList));
234for ilist=NbBuiltinTransform+1:numel(TransformList)
235    TransformCheckExist(ilist)=exist(fullfile(TransformPathList{ilist},[TransformList{ilist} '.m']),'file');
236end
237TransformPathList=TransformPathList(TransformCheckExist);
238TransformList=TransformList(TransformCheckExist);
239set(handles.TransformName,'String',[TransformList;{'more...'}])
240set(handles.TransformName,'UserData',TransformPathList)
241TransformIndex=[];
242if isfield(Param,'TransformName')% copy the selected menu index transferred in Param from uvmat
243    TransformIndex=find(strcmp(Param.TransformName,TransformList),1);
244end
245if isempty(TransformIndex)
246    TransformIndex=1;
247end
248set(handles.TransformName,'Value',TransformIndex)
249set(handles.TransformPath,'String',TransformPathList{TransformIndex})
250   
251%% fields input initialisation
252if isfield(Param,'list_fields')&& isfield(Param,'index_fields') &&~isempty(Param.list_fields) &&~isempty(Param.index_fields)
[992]253    set(handles.FieldName,'String',Param.list_fields); % list menu fields
254    set(handles.FieldName,'Value',Param.index_fields); % selected string index
[867]255end
[869]256if isfield(Param,'Coordinates')
257    if isfield(Param.Coordinates,'Coord_x')
258        set(handles.Coord_x,'String',Param.Coordinates.Coord_x)
259    end
260    if isfield(Param.Coordinates,'Coord_y')
261        set(handles.Coord_y,'String',Param.Coordinates.Coord_y)
262    end
263    if isfield(Param.Coordinates,'Coord_z')
264        set(handles.Coord_z,'String',Param.Coordinates.Coord_z)
265    end
[867]266end
267
268%% introduce the input file name(s) if defined from input Param,
[996]269set(handles.series,'UserData',SeriesData)% initiate Userdata
[867]270if isfield(Param,'InputFile')
271   
[1097]272    %% fill the list of input file series
[867]273    InputTable=[{Param.InputFile.RootPath},{Param.InputFile.SubDir},{Param.InputFile.RootFile},{Param.InputFile.NomType},{Param.InputFile.FileExt}];
[1097]274    if isempty(find(cellfun('isempty',InputTable)==0)) % if there is no input file, do not introduce input info
[909]275        set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
276        return
277    end
[867]278    TimeTable=[{Param.InputFile.TimeName},{[]},{[]},{[]},{[]}];
279    if isfield(Param.InputFile,'RootPath_1')
280        InputTable=[InputTable;[{Param.InputFile.RootPath_1},{Param.InputFile.SubDir_1},{Param.InputFile.RootFile_1},{Param.InputFile.NomType_1},{Param.InputFile.FileExt_1}]];
281        TimeTable=[TimeTable; [{Param.InputFile.TimeName_1},{[]},{[]},{[]},{[]}]];
282    end
283    set(handles.InputTable,'Data',InputTable)
[1097]284   
285    %% define the default path for the output files
286    [InputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
287    [InputPath,Experiment,ExperimentExt]=fileparts(InputPath);
288    set(handles.Device,'String',[Device DeviceExt])
289    set(handles.Experiment,'String',[Experiment ExperimentExt])
290    if ~isempty(regexp(InputTable{1,1},'(^http://)|(^https://)'))
291    set(handles.OutputPathBrowse,'Value',1)% an output folder needs to be specified for OpenDAP data
292    end
293
294    %update the output path if needed
295    if ~(isfield(SeriesData,'InputPath') && strcmp(SeriesData.InputPath,InputPath))
296    if get(handles.OutputPathBrowse,'Value')==1  % fix the output path in manual mode
297        OutputPathOld=get(handles.OutputPath,'String');
298        OutputPath=uigetdir(OutputPathOld,'pick a root folder for output data');
299        set(handles.OutputPath,'String',OutputPath)
300    else %reproduce the input path for output
301        set(handles.OutputPath,'String',InputPath)
302    end
303    end
304   
[867]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
[992]314    ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
[867]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
[992]322    ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
[867]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)
[869]328    if isfield(Param,'FileName_1')
[867]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
[869]334    ActionName_Callback([],[], handles)
335   
336    %% set length of waitbar
337    displ_time(handles)
338   
[867]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);
[992]463    MenuFile(str_find)=[]; % suppress the input file to the list
[867]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');
[937]488if ~isempty(InputTable)
[1037]489oldfile=[InputTable{1,1} InputTable{1,2}];
[937]490else
[867]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);
[937]496        if isfield(h,'MenuCampaign') && ~isempty(h.MenuCampaign)&& ischar(h.MenuCampaign{1})
497            oldfile=h.MenuCampaign{1};
[867]498        end
499    end
500end
[1059]501InputTable{1,1}='...';
[934]502set(handles.InputTable,'Data',InputTable)
[1059]503browse_data(oldfile,'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
504% NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
505% icount=0;
506% for iexp=1:numel(OutPut.Experiment)
507%     for idevice=1:numel(OutPut.DataSeries)
508%         icount=icount+1;
509%         InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp});
510%         InputTable{icount,2}=OutPut.DataSeries{idevice};
511%         if isempty(InputTable{icount,3})
512%             if icount>1
513%             InputTable{icount,3}=InputTable{icount-1,3};
514%             else
515%                 InputTable{icount,3}='';
516%             end
517%         end
518%         if isempty(InputTable{icount,4})
519%             if icount>1
520%             InputTable{icount,4}=InputTable{icount-1,4};
521%             else
522%                 InputTable{icount,4}='';
523%             end
524%         end
525%                 if isempty(InputTable{icount,5})
526%             if icount>1
527%             InputTable{icount,5}=InputTable{icount-1,5};
528%             else
529%                 InputTable{icount,5}='';
530%             end
531%         end
532%     end
533% end
534% if size(InputTable,1)>icount
535%     InputTable(icount+1:size(InputTable,1),:)=[];
536% end
537%REFRESH_Callback(hObject, eventdata, handles)
[867]538
539% --------------------------------------------------------------------
[1059]540% function MenuCampaign_Callback(hObject, eventdata, handles)
541% % --------------------------------------------------------------------
542%
543% OutPut=browse_data(get(hObject,'Label'),'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
544% if ~isfield(OutPut,'Campaign')
545%     return
546% end
547% NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
548% icount=0;
549% InputTable=get(handles.InputTable,'Data');
550% for iexp=1:numel(OutPut.Experiment)
551%     for idevice=1:numel(OutPut.DataSeries)
552%         icount=icount+1;
553%         InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp});
554%         InputTable{icount,2}=OutPut.DataSeries{idevice};
555%         if isempty(InputTable{icount,3})
556%             if icount>1
557%                 InputTable{icount,3}=InputTable{icount-1,3};
558%             else
559%                 InputTable{icount,3}='';
560%             end
561%         end
562%         if isempty(InputTable{icount,4})
563%             if icount>1
564%                 InputTable{icount,4}=InputTable{icount-1,4};
565%             else
566%                 InputTable{icount,4}='';
567%             end
568%         end
569%         if isempty(InputTable{icount,5})
570%             if icount>1
571%                 InputTable{icount,5}=InputTable{icount-1,5};
572%             else
573%                 InputTable{icount,5}='';
574%             end
575%         end
576%     end
577% end
578% if size(InputTable,1)>icount
579%     InputTable(icount+1:size(InputTable,1),:)=[];
580% end
581% set(handles.InputTable,'Data',InputTable)
582% REFRESH_Callback(hObject, eventdata, handles)
[937]583
[867]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
[880]598set(handles.OutputSubDir,'BackgroundColor',[1 0 1])% set edit box OutputSubDir to magenta color to indicate that refresh may be needed
[992]599xx=double(get(handles.series,'CurrentCharacter')); % get the keyboard character
[867]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
[992]606                InputTable=[InputTable;InputTable(iline,:)]; % create a new line as a copy of the last one
[867]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%------------------------------------------------------------------------
[1070]618check_input_file_series(handles)
619
620%% enable field and veltype menus, in accordance with the current action
621ActionInput_Callback([],[], handles)
622
623
624function check_input_file_series(handles)
[867]625InputTable=get(handles.InputTable,'Data');
626set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
627set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
628drawnow
629empty_line=false(size(InputTable,1),1);
630for iline=1:size(InputTable,1)
631    empty_line(iline)= isempty(cell2mat(InputTable(iline,1:3)));
632end
[1096]633if ~isempty(find(empty_line,1))
[992]634    InputTable(empty_line,:)=[]; % remove empty lines
[867]635    set(handles.InputTable,'Data',InputTable)
636    ListTable={'MinIndex_i','MaxIndex_i','MinIndex_j','MaxIndex_j','PairString','TimeTable'};
637    for ilist=1:numel(ListTable)
638        Table=get(handles.(ListTable{ilist}),'Data');
[992]639        Table(empty_line,:)=[]; % remove empty lines
[867]640        set(handles.(ListTable{ilist}),'Data',Table);
641    end
642    set(handles.series,'UserData',[])%refresh the stored info
643end
[883]644nbview=size(InputTable,1);
645for iview=1:nbview
[867]646    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
647    if ~exist(RootPath,'dir')
648        i1_series=[];
649        RootFile='';
650    else %scan the input folder
[1011]651        InputTable{iview,3}=regexprep(InputTable{iview,3},'^/','');
[963]652            [RootPath,~,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=...
653                find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]);
[867]654    end
655    % if no file is found, open a browser
656    if isempty(RootFile)&& isempty(i1_series)
657        fileinput=uigetfile_uvmat(['wrong input at line ' num2str(iview) ':pick a new input file'],RootPath);
658        if isempty(fileinput)
659            set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  back to red color
660            return
661        else
662            display_file_name(handles,fileinput,iview)
663        end
664    else
665       update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview)
666    end
667end
[883]668
669%% update MinIndex_i and MaxIndex_i if the input table content has been reduced in line nbre
[992]670MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
[883]671set(handles.MinIndex_i,'Data',MinIndex_i_table(1:nbview,:));
[992]672MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
[883]673set(handles.MinIndex_j,'Data',MinIndex_j_table(1:nbview,:));
[992]674MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
[991]675
[883]676set(handles.MaxIndex_i,'Data',MaxIndex_i_table(1:nbview,:));
[992]677MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
[883]678set(handles.MaxIndex_j,'Data',MaxIndex_j_table(1:nbview,:));
[992]679PairString=get(handles.PairString,'Data'); % retrieve the min indices in the table MinIndex
[883]680set(handles.PairString,'Data',PairString(1:nbview,:));
[992]681TimeTable=get(handles.TimeTable,'Data'); % retrieve the min indices in the table MinIndex
[883]682set(handles.TimeTable,'Data',TimeTable(1:nbview,:));
683
[867]684%% set length of waitbar
685displ_time(handles)
686set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (indicate activation finished)
687set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch'
688
[996]689
690
[867]691%------------------------------------------------------------------------
692% --- Function called when a new file is opened, either by series_OpeningFcn or by the browser
693%------------------------------------------------------------------------
694% INPUT:
695% handles: handles of elements in the GUI
696% Param: structure of input parameters, including  input file name and path
697% iview: line index in the input table
698%       or 'one': refresh the list
699%         'append': add a new line to the input table
700function errormsg=display_file_name(handles,Param,iview)
701 
702set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
703drawnow
[992]704errormsg=''; % default
[867]705if ischar(Param)
706    fileinput=Param;
707else% input set when series is opened (called by the GUI uvmat)
708    fileinput=Param.FileName;
709end
710   
711%% get the input root name, indices, file extension and nomenclature NomType
[1090]712if isempty(regexp(fileinput,'^http')) && ~exist(fileinput,'file')
[867]713    errormsg=['input file ' fileinput  ' does not exist'];
714    msgbox_uvmat('ERROR',errormsg)
715    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (refresh still needed)
716    return
717end
718
719%% detect root name, nomenclature and indices in the input file name:
720[FilePath,FileName,FileExt]=fileparts(fileinput);
721%%%%%%%%%%%%%%%%%%
722%TODO: case of input by uvmat: do not check agai the input seies %%%%%%%
723%%%%%%%%%%%%%%%%%%%
724% detect the file type, get the movie object if relevant, and look for the corresponding file series:
725% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
726[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
727FileType=FileInfo.FileType;
728if isempty(RootFile)&&isempty(i1_series)
729    errormsg='no input file in the series';
730    msgbox_uvmat('ERROR',errormsg)
731    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (end of activation)
732    return
733end
734if strcmp(FileType,'txt')
735    edit(fileinput)
736    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to  magenta color (end of activation)
737    return
738elseif strcmp(FileType,'xml')
739    editxml(fileinput)
740    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
741     return
742elseif strcmp(FileType,'figure')
743    open(fileinput)
744    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
745     return
746end
747
748%% enable other menus and uicontrols
749set(handles.RUN, 'Enable','On')
750set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
751set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
752drawnow
753
754
755%% fill the list of file series
756InputTable=get(handles.InputTable,'Data');
757SeriesData=get(handles.series,'UserData');
[1096]758
[867]759if strcmp(iview,'append') % display the input data as a new line in the table
[992]760    iview=size(InputTable,1)+1; % the next line in InputTable becomes the current line
[867]761elseif strcmp(iview,'one') % refresh the list of  input  file series
[992]762    iview=1; % the first line in InputTable becomes the current line
[867]763    InputTable={'','','','',''};
764    set(handles.TimeTable,'Data',[{''},{[]},{[]},{[]},{[]}])
765    set(handles.MinIndex_i,'Data',[])
766    set(handles.MaxIndex_i,'Data',[])
767    set(handles.MinIndex_j,'Data',[])
768    set(handles.MaxIndex_j,'Data',[])
769    set(handles.PairString,'Data',{''})
[992]770    SeriesData.CheckPair=0; % reset the list of input lines with pairs
[867]771    SeriesData.i1_series={};
772    SeriesData.i2_series={};
773    SeriesData.j1_series={};
774    SeriesData.j2_series={};
775    SeriesData.FileType={};
776    SeriesData.FileInfo={};
777    SeriesData.Time={};
778end
[883]779if isfield(SeriesData,'i1_series')
780    SeriesData.i1_series(iview+1:end)=[];
[867]781    SeriesData.i2_series(iview+1:end)=[];
782    SeriesData.j1_series(iview+1:end)=[];
783    SeriesData.j2_series(iview+1:end)=[];
784    SeriesData.FileType(iview+1:end)=[];
785    SeriesData.FileInfo(iview+1:end)=[];
786    SeriesData.Time(iview+1:end)=[];
[883]787end
788InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
[867]789if iview >1
790    set(handles.InputLine,'String',num2str(iview))
791end
792set(handles.InputTable,'Data',InputTable)
793
794%% determine the selected reference field indices for pair display
795if isempty(i1)
796    i1=1;
797end
798if isempty(i2)
799    i2=i1;
800end
[992]801ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
[867]802% set(handles.num_ref_i,'String',num2str(ref_i));
803if isempty(j1)
804    j1=1;
805end
806if isempty(j2)
807    j2=j1;
808end
[992]809ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
[867]810SeriesData.ref_i=ref_i;
811SeriesData.ref_j=ref_j;
812
813%% update first and last indices if they do not exist
814Param=read_GUI(handles.series);
815first_j=[];
816if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
817last_j=[];
818if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
819PairString='';
820if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
821[i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
822FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
823    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
824if ~exist(FirstFileName,'file')
825    set(handles.num_first_i,'String',num2str(ref_i))
826    set(handles.num_first_j,'String',num2str(ref_j))
827end
828[i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
829LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
830    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
831if ~exist(LastFileName,'file')
832    set(handles.num_last_i,'String',num2str(ref_i))
833    set(handles.num_last_j,'String',num2str(ref_j))
834end
835
836%% update the list of recent files in the menubar and save it for future opening
837MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
838    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
839str_find=strcmp(fileinput,MenuFile);
840if isempty(find(str_find,1))
[992]841    MenuFile=[{fileinput};MenuFile]; % insert the current file if not already in the list
[867]842end
843for ifile=1:min(length(MenuFile),5)
844    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
845end
846dir_perso=prefdir;
847profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
848if exist(profil_perso,'file')
[992]849    save (profil_perso,'MenuFile','-append'); % store the file names for future opening of uvmat
[867]850else
[992]851    save (profil_perso,'MenuFile','-V6'); % store the file names for future opening of uvmat
[867]852end
853% save the opened file to initiate future opening
[992]854SeriesData.RefFile{iview}=fileinput; % reference opening file for line iview
[867]855SeriesData.Ref_i1=i1;
856SeriesData.Ref_i2=i2;
857SeriesData.Ref_j1=j1;
858SeriesData.Ref_j2=j2;
[1096]859
860%% define the path for the output files
861[InputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
862[InputPath,Experiment,ExperimentExt]=fileparts(InputPath);
863set(handles.Device,'String',[Device DeviceExt])
864set(handles.Experiment,'String',[Experiment ExperimentExt])
865if ~isempty(regexp(InputTable{1,1},'(^http://)|(^https://)'))
866    set(handles.OutputPathBrowse,'Value',1)% an output folder needs to be specified for OpenDAP data
867end
868
869%update the output path if needed
870if ~(isfield(SeriesData,'InputPath') && strcmp(SeriesData.InputPath,InputPath))
871    if get(handles.OutputPathBrowse,'Value')==1  % fix the output path in manual mode
872        OutputPathOld=get(handles.OutputPath,'String');
873        OutputPath=uigetdir(OutputPathOld,'pick a root folder for output data');
874        set(handles.OutputPath,'String',OutputPath)
875    else %reproduce the input path for output
876        set(handles.OutputPath,'String',InputPath)
877    end
878    SeriesData.InputPath=InputPath;
879end
880
[867]881set(handles.series,'UserData',SeriesData)
882
883set(handles.InputTable,'BackgroundColor',[1 1 1])
884
885%% initiate input file series and refresh the current field view:     
886update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview);
887%% enable field and veltype menus, in accordance with the current action
888ActionName_Callback([],[], handles)
889
890%% set length of waitbar
891displ_time(handles)
892
893set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (end of activation)
894
895%------------------------------------------------------------------------
896% --- Update information about a new field series (indices to scan, timing,
897%     calibration from an xml file
898function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,VideoObject,iview)
899%------------------------------------------------------------------------
900InputTable=get(handles.InputTable,'Data');
901
902%% display the min and max indices for the whole file series
903if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
[992]904    MinIndex_j=1; % index j set to 1 by default
[867]905    MaxIndex_j=1;
[992]906    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)
907    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)
[867]908else
[992]909    ref_i=squeeze(max(i1_series(1,:,:),[],2)); % select ref_j index for each ref_i
910    ref_j=squeeze(max(j1_series(1,:,:),[],3)); % select ref_i index for each ref_j
[867]911     MinIndex_i=min(find(ref_i))-1;
912     MaxIndex_i=max(find(ref_i))-1;
913     MaxIndex_j=max(find(ref_j))-1;
914     MinIndex_j=min(find(ref_j))-1;
915    diff_j_max=diff(ref_j);
916    diff_i_max=diff(ref_i);
917    if ~isempty(diff_i_max) && isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max)))
918        set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to dispaly by default
919    end
920    if ~isempty(diff_j_max) && isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max)))
921        set(handles.num_incr_j,'String',num2str(diff_j_max(1)))
922    end
923end
924if isequal(MinIndex_i,-1)
925    MinIndex_i=0;
926end
927if isequal(MinIndex_j,-1)
928    MinIndex_j=0;
929end
[992]930MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
931MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
932MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
933MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
[867]934if ~isempty(MinIndex_i)&&~isempty(MaxIndex_i)
935    MinIndex_i_table(iview,1)=MinIndex_i;
936    MaxIndex_i_table(iview,1)=MaxIndex_i;
937end
938if ~isempty(MinIndex_j)&&~isempty(MaxIndex_j)
939    MinIndex_j_table(iview,1)=MinIndex_j;
940    MaxIndex_j_table(iview,1)=MaxIndex_j;
941end
942set(handles.MinIndex_i,'Data',MinIndex_i_table)%display the min indices in the table MinIndex
943set(handles.MinIndex_j,'Data',MinIndex_j_table)%display the max indices in the table MaxIndex
944set(handles.MaxIndex_i,'Data',MaxIndex_i_table)%display the min indices in the table MinIndex
945set(handles.MaxIndex_j,'Data',MaxIndex_j_table)%display the max indices in the table MaxIndex
946SeriesData=get(handles.series,'UserData');
947
948%% adjust the first and last indices for the selected series, only if requested by the bounds
949% i index, compare input to min index i
[992]950first_i=str2num(get(handles.num_first_i,'String')); % retrieve previous first i
951% ref_i=str2num(get(handles.num_ref_i,'String')); % index i given by the input field
[867]952ref_i=1;
953if isfield(SeriesData,'ref_i')
[937]954    ref_i=SeriesData.ref_i;
[867]955end
956if isempty(first_i)
[992]957    first_i=ref_i; % first_i updated by the input value
[867]958elseif first_i < MinIndex_i
959    first_i=MinIndex_i; % first_i set to the min i index (restricted by oter input lines)
960elseif first_i >MaxIndex_i
[992]961    first_i=MaxIndex_i; % first_i set to the max i index (restricted by oter input lines)
[867]962end
963% j index,  compare input to min index j
964first_j=str2num(get(handles.num_first_j,'String'));
965ref_j=1;
966if isfield(SeriesData,'ref_j')
[937]967    ref_j=SeriesData.ref_j;
[867]968end
969if isempty(first_j)
[992]970    first_j=ref_j; % first_j updated by the input value
[867]971elseif first_j<MinIndex_j
972    first_j=MinIndex_j; % first_j set to the min j index (restricted by oter input lines)
973elseif first_j >MaxIndex_j
974    first_j=MaxIndex_j; % first_j set to the max j index (restricted by oter input lines)
975end
976% i index, compare input to max index i
977last_i=str2num(get(handles.num_last_i,'String'));
978if isempty(last_i)
979    last_i=ref_i;
980elseif last_i > MaxIndex_i
981    last_i=MaxIndex_i;
982elseif last_i<first_i
983    last_i=first_i;
984end
985% j index, compare input to max index j
986last_j=str2num(get(handles.num_last_j,'String'));
987if isempty(last_j)
988    last_j=ref_j;
989elseif last_j>MaxIndex_j
990    last_j=MaxIndex_j;
991elseif last_j<first_j
992    last_j=first_j;
993end
[937]994set(handles.num_first_i,'String',num2str(first_i));
[867]995set(handles.num_first_j,'String',num2str(first_j));
[937]996set(handles.num_last_i,'String',num2str(last_i));
[867]997set(handles.num_last_j,'String',num2str(last_j));
998
999%% number of slices set by default
[992]1000NbSlice=[]; % default
[867]1001% read  value set by the first series for the append mode (iwiew >1)
1002if iview>1 && strcmp(get(handles.num_NbSlice,'Visible'),'on')
[937]1003    NbSlice=str2double(get(handles.num_NbSlice,'String'));
[867]1004end
1005
1006%% default time settings
1007TimeUnit='';
1008% read  value set by the first series for the append mode (iwiew >1)
[937]1009if iview>1
[867]1010    TimeUnit=get(handles.TimeUnit,'String');
1011end
1012TimeName='';
[992]1013Time=[]; % default
[867]1014TimeMin=[];
1015TimeFirst=[];
1016TimeLast=[];
1017TimeMax=[];
1018
1019%%  read image documentation file if found
1020XmlData=[];
1021check_calib=0;
1022XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
1023if ~isempty(XmlFileName)
1024    [XmlData,errormsg]=imadoc2struct(XmlFileName);
1025    if ~isempty(errormsg)
[937]1026        msgbox_uvmat('WARNING',['error in reading ' XmlFileName ': ' errormsg]);
[867]1027    end
1028    % read time if available
1029    if isfield(XmlData,'Time')
[937]1030        Time=XmlData.Time;
[867]1031        TimeName='xml';
1032    end
1033    if isfield(XmlData,'Camera')
1034        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
1035            if iview>1 && ~isempty(TimeUnit) && ~strcmp(TimeUnit,XmlData.Camera.TimeUnit)
1036                msgbox_uvmat('WARNING','inconsistent time unit with the first field series');
1037            end
1038            TimeUnit=XmlData.Camera.TimeUnit;
1039        end
1040    end
1041    % number of slices
[937]1042    if isfield(XmlData,'TranslationMotor')&& isfield(XmlData.TranslationMotor,'NbSlice')
1043        NbSlice_motor=XmlData.TranslationMotor.NbSlice;
1044        if ~isempty(NbSlice) && ~isequal(NbSlice_motor,NbSlice)
1045                msgbox_uvmat('WARNING','inconsistent Z numbers of Z indices');
1046        else
1047            NbSlice=NbSlice_motor;
1048        end
1049    end
[867]1050end
[937]1051if ~isempty(NbSlice)
1052set(handles.num_NbSlice,'String',num2str(NbSlice))
1053set(handles.num_NbSlice,'Visible','on')
1054end
[867]1055
1056%% read timing  from the current file (prioritary)
1057if ~isempty(VideoObject)% case of movies
1058    imainfo=get(VideoObject);
[1108]1059    if isfield(imainfo,'NumFrames')
1060        imainfo.NumberOfFrames=imainfo.NumFrames;
1061    end
[1096]1062    if isempty(j1_series) % frame index along i
[867]1063        Time=zeros(imainfo.NumberOfFrames+1,2);
1064        Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
1065    else
1066        Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
1067    end
1068    TimeName='video';
1069end
1070
1071
1072%% determine the min and max times: case of Netcdf files will be treated later in FieldName_Callback
1073if ~isempty(TimeName)
1074    TimeMin=Time(MinIndex_i+1,MinIndex_j+1);
1075    if size(Time)>=[first_i+1 first_j+1]
1076        TimeFirst=Time(first_i+1,first_j+1);
1077    end
1078    if size(Time)>=[last_i+1 last_j+1]
1079        TimeLast=Time(last_i+1,last_j+1);
1080    end
[1096]1081    if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1]
[867]1082        TimeMax=Time(MaxIndex_i+1,MaxIndex_j+1);
1083    end
1084end
1085
1086%% update the time table
1087TimeTable=get(handles.TimeTable,'Data');
1088TimeTable{iview,1}=TimeName;
1089TimeTable{iview,2}=TimeMin;
1090TimeTable{iview,3}=TimeFirst;
1091TimeTable{iview,4}=TimeLast;
1092TimeTable{iview,5}=TimeMax;
1093set(handles.TimeTable,'Data',TimeTable)
1094
1095%% update the series info in 'UserData'
1096SeriesData.i1_series{iview}=i1_series;
1097SeriesData.i2_series{iview}=i2_series;
1098SeriesData.j1_series{iview}=j1_series;
1099SeriesData.j2_series{iview}=j2_series;
1100SeriesData.FileType{iview}=FileInfo.FileType;
1101SeriesData.FileInfo{iview}=FileInfo;
1102SeriesData.Time{iview}=Time;
[1016]1103
1104SeriesData.TimeName=TimeName;
1105
[867]1106if check_calib
1107    SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib;
1108end
1109set(handles.series,'UserData',SeriesData)
1110
1111%% update pair menus
1112hset_pair=findobj(allchild(0),'Tag','set_pairs');
1113if ~isempty(hset_pair), delete(hset_pair); end % delete the GUI set_pair if opened
1114CheckPair= ~isempty(i2_series)||~isempty(j2_series); % check whether index pairs need to be defined
1115PairString=get(handles.PairString,'Data');
1116if CheckPair% if pairs need to be display for line iview
1117    [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series);
1118    Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,ModeMenu{ModeValue},Time,TimeUnit,ref_i,ref_j,TimeName,InputTable(iview,:),FileInfo);
1119    PairString{iview,1}=Menu{1};
1120else
[992]1121    PairString{iview,1}=''; % no pair for #iview
[867]1122end
1123set(handles.PairString,'Data',PairString)
1124if isempty(find(cellfun('isempty',get(handles.PairString,'Data'))==0, 1))% if all lines of pairs are empty
1125    set(handles.PairString,'Visible','off')
1126    set(handles.SetPairs,'Visible','off')
1127else
1128    set(handles.PairString,'Visible','on')
1129    set(handles.SetPairs,'Visible','on')
1130end
1131
1132
1133%% display the set of existing files as an image
1134set(handles.FileStatus,'Units','pixels')
1135Position=get(handles.FileStatus,'Position');
1136set(handles.FileStatus,'Units','normalized')
1137%xI=0.5:Position(3)-0.5;
1138nbview=numel(SeriesData.i1_series);
1139j_max=cell(1,nbview);
[992]1140MaxIndex_i=ones(1,nbview); % default
1141MinIndex_i=ones(1,nbview); % default
[867]1142for iline=1:nbview
[992]1143    pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); % max on pair index
1144    j_max{iline}=max(pair_max,[],1); % max on j index
[867]1145    if ~isempty(j_max{iline})
[1096]1146    MaxIndex_i(iline)=find(j_max{iline}, 1, 'last' )-1; % max ref index i
1147    MinIndex_i(iline)=find(j_max{iline}, 1 )-1; % min ref index i
[867]1148    end
1149end
1150MinIndex_i=min(MinIndex_i);
1151MaxIndex_i=max(MaxIndex_i);
1152range_index=MaxIndex_i-MinIndex_i+1;
1153range_y=max(1,floor(Position(4)/nbview));
1154npx=floor(Position(3));
1155file_indices=MinIndex_i+floor(((0.5:npx-0.5)/npx)*range_index)+1;
[992]1156CData=zeros(nbview*range_y,npx); % initiate the image representing the existing files
[867]1157for iline=1:nbview
1158    ind_y=1+(iline-1)*range_y:iline*range_y;
1159    LineData=zeros(size(file_indices));
1160    file_select=file_indices(file_indices<=numel(j_max{iline}));
[1096]1161    ind_select=file_indices<=numel(j_max{iline});
[867]1162    LineData(ind_select)=j_max{iline}(file_select)~=0;
1163    CData(ind_y,:)=ones(size(ind_y'))*LineData;
1164end
[992]1165CData=cat(3,zeros(size(CData)),CData,zeros(size(CData))); % make color images r=0,g,b=0
[867]1166set(handles.FileStatus,'CData',CData);
1167
1168%-----------------------------------------------------------guide -------------
1169%------------------------------------------------------------------------
1170%  III - FUNCTIONS ASSOCIATED TO THE FRAME IndexRange
1171%------------------------------------------------------------------------
1172
1173
1174% ---- determine the menu to put in mode and advice a default choice
1175%------------------------------------------------------------------------
1176function [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series)
1177%------------------------------------------------------------------------   
1178ModeMenu={''};
1179if isempty(j2_series)% no j pair
1180    ModeValue=1;
1181    if ~isempty(i2_series)
1182        ModeMenu={'series(Di)'}; % pair menu with only option Di
1183    end
1184else %existence of j pairs
[992]1185    pair_max=squeeze(max(i1_series,[],1)); % max on pair index
[867]1186    j_max=max(pair_max,[],1);
[992]1187    MaxIndex_i=find(j_max, 1, 'last' )-1; % max ref index i
1188    MinIndex_i=find(j_max, 1 )-1; % min ref index i
[867]1189    i_max=max(pair_max,[],2);
[992]1190    MaxIndex_j=find(i_max, 1, 'last' )-1; % max ref index i
1191    MinIndex_j=find(i_max, 1 )-1; % min ref index i
[867]1192    if MaxIndex_j==MinIndex_j
1193        ModeValue=1;
1194        ModeMenu={'bursts'};
1195    elseif MaxIndex_i==MinIndex_i
1196        ModeValue=1;
1197        ModeMenu={'series(Dj)'};
1198    else
1199        ModeMenu={'bursts';'series(Dj)'};
1200        if (MaxIndex_j-MinIndex_j)>10
[992]1201            ModeValue=2; % set mode to series(Dj) if more than 10 j values
[867]1202        else
1203            ModeValue=1;
1204        end
1205    end
1206end
1207
1208
1209%------------------------------------------------------------------------
[1096]1210%fill the menu of possible pairs as input
[867]1211function displ_pair=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo)
1212%------------------------------------------------------------------------
1213displ_pair={};
1214if isempty(TimeUnit)
1215    dtunit='e-03';
1216else
1217    dtunit=['m' TimeUnit];
1218end
1219switch mode
1220    case 'series(Di)'
1221        diff_i=i2_series-i1_series;
1222        min_diff=min(diff_i(diff_i>0));
1223        max_diff=max(diff_i(diff_i>0));
1224        for ipair=min_diff:max_diff
[1096]1225            if ~isempty(find(diff_i==ipair,1))% if the considered difference exists as input
[867]1226                pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
[1096]1227                if size(time,1)>=ref_i+ceil(ipair/2)
[867]1228                    if ref_i<=floor(ipair/2)
[992]1229                        ref_i=floor(ipair/2)+1; % shift ref_i to get the first pair
[867]1230                    end
1231                    Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1232                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1233                end
1234                displ_pair=[displ_pair;{pair_string}];
1235            end
1236        end
1237        if ~isempty(displ_pair)
1238            displ_pair=[displ_pair;{'Di=*|*'}];
1239        end
1240    case 'series(Dj)'
1241        if isempty(j2_series)
1242            msgbox_uvmat('ERROR','no j1-j2 pair available')
1243            return
1244        end
1245        diff_j=j2_series-j1_series;
1246        min_diff=min(diff_j(diff_j>0));
1247        max_diff=max(diff_j(diff_j>0));
1248        for ipair=min_diff:max_diff
1249            if numel(diff_j(diff_j==ipair))>0
1250                pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1251                if ~isempty(time)
1252                    if ref_j<=floor(ipair/2)
[992]1253                        ref_j=floor(ipair/2)+1; % shift ref_i to get the first pair
[867]1254                    end
1255                    Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1256                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1257                end
1258                displ_pair=[displ_pair;{pair_string}];
1259            end
1260        end
1261        if ~isempty(displ_pair)
1262            displ_pair=[displ_pair;{'Dj=*|*'}];
1263        end
1264    case 'bursts'
1265        if isempty(j2_series)
1266            msgbox_uvmat('ERROR','no j1-j2 pair available')
1267            return
1268        end
1269        %diff_j=j2_series-j1_series;
1270        min_j1=min(j1_series(j1_series>0));
1271        max_j1=max(j1_series(j1_series>0));
1272        min_j2=min(j2_series(j2_series>0));
1273        max_j2=max(j2_series(j2_series>0));
1274        for pair1=min_j1:min(max_j1,min_j1+20)
1275            for pair2=min_j2:min(max_j2,min_j2+20)
1276                if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1277                    pair_string=['j= ' num2str(pair1) '-' num2str(pair2)];
1278                    [TimeValue,DtValue]=get_time(ref_i,[],pair_string,InputTable,FileInfo,TimeName,'Dt');
1279                    %Dt=time(ref_i,pair2+1)-time(ref_i,pair1+1);
1280                    pair_string=[pair_string ', Dt=' num2str(DtValue) ' ' dtunit];
1281                    displ_pair=[displ_pair;{pair_string}];
1282                end
1283            end
1284        end
1285        if ~isempty(displ_pair)
1286            displ_pair=[displ_pair;{'j=*-*'}];
1287        end
1288end
1289
1290%------------------------------------------------------------------------
1291function num_first_i_Callback(hObject, eventdata, handles)
1292%------------------------------------------------------------------------
1293num_last_i_Callback(hObject, eventdata, handles)
1294
1295%------------------------------------------------------------------------
1296function num_last_i_Callback(hObject, eventdata, handles)
1297%------------------------------------------------------------------------
1298SeriesData=get(handles.series,'UserData');
1299if ~isfield(SeriesData,'Time')
1300    SeriesData.Time{1}=[];
1301end
1302displ_time(handles);
1303
1304%------------------------------------------------------------------------
1305function num_first_j_Callback(hObject, eventdata, handles)
1306%------------------------------------------------------------------------
1307 num_last_j_Callback(hObject, eventdata, handles)
1308
1309%------------------------------------------------------------------------
1310function num_last_j_Callback(hObject, eventdata, handles)
1311%------------------------------------------------------------------------
1312% first_j=str2num(get(handles.num_first_j,'String'));
1313% last_j=str2num(get(handles.num_last_j,'String'));
1314% ref_j=ceil((first_j+last_j)/2);
1315% set(handles.num_ref_j,'String', num2str(ref_j))
1316% num_ref_j_Callback(hObject, eventdata, handles)
1317SeriesData=get(handles.series,'UserData');
1318if ~isfield(SeriesData,'Time')
1319    SeriesData.Time{1}=[];
1320end
1321displ_time(handles);
1322
1323%------------------------------------------------------------------------
1324% ---- find the times corresponding to the first and last indices of a series
1325function displ_time(handles)
1326%------------------------------------------------------------------------
[992]1327SeriesData=get(handles.series,'UserData'); %
[867]1328if ~isfield(SeriesData,'Time')
1329    return
1330end
1331PairString=get(handles.PairString,'Data');
[992]1332ref_i_1=str2num(get(handles.num_first_i,'String')); % first reference index
1333ref_i_2=str2num(get(handles.num_last_i,'String')); % last reference index
[867]1334ref_j_1=[];ref_j_2=[];
1335if strcmp(get(handles.num_first_j,'Visible'),'on')
1336ref_j_1=str2num(get(handles.num_first_j,'String'));
1337ref_j_2=str2num(get(handles.num_last_j,'String'));
1338end
1339[i1_1,i2_1,j1_1,j2_1] = get_file_index(ref_i_1,ref_j_1,PairString);
1340[i1_2,i2_2,j1_2,j2_2] = get_file_index(ref_i_2,ref_j_2,PairString);
1341TimeTable=get(handles.TimeTable,'Data');
1342%%%%%%
1343%TODO: read time in netcdf file, see ActionName_Callback
1344%%%%%%%
1345%Pairs=get(handles.PairString,'Data');
1346for iview=1:size(TimeTable,1)
1347    if size(SeriesData.Time,1)<iview
1348        break
1349    end
1350    TimeTable{iview,3}=[];
1351    TimeTable{iview,4}=[];
1352    if size(SeriesData.Time{iview},1)>=i2_2+1 && (isempty(ref_j_1)||size(SeriesData.Time{iview},2)>=j2_2+1)
1353        if isempty(ref_j_1)
1354            time_first=(SeriesData.Time{iview}(i1_1+1,2)+SeriesData.Time{iview}(i2_1+1,2))/2;
1355            time_last=(SeriesData.Time{iview}(i1_2+1,2)+SeriesData.Time{iview}(i2_2+1,2))/2;
1356        else
1357            time_first=(SeriesData.Time{iview}(i1_1+1,j1_1+1)+SeriesData.Time{iview}(i2_1+1,j2_1+1))/2;
1358            time_last=(SeriesData.Time{iview}(i1_2+1,j1_2+1)+SeriesData.Time{iview}(i2_2+1,j2_1+1))/2;
1359        end
[992]1360        TimeTable{iview,3}=time_first; % TODO: take into account pairs
1361        TimeTable{iview,4}=time_last; % TODO: take into account pairs
[867]1362    end
1363end
1364set(handles.TimeTable,'Data',TimeTable)
1365
1366%% set the waitbar position with respect to the min and max in the series
1367MinIndex_i=min(get(handles.MinIndex_i,'Data'));
1368MaxIndex_i=max(get(handles.MaxIndex_i,'Data'));
1369pos_first=(ref_i_1-MinIndex_i)/(MaxIndex_i-MinIndex_i+1);
1370pos_last=(ref_i_2-MinIndex_i+1)/(MaxIndex_i-MinIndex_i+1);
1371if isempty(pos_first), pos_first=0; end
1372if isempty(pos_last), pos_last=1; end
[992]1373Position=get(handles.Waitbar,'Position'); % position of the waitbar:= [ x,y, width, height]
[867]1374Position_status=get(handles.FileStatus,'Position');
1375Position(1)=Position_status(1)+Position_status(3)*pos_first;
[992]1376Position(3)=max(Position_status(3)*(pos_last-pos_first),0.001); % width must remain positive
[867]1377set(handles.Waitbar,'Position',Position)
1378update_waitbar(handles.Waitbar,0)
1379
1380%------------------------------------------------------------------------
1381% --- Executes when selected cell(s) is changed in PairString.
1382function PairString_CellSelectionCallback(hObject, eventdata, handles)
1383%------------------------------------------------------------------------   
1384if numel(eventdata.Indices)>=1
1385    PairString=get(hObject,'Data');
1386    if ~isempty(PairString{eventdata.Indices(1)})
1387        SetPairs_Callback(hObject, eventdata.Indices(1), handles)
1388    end
1389end
1390
1391%-------------------------------------
1392function enable_i(handles,state)
1393set(handles.i_txt,'Visible',state)
1394set(handles.num_first_i,'Visible',state)
1395set(handles.num_last_i,'Visible',state)
1396set(handles.num_incr_i,'Visible',state)
1397
1398%-----------------------------------
1399function enable_j(handles,state)
1400set(handles.j_txt,'Visible',state)
1401set(handles.num_first_j,'Visible',state)
1402set(handles.num_last_j,'Visible',state)
1403set(handles.num_incr_j,'Visible',state)
1404set(handles.MinIndex_j,'Visible',state)
1405set(handles.MaxIndex_j,'Visible',state)
1406
1407
1408%%%%%%%%%%%%%%%%%%%%
1409%%  MAIN ActionName FUNCTIONS
1410%%%%%%%%%%%%%%%%%%%%
1411%------------------------------------------------------------------------
1412% --- Executes on button press in RUN.
1413%------------------------------------------------------------------------
1414function RUN_Callback(hObject, eventdata, handles)
1415
1416%% settings of the button RUN
[996]1417if ~isequal(get(handles.ActionInput,'BackgroundColor'),[1 0 0])
1418    msgbox_uvmat('ERROR','first activate the button ActionInput')
1419    return
1420end
[992]1421set(handles.RUN,'BusyAction','queue'); % activation of STOP button will set BusyAction to 'cancel'
[867]1422set(handles.RUN, 'Enable','Off')% avoid further RUN action until the current one is finished
1423set(handles.RUN,'BackgroundColor',[1 1 0])%show activation of RUN by yellow color
1424drawnow
1425set(handles.status,'Value',0)% desable status display if relevant
1426status_Callback([], eventdata, handles)
1427
1428%% launch action
1429errormsg=launch_action(handles);
1430if ~isempty(errormsg)
1431     msgbox_uvmat('ERROR',errormsg)
1432end
1433
1434%% reset the GUI series
1435update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate launching is finished
1436set(handles.RUN, 'Enable','On')
1437set(handles.RUN,'BackgroundColor',[1 0 0])
1438set(handles.RUN, 'Value',0)
1439
1440%------------------------------------------------------------------------
1441% --- called by RUN_Callback
1442%------------------------------------------------------------------------
[997]1443% The calculations are launched in three different ways:
1444% RunMode='local': calculation on the local Matlab session, will prevent other actions during that time.
1445% RunMode='background': calculation on the local computer, but in a new Matlab session (with no graphic output).
1446% RunMode='cluster': calculations dispatched in a cluster, using a managing system, 'oar, 'sge, or 'sgb'.
1447% In the latter case, the calculation is split in 'packets' of i index (all j indices are contained in a single packet).
1448% This splitting is possible only if the different calculations in the series are independent. Otherwise the action
1449% function imposes a number of processes NbSlice in input, for instance NbSlice=1 for a time series.
1450% If NbSlice is not imposed, the splitting in packets (jobs) is determined
1451% so that a job is optimum length AdvisedJobCPUTime), and the total job number in any case smaller
1452% than MaxJobNumber (these parameters are defined in the file series.xml in
1453% accordance with the management strategy for the cluster). The jobs are
1454% dispatched in parallel into NbCore processors by the cluster managing system.
1455
[867]1456function errormsg=launch_action(handles)
[992]1457errormsg=''; % default
[867]1458
1459%% read the data on the GUI series
[992]1460Param=read_GUI_series(handles); % displayed parameters
1461SeriesData=get(handles.series,'UserData'); % hidden parameters
[883]1462if isfield(SeriesData,'TransformInput')
1463    Param.TransformInput=SeriesData.TransformInput;
1464end
[1072]1465if isfield(SeriesData,'ProjObject')
1466    Param.ProjObject=SeriesData.ProjObject;
1467end
[867]1468if ~isfield(SeriesData,'i1_series')
1469    errormsg='The input field series needs to be refreshed: press REFRESH';
1470    return
1471end
[1078]1472if isfield(Param,'InputFields')&& isfield(Param.InputFields,'FieldName')&& isequal(Param.InputFields.FieldName,'add_field...')
1473    errormsg='input field name(s) not defined, select add_field...';
[867]1474    return
1475end
1476
1477%% select the Action mode, 'local', 'background' or 'cluster' (if available)
[992]1478RunMode='local'; % default (needed for first opening of the GUI series)
[867]1479if isfield(Param.Action,'RunMode')
1480    RunMode=Param.Action.RunMode;
[992]1481    Param.Action=rmfield(Param.Action,'RunMode'); % remove from the recorded xml file to avoid interference during ImportConfig
[1051]1482    Param.RunMode=RunMode; % keep track of the mode
[867]1483end
[992]1484ActionExt='.m'; % default
[867]1485if isfield(Param.Action,'ActionExt')
[992]1486    ActionExt=Param.Action.ActionExt; % '.m', '.sh' (compiled)  or '.py' (Python)
1487    Param.Action=rmfield(Param.Action,'ActionExt'); % remove from the recorded xml file to avoid interference during ImportConfig
[867]1488end
1489ActionName=Param.Action.ActionName;
1490ActionPath=Param.Action.ActionPath;
1491path_series=fileparts(which('series'));
1492
1493%% create the Action fct handle if RunMode option = 'local'
1494if strcmp(RunMode,'local')
1495    if ~isequal(ActionPath,path_series)
1496        eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1497        if ~exist(ActionPath,'dir')
1498            errormsg=['The prescribed function path ' ActionPath ' does not exist'];
1499            return
1500        end
1501        if ~isequal(spath,ActionPath)
1502            addpath(ActionPath)% add the prescribed path if not the current one
1503        end
1504    end
1505    eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1506    if ~isequal(ActionPath,path_series)
1507        rmpath(ActionPath)% add the prescribed path if not the current one
1508    end
1509end
1510
[994]1511%% Get  parameters from series.xml
[992]1512errormsg=''; % default error message
[928]1513ActionFullName=fullfile(get(handles.ActionPath,'String'),ActionName);
[934]1514
1515%% If a compiled version has been selected (ext .sh) check wether it needs to be recompiled
[867]1516if strcmp(ActionExt,'.sh')
1517    TransformPath='';
[1001]1518    if isfield(SeriesData,'TransformPath')
1519        TransformPath=SeriesData.TransformPath;
1520        if isfield(SeriesData,'TransformList')
1521            TransformList=get(handles.TransformName,'String');
1522            TransformIndex=get(handles.TransformName,'Value');
1523            TransformName=TransformList{TransformIndex};
1524            if ~ismember(TransformName,SeriesData.TransformList)
1525                TransformPath='';
1526            end
1527        end
[867]1528    end
[1001]1529    if ~isempty(TransformPath)&&...
1530          ~strcmp(TransformPath,get(handles.TransformPath,'String'))% if the transform is not in paths set for compilation
1531        msgbox_uvmat('ERROR', 'compilation not available for this transform function, select .m')
1532        return
1533    end
[867]1534    set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
1535    set(handles.ActionExt,'BackgroundColor',[1 1 0])
[923]1536    [mcrmajor, mcrminor] = mcrversion;   
1537    MCRROOT = ['MCRROOT',int2str(mcrmajor),int2str(mcrminor)];
[1035]1538    RunTime = getenv('MCRROOT'); % Just variable MCRROOT with no version in it's name
[1036]1539    if strcmp(RunTime,'')
1540        RunTime = getenv(MCRROOT); % Use specialize MCRROOT with version
1541    end
[895]1542    ActionNameVersion=[ActionName '_' MCRROOT];
1543    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']);
[934]1544    % compile the .m file if the .sh file does not exist yet
[867]1545    if ~exist(ActionFullName,'file')
1546        answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
1547        if strcmp(answer,'Yes')
1548            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1549            path_uvmat=fileparts(which('series'));
1550            currentdir=pwd;
1551            cd(get(handles.ActionPath,'String'))% go to the directory of Action
1552            addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1553            compile(ActionName,TransformPath)
1554            cd(currentdir)
[880]1555        else
1556            errormsg='Action launch interrupted';
1557            return
[867]1558        end       
1559    else
[895]1560        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']));
[867]1561        m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
1562        if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
1563            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1564            drawnow
[895]1565            answer=msgbox_uvmat('INPUT_Y-N',[ActionNameVersion '.sh needs to be updated: recompile now?']);
[867]1566            if strcmp(answer,'Yes')
1567                path_uvmat=fileparts(which('series'));
1568                currentdir=pwd;
1569                cd(get(handles.ActionPath,'String'))% go to the directory of Action
1570                addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
[1030]1571                addpath(fullfile(path_uvmat,'transform_field'))% add the path to transform functions to run the fct 'compile'
[867]1572                compile(ActionName,TransformPath)
1573                cd(currentdir)
1574            end
1575        end
1576    end
[934]1577
[867]1578    set(handles.ActionExt,'BackgroundColor',[1 1 1])
1579     set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch
1580end
1581
[897]1582%% set nbre of cluster cores and processes:
1583% NbCore is the number of computer processors used
[917]1584% NbProcess is the number of independent processes in which the required calculation is split.
[1114]1585% switch RunMode
1586%     case {'local','background'}
1587%         NbCore=1; % no need to split the calculation
1588%     case 'cluster'
1589%         %proposed number of cores to reserve in the cluster
1590%         NbCoreAdvised=SeriesData.SeriesParam.ClusterParam.NbCoreAdvised;
1591%         NbCoreMax=min(NbProcess,SeriesData.SeriesParam.ClusterParam.NbCoreMax);
1592%         if NbCoreMax~=1
1593%             if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1594%                 warning_string=', preferably use .sh option to save Matlab licences';
1595%             else
1596%                 warning_string=')';
1597%             end
1598%             answer=msgbox_uvmat('INPUT_TXT',['Number of cores (max ' num2str(NbCoreMax) ', ' warning_string],num2str(NbCoreAdvised));
1599%             if isempty(answer)
1600%                 errormsg='Action launch interrupted by user';
1601%                 return
1602%             end
1603%             NbCore=str2double(answer);
1604%             if NbCore > NbCoreMax
1605%                 NbCore=NbCoreMax;
1606%             end
1607%         else
1608%             NbCore=1;
1609%         end
1610% end
[867]1611if ~isfield(Param.IndexRange,'NbSlice')
1612    Param.IndexRange.NbSlice=[];
1613end
[1090]1614OutputPath=get(handles.OutputPath,'String');
[867]1615
[1068]1616%% Look for processing on multiple experiments set by the GUI browse_data
1617NbExp=1;% initiate the number of experiments set by the GUI browse_data, =1 otherwise
[1059]1618if get(handles.Replicate,'Value')
1619    hh=findobj(allchild(0),'Tag','browse_data');
[1072]1620    if isempty(hh)
1621        set(handles.Replicate,'Value',0)
1622    else
1623        set(handles.Replicate,'BackgroundColor',[1 1 0])%paint Relicate button in yellow
1624        BrowseData=guidata(hh);
1625        SourceDir=get(BrowseData.SourceDir,'String');
1626        ListExp=get(BrowseData.ListExperiments,'String');
1627        ExpIndices=get(BrowseData.ListExperiments,'Value');
1628        ListExp=ListExp(ExpIndices);
1629        ListDevices=get(BrowseData.ListDevices,'String');
1630        DeviceIndices=get(BrowseData.ListDevices,'Value');
1631        ListDevices=ListDevices(DeviceIndices);
1632        ListDataSeries=get(BrowseData.DataSeries,'String');
1633        DataSeriesIndices=get(BrowseData.DataSeries,'Value');
1634        ListDataSeries=ListDataSeries(DataSeriesIndices);
1635        NbExp=0; % counter of the number of experiments set by the GUI browse_data
1636        for iexp=1:numel(ListExp)
1637            if ~isempty(regexp(ListExp{iexp},'^\+/'))% if it is a folder
[1104]1638               %if strcmp(get(BrowseData.DataSeries,'enable'),'off') %case of a multiple input line for series
1639%                     NbExp=NbExp+1;
1640%                     ExpIndex{NbExp}=iexp;
1641%                     for idevice=1:numel(ListDevices)
1642%                         lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),...
1643%                             regexprep(ListDevices{idevice},'^\+/',''));
1644%                         lpathout=fullfile(OutputPath,regexprep(ListExp{iexp},'^\+/',''),...
1645%                             regexprep(ListDevices{idevice},'^\+/',''));
1646%                         ldir=regexprep(ListDataSeries{idevice},'^\+/','');
1647%                         ListPath{idevice,NbExp}=lpath;
1648%                         ListPathOut{idevice,NbExp}=lpathout;
1649%                         ListSubdir{idevice,NbExp}=ldir;
1650%                     end
1651                %else
[1072]1652                    for idevice=1:numel(ListDevices)
1653                        if ~isempty(regexp(ListDevices{idevice},'^\+/'))% if it is a folder
1654                            for isubdir=1:numel(ListDataSeries)
1655                                if ~isempty(regexp(ListDataSeries{isubdir},'^\+/'))% if it is a folder
1656                                    lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),...
1657                                        regexprep(ListDevices{idevice},'^\+/',''));
[1090]1658                                    lpathout= fullfile(OutputPath,regexprep(ListExp{iexp},'^\+/',''),...
1659                                        regexprep(ListDevices{idevice},'^\+/',''));
[1072]1660                                    ldir= regexprep(ListDataSeries{isubdir},'^\+/','');
1661                                    if exist(fullfile(lpath,ldir),'dir')
1662                                        NbExp=NbExp+1;
[1104]1663                                        ExpIndex(NbExp)=ExpIndices(iexp);
1664                                        DeviceIndex(NbExp)=DeviceIndices(idevice);
[1072]1665                                        ListPath{NbExp}=lpath;
[1090]1666                                        ListPathOut{NbExp}=lpathout;
[1104]1667                                        ListDeviceOut{NbExp}=regexprep(ListDevices{idevice},'^\+/','');
1668                                        ListExpOut{NbExp}=regexprep(ListExp{iexp},'^\+/','');
[1072]1669                                        ListSubdir{NbExp}=ldir;
1670                                    end
[1069]1671                                end
[1068]1672                            end
1673                        end
1674                    end
[1104]1675%                 end
[1068]1676            end
1677        end
[1072]1678        answer=msgbox_uvmat('INPUT_Y-N-Cancel',['replicate the processing on ' num2str(NbExp) ' data series']);
1679        if strcmp(answer,'Cancel')||strcmp(answer,'No')
1680            return
1681        end
[905]1682    end
[1059]1683end
[1090]1684
[1059]1685%%%%%%%%%%%%%%%%%%% LOOP ON EXPERIMENTS POSSIBLY SET BY THE GUI browse_data, NbExp=1 otherwise %%%%%%%%%
[1090]1686
[1059]1687for iexp=1:NbExp
[1068]1688    if get(handles.Replicate,'Value')
1689        if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1690            disp('program stopped by user')
1691            return
1692        end
[1104]1693        set(BrowseData.ListExperiments,'Value',ExpIndex(iexp))
1694        set(BrowseData.ListDevices,'Value',DeviceIndex(iexp))
[1069]1695        Param.InputTable(:,1)=ListPath(:,iexp);
1696        Param.InputTable(:,2)=ListSubdir(:,iexp);
[1070]1697        OutputSubDir=unique(ListSubdir(:,iexp));
1698        Param.OutputSubDir=OutputSubDir{1};
1699        if numel(OutputSubDir)>1% case
1700            for iout=2:numel(OutputSubDir)
1701                Param.OutputSubDir=[Param.OutputSubDir '-' OutputSubDir{iout}];
1702            end               
1703        end       
[1068]1704    end
1705    [xx,ExpName]=fileparts(Param.InputTable{1,1});
[1059]1706    Param.IndexRange.first_i=str2num(get(handles.num_first_i,'String'));%reset the firrst_i and last_i for multiple experiments, modified by the splitting into NbProcess
1707    Param.IndexRange.last_i=str2num(get(handles.num_last_i,'String'));
[1070]1708   
[1072]1709    %% create the output data directory if needed, after checking its existence
[1059]1710    OutputDir='';
1711    answer='';
[1108]1712    if isfield(Param,'OutputSubDir')&& isfield(Param,'OutputDirExt')% possibly update the output dir if it already exists
[1090]1713        PathOut=get(handles.OutputPath,'String');
1714        if ~exist(PathOut,'dir') % test if  the dir  already exist
[1104]1715            PathOut=uigetdir(PathOut,'pick the output root path');
1716            set(handles.OutputPath,'String',PathOut);
[1090]1717        end
[1105]1718        if get(handles.Replicate,'Value')
[1104]1719        PathExpOut=fileparts(ListPath{iexp});
[1105]1720        PathExpDeviceOut=ListPath{iexp};
1721        else
1722            PathExpOut=fullfile(PathOut,get(handles.Experiment,'String'));
1723            PathExpDeviceOut=fullfile(PathExpOut,get(handles.Device,'String'))
1724        end
[1090]1725        if ~exist(PathExpOut,'dir')
1726            [tild,msg1]=mkdir(PathExpOut);
1727            if ~strcmp(msg1,'')
1728                errormsg=['cannot create ' PathExpOut ': ' msg1]; % error message for directory creation
1729                return
1730            end
1731        end
1732        if ~exist(PathExpDeviceOut,'dir')
1733            [tild,msg1]=mkdir(PathExpDeviceOut);
1734            if ~strcmp(msg1,'')
1735                errormsg=['cannot create ' PathExpDeviceOut ': ' msg1]; % error message for directory creation
1736                return
1737            end
1738        end
[1108]1739
[1070]1740        SubDirOut=[Param.OutputSubDir Param.OutputDirExt];
[1059]1741        SubDirOutNew=SubDirOut;
[1090]1742        detect=exist(fullfile(PathExpDeviceOut,SubDirOutNew),'dir'); % test if  the dir  already exist
[1059]1743        check_create=1; % need to create the result directory by default
1744        CheckOverwrite=1;
1745        if isfield(Param,'CheckOverwrite')
[1090]1746            CheckOverwrite=Param.CheckOverwrite;% will overwrite previous data if it is equal to 1
[904]1747        end
[1059]1748        while detect
1749            if CheckOverwrite
1750                comment=', possibly overwrite previous data';
1751            else
1752                comment=', will complement existing result files (no overwriting)';
1753            end
[1090]1754            answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(PathExpDeviceOut,SubDirOutNew) comment]);
[1059]1755            if strcmp(answer,'Cancel')
1756                break
1757            elseif strcmp(answer,'Yes')
1758                detect=0;
1759                check_create=0;
1760            else
1761                r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names'); % detect whether name ends by a number
1762                if isempty(r)
1763                    r(1).root=[SubDirOutNew '_'];
1764                    r(1).num1='0';
1765                end
1766                SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)]; % increment the index by 1 or put 1
[1090]1767                detect=exist(fullfile(PathExpDeviceOut,SubDirOutNew),'dir'); % test if  the dir  already exists
[1059]1768                check_create=1;
1769            end
1770        end
[867]1771        if strcmp(answer,'Cancel')
[1059]1772            continue
1773        end
[1070]1774        Param.OutputDirExt=regexprep(SubDirOutNew,['^' Param.OutputSubDir],'');
[1059]1775        Param.OutputRootFile=Param.InputTable{1,3}; % the first sorted RootFile taken for output
[1090]1776        OutputDir=fullfile(PathExpDeviceOut,[Param.OutputSubDir Param.OutputDirExt]); % full name (with path) of output directory
[1059]1777        if check_create    % create output directory if it does not exist
1778            [tild,msg1]=mkdir(OutputDir);
1779            if ~strcmp(msg1,'')
1780                errormsg=['cannot create ' OutputDir ': ' msg1]; % error message for directory creation
1781                return
[867]1782            end
1783        end
[1059]1784       
1785    elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir
1786        OutputDir=Param.ActionInput.LogPath;
[867]1787    end
[1108]1788    if isfield(Param,'OutputSubDir')&& isfield(Param,'OutputDirExt')
1789        set(handles.OutputSubDir,'String',Param.OutputSubDir)
1790        set(handles.OutputDirExt,'String',Param.OutputDirExt)
1791        drawnow
[1100]1792    end
[1070]1793    if get(handles.Replicate,'Value')
1794        set(handles.InputTable,'Data',Param.InputTable)
[1104]1795        set(handles.OutputPath,'String',OutputPath)
1796         set(handles.Experiment,'String',ListExpOut{iexp})
1797        set(handles.Device,'String',ListDeviceOut{iexp})
1798        Param.Experiment=ListExpOut{iexp};
1799        Param.Device=ListDeviceOut{iexp};
[1100]1800        check_input_file_series(handles)     
[1070]1801    end
[1059]1802    DirXml=fullfile(OutputDir,'0_XML');
1803    if ~exist(DirXml,'dir')
1804        [~,msg1]=mkdir(DirXml);
[867]1805        if ~strcmp(msg1,'')
[1059]1806            errormsg=['cannot create ' DirXml ': ' msg1]; % error message for directory creation
[867]1807            return
1808        end
[1068]1809        [success,msg] = fileattrib(DirXml,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
1810        if success==0
1811            msgbox_uvmat('WARNING',{['unable to set group write access to ' DirXml ':']; msg}); % error message for directory creation
1812        end
[867]1813    end
[1059]1814    OutputNomType=nomtype2pair(Param.InputTable{1,4}); % nomenclature for output files
[867]1815   
[1059]1816    %% get the set of reference input field indices
1817    first_i=1; % first i index to process
1818    last_i=1; % last i index to process
1819    incr_i=1; % increment step in i index
1820    first_j=1; % first j index to process
1821    last_j=1; % last j index to process
1822    incr_j=1; % increment step in j index
1823    if isfield(Param.IndexRange,'first_i')
1824        first_i=Param.IndexRange.first_i;
1825        incr_i=Param.IndexRange.incr_i;
1826        last_i=Param.IndexRange.last_i;
1827    end
1828    if isfield(Param.IndexRange,'incr_j')
1829        first_j=Param.IndexRange.first_j;
1830        last_j=Param.IndexRange.last_j;
1831        incr_j=Param.IndexRange.incr_j;
1832    end
1833    if last_i < first_i || last_j < first_j
1834        errormsg= 'series/Run_Callback:last field index must be larger or equal to the first one';
[867]1835        return
1836    end
[1059]1837    %incr_i must be defined, =1 by default, if NbSlice is active
1838    if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice)
1839        incr_i=1;
1840        set(handles.num_incr_i,'String','1')
[867]1841    end
[1059]1842    % case of no increment i defined: processing is done on the available files found in i1_series
1843    if isempty(incr_i)
1844        if isempty(incr_j)
1845            [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1846            ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1847            ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1848            ref_j=ref_j-1;
1849            ref_i=ref_i-1;
1850        else
1851            ref_j=first_j:incr_j:last_j;
1852            [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1853            ref_i=ref_i-1;
1854            ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1855        end
1856        % increment i is defined: processing is done on first_i:incr_i:last_i;
[867]1857    else
[1059]1858        ref_i=first_i:incr_i:last_i;
1859        if isempty(incr_j)% automatic finding of the existing j indices
1860            [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1861            ref_j=ref_j-1;
1862            ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
[910]1863        else
[1059]1864            ref_j=first_j:incr_j:last_j;
[910]1865        end
[867]1866    end
[1059]1867    nbfield_j=numel(ref_j); % number of j indices
[1114]1868    BlockLength=numel(ref_i); % by default, job involves the full set of i field indicesNbProcess
[1059]1869    NbProcess=1;
[1114]1870    NbCore=1;
[1059]1871    switch RunMode
1872        case 'cluster'
[1114]1873            if (isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime) && isnumeric(Param.Action.CPUTime))
[1104]1874                CPUTime=Param.Action.CPUTime; % Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j
[1097]1875            else
[1104]1876                answer=msgbox_uvmat('INPUT_TXT','estimate the CPU time(in minutes) for each value of index i:' ,'');
1877                CPUTime=str2num(answer);
1878                set(handles.num_CPUTime,'String',answer)
1879                Param.Action.CPUTime=CPUTime;
[1097]1880            end
[1059]1881            JobNumberMax=SeriesData.SeriesParam.ClusterParam.JobNumberMax;
1882            JobCPUTimeAdvised=SeriesData.SeriesParam.ClusterParam.JobCPUTimeAdvised;
1883            if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined
1884                BlockLength= ceil(JobCPUTimeAdvised/(CPUTime*nbfield_j)); % iterations are grouped in sets with length BlockLength  such that the typical CPU time of a job is JobCPUTimeAdvised.
1885                BlockLength=max(BlockLength,ceil(numel(ref_i)*NbExp/JobNumberMax)); % possibly increase the BlockLength to have less than MaxJobNumber jobs
1886                NbProcess=ceil(numel(ref_i)/BlockLength) ; % nbre of processes sent to oar
1887            else
1888                NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1889            end
[1114]1890
1891            %         %proposed number of cores to reserve in the cluster
1892            NbCoreAdvised=SeriesData.SeriesParam.ClusterParam.NbCoreAdvised;
1893            NbCoreMax=min(NbProcess,SeriesData.SeriesParam.ClusterParam.NbCoreMax);% reduces the number of cores if it exceeds the number of processes
1894            if NbCoreMax~=1
1895                if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1896                    warning_string=', preferably use .sh option to save Matlab licences';
1897                else
1898                    warning_string=')';
1899                end
1900                answer=msgbox_uvmat('INPUT_TXT',['Number of cores (max ' num2str(NbCoreMax) ', ' warning_string],num2str(NbCoreAdvised));
1901                if isempty(answer)
1902                    errormsg='Action launch interrupted by user';
1903                    return
1904                end
1905                NbCore=str2double(answer);
1906                if NbCore > NbCoreMax
1907                    NbCore=NbCoreMax;
1908                end
1909            end
[1059]1910        otherwise
1911            if ~isempty(Param.IndexRange.NbSlice)
1912                NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1913            end
1914    end
[1114]1915
[1059]1916    %% record nbre of output files and starting time for computation for status
1917    StatusData=get(handles.status,'UserData');
1918    if isfield(StatusData,'OutputFileMode')
1919        switch StatusData.OutputFileMode
1920            case 'NbInput'
1921                StatusData.NbOutputFile=numel(ref_i)*nbfield_j;
1922            case 'NbInput_i'
1923                StatusData.NbOutputFile=numel(ref_i);
1924            case 'NbSlice'
1925                StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
[917]1926        end
[918]1927    end
[1059]1928    StatusData.TimeStart=now;
1929    set(handles.status,'UserData',StatusData)
[1114]1930
[1059]1931    %% case of a function in Python
1932    if strcmp(ActionExt, '.py (in dev.)')
1933        fprintf([
1934            '\n' ...
1935            '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ...
1936            'The option .py is used. It is still in development.\n' ...
1937            'To try it, first install pyper and the most recent version of fluidimage\n' ...
1938            '(see https://bitbucket.org/fluiddyn/fluidimage).\n' ...
1939            'Warning: there is no direct correspondance between UVMAT and fluidimage parameters\n' ...
1940            '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n'])
1941        RunMode = 'python';
[918]1942    end
1943   
[1059]1944   
1945    %% direct processing on the current Matlab session or creation of command files
1946    filexml=cell(1,NbProcess); % initialisation of the names of the files containing the processing parameters
1947    extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process
1948    for iprocess=1:NbProcess
1949        extxml{iprocess}='.xml';
1950    end
1951    for iprocess=1:NbProcess
1952        if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1953            disp('program stopped by user')
1954            return
1955        end
[1091]1956        Param.IndexRange.incr_slice=incr_i;
[1059]1957        if isempty(Param.IndexRange.NbSlice)
1958            Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1959            if Param.IndexRange.first_i>last_i
1960                NbProcess=iprocess-1; % leave the loop, we are at the end of the calculation
1961                break
[919]1962            end
[1059]1963            Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
1964        else %multislices (then incr_i is not empty)
1965            Param.IndexRange.first_i= first_i+iprocess-1;
[1091]1966            Param.IndexRange.incr_slice=incr_i*Param.IndexRange.NbSlice;
[919]1967        end
[1059]1968        for ilist=1:size(Param.InputTable,1)
1969            Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/'); % correct path name for PCWIN system
1970        end
1971       
1972        if isfield(Param,'OutputSubDir')
1973            t=struct2xml(Param);
1974            t=set(t,1,'name','Series');
1975            extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,...
1976                Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1977            filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess});
1978            try
1979                save(t, filexml{iprocess}); % save the xml file containing the processing parameters
1980            catch ME
1981                if ~strcmp (RunMode,'local')
1982                    errormsg=['error writting ' filexml{iprocess} ': ' ME.message];
1983                    return
[867]1984                end
[1059]1985            end
[867]1986        end
[1059]1987        if strcmp (RunMode,'local')
1988            switch ActionExt
1989                case '.m'
1990                    h_fun(Param); % direct launching
1991                   
1992                case '.sh'
1993                    switch computer
1994                        case {'PCWIN','PCWIN64'} %Windows system
1995                            filexml=regexprep(filexml,'\\','\\\\'); % add '\' so that '\' are left as characters
1996                            system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); % TODO: adapt to DOS system
1997                        case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1998                            system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]);
1999                    end
2000            end
[867]2001        end
2002    end
[1059]2003   
2004    if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python')
2005        %% processing on a different session of the same computer (background) or cluster, create executable files
2006        batch_file_list=cell(NbProcess,1); % initiate the list of executable files
2007        DirExe=fullfile(OutputDir,'0_EXE'); % directory name for executable files
2008        switch computer
2009            case {'PCWIN','PCWIN64'} %Windows system
2010                ExeExt='.bat';
2011            case {'GLNX86','GLNXA64','MACI64'}%Linux  system
2012                ExeExt='.sh';
[867]2013        end
[1059]2014        %create subdirectory for executable files
2015        if ~exist(DirExe,'dir')
2016            [tild,msg1]=mkdir(DirExe);
2017            if ~strcmp(msg1,'')
2018                errormsg=['cannot create ' DirExe ': ' msg1]; % error message for directory creation
2019                return
2020            end
[1068]2021            [success,msg] = fileattrib(DirExe,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2022            if success==0
2023                msgbox_uvmat('WARNING',{['unable to set group write access to ' DirExe ':']; msg}); % error message for directory creation
2024            end
[1059]2025        end
2026        %create subdirectory for log files
2027        DirLog=fullfile(OutputDir,'0_LOG');
2028        if ~exist(DirLog,'dir')
2029            [tild,msg1]=mkdir(DirLog);
2030            if ~strcmp(msg1,'')
2031                errormsg=['cannot create ' DirLog ': ' msg1]; % error message for directory creation
2032                return
2033            end
[1068]2034            [success,msg] = fileattrib(DirLog,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2035            if success==0
2036                msgbox_uvmat('WARNING',{['unable to set group write access to ' DirLog ':']; msg}); % error message for directory creation
2037            end
[1059]2038        end
2039       
2040        %create the executable file
2041        file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,...
2042            first_i,last_i,first_j,last_j);
2043        file_exe_global=fullfile(OutputDir,'0_EXE',file_exe_global);
2044        filelog_global=fullfile_uvmat('','',Param.InputTable{1,3},'.log',OutputNomType,...
2045            first_i,last_i,first_j,last_j);
2046        filelog_global=fullfile(OutputDir,'0_LOG',filelog_global);
2047       
2048        for iprocess=1:NbProcess
2049            %create the executable file
2050            batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt));
2051           
2052            % set the log file name
2053            filelog{iprocess}=fullfile(OutputDir,'0_LOG',regexprep(extxml{iprocess},'.xml$','.log'));
2054        end
[867]2055    end
[932]2056   
[1059]2057    %% launch the executable files for background or cluster processing
2058   
2059    switch RunMode
[918]2060       
[1059]2061        case 'background'
2062            [fid,message]=fopen(file_exe_global,'w');
2063            if isequal(fid,-1)
2064                errormsg=['creation of ' file_exe_global ':' message];
2065                return
2066            end
2067            switch ActionExt
2068                case '.m'% Matlab function
[918]2069                    switch computer
2070                        case {'GLNX86','GLNXA64','MACI64'}
[1059]2071                            matlab_ver = ver('MATLAB');
2072                            matlab_version = matlab_ver.Version;
2073                            cmd=[...
2074                                '#!/bin/bash\n'...
2075                                'source /etc/profile\n'...
2076                                'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
2077                                'time_start=$(date +%%s)\n'...
2078                                'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog_global ''' <<END_MATLAB\n'...
2079                                'addpath(''' path_series ''');\n'...
2080                                'addpath(''' Param.Action.ActionPath ''');\n'];
2081                            for iprocess=1:NbProcess
2082                                cmd=[cmd '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'];
[918]2083                            end
[1059]2084                            cmd=[cmd  'exit\n' 'END_MATLAB\n'...
2085                                'time_end=$(date +%%s)\n'...
2086                                'echo "global time = " $(($time_end - $time_start)) >> ''' filelog_global '''\n'];
[992]2087                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
[1059]2088                            fclose(fid); % close the executable filefilelog_global
2089                            system(['chmod +x ' file_exe_global]); % set the file to executable
2090                        case {'PCWIN','PCWIN64'}
2091                            cmd=['matlab -automation -logfile ' regexprep(filelog{iprocess},'\\','\\\\')...
2092                                ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
2093                                'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');'];
2094                            for iprocess=1:NbProcess
2095                                cmd=[cmd '' Param.Action.ActionName  '( ''' regexprep(filexml{iprocess},'\\','\\\\') ''');']
2096                            end
2097                            cmd=[cmd ';exit"'];
2098                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
[992]2099                            fclose(fid); % close the executable file
[918]2100                    end
[1059]2101                    system([file_exe_global ' &'])% directly execute the command file
2102                case '.sh' % compiled Matlab function
2103                    for iprocess=1:NbProcess
2104                        switch computer
2105                            case {'GLNX86','GLNXA64','MACI64'}
2106                                [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
2107                                if isequal(fid,-1)
2108                                    errormsg=['creation of .bat file: ' message];
2109                                    return
2110                                end
2111                                cmd=['#!/bin/bash \n '...
2112                                    '#$ -cwd \n '...
2113                                    'hostname && date \n '...
2114                                    'umask 002 \n'...
2115                                    ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
2116                                fprintf(fid,cmd); % fill the executable file with the  char string cmd
2117                                fclose(fid); % close the executable file
2118                                system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
2119                                system([batch_file_list{iprocess} ' &'])% directly execute the command file
2120                            case {'PCWIN','PCWIN64'}
2121                                msgbox_uvmat('ERROR','option for compiled Matlab functions not implemented for Windows system')
2122                                return
2123                        end
2124                    end
2125                    msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched in background for ' ExpName ': press STATUS to see results'])
2126            end
2127           
2128        case 'cluster' % option 'oar-parexec' used
2129            %create subdirectory for oar commands
2130            for iprocess=1:NbProcess
2131                [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
2132                if isequal(fid,-1)
2133                    errormsg=['creation of .bat file: ' message];
2134                    return
[867]2135                end
[1059]2136                if  strcmp(ActionExt,'.sh')
2137                    cmd=['#!/bin/bash \n '...
2138                        '#$ -cwd \n '...
2139                        'hostname && date \n '...
2140                        'umask 002 \n'...
2141                        ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
2142                else
2143                    matlab_ver = ver('MATLAB');
2144                    matlab_version = matlab_ver.Version;
2145                    cmd=[...
2146                        '#!/bin/bash\n'...
2147                        'source /etc/profile\n'...
2148                        'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
2149                        'matlab -nodisplay -nosplash -nojvm -singleCompThread -logfile ''' filelog{iprocess} ''' <<END_MATLAB\n'...
2150                        'addpath(''' path_series ''');\n'...
2151                        'addpath(''' Param.Action.ActionPath ''');\n'...
2152                        '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'...
2153                        'exit\n'...
2154                        'END_MATLAB\n'];
2155                end
2156                fprintf(fid,cmd); % fill the executable file with the  char string cmd
2157                fclose(fid); % close the executable file
2158                system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
[918]2159            end
[1059]2160            DIR_CLUSTER=fullfile(OutputDir,'0_CLUSTER');
2161            if exist(DIR_CLUSTER,'dir')% delete the content of the dir 0_LOG to allow new input
2162                curdir=pwd;
2163                cd(DIR_CLUSTER)
2164                delete('*')
2165                cd(curdir)
[918]2166            else
[1059]2167                [tild,msg1]=mkdir(DIR_CLUSTER);
2168                if ~strcmp(msg1,'')
2169                    errormsg=['cannot create ' DIR_CLUSTER ': ' msg1]; % error message for directory creation
2170                    return
2171                end
[918]2172            end
[1059]2173            % create file containing the list of jobs
2174            ListProcess=fullfile(DIR_CLUSTER,'job_list.txt'); % name of the file containing the list of executables
[1085]2175            [fid,errormsg]=fopen(ListProcess,'w'); % open it for writting
2176            if isempty(errormsg)
[1059]2177            for iprocess=1:length(batch_file_list)
2178                fprintf(fid,[batch_file_list{iprocess} '\n']); % write list of exe files
[918]2179            end
[1059]2180            fclose(fid);
2181            system(['chmod +x ' ListProcess]); % set the file to executable
[1085]2182            else
2183                errormsg=['error for writting the executable file:' errormsg];
2184            end       
[1059]2185            CPUTimeProcess=CPUTime*BlockLength*nbfield_j; % estimated CPU time for one individual process (in minutes)
2186            LaunchCmdFcn=SeriesData.SeriesParam.ClusterParam.LaunchCmdFcn;
2187            oar_command=feval(LaunchCmdFcn,ListProcess,ActionFullName,DirLog,NbProcess, NbCore,CPUTimeProcess)
2188            [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window
2189            filename_oarcommand=fullfile(DIR_CLUSTER,'0_cluster_command'); % keep track of the command in file '0-OAR/0_cluster_command'
[1096]2190            [fid,errormsg]=fopen(filename_oarcommand,'w');
2191            if ~isempty(errormsg)
2192                msgbox_uvmat('ERROR',['cannot create ' filename_oarcommand ': ' errormsg])
2193                return
2194            end
[1059]2195            fprintf(fid,oar_command); % store the command
2196            fprintf(fid,result); % store the result (job ID number)
2197            fclose(fid);
2198            if status==0
[1068]2199                msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched for ' ExpName ' as ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
[1059]2200            else
[1068]2201                msgbox_uvmat('ERROR',result)
[984]2202            end
[1059]2203            %     case 'cluster_pbs' % for LMFA Kepler machine:  trqnsferred to fct
2204           
2205            %         %create subdirectory for pbs command and log files
2206            %         DirPBS=fullfile(OutputDir,'0_PBS'); % todo : common name OAR/PBS
2207            %         if exist(DirPBS,'dir')% delete the content of the dir 0_LOG to allow new input
2208            %             curdir=pwd;
2209            %             cd(DirPBS)
2210            %             delete('*')
2211            %             cd(curdir)
2212            %         else
2213            %             [tild,msg1]=mkdir(DirPBS);
2214            %             if ~strcmp(msg1,'')
2215            %                 errormsg=['cannot create ' DirPBS ': ' msg1]; % error message for directory creation
2216            %                 return
2217            %             end
2218            %         end
2219            %         max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h)
2220            %         walltime_onejob=1800; % seconds, max estimated time for asingle file index value
2221            %         ListProcess=fullfile(DirPBS,'job_list.txt'); % create name of the global executable file
2222            %         fid=fopen(ListProcess,'w');
2223            %         for iprocess=1:length(batch_file_list)
2224            %             fprintf(fid,[batch_file_list{iprocess} '\n']); % list of exe files
2225            %         end
2226            %         fclose(fid);
2227            %         system(['chmod +x ' ListProcess]); % set the file to executable
2228            %         pbs_command=['qsub -n CIVX '...
2229            %             '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
2230            %             '-l /core=' num2str(NbCore) ','...
2231            %             'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
2232            %             '-E ' regexprep(ListProcess,'\.txt\>','.stderr') ' '...
2233            %             '-O ' regexprep(ListProcess,'\.txt\>','.log') ' '...
2234            %             extra_qstat ' '...
2235            %             '"oar-parexec -s -f ' ListProcess ' '...
2236            %             '-l ' ListProcess '.log"'];
2237            %         filename_oarcommand=fullfile(DirPBS,'pbs_command');
2238            %         fid=fopen(filename_oarcommand,'w');
2239            %         fprintf(fid,pbs_command);
2240            %         fclose(fid);
2241            %         fprintf(pbs_command); % display in command line
2242            %         %system(pbs_command);
2243            %         msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster'])
2244           
2245        case 'cluster_sge' % for PSMN % TODO: use the standard 'cluster' config with an external fct
2246            % Au PSMN, on ne cr??e pas 1 job avec plusieurs c??urs, mais N jobs de 1 c??urs
2247            % o?? N < 1000.
2248            %create subdirectory for pbs command and log files
2249           
2250            DirSGE=fullfile(OutputDir,'0_SGE');
2251            if exist(DirSGE,'dir')% delete the content of the dir 0_LOG to allow new input
2252                curdir=pwd;
2253                cd(DirSGE)
2254                delete('*')
2255                cd(curdir)
2256            else
2257                [tild,msg1]=mkdir(DirSGE);
2258                if ~strcmp(msg1,'')
2259                    errormsg=['cannot create ' DirSGE ': ' msg1]; % error message for directory creation
2260                    return
2261                end
[984]2262            end
[1059]2263            maxImgsPerJob = ceil(length(batch_file_list)/NbCore);
2264            disp(['Max number of jobs: ' num2str(NbCore)])
2265            disp(['Images per job: ' num2str(maxImgsPerJob)])
2266           
2267            iprocess = 1;
2268            imgsInJob = [];
2269            currJobIndex = 1;
2270            done = 0;
2271            while(~done)
2272                if(iprocess <= length(batch_file_list))
2273                    imgsInJob = [imgsInJob, iprocess];
[984]2274                end
[1059]2275                if((numel(imgsInJob) >= maxImgsPerJob) || (iprocess == length(batch_file_list)))
2276                    cmd=['#!/bin/sh \n'...
2277                        '#$ -cwd \n'...
2278                        'hostname && date\n']
2279                    for ii=1:numel(imgsInJob)
2280                        cmd=[cmd ActionFullName ' /softs/matlab ' filexml{imgsInJob(ii)} '\n'];
2281                    end
2282                    [fid, message] = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w');
2283                    fprintf(fid, cmd);
2284                    fclose(fid);
2285                    system(['chmod +x ' DirSGE '/job' num2str(currJobIndex) '.sh'])
2286                    sge_command=['qsub -N civ_' num2str(currJobIndex) ' '...
2287                        '-q ' qstat_Queue ' '...
2288                        '-e ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2289                        '-o ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2290                        fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])];
2291                    fprintf(sge_command); % display in command line
2292                    [status, result] = system(sge_command);
2293                    fprintf(result);
2294                    currJobIndex = currJobIndex + 1;
2295                    imgsInJob = [];
2296                end
2297                if(iprocess == length(batch_file_list))
2298                    done = 1;
2299                end
2300                iprocess = iprocess + 1;
[984]2301            end
[1059]2302            msgbox_uvmat('CONFIRMATION',[num2str(currJobIndex-1) ' jobs launched on queue ' qstat_Queue '.'])
2303        case 'python'
2304            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))") ' ...
2305                'python -m fluidimage.run_from_xml ' filexml{iprocess}];
2306            fprintf(['command:\n' command '\n\n'])
2307            system(command, '-echo');
2308    end
2309    if exist(OutputDir,'dir')
2310        [SUCCESS,MESSAGE,MESSAGEID] = fileattrib (OutputDir);
2311        if MESSAGE.GroupWrite~=1
2312            [success,msg] = fileattrib(OutputDir,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2313            if success==0
2314                msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg}); % error message for directory creation
[984]2315            end
2316        end
[932]2317    end
2318end
[1068]2319set(handles.Replicate,'BackgroundColor',[0 1 0])
[1070]2320
[867]2321%------------------------------------------------------------------------
2322function STOP_Callback(hObject, eventdata, handles)
2323%------------------------------------------------------------------------
2324set(handles.RUN, 'BusyAction','cancel')
2325set(handles.RUN,'BackgroundColor',[1 0 0])
2326set(handles.RUN,'enable','on')
2327set(handles.RUN, 'Value',0)
2328
2329%------------------------------------------------------------------------
2330% --- read parameters from the GUI series
2331%------------------------------------------------------------------------
2332function Param=read_GUI_series(handles)
2333
2334%% read raw parameters from the GUI series
2335Param=read_GUI(handles.series);
2336
[1068]2337%% clean the output structure by removing unused information
[867]2338if isfield(Param,'Pairs')
[992]2339    Param=rmfield(Param,'Pairs'); % info Pairs not needed for output
[867]2340end
2341if isfield(Param,'InputLine')
2342    Param=rmfield(Param,'InputLine');
2343end
2344if isfield(Param,'EditObject')
2345    Param=rmfield(Param,'EditObject');
2346end
2347Param.IndexRange.TimeSource=Param.IndexRange.TimeTable{end,1};
2348Param.IndexRange=rmfield(Param.IndexRange,'TimeTable');
2349empty_line=false(size(Param.InputTable,1),1);
2350for iline=1:size(Param.InputTable,1)
2351    empty_line(iline)=isempty(cell2mat(Param.InputTable(iline,1:3)));
2352end
2353Param.InputTable(empty_line,:)=[];
2354
2355%------------------------------------------------------------------------
2356% --- Executes on selection change in ActionName.
[1033]2357function ActionName_Callback(hObject, ActionPath, handles)
[867]2358%------------------------------------------------------------------------
2359
2360%% stop any ongoing series processing
2361if isequal(get(handles.RUN,'Value'),1)
2362    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
2363    if strcmp(answer,'Yes')
[1033]2364        STOP_Callback(hObject, [], handles)
[867]2365    else
2366        return
2367    end
2368end
2369set(handles.ActionName,'BackgroundColor',[1 1 0])
2370huigetfile=findobj(allchild(0),'tag','status_display');
2371if ~isempty(huigetfile)
2372    delete(huigetfile)
2373end
2374drawnow
2375
2376%% get Action name and path
[992]2377NbBuiltinAction=get(handles.Action,'UserData'); % nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
2378ActionList=get(handles.ActionName,'String'); % list menu fields
[867]2379ActionIndex=get(handles.ActionName,'Value');
[1068]2380if ~isequal(ActionIndex,1)% if we are not just opening series
[867]2381    InputTable=get(handles.InputTable,'Data');
2382    if isempty(InputTable{1,4})
2383        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
2384        return
2385    end
2386end
2387ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
[992]2388ActionPathList=get(handles.ActionName,'UserData'); % list of recorded paths to functions of the list ActionName
[867]2389
2390%% add a new function to the menu if 'more...' has been selected in the menu ActionName
2391if isequal(ActionName,'more...')
[1040]2392    if ~ischar(ActionPath)
[1033]2393        ActionPath=get(handles.ActionPath,'String');
2394    end
[867]2395    [FileName, PathName] = uigetfile( ...
2396        {'*.m', ' (*.m)';
2397        '*.m',  '.m files '; ...
2398        '*.*', 'All Files (*.*)'}, ...
[1033]2399        'Pick a series processing function ',ActionPath);
[867]2400    if length(FileName)<2
2401        return
2402    end
2403    [tild,ActionName,ActionExt]=fileparts(FileName);
2404   
2405    % insert the choice in the menu ActionName
[992]2406    ActionIndex=find(strcmp(ActionName,ActionList),1); % look for the selected function in the menu Action
[867]2407    PathName=regexprep(PathName,'/$','');
2408    if ~isempty(ActionIndex) && ~strcmp(ActionPathList{ActionIndex},PathName)%compare the path to the existing fct
2409        ActionIndex=[]; % the selected path is different than the recorded one
2410    end
2411    if isempty(ActionIndex)%the qselected fct (with selected path) does not exist in the menu
2412        ActionIndex= length(ActionList);
[992]2413        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)]; % the selected function is appended in the menu, before the last item 'more...'
[867]2414         ActionPathList=[ActionPathList; PathName];
2415    end
2416   
2417    % record the file extension and extend the path list if it is a new extension
[886]2418    ActionExtList=get(handles.ActionExt,'String');
2419    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
2420    if isempty(ActionExtIndex)
2421        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
2422    end
[867]2423
2424    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
[992]2425    if length(ActionList)>NbBuiltinAction+5; % nb_builtin_ACTION=nbre of functions always remaining in the initial menu
[867]2426        nbremove=length(ActionList)-NbBuiltinAction-5;
2427        ActionList(NbBuiltinAction+1:end-5)=[];
2428        ActionPathList(NbBuiltinAction+1:end-4,:)=[];
2429        ActionIndex=ActionIndex-nbremove;
2430    end
2431   
2432    % record action menu, choice and path
2433    set(handles.ActionName,'Value',ActionIndex)
2434    set(handles.ActionName,'String',ActionList)
2435       set(handles.ActionName,'UserData',ActionPathList);
2436    set(handles.ActionExt,'Value',ActionExtIndex)
2437       
2438    %record the user defined menu additions in personal file profil_perso
2439    dir_perso=prefdir;
2440    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2441    if NbBuiltinAction+1<=numel(ActionList)-1
2442        ActionListUser=ActionList(NbBuiltinAction+1:numel(ActionList)-1);
2443        ActionPathListUser=ActionPathList(NbBuiltinAction+1:numel(ActionList)-1);
[886]2444        ActionExtListUser={};
2445        if numel(ActionExtList)>2
2446            ActionExtListUser=ActionExtList(3:end);
2447        end
[867]2448        if exist(profil_perso,'file')
2449            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
2450        else
2451            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
2452        end
2453    end
2454end
2455
2456%% check the current ActionPath to the selected function
[992]2457ActionPath=ActionPathList{ActionIndex}; % current recorded path
2458set(handles.ActionPath,'String',ActionPath); % show the path to the senlected function
[867]2459
2460%% reinitialise the waitbar
2461update_waitbar(handles.Waitbar,0)
2462
[996]2463%% Put the first line of the selected Action fct as tooltip help
2464try
2465    [fid,errormsg] =fopen([ActionName '.m']);
2466    InputText=textscan(fid,'%s',1,'delimiter','\n');
2467    fclose(fid);
2468    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
2469end
2470set(handles.ActionName,'BackgroundColor',[1 1 1])
2471set(handles.ActionInput,'BackgroundColor',[1 0 1])% set ActionInput button to magenta color to indicate that input refr
[1097]2472set(handles.num_CPUTime,'String','')
[996]2473
2474% --- Executes on button press in ActionInput.
2475function ActionInput_Callback(hObject, eventdata, handles)
2476
2477set(handles.ActionInput,'BackgroundColor',[1 1 0])
[1068]2478SeriesData=get(handles.series,'UserData'); % info on the input file series
[996]2479
[867]2480%% create the function handle for Action
[996]2481ActionPath=get(handles.ActionPath,'String');
2482ActionList=get(handles.ActionName,'String');
2483ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
[897]2484if ~exist(ActionPath,'dir')
[1033]2485    ActionName_Callback(handles.ActionName, ActionPath, handles)% update the function
[897]2486    return
[867]2487end
[992]2488current_dir=pwd; % current working dir
[897]2489cd(ActionPath)
[1114]2490h_fun=str2func(ActionName);% create the function handle for the function ActionName
[897]2491cd(current_dir)
[867]2492
2493%% Activate the Action fct to adapt the configuration of the GUI series and bring specific parameters in SeriesData
[992]2494Param=read_GUI_series(handles); % read the parameters from the GUI series
[997]2495Param.Action.RUN=0;
[1068]2496Param.SeriesData=SeriesData;
[992]2497ParamOut=h_fun(Param); % run the selected Action function to get the relevant input
[867]2498
2499
2500%% Visibility of VelType and VelType_1 menus asked by ActionName
[992]2501VelTypeRequest=1; % VelType requested by default
2502VelTypeRequest_1=1; % VelType requested by default
[867]2503if isfield(ParamOut,'VelType')
2504    VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'});
2505    VelTypeRequest_1=strcmp( ParamOut.VelType,'two');
2506end
2507FieldNameRequest=0;  %hidden by default
2508FieldNameRequest_1=0;  %hidden by default
2509if isfield(ParamOut,'FieldName')
2510    FieldNameRequest=ismember(ParamOut.FieldName,{'on','one','two'});
2511    FieldNameRequest_1=strcmp( ParamOut.FieldName,'two');
2512end
2513
2514%% Detect the types of input files and set menus and default options in 'VelType'
[1100]2515if ~isfield(SeriesData,'FileType')
2516    SeriesData.FileType={'none'};
2517end
2518iview_civ=find( strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));
[992]2519iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)); % all nc files, icluding civ
2520FieldList=get(handles.FieldName,'String'); % previous list as default
[867]2521if ~iscell(FieldList),FieldList={FieldList};end
[992]2522FieldList_1=get(handles.FieldName_1,'String'); % previous list as default
[867]2523if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
[992]2524CheckList_1=1; % indicate whether FieldName_1 has been updated
[867]2525handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title];
[954]2526if VelTypeRequest && numel(iview_civ)>=1
[867]2527    menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)});
2528    set(handles.VelType,'Value',1)% set first choice by default
2529    set(handles.VelType,'String',[{'*'};menu])
2530    set(handles.VelType,'Visible','on')
2531    set(handles.VelType_title,'Visible','on')
[1030]2532    FieldList=set_field_list('U','V'); % standard menu for civx data
[1051]2533    if max(get(handles.FieldName,'Value'))>numel(FieldList)
[1090]2534        set(handles.FieldName,'Value',1); % velocity vector choice by default
[1051]2535    end
[954]2536    if  VelTypeRequest_1 && numel(iview_civ)>=2
[867]2537        menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});
2538        set(handles.VelType_1,'Value',1)% set first choice by default
2539        set(handles.VelType_1,'String',[{'*'};menu])
2540        set(handles.VelType_1,'Visible','on')
2541        set(handles.VelType_title_1,'Visible','on')
[1078]2542        FieldList_1=[set_field_list('U','V');{'C'};{'add_field...'}]; % standard menu for civx data
[867]2543        CheckList_1=1;
[992]2544        set(handles.FieldName_1,'Value',1); % velocity vector choice by default
[867]2545    else
2546        set(handles.VelType_1,'Visible','off')
2547        set(handles.VelType_title_1,'Visible','off')
2548    end
2549else
2550    set(handles.VelType,'Visible','off')
2551    set(handles.VelType_title,'Visible','off')
[954]2552end
[867]2553
2554%% Detect the types of input files and set menus and default options in 'FieldName'
[940]2555if (FieldNameRequest || VelTypeRequest) && numel(iview_netcdf)>=1
[954]2556    set(handles.InputFields,'Visible','on')% set the frame InputFields visible
[940]2557    if FieldNameRequest && isfield(SeriesData.FileInfo{iview_netcdf(1)},'ListVarName')
2558        set(handles.FieldName,'Visible','on')
[1078]2559        set(handles.Field_text,'Visible','on')
[867]2560        ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName;
[992]2561        ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
[867]2562        for ilist=1:numel(ind_var)
2563            if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
[992]2564                FieldList={}; % previous choice not consistent with new input field
[867]2565                set(handles.FieldName,'Value',1)
2566                break
2567            end
2568        end
2569        if ~isempty(FieldList)
2570            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2571                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2572                FieldList={};
2573                set(handles.Coord_x,'String','')
2574                set(handles.Coord_y,'String','')
2575            end
2576            Coord_z=get(handles.Coord_z,'String');
[1108]2577            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))REFRESH
[867]2578                FieldList={};
2579                set(handles.Coord_z,'String','')
2580            end
2581        end
[984]2582    else
2583        set(handles.FieldName,'Visible','off')
[1078]2584        set(handles.Field_text,'Visible','off')
[954]2585    end
2586   
2587    set(handles_coord,'Visible','on')
[1078]2588    if isempty(find(strcmp('add_field...',FieldList)))
[1090]2589        FieldList=[FieldList;{'add_field...'}];%add 'add_field...' to the menu FieldName if it is not already
[1030]2590    end
[954]2591    if FieldNameRequest_1 && numel(iview_netcdf)>=2
2592        set(handles.FieldName_1,'Visible','on')
2593        if CheckList_1==0        % not civ input made
2594            ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName;
[992]2595            ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
[954]2596            for ilist=1:numel(ind_var)
2597                if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
[992]2598                    FieldList_1={}; % previous choice not consistent with new input field
[954]2599                    set(handles.FieldName_1,'Value',1)
2600                    break
[867]2601                end
2602            end
[954]2603            warn_coord=0;
2604            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2605                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2606                warn_coord=1;
2607            end
2608            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2609                FieldList_1={};
2610                warn_coord=1;
2611            end
2612            if warn_coord
[984]2613                msgbox_uvmat('WARNING','coordinate names do not exist in the second netcdf input file')
[954]2614            end
2615           
2616            set(handles.FieldName_1,'Visible','on')
2617            set(handles.FieldName_1,'Value',1)
2618            set(handles.FieldName_1,'String',FieldList_1)
[867]2619        end
[940]2620    else
[954]2621        set(handles.FieldName_1,'Visible','off')
2622    end
2623    if isempty(FieldList)
[1078]2624        set(handles.Field_text,'Visible','off')
[940]2625        set(handles.FieldName,'Visible','off')
[954]2626    else
[1078]2627        set(handles.Field_text,'Visible','on')
[954]2628        set(handles.FieldName,'Visible','on')
2629        set(handles.FieldName,'String',FieldList)
[940]2630    end
[867]2631else
2632    set(handles.InputFields,'Visible','off')
2633end
2634
[904]2635%% Introduce visibility of file overwrite option
2636if isfield(ParamOut,'CheckOverwriteVisible')&& strcmp(ParamOut.CheckOverwriteVisible,'on')
2637    set(handles.CheckOverwrite,'Visible','on')
2638else
2639    set(handles.CheckOverwrite,'Visible','off')
2640end
[867]2641
2642%% Check whether alphabetical sorting of input Subdir is allowed by the Action fct  (for multiples series entries)
2643if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Param.InputTable,1)>1
[1008]2644    [tild,iview]=sort(Param.InputTable(:,2)); % subdirectories sorted in alphabetical order
2645    set(handles.InputTable,'Data',Param.InputTable(iview,:));
[867]2646    MinIndex_i=get(handles.MinIndex_i,'Data');
2647    MinIndex_j=get(handles.MinIndex_j,'Data');
2648    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2649    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2650    set(handles.MinIndex_i,'Data',MinIndex_i(iview,:));
2651    set(handles.MinIndex_j,'Data',MinIndex_j(iview,:));
2652    set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:));
[1090]2653    set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));
[867]2654    TimeTable=get(handles.TimeTable,'Data');
[1068]2655    if size(TimeTable,1)<size(Param.InputTable,1)%if the time table is not complete, copy the missing lines from the previous ones
2656        for iline=size(TimeTable,1)+1:size(Param.InputTable,1)
2657            TimeTable(iline,:)=TimeTable(iline-1,:);
2658        end
2659    end
2660    set(handles.TimeTable,'Data',TimeTable(iview,:));% sort the time tables
[867]2661    PairString=get(handles.PairString,'Data');
2662    set(handles.PairString,'Data',PairString(iview,:));
2663end
2664
2665%% Impose the whole input file index range if requested
2666if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on')
2667    MinIndex_i=get(handles.MinIndex_i,'Data');
2668    MinIndex_j=get(handles.MinIndex_j,'Data');
2669    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2670    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2671    set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line)
2672    set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line)
2673    set(handles.num_incr_i,'String','1')
2674    set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line)
2675    set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line)
2676    set(handles.num_incr_j,'String','1')
2677else  % check index ranges
2678    first_i=1;last_i=1;first_j=1;last_j=1;
2679    if isfield(Param.IndexRange,'first_i')
2680        first_i=Param.IndexRange.first_i;
2681        last_i=Param.IndexRange.last_i;
2682    end
2683    if isfield(Param.IndexRange,'first_j')
2684        first_j=Param.IndexRange.first_j;
2685        last_j=Param.IndexRange.last_j;
2686    end
2687    if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
[1097]2688            set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end
[867]2689end
2690
2691%% enable or desable j index visibility
[992]2692status_j='on'; % default
[1100]2693if isfield(SeriesData,'j1_series') && isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)) % case of empty j indices
[867]2694    status_j='off'; % no j index needed
2695elseif strcmp(get(handles.PairString,'Visible'),'on')
[992]2696    check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j')); % =0 for burst case, 1 otherwise
[867]2697    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
2698        status_j='off'; % no j index needed for bust case
2699    end
2700end
2701enable_j(handles,status_j) % no j index needed
[994]2702if isfield(ParamOut,'j_index_1')&& isfield(ParamOut,'j_index_2')%strcmp(ParamOut.Desable_j_index,'on')
2703    %status_j='off';
2704    set(handles.num_first_j,'String',num2str(ParamOut.j_index_1))
2705    set(handles.num_last_j,'String',num2str(ParamOut.j_index_2))
2706    set(handles.num_first_j,'enable','off')
2707    set(handles.num_last_j,'enable','off')
2708    set(handles.num_incr_j,'visible','off')
2709else
2710    set(handles.num_first_j,'enable','on')
2711    set(handles.num_last_j,'enable','on')
2712    set(handles.num_incr_j,'visible',status_j)
2713end
[867]2714
2715%% NbSlice visibility
[897]2716if isfield(ParamOut,'NbSlice') && (strcmp(ParamOut.NbSlice,'on')||isnumeric(ParamOut.NbSlice))
2717    set(handles.num_NbSlice,'Visible','on')
2718    set(handles.NbSlice_title,'Visible','on')
[867]2719else
[897]2720    set(handles.num_NbSlice,'Visible','off')
2721    set(handles.NbSlice_title,'Visible','off')
[867]2722end
[997]2723if isfield(ParamOut,'NbSlice') && isnumeric(ParamOut.NbSlice)
[897]2724    set(handles.num_NbSlice,'String',num2str(ParamOut.NbSlice))
2725    set(handles.num_NbSlice,'Enable','off'); % NbSlice set by the activation of the Action function
2726else
2727    set(handles.num_NbSlice,'Enable','on'); % NbSlice can be modified on the GUI series
2728end
[867]2729
2730%% Visibility of FieldTransform menu
2731FieldTransformVisible='off';  %hidden by default
2732if isfield(ParamOut,'FieldTransform')
[1001]2733    if ~strcmp(ParamOut.FieldTransform,'off')
2734    FieldTransformVisible='on'; 
2735    end
2736    if iscell(ParamOut.FieldTransform)
2737        SeriesData.TransformList=ParamOut.FieldTransform;
2738    end
[867]2739    TransformName_Callback([],[], handles)
2740end
2741set(handles.FieldTransform,'Visible',FieldTransformVisible)
[1090]2742if isfield(ParamOut,'TransformPath')% record the path of transform function requested for compilation
[1001]2743    set(handles.TransformPath,'UserData',ParamOut.TransformPath)
[867]2744else
[1001]2745    set(handles.TransformPath,'UserData',[])
[867]2746end
2747
2748%% Visibility of projection object
2749ProjObjectVisible='off';  %hidden by default
2750if isfield(ParamOut,'ProjObject')
2751    ProjObjectVisible=ParamOut.ProjObject;
2752end
2753set(handles.CheckObject,'Visible',ProjObjectVisible)
2754if ~get(handles.CheckObject,'Value')
2755    ProjObjectVisible='off';
2756end
[1072]2757set(handles.ProjObjectName,'Visible',ProjObjectVisible)
[867]2758set(handles.DeleteObject,'Visible',ProjObjectVisible)
2759set(handles.ViewObject,'Visible',ProjObjectVisible)
2760set(handles.EditObject,'Visible',ProjObjectVisible)
2761
2762%% Visibility of mask input
2763MaskVisible='off';  %hidden by default
2764if isfield(ParamOut,'Mask')
2765    MaskVisible=ParamOut.Mask;
2766end
2767set(handles.CheckMask,'Visible',MaskVisible);
[1065]2768%% Setting of expected iteration time
2769if isfield(ParamOut,'CPUTime')
2770    set(handles.num_CPUTime,'String',num2str(ParamOut.CPUTime));
2771end
[867]2772
[1090]2773%% definition of the path for the output files
2774InputTable=get(handles.InputTable,'Data');
2775[OutputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
2776[OutputPath,Experiment,ExperimentExt]=fileparts(OutputPath);
2777set(handles.Device,'String',[Device DeviceExt])
2778set(handles.Device,'Visible','on')
2779set(handles.Device_title,'Visible','on')
2780set(handles.Experiment,'String',[Experiment ExperimentExt])
2781set(handles.Experiment,'Visible','on')
2782set(handles.Experiment_title,'Visible','on')
2783set(handles.Experiment_title,'Visible','on')
2784set(handles.OutputPath,'Visible','on')
2785set(handles.OutputPathBrowse,'Visible','on')
2786   
2787%% definition of the subdirectory containing the output files
2788
[867]2789if  ~(isfield(SeriesData,'ActionName') && strcmp(ActionName,SeriesData.ActionName))
[992]2790    OutputDirExt='.series'; % default
[867]2791    if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
2792        OutputDirExt=ParamOut.OutputDirExt;
2793    end
2794    set(handles.OutputDirExt,'String',OutputDirExt)
2795end
2796OutputDirVisible='off';
[992]2797OutputSubDirMode='auto'; % default
[867]2798SubDirOut='';
2799if isfield(ParamOut,'OutputSubDirMode')
2800    OutputSubDirMode=ParamOut.OutputSubDirMode;
2801end
2802switch OutputSubDirMode
[1090]2803    case 'auto' % default
[867]2804        OutputDirVisible='on';
[992]2805        SubDir=InputTable(1:end,2); % set of subdirectories
[867]2806        SubDirOut=SubDir{1};
2807        if numel(SubDir)>1
2808            for ilist=2:numel(SubDir)
2809                SubDirOut=[SubDirOut '-' regexprep(SubDir{ilist},'^/','')];
2810            end
2811        end
2812    case 'one'
2813        OutputDirVisible='on';
[992]2814        SubDirOut=InputTable{1,2}; % use the first subdir name (+OutputDirExt) as output  subdirectory
[867]2815    case 'two'
2816        OutputDirVisible='on';   
[992]2817        SubDir=InputTable(1:2,2); % set of subdirectories
[867]2818        SubDirOut=SubDir{1};
2819        if numel(SubDir)>1
2820                SubDirOut=[SubDirOut '-' regexprep(SubDir{2},'^/','')];
2821        end
2822    case 'last'
2823        OutputDirVisible='on';
[992]2824        SubDirOut=InputTable{end,2}; % use the last subdir name (+OutputDirExt) as output  subdirectory
[867]2825end
2826set(handles.OutputSubDir,'String',SubDirOut)
[883]2827set(handles.OutputSubDir,'BackgroundColor',[1 1 1])% set edit box to white color to indicate refreshment
[867]2828set(handles.OutputDirExt,'Visible',OutputDirVisible)
2829set(handles.OutputSubDir,'Visible',OutputDirVisible)
[1096]2830% set(handles.OutputDir_title,'Visible',OutputDirVisible)
[992]2831SeriesData.ActionName=ActionName; % record ActionName for next use
[867]2832
2833
2834%% visibility of the run mode (local or background or cluster)
2835if strcmp(OutputSubDirMode,'none')
[992]2836    RunModeVisible='off'; % only local mode available if no output file is produced
[867]2837else
2838    RunModeVisible='on';
2839end
2840set(handles.RunMode,'Visible',RunModeVisible)
2841set(handles.ActionExt,'Visible',RunModeVisible)
2842set(handles.RunMode_title,'Visible',RunModeVisible)
2843set(handles.ActionExt_title,'Visible',RunModeVisible)
2844
2845
2846%% Expected nbre of output files
2847if isfield(ParamOut,'OutputFileMode')
2848    StatusData.OutputFileMode=ParamOut.OutputFileMode;
2849    set(handles.status,'UserData',StatusData)
2850end
2851
2852%% definition of an additional parameter set, determined by an ancillary GUI
2853if isfield(ParamOut,'ActionInput')
[996]2854%     set(handles.ActionInput,'Visible','on')
[867]2855    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
2856    SeriesData.ActionInput=ParamOut.ActionInput;
2857else
[996]2858%     set(handles.ActionInput,'Visible','off')
[867]2859    if isfield(SeriesData,'ActionInput')
2860        SeriesData=rmfield(SeriesData,'ActionInput');
2861    end
2862end
2863set(handles.series,'UserData',SeriesData)
[996]2864set(handles.ActionInput,'BackgroundColor',[1 0 0])
[867]2865
[1078]2866
[867]2867%------------------------------------------------------------------------
[1078]2868% --- Executes on button press in RefreshField.
2869function RefreshField_Callback(hObject, eventdata, handles)
2870%------------------------------------------------------------------------
2871set(handles.FieldName,'String',{'add_field...'});
2872set(handles.FieldName,'Value',1);
2873FieldName_Callback(hObject, eventdata, handles)
2874
2875
2876%------------------------------------------------------------------------
[867]2877% --- Executes on selection change in FieldName.
2878function FieldName_Callback(hObject, eventdata, handles)
2879%------------------------------------------------------------------------
[1078]2880FieldListInit=get(handles.FieldName,'String');
[867]2881field_index=get(handles.FieldName,'Value');
[1078]2882field=FieldListInit{field_index(1)};
2883if isequal(field,'add_field...')
2884    FieldListInit(field_index(1))=[];
[867]2885    SeriesData=get(handles.series,'UserData');
2886    % input line for which the field choice is relevant
[992]2887    iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ
[867]2888    hget_field=findobj(allchild(0),'name','get_field');
2889    if ~isempty(hget_field)
2890        delete(hget_field)%delete opened versions of get_field
2891    end
2892    Param=read_GUI(handles.series);
2893    InputTable=Param.InputTable(iview,:);
2894    % check the existence of the first file in the series
[992]2895    first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1; % default setting for index j
[1078]2896    if isfield(Param.IndexRange,'first_j') % if index j is used     
[867]2897        first_j=Param.IndexRange.first_j;
2898        last_j=Param.IndexRange.last_j;
2899        MinIndex_j=Param.IndexRange.MinIndex_j(iview);
2900        MaxIndex_j=Param.IndexRange.MaxIndex_j(iview);
2901    end
2902    PairString='';
2903    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end
2904    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2905    LineIndex=iview(1);
2906    if numel(iview)>1     
2907        answer=msgbox_uvmat('INPUT_TXT',['select the line of the input table:' num2str(iview)] ,num2str(iview(1)));
2908        LineIndex=str2num(answer);
2909    end
2910    FirstFileName=fullfile_uvmat(InputTable{LineIndex,1},InputTable{LineIndex,2},InputTable{LineIndex,3},...
2911        InputTable{LineIndex,5},InputTable{LineIndex,4},i1,i2,j1,j2);
[1090]2912    if exist(FirstFileName,'file') || ~isempty(regexp(InputTable{LineIndex,1},'^http'))
[867]2913        ParamIn.Title='get_field: pick input variables and coordinates for series processing';
2914        ParamIn.SeriesInput=1;
2915        GetFieldData=get_field(FirstFileName,ParamIn);
2916        FieldList={};
[876]2917        if isfield(GetFieldData,'FieldOption')% if a field has been selected
[867]2918        switch GetFieldData.FieldOption
2919            case 'vectors'
2920                UName=GetFieldData.PanelVectors.vector_x;
2921                VName=GetFieldData.PanelVectors.vector_y;
2922                YName={GetFieldData.Coordinates.Coord_y};
2923                FieldList={['vec(' UName ',' VName ')'];...
2924                    ['norm(' UName ',' VName ')'];...
2925                    UName;VName};
[1030]2926                set(handles.VelType,'Visible','off')
[867]2927            case {'scalar'}
2928                FieldList=GetFieldData.PanelScalar.scalar;
2929                YName={GetFieldData.Coordinates.Coord_y};
2930                if ischar(FieldList)
2931                    FieldList={FieldList};
2932                end
[1030]2933                set(handles.VelType,'Visible','off')
[867]2934            case 'civdata...'
2935                FieldList=[set_field_list('U','V') ;{'C'}];
2936                set(handles.FieldName,'Value',1) % set menu to 'velocity
2937                XName='X';
2938                YName='y';
[1030]2939                set(handles.VelType,'Visible','on')
[867]2940        end
2941        set(handles.FieldName,'Value',1)
[1078]2942        set(handles.FieldName,'String',[FieldListInit; FieldList; {'add_field...'}]);
[867]2943        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2944           if ~isempty(regexp(FieldList{1},'^vec'))
2945                set(handles.FieldName,'Value',1)
2946           else
2947                set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
2948           end
2949            XName=GetFieldData.Coordinates.Coord_x;
2950            YName=GetFieldData.Coordinates.Coord_y;
2951            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2952            % get the time info                     
2953            TimeTable=get(handles.TimeTable,'Data');
2954            switch TimeNameStr
2955                case 'file index'
2956                    TimeName='';
2957                case 'attribute'
2958                    TimeName=['att:' GetFieldData.Time.TimeName];
2959                    % update the time table
2960                    TimeTable{LineIndex,2}=get_time(Param.IndexRange.MinIndex_i(LineIndex),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Min time     
2961                    TimeTable{LineIndex,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % first time             
2962                    TimeTable{LineIndex,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % last time                     
2963                    TimeTable{LineIndex,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Max time
2964                case 'variable'
2965                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2966                    set(handles.NomType,'String','*')
2967                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2968                    set(handles.FileIndex,'String','')
2969                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2970                case 'matrix_index'
2971                    TimeName=['dim:' GetFieldData.Time.TimeName];
2972                    set(handles.NomType,'String','*')
2973                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2974                    set(handles.FileIndex,'String','')
2975                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2976            end
2977            TimeTable{LineIndex,1}=TimeName;
2978            set(handles.TimeTable,'Data',TimeTable);
2979        end
2980        set(handles.Coord_x,'String',XName)
2981        set(handles.Coord_y,'String',YName)
2982        set(handles.Coord_x,'Visible','on')
2983        set(handles.Coord_y,'Visible','on')
[876]2984        end
[867]2985    else
2986        msgbox_uvmat('ERROR',[FirstFileName ' does not exist'])
2987    end
2988end
2989
[972]2990
[867]2991function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
2992[i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
2993FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2);
2994Data=nc2struct(FileName,[]);
2995TimeValue=[];
2996DtValue=[];
2997if isequal(FileInfo.FileType,'civdata')
2998    if ismember(TimeName,{'civ1','filter1'})
[970]2999        if isfield(Data,'Civ1_Time')
[867]3000        TimeValue=Data.Civ1_Time;
[970]3001        end
3002        if isfield(Data,'Civ1_Dt')
[867]3003        DtValue=Data.Civ1_Dt;
[970]3004        end
[867]3005    else
[970]3006        if isfield(Data,'Civ2_Time')
[867]3007        TimeValue=Data.Civ2_Time;
[970]3008        end
3009        if isfield(Data,'Civ2_Dt')
[867]3010        DtValue=Data.Civ2_Dt;
[970]3011        end
[867]3012    end
3013else
3014    if ~isempty(TimeName)&& isfield(Data,TimeName)
3015        TimeValue=Data.(TimeName);
3016    end
3017    if exist('DtName','var') && isfield(Data,DtName)
3018        DtValue=Data.(DtName);
3019    end
3020end
3021
3022%------------------------------------------------------------------------
3023% --- Executes on selection change in FieldName_1.
3024function FieldName_1_Callback(hObject, eventdata, handles)
3025%------------------------------------------------------------------------
3026field_str=get(handles.FieldName_1,'String');
3027field_index=get(handles.FieldName_1,'Value');
3028field=field_str{field_index(1)};
[1078]3029if isequal(field,'add_field...')
[867]3030    hget_field=findobj(allchild(0),'name','get_field');
3031    if ~isempty(hget_field)
3032        delete(hget_field)%delete opened versions of get_field
3033    end
3034    Param=read_GUI(handles.series);
3035    Param.InputTable=Param.InputTable(1,:);
3036    % check the existence of the first file in the series
3037    first_j=[];
3038    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
3039    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
3040    PairString='';
3041    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
3042    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
3043    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
3044        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
3045    if exist(FirstFileName,'file')
3046        ParamIn.SeriesInput=1;
3047        GetFieldData=get_field(FirstFileName,ParamIn);
3048        FieldList={};
3049        switch GetFieldData.FieldOption
3050            case 'vectors'
3051                UName=GetFieldData.PanelVectors.vector_x;
3052                VName=GetFieldData.PanelVectors.vector_y;
3053                FieldList={['vec(' UName ',' VName ')'];...
3054                    ['norm(' UName ',' VName ')'];...
3055                    UName;VName};
3056            case {'scalar','pick variables'}
3057                FieldList=GetFieldData.PanelScalar.scalar;
3058                if ischar(FieldList)
3059                    FieldList={FieldList};
3060                end
3061            case '1D plot'
3062
3063            case 'civdata...'
3064                FieldList=set_field_list('U','V','C');
3065                set(handles.FieldName,'Value',2) % set menu to 'velocity
3066        end
3067        if ~strcmp(GetFieldData.FieldOption,'civdata...')
3068            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
3069            switch TimeNameStr
3070                case 'file index'
3071                    set(handles.TimeName,'String','');
3072                case 'attribute'
3073                    set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
3074                case 'variable'
3075                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
3076                    set(handles.NomType,'String','*')
3077                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
3078                    set(handles.FileIndex,'String','')
3079                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
3080                case 'matrix_index'
3081                    set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]);
3082                    set(handles.NomType,'String','*')
3083                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
3084                    set(handles.FileIndex,'String','')
3085                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
3086            end
3087        end
3088        set(handles.FieldName_1,'Value',1)
[1078]3089        set(handles.FieldName_1,'String',[FieldList; {'add_field...'}]);
[867]3090    end
3091end   
3092
3093
3094%%%%%%%%%%%%%
3095function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
3096indsel=ind_i;
[992]3097indiff=diff(ind_i); % test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
3098indiff=[1 indiff last_i-ind_i(end)+1]; % for testing gaps with the imposed bounds
[867]3099if ~isempty(indiff)
3100    indiff2=diff(indiff);
3101    indiffp=[indiff2 1];
3102    indiffm=[1 indiff2];
[992]3103    ind_multi_m=find((indiff==0)&(indiffm<0))-1; % indices of first members of multiplets
3104    ind_multi_p=find((indiff==0)&(indiffp>0)); % indices of last members of multiplets
[867]3105    %for each multiplet, select the most recent file
3106    ind_remove=[];
3107    for i=1:length(ind_multi_m)
3108        ind_pairs=ind_multi_m(i):ind_multi_p(i);
3109        for imulti=1:length(ind_pairs)
[992]3110            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date); % dates of creation
[867]3111        end
[992]3112        [datenew,indsort2]=sort(datepair); % sort the multiplet by creation date
3113        ind_s=indsort2(1:end-1); %
3114        ind_remove=[ind_remove ind_pairs(ind_s)]; % remove these indices, leave the last one
[867]3115    end
3116end
3117
3118%------------------------------------------------------------------------
3119% --- determine the list of index pairstring of processing file
3120function [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)
3121%------------------------------------------------------------------------
[992]3122num_i1=num_i; % set of first image numbers by default
[867]3123num_i2=num_i;
3124num_j1=num_j;
3125num_j2=num_j;
3126num_i_out=num_i;
3127num_j_out=num_j;
3128% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
3129if isequal(mode,'series(Di)')
[992]3130    num_i1_line=num_i+ind_shift(3); % set of first image numbers
[867]3131    num_i2_line=num_i+ind_shift(4);
3132    % adjust the first and last field number
3133        indsel=find(num_i1_line >= 1);
3134    num_i_out=num_i(indsel);
3135    num_i1_line=num_i1_line(indsel);
3136    num_i2_line=num_i2_line(indsel);
3137    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
3138    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
3139    [xx,num_i1]=meshgrid(num_j,num_i1_line);
3140    [xx,num_i2]=meshgrid(num_j,num_i2_line);
3141elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
3142    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
3143        num_j1=ind_shift(1)*ones(size(num_i));
3144        num_j2=ind_shift(2)*ones(size(num_i));
3145    else
[992]3146        num_j1_col=num_j+ind_shift(1); % set of first image numbers
[867]3147        num_j2_col=num_j+ind_shift(2);
3148        % adjust the first field number
3149        indsel=find((num_j1_col >= 1));   
3150        num_j_out=num_j(indsel);
3151        num_j1_col=num_j1_col(indsel);
3152        num_j2_col=num_j2_col(indsel);
3153        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
3154        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
3155    end   
3156end
3157
3158%------------------------------------------------------------------------
3159% --- Executes on button press in CheckObject.
3160function CheckObject_Callback(hObject, eventdata, handles)
3161%------------------------------------------------------------------------
[992]3162hset_object=findobj(allchild(0),'tag','set_object'); % find the set_object interface handle
[867]3163if get(handles.CheckObject,'Value')
3164    SeriesData=get(handles.series,'UserData');
[1113]3165    if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject)% a projection object is already loaded in the GUI series
[867]3166        set(handles.ViewObject,'Value',1)
3167        ViewObject_Callback(hObject, eventdata, handles)
3168    else
[1113]3169        if ishandle(hset_object)% a projection object is already displayed in a GUI set_object
[867]3170            uistack(hset_object,'top')% show the GUI set_object if opened
3171        else
3172            %get the object file
3173            InputTable=get(handles.InputTable,'Data');
3174            defaultname=InputTable{1,1};
3175            if isempty(defaultname)
3176                defaultname={''};
3177            end
3178            fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml');
3179            if isempty(fileinput)% exit if no object file is selected
3180                set(handles.CheckObject,'Value',0)
3181                return
3182            end
3183            %read the file
3184            data=xml2struct(fileinput);
3185            if ~isfield(data,'Type')
3186                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
3187                set(handles.CheckObject,'Value',0)
3188                return
3189            end
3190            if ~isfield(data,'ProjMode')
3191                data.ProjMode='none';
3192            end
[992]3193            hset_object=set_object(data); % call the set_object interface
[867]3194            set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat
3195        end
3196        ProjObject=read_GUI(hset_object);
[1072]3197        set(handles.ProjObjectName,'String',ProjObject.Name); % display the object name
[867]3198        SeriesData=get(handles.series,'UserData');
3199        SeriesData.ProjObject=ProjObject;
3200        set(handles.series,'UserData',SeriesData);
3201    end
3202    set(handles.EditObject,'Visible','on');
3203    set(handles.DeleteObject,'Visible','on');
3204    set(handles.ViewObject,'Visible','on');
[1072]3205    set(handles.ProjObjectName,'Visible','on');
[867]3206else
3207    set(handles.EditObject,'Visible','off');
3208    set(handles.DeleteObject,'Visible','off');
3209    set(handles.ViewObject,'Visible','off');
3210    if ~ishandle(hset_object)
3211        set(handles.ViewObject,'Value',0);
3212    end
[1072]3213    set(handles.ProjObjectName,'Visible','off');
[867]3214end
3215
3216%------------------------------------------------------------------------
3217% --- Executes on button press in ViewObject.
3218%------------------------------------------------------------------------
3219function ViewObject_Callback(hObject, eventdata, handles)
3220
3221UserData=get(handles.series,'UserData');
3222hset_object=findobj(allchild(0),'Tag','set_object');
3223if ~isempty(hset_object)
3224    delete(hset_object)% refresh set_object if already opened
3225end
3226hset_object=set_object(UserData.ProjObject);
3227set(hset_object,'Name','view_object_series')
3228
3229
3230%------------------------------------------------------------------------
3231% --- Executes on button press in EditObject.
3232function EditObject_Callback(hObject, eventdata, handles)
3233%------------------------------------------------------------------------
3234if get(handles.EditObject,'Value')
3235    set(handles.ViewObject,'Value',0)
[998]3236    UserData=get(handles.series,'UserData');
[1113]3237    if isfield(UserData,'ProjObject')
[867]3238    hset_object=set_object(UserData.ProjObject);
3239    set(hset_object,'Name','edit_object_series')
3240    set(get(hset_object,'Children'),'Enable','on')
[1113]3241    else
3242        msgbox_uvmat('ERROR','no projection object available');
3243    end
[867]3244else
3245    hset_object=findobj(allchild(0),'Tag','set_object');
3246    if ~isempty(hset_object)
3247        set(get(hset_object,'Children'),'Enable','off')
3248    end
3249end
3250
3251%------------------------------------------------------------------------
3252% --- Executes on button press in DeleteObject.
3253function DeleteObject_Callback(hObject, eventdata, handles)
3254%------------------------------------------------------------------------
3255SeriesData=get(handles.series,'UserData');
3256SeriesData.ProjObject=[];
3257set(handles.series,'UserData',SeriesData)
[1072]3258set(handles.ProjObjectName,'String','')
3259set(handles.ProjObjectName,'Visible','off')
[867]3260set(handles.CheckObject,'Value',0)
3261set(handles.ViewObject,'Visible','off')
3262set(handles.EditObject,'Visible','off')
3263hset_object=findobj(allchild(0),'name','set_object_series');
3264if ~isempty(hset_object)
3265    delete(hset_object)
3266end
3267set(handles.DeleteObject,'Visible','off')
3268
3269%------------------------------------------------------------------------
3270% --- Executed when CheckMask is activated
3271%------------------------------------------------------------------------
3272function CheckMask_Callback(hObject, eventdata, handles)
3273
3274if get(handles.CheckMask,'Value')
3275    InputTable=get(handles.InputTable,'Data');
3276    nbview=size(InputTable,1);
[992]3277    MaskTable=cell(nbview,1); % default
3278    ListMask=cell(nbview,1); % default
[867]3279    MaskData=get(handles.MaskTable,'Data');
[992]3280    MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1); % complement if undefined lines
[867]3281    for iview=1:nbview
3282        ListMask{iview,1}=num2str(iview);
3283        RootPath=InputTable{iview,1};
3284        if ~isempty(RootPath)
3285            if isempty(MaskData{iview})
3286                SubDir=InputTable{iview,2};
[992]3287                MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']); % take the root part of SubDir, before the first dot '.'
[867]3288                if exist(MaskPath,'dir')
[992]3289                    ListStruct=dir(MaskPath); % look for a mask file
3290                    ListCells=struct2cell(ListStruct); % transform dir struct to a cell arrray
3291                    check_dir=cell2mat(ListCells(4,:)); % =1 for directories, =0 for files
3292                    ListFiles=ListCells(1,:); % list of file and dri names
3293                    ListFiles=ListFiles(~check_dir); % list of file names (excluding dir)
[867]3294                    mdetect=0;
3295                    if ~isempty(ListFiles)
3296                        for ifile=1:numel(ListFiles)
3297                            [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0);
3298                            if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series)
3299                                mdetect=1;
3300                                MaskName=ListFiles{ifile};
3301                            end
3302                            if ~strcmp(MaskFile{ifile},MaskFile{1})
[992]3303                                mdetect=0; % cancel detection test in case of multiple masks, use the brower for selection
[867]3304                                break
3305                            end
3306                        end
3307                    end
3308                    if mdetect==1
3309                        MaskName=fullfile(MaskPath,'mask_1.png');
3310                    else
3311                        MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image');
3312                    end
3313                else
3314                    MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3315                end
3316                MaskTable{iview,1}=MaskName ;
3317                ListMask{iview,1}=num2str(iview);
3318            end
3319        end
3320    end
3321    set(handles.MaskTable,'Data',MaskTable)
3322    set(handles.MaskTable,'Visible','on')
3323    set(handles.MaskBrowse,'Visible','on')
3324    set(handles.ListMask,'Visible','on')
3325    set(handles.ListMask,'String',ListMask)
3326    set(handles.ListMask,'Value',1)
3327else
3328    set(handles.MaskTable,'Visible','off')
3329    set(handles.MaskBrowse,'Visible','off')
3330    set(handles.ListMask,'Visible','off')
3331end
3332
3333%------------------------------------------------------------------------
3334% --- Executes on button press in MaskBrowse.
3335%------------------------------------------------------------------------
3336function MaskBrowse_Callback(hObject, eventdata, handles)
3337
3338InputTable=get(handles.InputTable,'Data');
3339iview=get(handles.ListMask,'Value');
3340RootPath=InputTable{iview,1};
3341MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3342if ~isempty(MaskName)
3343    MaskTable=get(handles.MaskTable,'Data');
3344    MaskTable{iview,1}=MaskName ;
3345    set(handles.MaskTable,'Data',MaskTable)
3346end
3347
3348%------------------------------------------------------------------------
3349% --- Executes when selected cell(s) is changed in MaskTable.
3350%------------------------------------------------------------------------
3351function MaskTable_CellSelectionCallback(hObject, eventdata, handles)
3352
3353if numel(eventdata.Indices)>=1
3354set(handles.ListMask,'Value',eventdata.Indices(1))
3355end
3356
3357%-------------------------------------------------------------------
3358function MenuHelp_Callback(hObject, eventdata, handles)
3359%-------------------------------------------------------------------
3360
3361
[992]3362% path_to_uvmat=which ('uvmat'); % check the path of uvmat
[867]3363% pathelp=fileparts(path_to_uvmat);
3364% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
3365% 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')
3366% else
3367%     addpath (fullfile(pathelp,'uvmat_doc'))
3368%     web([helpfile '#series'])
3369% end
3370
3371%-------------------------------------------------------------------
3372% --- Executes on selection change in TransformName.
3373function TransformName_Callback(hObject, eventdata, handles)
3374%----------------------------------------------------------------------
3375TransformList=get(handles.TransformName,'String');
3376TransformIndex=get(handles.TransformName,'Value');
3377TransformName=TransformList{TransformIndex};
3378TransformPathList=get(handles.TransformName,'UserData');
3379nb_builtin_transform=4;
[1114]3380
3381%% browse transform functions with the input menu option more...
3382if isequal(TransformName,'more...')% browse transform functions     
[867]3383    FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
3384    if isempty(FileName)
3385        return     %browser closed without choice
3386    end
[992]3387    [TransformPath,TransformName,TransformExt]=fileparts(FileName); % removes extension .m
[867]3388    if ~strcmp(TransformExt,'.m')
3389        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3390        return
3391    end
3392     % insert the choice in the menu
[992]3393    TransformIndex=find(strcmp(TransformName,TransformList),1); % look for the selected function in the menu Action
[867]3394    if isempty(TransformIndex)%the input string does not exist in the menu
3395        TransformIndex= length(TransformList);
[992]3396        TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)]; % the selected function is appended in the menu, before the last item 'more...'
[867]3397        set(handles.TransformName,'String',TransformList)
3398        TransformPathList=[TransformPathList;{TransformPath}];
3399    else% the input function already exist, we update its path (possibly new)
[992]3400        TransformPathList{TransformIndex}=TransformPath; %
[867]3401        set(handles.TransformName,'Value',TransformIndex)
3402    end
3403   % save the new menu in the personal file 'uvmat_perso.mat'
[992]3404   dir_perso=prefdir; % personal Matalb directory
[867]3405   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3406   if exist(profil_perso,'file')
3407       for ilist=nb_builtin_transform+1:numel(TransformPathList)
3408           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
3409           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
3410       end
3411       TransformPathListUser=TransformPathListUser';
3412       TransformListUser=TransformListUser';
[992]3413       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); % store the root name for future opening of uvmat
[867]3414   end
3415end
3416
[1114]3417%% display the current function path
[992]3418set(handles.TransformPath,'String',TransformPathList{TransformIndex}); % show the path to the senlected function
[867]3419set(handles.TransformName,'UserData',TransformPathList);
3420
[883]3421%% create the function handle of the selected fct
3422if ~isempty(TransformName)
[897]3423    if ~exist(TransformPathList{TransformIndex},'dir')
3424        msgbox_uvmat('ERROR',['The prescribed transform function path ' TransformPathList{TransformIndex} ' does not exist']);
3425        return
3426    end
[992]3427    current_dir=pwd; % current working dir
[883]3428    cd(TransformPathList{TransformIndex})
3429    transform_handle=str2func(TransformName);
3430    cd(current_dir)
[994]3431    Field.Action.RUN=0;% indicate that the transform fct is called only to get input param
3432    SeriesData=get(handles.series,'UserData');
3433    ParamIn=[];
3434    if isfield(SeriesData,'TransformInput')
3435        ParamIn.TransformInput=SeriesData.TransformInput;
3436    end
[1114]3437    DataOut=feval(transform_handle,Field,ParamIn);% execute the transform fct to get its input parameters
[883]3438    if isfield(DataOut,'TransformInput')%  used to add transform parameters at selection of the transform fct
3439        SeriesData.TransformInput=DataOut.TransformInput;
3440        set(handles.series,'UserData',SeriesData)
3441    end
3442end
3443
[867]3444%------------------------------------------------------------------------
3445% --- fct activated by the upper bar menu ExportConfig
3446%------------------------------------------------------------------------
3447function MenuDisplayConfig_Callback(hObject, eventdata, handles)
3448
3449global Param
3450Param=read_GUI_series(handles);
3451evalin('base','global Param')%make CurData global in the workspace
3452display('current series config :')
3453evalin('base','Param') %display CurData in the workspace
[992]3454commandwindow; % brings the Matlab command window to the front
[867]3455
3456%------------------------------------------------------------------------
3457% --- fct activated by the upper bar menu InportConfig: import
3458%     menu settings from an xml file (stored in /0_XML for each run)
3459%------------------------------------------------------------------------
3460function MenuImportConfig_Callback(hObject, eventdata, handles)
3461
3462%% use a browser to choose the xml file containing the processing config
3463InputTable=get(handles.InputTable,'Data');
[992]3464oldfile=InputTable{1,1}; % current path in InputTable
[867]3465if isempty(oldfile)
3466    % use a file name stored in prefdir
3467    dir_perso=prefdir;
3468    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3469    if exist(profil_perso,'file')
3470        h=load (profil_perso);
3471        if isfield(h,'RootPath') && ischar(h.RootPath)
3472            oldfile=h.RootPath;
3473        end
3474    end
3475end
[992]3476filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml'); % get the xml file containing processing parameters
[867]3477if isempty(filexml), return, end % quit function if an xml file has not been opened
3478
3479%% fill the GUI series with the content of the xml file
[1095]3480[Param,RootTag,errormsg]=xml2struct(filexml); % read the input xml file as a Matlab structure
3481if ~isempty(errormsg)
3482    msgbox_uvmat('ERROR',errormsg);
3483    return
3484end
[867]3485% ask to stop current Action if button RUN is in action (another process is already running)
3486if isequal(get(handles.RUN,'Value'),1)
3487    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
3488    if strcmp(answer,'Yes')
3489        STOP_Callback(hObject, eventdata, handles)
3490    else
3491        return
3492    end
3493end
[992]3494Param.Action.RUN=0; % desactivate the input RUN=1
[867]3495
3496fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
3497SeriesData=get(handles.series,'UserData');
3498if isfield(Param,'InputFields')
3499    ListField=Param.InputFields.FieldName;
3500    if ischar(ListField),ListField={ListField}; end
[1078]3501    set(handles.FieldName,'String',[ListField;{'add_field...'}])
[867]3502     set(handles.FieldName,'Value',1:numel(ListField))
3503     set(handles.FieldName,'Visible','on')
3504end       
3505if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
[996]3506%     set(handles.ActionInput,'Visible','on')
3507%     set(handles.ActionInput,'Value',0)
[992]3508    Param.ActionInput.ConfigSource=filexml; % record the source of config for future info
[867]3509    SeriesData.ActionInput=Param.ActionInput;
3510end
[883]3511if isfield(Param,'TransformInput')%  introduce  parameters specific to a transform fct
3512    SeriesData.TransformInput=Param.TransformInput;
3513end
[867]3514if isfield(Param,'ProjObject') %introduce projection object if relevant
3515    SeriesData.ProjObject=Param.ProjObject;
3516end
3517set(handles.series,'UserData',SeriesData)
3518if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
[1072]3519    set(handles.ProjObjectName,'String',Param.ProjObject.Name)
[867]3520    set(handles.ViewObject,'Visible','on')
3521    set(handles.EditObject,'Visible','on')
3522    set(handles.DeleteObject,'Visible','on')
3523else     
[1072]3524    set(handles.ProjObjectName,'String','')
3525    set(handles.ProjObjectName,'Visible','off')
[867]3526    set(handles.ViewObject,'Visible','off')
3527    set(handles.EditObject,'Visible','off')
3528    set(handles.DeleteObject,'Visible','off')     
3529end     
[992]3530set(handles.REFRESH,'BackgroundColor',[1 0 1]); % paint REFRESH button in magenta to indicate that it should be activated
[867]3531
3532
3533%------------------------------------------------------------------------
3534% --- Executes when the GUI series is resized.
3535%------------------------------------------------------------------------
3536function series_ResizeFcn(hObject, eventdata, handles)
3537
3538%% input table
3539set(handles.InputTable,'Unit','pixel')
3540Pos=get(handles.InputTable,'Position');
3541set(handles.InputTable,'Unit','normalized')
3542ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
3543ColumnWidth=num2cell(ColumnWidth);
3544set(handles.InputTable,'ColumnWidth',ColumnWidth)
3545
3546%% MinIndex_j and MaxIndex_i
3547unit=get(handles.MinIndex_i,'Unit');
3548set(handles.MinIndex_i,'Unit','pixel')
3549Pos=get(handles.MinIndex_i,'Position');
3550set(handles.MinIndex_i,'Unit',unit)
3551set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18})
3552set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18})
3553set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18})
3554set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18})
3555
3556%% TimeTable
3557set(handles.TimeTable,'Unit','pixel')
3558Pos=get(handles.TimeTable,'Position');
3559set(handles.TimeTable,'Unit','normalized')
3560% ColumnWidth=get(handles.TimeTable,'ColumnWidth');
3561ColumnWidth=num2cell(floor([0.2 0.2 0.2 0.2 0.2]*(Pos(3)-20)));
3562set(handles.TimeTable,'ColumnWidth',ColumnWidth)
3563
3564
3565%% PairString
3566set(handles.PairString,'Unit','pixel')
3567Pos=get(handles.PairString,'Position');
3568set(handles.PairString,'Unit','normalized')
3569set(handles.PairString,'ColumnWidth',{Pos(3)-5})
3570
3571%% MaskTable
3572set(handles.MaskTable,'Unit','pixel')
3573Pos=get(handles.MaskTable,'Position');
3574set(handles.MaskTable,'Unit','normalized')
3575set(handles.MaskTable,'ColumnWidth',{Pos(3)-5})
3576
3577%------------------------------------------------------------------------
3578% --- Executes on button press in status.
3579%------------------------------------------------------------------------
3580function status_Callback(hObject, eventdata, handles)
3581
3582if get(handles.status,'Value')
3583    set(handles.status,'BackgroundColor',[1 1 0])
3584    drawnow
3585    Param=read_GUI(handles.series);
[1090]3586    RootPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device);
[867]3587    if ~isfield(Param,'OutputSubDir')   
3588        msgbox_uvmat('ERROR','no standard sub-directory definition for output files, use a browser to check the output')
3589        set(handles.status,'BackgroundColor',[0 1 0])
3590        return
3591    end
[992]3592    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt]; % subdirectory for output files
[867]3593    OutputDir=fullfile(RootPath,OutputSubDir);
3594    if exist(OutputDir,'dir')
3595        uigetfile_uvmat('status_display',OutputDir)
3596    else
3597        msgbox_uvmat('ERROR','output folder not created yet: calculation did not start')
3598        set(handles.status,'BackgroundColor',[0 1 0])
3599    end
3600else
3601    %% delete current display fig if selection is off
3602    set(handles.status,'BackgroundColor',[0 1 0])
3603    hfig=findobj(allchild(0),'name','status_display');
3604    if ~isempty(hfig)
3605        delete(hfig)
3606    end
3607    return
3608end
3609
3610
3611%------------------------------------------------------------------------   
3612% launched by selecting a file on the list
3613%------------------------------------------------------------------------
3614function view_file(hObject, eventdata)
3615
3616list=get(hObject,'String');
3617index=get(hObject,'Value');
3618rootroot=get(hObject,'UserData');
3619selectname=list{index};
3620ind_dot=regexp(selectname,'\.\.\.');
3621if ~isempty(ind_dot)
3622    selectname=selectname(1:ind_dot-1);
3623end
3624FullSelectName=fullfile(rootroot,selectname);
3625if exist(FullSelectName,'dir')% a directory has been selected
3626    ListFiles=dir(FullSelectName);
3627    ListDisplay=cell(numel(ListFiles),1);
3628    for ilist=2:numel(ListDisplay)% suppress the first line '.'
3629        ListDisplay{ilist-1}=ListFiles(ilist).name;
3630    end
3631    set(hObject,'Value',1)
3632    set(hObject,'String',ListDisplay)
3633    if strcmp(selectname,'..')
3634        FullSelectName=fileparts(fileparts(FullSelectName));
3635    end
3636    set(hObject,'UserData',FullSelectName)
3637    hfig=get(hObject,'parent');
3638    htitlebox=findobj(hfig,'tag','titlebox');   
3639    set(htitlebox,'String',FullSelectName)
3640elseif exist(FullSelectName,'file')%visualise the vel field if it exists
3641    FileInfo=get_file_info(FullSelectName);   
3642    if strcmp(FileInfo.FileType,'txt')
3643        edit(FullSelectName)
3644    elseif strcmp(FileInfo.FileType,'xml')
3645        editxml(FullSelectName)
3646    else
3647        uvmat(FullSelectName)
3648    end
3649    set(gcbo,'Value',1)
3650end
3651
3652
3653%------------------------------------------------------------------------   
3654% launched by refreshing the status figure
3655%------------------------------------------------------------------------
3656function refresh_GUI(hfig)
3657
3658htitlebox=findobj(hfig,'tag','titlebox');
3659hlist=findobj(hfig,'tag','list');
3660hseries=findobj(allchild(0),'tag','series');
3661hstatus=findobj(hseries,'tag','status');
3662StatusData=get(hstatus,'UserData');
3663OutputDir=get(htitlebox,'String');
3664if ischar(OutputDir),OutputDir={OutputDir};end
3665ListFiles=dir(OutputDir{1});
3666if numel(ListFiles)<1
3667    return
3668end
[992]3669ListFiles(1)=[]; % removes the first line ='.'
[867]3670ListDisplay=cell(numel(ListFiles),1);
3671testrecent=0;
3672datnum=zeros(numel(ListDisplay),1);
3673for ilist=1:numel(ListDisplay)
3674    ListDisplay{ilist}=ListFiles(ilist).name;
3675      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
[992]3676            datnum(ilist)=ListFiles(ilist).datenum; % only available in recent matlab versions
[867]3677            testrecent=1;
3678       end
3679end
3680set(hlist,'String',ListDisplay)
3681
3682%% Look at date of creation
3683ListDisplay=ListDisplay(datnum~=0);
[992]3684datnum=datnum(datnum~=0); % keep the non zero values corresponding to existing files
[867]3685NbOutputFile=[];
3686if isempty(datnum)
3687    if testrecent
3688        message='no civ result created yet';
3689    else
3690        message='';
3691    end
3692else
3693    [first,indfirst]=min(datnum);
3694    [last,indlast]=max(datnum);
3695    NbOutputFile_str='?';
3696    NbOutputFile=[];
3697    if isfield(StatusData,'NbOutputFile')
3698        NbOutputFile=StatusData.NbOutputFile;
3699        NbOutputFile_str=num2str(NbOutputFile);
3700    end
3701    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
3702        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
3703end
3704set(htitlebox,'String', [OutputDir{1};message])
3705
3706%% update the waitbar
3707hwaitbar=findobj(hfig,'tag','waitbar');
3708if ~isempty(NbOutputFile)
3709    BarPosition=get(hwaitbar,'Position');
3710    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
3711    set(hwaitbar,'Position',BarPosition)
3712end
3713
3714%------------------------------------------------------------------------
3715% --- Executes on selection change in ActionExt.
3716%------------------------------------------------------------------------
3717function ActionExt_Callback(hObject, eventdata, handles)
3718
3719ActionExtList=get(handles.ActionExt,'String');
3720ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
3721if strcmp(ActionExt,'.py (in dev.)')
3722    set(handles.RunMode,'Value',2)
3723end
3724
3725
3726function num_NbSlice_Callback(hObject, eventdata, handles)
3727NbSlice=str2num(get(handles.num_NbSlice,'String'));
3728
3729%------------------------------------------------------------------------
3730% --- set the visibility of relevant velocity type menus:
3731function menu=set_veltype_display(Civ,FileType)
3732%------------------------------------------------------------------------
3733if ~exist('FileType','var')
3734    FileType='civx';
3735end
3736switch FileType
3737    case 'civx'
3738        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3739        if isequal(Civ,0)
3740            imax=0;
3741        elseif isequal(Civ,1) || isequal(Civ,2)
3742            imax=1;
3743        elseif isequal(Civ,3)
3744            imax=3;
3745        elseif isequal(Civ,4) || isequal(Civ,5)
3746            imax=4;
3747        elseif isequal(Civ,6) %patch2
3748            imax=6;
3749        end
3750    case 'civdata'
3751        menu={'civ1';'filter1';'civ2';'filter2'};
3752        if isequal(Civ,0)
3753            imax=0;
3754        elseif isequal(Civ,1) || isequal(Civ,2)
3755            imax=1;
3756        elseif isequal(Civ,3)
3757            imax=2;
3758        elseif isequal(Civ,4) || isequal(Civ,5)
3759            imax=3;
[912]3760        else%if isequal(Civ,6) %patch2
[867]3761            imax=4;
3762        end
3763end
3764menu=menu(1:imax);
3765
3766
3767% --- Executes on mouse motion over figure - except title and menu.
[1059]3768% function series_WindowButtonMotionFcn(hObject, eventdata, handles)
3769% set(hObject,'Pointer','arrow');
[867]3770
3771
3772% --- Executes on button press in SetPairs.
[972]3773function SetPairs_Callback(hObject, eventdata, handles)
[867]3774
3775%% delete previous occurrence of 'set_pairs'
3776hfig=findobj(allchild(0),'Tag','set_pairs');
3777if ~isempty(hfig)
3778delete(hfig)
3779end
3780
3781%% create the GUI set_pairs
3782set(0,'Unit','points')
[992]3783ScreenSize=get(0,'ScreenSize'); % get the size of the screen, to put the fig on the upper right
3784Width=220; % fig width in points (1/72 inch)
[867]3785Height=min(0.8*ScreenSize(4),300);
[992]3786Left=ScreenSize(3)- Width-40; % right edge close to the right, with margin=40
3787Bottom=ScreenSize(4)-Height-40; % put fig at top right
[867]3788hfig=findobj(allchild(0),'Tag','set_slice');
[992]3789if ~isempty(hfig),delete(hfig), end; % delete existing version of the GUI
[867]3790hfig=figure('name','set_pairs','tag','set_pairs','MenuBar','none','NumberTitle','off','Unit','points','Position',[Left,Bottom,Width,Height]);
3791BackgroundColor=get(hfig,'Color');
3792SeriesData=get(handles.series,'UserData');
3793TimeUnit=get(handles.TimeUnit,'String');
3794PairString=get(handles.PairString,'Data');
[992]3795ListViewLines=find(cellfun('isempty',PairString)==0); % find list of non empty pairs
[867]3796ListViewMenu=cell(numel(ListViewLines),1);
[1011]3797%iview=get(handles.PairString,'Value');
3798iview=[];
[867]3799for ilist=1:numel(ListViewLines)
3800    ListViewMenu{ilist}=num2str(ListViewLines(ilist));
3801end
3802if isempty(iview)
[992]3803    ListViewValue=numel(ListViewLines); % we work by default on the pair option for the last line which requires pairs
[867]3804    iview=ListViewLines(end);
3805else
3806    ListViewValue=find(ListViewLines==iview);
3807end
3808ref_i=str2num(get(handles.num_first_i,'String'));
[992]3809ref_j=1; % default
[867]3810if strcmp(get(handles.num_first_j,'String'),'Visible')
3811    ref_j=str2num(get(handles.num_first_j,'String'));
3812end
[1016]3813[ModeMenu,ModeValue]=update_mode(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j2_series{1});
3814InputTable=get(handles.InputTable,'Data');
3815displ_pair=update_listpair(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j1_series{1},SeriesData.j2_series{1},ModeMenu{ModeValue},...
3816                                                 SeriesData.Time{1},TimeUnit,ref_i,ref_j,SeriesData.TimeName,InputTable,SeriesData.FileInfo{1});
3817for iline=1:size(InputTable,1)
3818    viewcell{iline}=num2str(iline);
3819end
3820viewcell=viewcell';
3821ModeMenu={'bursts';'series(Dj)'};
3822ModeValue=1;                                               
3823                   %i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo                             
[867]3824% first raw of the GUI
3825uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,...
[992]3826    'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right'); % title
[867]3827uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.54 0.8 0.3 0.2],'BackgroundColor',[1 1 1],...
[1016]3828    'Callback',@(hObject,eventdata)ListView_Callback(hObject,eventdata),'String',viewcell,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
[867]3829    'Tag','ListView','TooltipString','''ListView'':choice of the file series w for pair display');
3830% second raw of the GUI
3831uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.79 0.7 0.1],'BackgroundColor',BackgroundColor,...
[992]3832    'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
[867]3833uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.05 0.62 0.9 0.2],'BackgroundColor',[1 1 1],...
3834    'Callback',@(hObject,eventdata)Mode_Callback(hObject,eventdata),'String',ModeMenu,'Value',ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3835    'Tag','Mode','TooltipString','''Mode'': choice of the image pair mode');
3836% third raw
3837uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.6 0.7 0.1],'BackgroundColor',BackgroundColor,...
[992]3838    'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
[867]3839uicontrol('Style','listbox','Units','normalized', 'Position', [0.05 0.42 0.9 0.2],'BackgroundColor',[1 1 1],...
3840    'Callback',@(hObject,eventdata)ListPair_Callback(hObject,eventdata),'String',displ_pair,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3841    'Tag','ListPair','TooltipString','''ListPair'': menu for selecting the image pair');
3842uicontrol('Style','text','Units','normalized', 'Position', [0.1 0.22 0.8 0.1],'BackgroundColor',BackgroundColor,...
[992]3843    'String','ref_i           ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center'); % title
[867]3844uicontrol('Style','edit','Units','normalized', 'Position', [0.15 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3845    'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),'String',num2str(ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3846    'Tag','num_ref_i','TooltipString','''num_ref_i'': reference field index i used to display dt in ''list_pair_civ''');
3847uicontrol('Style','edit','Units','normalized', 'Position', [0.55 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3848    'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),'String',num2str(ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3849    'Tag','num_ref_j','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ''');
[880]3850uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.01 0.01 0.3 0.12],'BackgroundColor',[0 1 0],...
3851    'Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),'String','OK','FontUnits','points','FontSize',12,'FontWeight','bold',...
3852    'Tag','OK','TooltipString','''OK'': validate the choice');
[867]3853%  last raw  of the GUI: pushbuttons
3854% 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),...
3855%     'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''OK'': apply the output to the current field series in uvmat');
3856drawnow
3857
3858%------------------------------------------------------------------------
3859function ListView_Callback(hObject,eventdata)
3860Mode_Callback(hObject,eventdata)
3861
3862%------------------------------------------------------------------------   
3863function Mode_Callback(hObject,eventdata)
3864%% get input info
[992]3865hseries=findobj(allchild(0),'tag','series'); % handles of the GUI series
3866hhseries=guidata(hseries); % handles of the elements in the GUI series
[867]3867TimeUnit=get(hhseries.TimeUnit,'String');
3868SeriesData=get(hseries,'UserData');
3869mode_list=get(hObject,'String');
3870mode=mode_list{get(hObject,'Value')};
3871hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3872iview=get(hListView,'Value');
3873i1_series=SeriesData.i1_series{iview};
3874i2_series=SeriesData.i2_series{iview};
3875j1_series=SeriesData.j1_series{iview};
3876j2_series=SeriesData.j2_series{iview};
3877
3878%% enable j index visibility after the new choice
[1016]3879
3880if strcmp(mode,'series(Dj)')
3881   status_j='on'; % default
3882else
3883       status_j='off'; % no j index needed for bust case
[867]3884end
[1016]3885enable_j(hhseries,status_j) % no j index needed
[867]3886
3887%% get the reference indices for the time interval Dt
3888href_i=findobj(get(hObject,'parent'),'Tag','ref_i');
3889ref_i=[];ref_j=[];
3890if strcmp(get(href_i,'Visible'),'on')
3891    ref_i=str2num(get(href_i,'String'));
3892end
3893if isempty(ref_i)
3894    ref_i=1;
3895end
3896if isempty(ref_j)
3897    ref_j=1;
3898end
3899
3900%% update the menu ListPair
[1016]3901Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo);
[867]3902hlist_pairs=findobj(get(hObject,'parent'),'Tag','ListPair');
3903set(hlist_pairs,'Value',1)% set the first choice by default in ListPair
3904set(hlist_pairs,'String',Menu)% set the menu in ListPair
3905ListPair_Callback(hlist_pairs,[])% apply the default choice in ListPair
3906
3907%-------------------------------------------------------------
3908% --- Executes on selection in ListPair.
3909function ListPair_Callback(hObject,eventdata)
3910%------------------------------------------------------------
[992]3911list_pair=get(hObject,'String'); % get the menu of image pairs
[867]3912if isempty(list_pair)
3913    string='';
3914else
3915    string=list_pair{get(hObject,'Value')};
[992]3916   % string=regexprep(string,',.*',''); % removes time indication (after ',')
[867]3917end
3918hseries=findobj(allchild(0),'tag','series');
3919hPairString=findobj(hseries,'tag','PairString');
3920PairString=get(hPairString,'Data');
3921hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3922iview=get(hListView,'Value');
3923PairString{iview,1}=string;
3924% report the selected pair string to the table PairString
3925set(hPairString,'Data',PairString)
3926
3927
3928%------------------------------------------------------------------------
3929function num_ref_i_Callback(hObject, eventdata)
3930%------------------------------------------------------------------------
3931Mode_Callback([],[])
3932
3933%------------------------------------------------------------------------
3934function num_ref_j_Callback(hObject, eventdata)
3935%------------------------------------------------------------------------
3936Mode_Callback([],[])
3937
3938%------------------------------------------------------------------------
[880]3939function OK_Callback(hObject, eventdata)
3940%------------------------------------------------------------------------
3941delete(get(hObject,'parent'))
3942
3943
3944%------------------------------------------------------------------------
[867]3945% --- Executes on button press in ClearLine.
3946%------------------------------------------------------------------------
3947function ClearLine_Callback(hObject, eventdata, handles)
3948InputTable=get(handles.InputTable,'Data');
3949iline=str2double(get(handles.InputLine,'String'));
3950if size(InputTable,1)>1
[992]3951    InputTable(iline,:)=[]; % suppress the current line if not the first
[867]3952    set(handles.InputTable,'Data',InputTable);
3953end
[883]3954set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refr
[880]3955
3956
3957% --- Executes on button press in MonitorCluster.
3958function MonitorCluster_Callback(hObject, eventdata, handles)
3959
[1070]3960[rr,ss]=system('oarstat |grep N=UVmat');% check the list of jobs launched with uvmat
3961if isempty(ss)
3962   disp( 'no job presently submitted with uvmat')
3963else
3964    disp('format: R/W=run/wait, time lapsed, R=nbre of cores,W=walltime')
3965    disp(ss)
3966end
[991]3967
[1070]3968
[880]3969function OutputSubDir_Callback(hObject, eventdata, handles)
3970set(handles.OutputSubDir,'BackgroundColor',[1 1 1])
[904]3971
3972
3973% --- Executes on button press in CheckOverwrite.
3974function CheckOverwrite_Callback(hObject, eventdata, handles)
[880]3975
[904]3976% --- Executes on button press in TestCPUTime.
3977function TestCPUTime_Callback(hObject, eventdata, handles)
3978% hObject    handle to TestCPUTime (see GCBO)
3979% eventdata  reserved - to be defined in a future version of MATLAB
3980% handles    structure with handles and user data (see GUIDATA)
3981
3982
[994]3983% --- Executes on button press in DiskQuota.
3984function DiskQuota_Callback(hObject, eventdata, handles)
[996]3985SeriesData=get(handles.series,'UserData');
3986system(SeriesData.SeriesParam.DiskQuotaCmd)
3987
3988
[1059]3989% --- Executes on button press in Replicate.
3990function Replicate_Callback(hObject, eventdata, handles)
3991if get(handles.Replicate,'Value')
[1069]3992    InputTable=get(handles.InputTable,'Data');
3993    for ilist=1:size(InputTable,1)
3994        InputDir{ilist}=fullfile(InputTable{ilist,1},InputTable{ilist,2});
3995    end
3996    browse_data(InputDir)
[1059]3997else
3998    hh=findobj(allchild(0),'Tag','browse_data');
3999    if ~isempty(hh)
4000        delete(hh)
4001    end
[1065]4002end
[1072]4003
[1090]4004
4005
4006
4007function OutputPath_Callback(hObject, eventdata, handles)
4008
4009
4010function Experiment_Callback(hObject, eventdata, handles)
4011
4012
4013function Device_Callback(hObject, eventdata, handles)
4014
4015
4016% --- Executes on button press in OutputPathBrowse.
4017function OutputPathBrowse_Callback(hObject, eventdata, handles)
[1096]4018CheckValue=get(handles.OutputPathBrowse,'Value');
4019if CheckValue
[1090]4020OutputPath=uigetdir(get(handles.OutputPath,'String'));
4021set(handles.OutputPath,'String',OutputPath)
[1096]4022else
4023    InputTable=get(handles.InputTable,'Data');
4024    set(handles.OutputPath,'String',InputTable{1,1})
4025end
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