%'series': master function associated to the GUI series.m for analysis field series %------------------------------------------------------------------------ % function varargout = series(varargin) % associated with the GUI series.fig % %INPUT % param: structure with input parameters (link with the GUI uvmat) % .menu_coord_str: string for the TransformName (menu for coordinate transforms) % .menu_coord_val: value for TransformName (menu for coordinate transforms) % .FileName: input file name % .FileName_1: second input file name % .list_field: menu of input fields % .index_fields: chosen index % .civ1=0 or 1, .interp1, ... : input civ field type % %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA % Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA % This file is part of the toolbox UVMAT. % % UVMAT is free software; you can redistribute it and/or modify % it under the terms of the GNU General Public License as published by % the Free Software Foundation; either version 2 of the License, or % (at your option) any later version. % % UVMAT is distributed in the hope that it will be useful, % but WITHOUT ANY WARRANTY; without even the implied warranty of % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the % GNU General Public License (file UVMAT/COPYING.txt) for more details. %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA %------------------------------------------------------------------------ %------------------------------------------------------------------------ % I - MAIN FUNCTION series %------------------------------------------------------------------------ %------------------------------------------------------------------------ function varargout = series(varargin) % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name', mfilename, ... 'gui_Singleton', gui_Singleton, ... 'gui_OpeningFcn', @series_OpeningFcn, ... 'gui_OutputFcn', @series_OutputFcn, ... 'gui_LayoutFcn', [] , ... 'gui_Callback', []); if nargin && ischar(varargin{1}) gui_State.gui_Callback = str2func(varargin{1}); end if nargout [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); else gui_mainfcn(gui_State, varargin{:}); end % End initialization code - DO NOT EDIT %-------------------------------------------------------------------------- % --- Executes just before series is made visible. %-------------------------------------------------------------------------- function series_OpeningFcn(hObject, eventdata, handles,Param) % Choose default command line output for series handles.output = hObject; % Update handles structure guidata(hObject, handles); %% initial settings % position and size of the GUI at opening set(0,'Unit','points') ScreenSize=get(0,'ScreenSize');%size of the current screen, in points (1/72 inch) Width=900;% prefered width of the GUI in points (1/72 inch) Height=624;% prefered height of the GUI in points (1/72 inch) %adjust to screen size (reduced by a min margin) RescaleFactor=min((ScreenSize(3)-80)/Width,(ScreenSize(4)-80)/Height); if RescaleFactor>1 RescaleFactor=min(RescaleFactor,1); end Width=Width*RescaleFactor; Height=Height*RescaleFactor; LeftX=80*RescaleFactor;%position of the left fig side, in pixels (put to the left side, with some margin) LowY=round(ScreenSize(4)/2-Height/2); % put at the middle height on the screen set(hObject,'Units','points') set(hObject,'Position',[LeftX LowY Width Height])% position and size of the GUI at opening % settings of table MinIndex_j set(handles.MinIndex_i,'ColumnFormat',{'numeric'}) set(handles.MinIndex_i,'ColumnEditable',false) set(handles.MinIndex_i,'ColumnName',{'i min'}) set(handles.MinIndex_i,'Data',[])% initiate Data to double (not cell) % settings of table MinIndex_j set(handles.MinIndex_j,'ColumnFormat',{'numeric'}) set(handles.MinIndex_j,'ColumnEditable',false) set(handles.MinIndex_j,'ColumnName',{'j min'}) set(handles.MinIndex_j,'Data',[])% initiate Data to double (not cell) % settings of table MaxIndex_i set(handles.MaxIndex_i,'ColumnFormat',{'numeric'}) set(handles.MaxIndex_i,'ColumnEditable',false) set(handles.MaxIndex_i,'ColumnName',{'i max'}) set(handles.MaxIndex_i,'Data',[])% initiate Data to double (not cell) % settings of table MaxIndex_j set(handles.MaxIndex_j,'ColumnFormat',{'numeric'}) set(handles.MaxIndex_j,'ColumnEditable',false) set(handles.MaxIndex_j,'ColumnName',{'j max'}) set(handles.MaxIndex_j,'Data',[])% initiate Data to double (not cell) % settings of table PairString set(handles.PairString,'ColumnName',{'pairs'}) set(handles.PairString,'ColumnEditable',false) set(handles.PairString,'ColumnFormat',{'char'}) set(handles.PairString,'Data',{''}) % settings of table MaskTable set(handles.MaskTable,'ColumnName',{'mask name'}) set(handles.PairString,'ColumnEditable',false) set(handles.PairString,'ColumnFormat',{'char'}) set(handles.PairString,'Data',{''}) series_ResizeFcn(hObject, eventdata, handles)%resize table according to series GUI size set(hObject,'WindowButtonDownFcn',{'mouse_down'})%allows mouse action with right button (zoom for uicontrol display) set(handles.InputTable,'KeyPressFcn',{@key_press_fcn,handles})%set keyboard action function (allow action on uvmat when set_object is in front) set(hObject,'DeleteFcn',{@closefcn})% % check default input data if ~exist('Param','var') Param=[]; %default end %% list of builtin functions in the mebu ActionName ActionList={'check_data_files';'aver_stat';'time_series';'civ_series';'merge_proj'};% WARNING: fits with nb_builtin_ACTION=4 in ActionName_callback NbBuiltinAction=numel(ActionList); [path_series,name,ext]=fileparts(which('series'));% path to the GUI series path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series' ActionExtList={'.m';'.sh'};% default choice of extensions (Matlab fct .m or compiled version .sh ActionPathList=cell(NbBuiltinAction,numel(ActionExtList));%initiate the cell matrix of Action fct paths ActionPathList(:)={path_series_fct}; %set the default path to series fcts to all list members RunModeList={'local';'background'};% default choice of extensions (Matlab fct .m or compiled version .sh) [s,w]=system('oarstat');% look for cluster system 'oar' if isequal(s,0) RunModeList=[RunModeList;{'cluster_oar'}]; end [s,w]=system('qstat');% look for cluster system 'sge' if isequal(s,0) RunModeList=[RunModeList;{'cluster_sge'}]; end set(handles.RunMode,'String',RunModeList) %% list of builtin transform functions in the mebu TransformName TransformList={'';'sub_field';'phys';'phys_polar'};% WARNING: must fit with the corresponding menu in uvmat and nb_builtin_transform=4 in TransformName_callback NbBuiltinTransform=numel(TransformList); path_transform_fct=fullfile(path_series,'transform_field'); TransformPathList=cell(NbBuiltinTransform,1);%initiate the cell matrix of Action fct paths TransformPathList(:)={path_transform_fct}; %set the default path to series fcts to all list members %% get the user defined functions stored in the personal file uvmat_perso.mat dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') h=load (profil_perso); %get the list of previous input files in the upper bar menu Open if isfield(h,'MenuFile') for ifile=1:min(length(h.MenuFile),5) set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile}); set(handles.(['MenuFile_' num2str(ifile+5)]),'Label',h.MenuFile{ifile}); end end %get the list of previous camapigns in the upper bar menu Open campaign if isfield(h,'MenuCampaign') for ifile=1:min(length(h.MenuCampaign),5) set(handles.(['MenuCampaign_' num2str(ifile)]),'Label',h.MenuCampaign{ifile}); end end %get the menu of actions if isfield(h,'ActionExtListUser') && iscell(h.ActionExtListUser) ActionExtList=[ActionExtList; h.ActionExtListUser]; end if isfield(h,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser) ActionList=[ActionList;h.ActionListUser]; ActionPathList=[ActionPathList;h.ActionPathListUser]; end %get the menu of transform fct if isfield(h,'TransformListUser') && iscell(h.TransformListUser) && isfield(h,'TransformPathListUser') && iscell(h.TransformPathListUser) TransformList=[TransformList;h.TransformListUser]; TransformPathList=[TransformPathList;h.TransformPathListUser]; end end %% selection of the input Action fct ActionCheckExist=true(size(ActionList));%initiate the check of the path to the listed action fct for ilist=NbBuiltinAction+1:numel(ActionList)%check the validity of the path of the user defined Action fct ActionCheckExist(ilist)=exist(fullfile(ActionPathList{ilist},[ActionList{ilist} '.m']),'file'); end ActionPathList=ActionPathList(ActionCheckExist,:);% suppress the menu options which are not valid anymore ActionList=ActionList(ActionCheckExist); set(handles.ActionName,'String',[ActionList;{'more...'}]) set(handles.ActionName,'UserData',ActionPathList) ActionIndex=[]; if isfield(Param,'ActionName')% copy the selected menu index transferred in Param from uvmat ActionIndex=find(strcmp(Param.ActionName,ActionList),1); end if isempty(ActionIndex) ActionIndex=1; end set(handles.ActionName,'Value',ActionIndex) set(handles.ActionPath,'String',ActionPathList{ActionIndex}) set(handles.ActionExt,'Value',1) set(handles.ActionExt,'String',ActionExtList) %% selection of the input transform fct TransformCheckExist=true(size(TransformList)); for ilist=NbBuiltinTransform+1:numel(TransformList) TransformCheckExist(ilist)=exist(fullfile(TransformPathList{ilist},[TransformList{ilist} '.m']),'file'); end TransformPathList=TransformPathList(TransformCheckExist); TransformList=TransformList(TransformCheckExist); set(handles.TransformName,'String',[TransformList;{'more...'}]) set(handles.TransformName,'UserData',TransformPathList) TransformIndex=[]; if isfield(Param,'TransformName')% copy the selected menu index transferred in Param from uvmat TransformIndex=find(strcmp(Param.TransformName,TransformList),1); end if isempty(TransformIndex) TransformIndex=1; end set(handles.TransformName,'Value',TransformIndex) set(handles.TransformPath,'String',TransformPathList{TransformIndex}) %% fields input initialisation if isfield(Param,'list_fields')&& isfield(Param,'index_fields') &&~isempty(Param.list_fields) &&~isempty(Param.index_fields) set(handles.FieldName,'String',Param.list_fields);% list menu fields set(handles.FieldName,'Value',Param.index_fields);% selected string index end if isfield(Param,'Coord_x_str')&& isfield(Param,'Coord_x_val') set(handles.Coord_x,'String',Param.Coord_x_str);% list menu fields set(handles.Coord_x,'Value',Param.Coord_x_val);% selected string index end if isfield(Param,'Coord_y_str')&& isfield(Param,'Coord_y_val') set(handles.Coord_y,'String',Param.Coord_y_str);% list menu fields set(handles.Coord_y,'Value',Param.Coord_y_val);% selected string index end %% introduce the input file name(s) if defined from input Param if isfield(Param,'FileName')&&~isempty(Param.FileName) InputTable={}; set(handles.InputTable,'Data',InputTable) if isfield(Param,'FileName_1') display_file_name(handles,Param.FileName,'one')%refresh the input table display_file_name(handles,Param.FileName_1,1) else display_file_name(handles,Param.FileName,'one')%refresh the input table end end if isfield(Param,'incr_i') set(handles.num_incr_i,'String',num2str(Param.incr_i)) end if isfield(Param,'incr_j') set(handles.num_incr_j,'String',num2str(Param.incr_j)) end set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed %------------------------------------------------------------------------ % --- Outputs from this function are returned to the command line. function varargout = series_OutputFcn(hObject, eventdata, handles) %------------------------------------------------------------------------ varargout{1} = handles.output; %------------------------------------------------------------------------ % --- executed when closing uvmat: delete or desactivate the associated figures if exist function closefcn(gcbo,eventdata) %------------------------------------------------------------------------ % delete set_object_series if detected hh=findobj(allchild(0),'name','view_object_series'); if ~isempty(hh) delete(hh) end hh=findobj(allchild(0),'name','edit_object_series'); if ~isempty(hh) delete(hh) end %delete the bowser if detected hh=findobj(allchild(0),'tag','browser'); if ~isempty(hh) delete(hh) end %------------------------------------------------------------------------ %------------------------------------------------------------------------ % II - FUNCTIONS FOR INTRODUCING THE INPUT FILES % automatically sets the global properties when the rootfile name is introduced % then activate the view-field actionname if selected % it is activated either by clicking on the RootPath window or by the % browser %------------------------------------------------------------------------ %------------------------------------------------------------------------ % --- fct activated by the browser under 'Open' %------------------------------------------------------------------------ function MenuBrowse_Callback(hObject, eventdata, handles) %% look for the previously opened file 'oldfile' InputTable=get(handles.InputTable,'Data'); oldfile=InputTable{1,1}; if isempty(oldfile) % use a file name stored in prefdir dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') h=load (profil_perso); if isfield(h,'RootPath') && ischar(h.RootPath) oldfile=h.RootPath; end end end %% launch the browser fileinput=uigetfile_uvmat('pick an input file in the series',oldfile); hh=dir(fileinput); if numel(hh)>1 msgbox_uvmat('ERROR','invalid input, probably a broken link'); else if ~isempty(fileinput) display_file_name(handles,fileinput,'one') end end % -------------------------------------------------------------------- function MenuBrowseAppend_Callback(hObject, eventdata, handles) %% look for the previously opened file 'oldfile' InputTable=get(handles.InputTable,'Data'); RootPathCell=InputTable(:,1); if isempty(RootPathCell{1})% no input file in the table MenuBrowse_Callback(hObject, eventdata, handles)%refresh the input table, not append return end SubDirCell=InputTable(:,2); oldfile=fullfile(RootPathCell{1},SubDirCell{1}); %% use a file name stored in prefdir dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') h=load (profil_perso); if isfield(h,'RootPath') && ischar(h.RootPath) oldfile=h.RootPath; end end %% launch the browser fileinput=uigetfile_uvmat('pick a file to append in the input table',oldfile); hh=dir(fileinput); if numel(hh)>1 msgbox_uvmat('ERROR','invalid input, probably a broken link'); else if ~isempty(fileinput) display_file_name(handles,fileinput,'append') end end %------------------------------------------------------------------------ % --- fct activated by selecting a previous file under the menu Open %------------------------------------------------------------------------ function MenuFile_Callback(hObject, eventdata, handles) errormsg=display_file_name(handles,get(hObject,'Label'),'one'); if ~isempty(errormsg) set(hObject,'Label','') MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};... {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}]; str_find=strcmp(get(hObject,'Label'),MenuFile); MenuFile(str_find)=[];% suppress the input file to the list for ifile=1:numel(MenuFile) set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile}); end end %------------------------------------------------------------------------ % --- fct activated by selecting a previous file under the menu Open/append %------------------------------------------------------------------------ function MenuFile_append_Callback(hObject, eventdata, handles) InputTable=get(handles.InputTable,'Data'); if isempty(InputTable{1,1})% no input file in the table display_file_name(handles,get(hObject,'Label'),'one') %refresh the input table, not append else display_file_name(handles,get(hObject,'Label'),'append')% append the selected file to the current list of InputTable end %------------------------------------------------------------------------ % --- fct activated by the browser under 'Open campaign' %------------------------------------------------------------------------ function MenuBrowseCampaign_Callback(hObject, eventdata, handles) set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0]) drawnow InputTable=get(handles.InputTable,'Data'); RootPath=InputTable{1,1}; CampaignPath=fileparts(fileparts(RootPath)); DirFull=uigetfile_uvmat('define this path as the Campaign folder:',CampaignPath,'uigetdir'); if ~ischar(DirFull)|| ~exist(DirFull,'dir') return end OutPut=browse_data(DirFull);% open the GUI browse_data to get select a campaign dir, experiment and device if ~isfield(OutPut,'Campaign') return end DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1}); ListStruct=dir(DirName); %list files and the dir DataSeries % select the first appropriate file in the dir FileName=''; for ilist=1:numel(ListStruct) if ~isequal(ListStruct(ilist).isdir,1)%look for files, not dir FileName=ListStruct(ilist).name; FileType=get_file_type(fullfile(DirName,FileName)); switch FileType case {'image','multimage','civx','civdata','netcdf'} break end end end if isempty(FileName) msgbox_uvmat('ERROR',['no appropriate input file in the DataSeries folder ' fullfile(DirName)]) return end %% update the list of campaigns in the menubar MenuCampaign=[{get(handles.MenuCampaign_1,'Label')};{get(handles.MenuCampaign_2,'Label')};... {get(handles.MenuCampaign_3,'Label')};{get(handles.MenuCampaign_4,'Label')};{get(handles.MenuCampaign_5,'Label')}]; check_dir=isempty(find(strcmp(DirFull,MenuCampaign))); if check_dir %insert the new campaign in the list if it is not found MenuCampaign(end)=[]; %suppress the last item MenuCampaign=[{DirFull};MenuCampaign];%insert the new campaign for ilist=1:numel(MenuCampaign) set(handles.(['MenuCampaign_' num2str(ilist)]),'Label',MenuCampaign{ilist}) end % save the list for future opening: dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') save (profil_perso,'MenuCampaign','RootPath','-append'); %store the file names for future opening of uvmat else save (profil_perso,'MenuCampaign','RootPath','-V6'); %store the file names for future opening of uvmat end end %% display the selected field and related information if get(handles.CheckAppend,'Value') display_file_name(handles,fullfile(DirName,FileName),'append') else display_file_name(handles,fullfile(DirName,FileName),'one') end set(handles.MenuOpenCampaign,'ForegroundColor',[0 0 0]) % -------------------------------------------------------------------- function MenuCampaign_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0]) OutPut=browse_data(get(hObject,'Label'));% open the GUI browse_data to get select a campaign dir, experiment and device if ~isfield(OutPut,'Campaign') return end DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1}); hdir=dir(DirName); %list files and dirs for ilist=1:numel(hdir) if ~isequal(hdir(ilist).isdir,1)%look for files, not dir FileName=hdir(ilist).name; FileType=get_file_type(fullfile(DirName,FileName)); switch FileType case {'image','multimage','civx','civdata','netcdf'} break end end end if get(handles.CheckAppend,'Value') display_file_name(handles,fullfile(DirName,FileName),'append') else display_file_name(handles,fullfile(DirName,FileName),'one') end set(handles.MenuOpenCampaign,'ForegroundColor',[0 0 0]) %------------------------------------------------------------------------ % --- Executes when entered data in editable cell(s) in InputTable. function InputTable_CellEditCallback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed % set(handles.REFRESH_title,'Visible','on') iview=eventdata.Indices(1); view_set=get(handles.REFRESH,'UserData'); if isempty(find(view_set==iview)) set(handles.REFRESH,'UserData',[view_set iview]) end %% enable other menus and uicontrols set(handles.MenuOpenCampaign,'Enable','on') set(handles.MenuCampaign_1,'Enable','on') set(handles.MenuCampaign_2,'Enable','on') set(handles.MenuCampaign_3,'Enable','on') set(handles.MenuCampaign_4,'Enable','on') set(handles.MenuCampaign_5,'Enable','on') set(handles.RUN, 'Enable','On') set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red %------------------------------------------------------------------------ % --- 'key_press_fcn:' function activated when a key is pressed on the keyboard %------------------------------------------------------------------------ function key_press_fcn(hObject,eventdata,handles) xx=double(get(handles.series,'CurrentCharacter')); %get the keyboard character if ismember(xx,[8 127 31])%backspace or delete, or downward InputTable=get(handles.InputTable,'Data'); iline=get(handles.InputTable,'UserData'); if isequal(xx, 31) if isequal(iline,size(InputTable,1))% arrow downward InputTable=[InputTable;cell(1,size(InputTable,2))]; end else InputTable(iline,:)=[];% suppress the current line end set(handles.InputTable,'Data',InputTable); end %------------------------------------------------------------------------ % --- Executes on button press in REFRESH. function REFRESH_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ InputTable=get(handles.InputTable,'Data'); set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch' set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH button to yellow color (indicate activation) drawnow empty_line=false(size(InputTable,1),1); for iline=1:size(InputTable,1) empty_line(iline)= isempty(cell2mat(InputTable(iline,1:3))); end InputTable(empty_line,:)=[];%remove empty lines set(handles.InputTable,'Data',InputTable) for iview=1:size(InputTable,1) RootPath=fullfile(InputTable{iview,1},InputTable{iview,2}); if ~exist(RootPath,'dir') i1_series=[]; RootPath=fileparts(RootPath); %will try the upper folder else %scan the input folder [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,FileInfo,MovieObject]=... find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]); end % if no file is found, open a browser if isempty(i1_series) fileinput=uigetfile_uvmat(['wrong input at line ' num2str(iview) ':pick a new input file'],RootPath); if isempty(fileinput) set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH back to red color return else display_file_name(handles,fileinput,iview) end else update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,FileInfo,MovieObject,iview) end end set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH button to red color (indicate activation finished) set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch' %------------------------------------------------------------------------ % --- Function called when a new file is opened, either by series_OpeningFcn or by the browser function errormsg=display_file_name(handles,fileinput,iview) %------------------------------------------------------------------------ % % INPUT: % handles: handles of elements in the GUI % fileinput: input file name, including path % iview: line index in the input table % or 'one': refresh the list % 'append': add a new line to the input table set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH button to yellow color (indicate activation) drawnow errormsg='';%default %% get the input root name, indices, file extension and nomenclature NomType if ~exist(fileinput,'file') errormsg=['input file ' fileinput ' does not exist']; msgbox_uvmat('ERROR',errormsg) set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH button to red color (end of activation) return end %% detect root name, nomenclature and indices in the input file name: [FilePath,FileName,FileExt]=fileparts(fileinput); % detect the file type, get the movie object if relevant, and look for the corresponding file series: % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]); if isempty(RootFile)&&isempty(i1_series) errormsg='no input file in the series'; msgbox_uvmat('ERROR',errormsg) set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH button to red color (end of activation) return end if strcmp(FileType,'txt') edit(fileinput) set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH button to red color (end of activation) return elseif strcmp(FileType,'xml') editxml(fileinput) set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH button to red color (end of activation) return elseif strcmp(FileType,'figure') open(fileinput) set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH button to red color (end of activation) return end %% enable other menus and uicontrols set(handles.MenuOpenCampaign,'Enable','on') set(handles.MenuCampaign_1,'Enable','on') set(handles.MenuCampaign_2,'Enable','on') set(handles.MenuCampaign_3,'Enable','on') set(handles.MenuCampaign_4,'Enable','on') set(handles.MenuCampaign_5,'Enable','on') set(handles.RUN, 'Enable','On') set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box to yellow drawnow %% fill the list of file series InputTable=get(handles.InputTable,'Data'); SeriesData=get(handles.series,'UserData'); if strcmp(iview,'append') % display the input data as a new line in the table iview=size(InputTable,1)+1;% the next line in InputTable becomes the current line %InputTable(iview+1,:)={'','','','',''}; InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}]; elseif strcmp(iview,'one') % refresh the list of input file series iview=1; %the first line in InputTable becomes the current line InputTable={'','','','',''}; %InputTable=[{'','','','',''};{'','','','',''}]; InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}]; set(handles.TimeTable,'Data',[{[]},{[]},{[]},{[]}]) set(handles.MinIndex_i,'Data',[]) set(handles.MaxIndex_i,'Data',[]) set(handles.MinIndex_j,'Data',[]) set(handles.MaxIndex_j,'Data',[]) set(handles.ListView,'Value',1) set(handles.ListView,'String',{'1'}) set(handles.PairString,'Data',{''}) SeriesData.i1_series={}; SeriesData.i2_series={}; SeriesData.j1_series={}; SeriesData.j2_series={}; SeriesData.FileType={}; SeriesData.FileInfo={}; SeriesData.Time={}; end %nbview=size(InputTable,1)-1;% rmq: the last line is set blank to allow manual addition of a line nbview=size(InputTable,1); set(handles.ListView,'String',mat2cell((1:nbview)',ones(nbview,1))) set(handles.ListView,'Value',iview) set(handles.InputTable,'Data',InputTable) %% determine the selected reference field indices for pair display if isempty(i1) i1=1; end if isempty(i2) i2=i1; end ref_i=floor((i1+i2)/2);% reference image number corresponding to the file set(handles.num_ref_i,'String',num2str(ref_i)); % set(handles.num_ref_i,'UserData',[i1 i2])%store the indices for future opening if isempty(j1) j1=1; end if isempty(j2) j2=j1; end ref_j=floor((j1+j2)/2);% reference image number corresponding to the file set(handles.num_ref_j,'String',num2str(ref_j)); %% update first and last indices if they do not exist Param=read_GUI(handles.series); first_j=[]; if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end last_j=[]; if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end PairString=''; if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); if ~exist(FirstFileName,'file') set(handles.num_first_i,'String',num2str(ref_i)) set(handles.num_first_j,'String',num2str(ref_j)) end [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString); LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); if ~exist(LastFileName,'file') set(handles.num_last_i,'String',num2str(ref_i)) set(handles.num_last_j,'String',num2str(ref_j)) end %% update the list of recent files in the menubar and save it for future opening MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};... {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}]; str_find=strcmp(fileinput,MenuFile); if isempty(find(str_find,1)) MenuFile=[{fileinput};MenuFile];%insert the current file if not already in the list end for ifile=1:min(length(MenuFile),5) eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});']) end dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat else save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat end % save the opened file to initiate future opening SeriesData.RefFile{iview}=fileinput;% reference opening file for line iview SeriesData.Ref_i1=i1; SeriesData.Ref_i2=i2; SeriesData.Ref_j1=j1; SeriesData.Ref_j2=j2; set(handles.series,'UserData',SeriesData) set(handles.InputTable,'BackgroundColor',[1 1 1]) %% initiate input file series and refresh the current field view: update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,FileInfo,MovieObject,iview); set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH button to red color (end of activation) %------------------------------------------------------------------------ % --- Update information about a new field series (indices to scan, timing, % calibration from an xml file function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,FileInfo,VideoObject,iview) %------------------------------------------------------------------------ InputTable=get(handles.InputTable,'Data'); %% display the min and max indices for the whole file series if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0 MinIndex_j=1;% index j set to 1 by default MaxIndex_j=1; 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) 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) else ref_i=squeeze(max(i1_series(1,:,:),[],2));% select ref_j index for each ref_i ref_j=squeeze(max(j1_series(1,:,:),[],3));% select ref_i index for each ref_j MinIndex_i=min(find(ref_i))-1; MaxIndex_i=max(find(ref_i))-1; MaxIndex_j=max(find(ref_j))-1; MinIndex_j=min(find(ref_j))-1; diff_j_max=diff(ref_j); diff_i_max=diff(ref_i); if ~isempty(diff_i_max) && isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max))) set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to dispaly by default end if ~isempty(diff_j_max) && isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max))) set(handles.num_incr_j,'String',num2str(diff_j_max(1))) end end if isequal(MinIndex_i,-1) MinIndex_i=0; end if isequal(MinIndex_j,-1) MinIndex_j=0; end MinIndex_i_table=get(handles.MinIndex_i,'Data');%retrieve the min indices in the table MinIndex MinIndex_j_table=get(handles.MinIndex_j,'Data');%retrieve the min indices in the table MinIndex MaxIndex_i_table=get(handles.MaxIndex_i,'Data');%retrieve the min indices in the table MinIndex MaxIndex_j_table=get(handles.MaxIndex_j,'Data');%retrieve the min indices in the table MinIndex if ~isempty(MinIndex_i)&&~isempty(MaxIndex_i) MinIndex_i_table(iview,1)=MinIndex_i; MaxIndex_i_table(iview,1)=MaxIndex_i; end if ~isempty(MinIndex_j)&&~isempty(MaxIndex_j) MinIndex_j_table(iview,1)=MinIndex_j; MaxIndex_j_table(iview,1)=MaxIndex_j; end set(handles.MinIndex_i,'Data',MinIndex_i_table)%display the min indices in the table MinIndex set(handles.MinIndex_j,'Data',MinIndex_j_table)%display the max indices in the table MaxIndex set(handles.MaxIndex_i,'Data',MaxIndex_i_table)%display the min indices in the table MinIndex set(handles.MaxIndex_j,'Data',MaxIndex_j_table)%display the max indices in the table MaxIndex %% adjust the first and last indices for the selected series, only if requested by the bounds % i index, compare input to min index i first_i=str2num(get(handles.num_first_i,'String'));%retrieve previous first i ref_i=str2num(get(handles.num_ref_i,'String'));%index i given by the input field if isempty(first_i) first_i=ref_i;% first_i updated by the input value elseif first_i < MinIndex_i first_i=MinIndex_i; % first_i set to the min i index (restricted by oter input lines) elseif first_i >MaxIndex_i first_i=MaxIndex_i;% first_i set to the max i index (restricted by oter input lines) end % j index, compare input to min index j first_j=str2num(get(handles.num_first_j,'String')); ref_j=str2num(get(handles.num_ref_j,'String'));%index j given by the input field if isempty(first_j) first_j=ref_j;% first_j updated by the input value elseif first_jMaxIndex_j first_j=MaxIndex_j; % first_j set to the max j index (restricted by oter input lines) end % i index, compare input to max index i last_i=str2num(get(handles.num_last_i,'String')); if isempty(last_i) last_i=ref_i; elseif last_i > MaxIndex_i last_i=MaxIndex_i; elseif last_iMaxIndex_j last_j=MaxIndex_j; elseif last_j1) if iview>1 && strcmp(get(handles.num_NbSlice,'Visible'),'on') NbSlice=str2num(get(handles.num_NbSlice,'String')); end %% default time unit TimeUnit=''; % read value set by the first series for the checkappend mode (iwiew >1) if iview>1 TimeUnit=get(handles.TimeUnit,'String'); end TimeSource=''; Time=[];%default %% read image documentation file if found XmlData=[]; check_calib=0; XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5}); if ~isempty(XmlFileName) [XmlData,errormsg]=imadoc2struct(XmlFileName); if ~isempty(errormsg) msgbox_uvmat('WARNING',['error in reading ' XmlFileName ': ' errormsg]); end % read time if available if isfield(XmlData,'Time') Time=XmlData.Time; TimeSource='xml'; end if isfield(XmlData,'Camera') if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice) if iview>1 && ~isempty(NbSlice) && ~strcmp(NbSlice,XmlData.Camera.NbSlice) msgbox_uvmat('WARNING','inconsistent number of slices with the first field series'); end NbSlice=XmlData.Camera.NbSlice;% Nbre of slices from camera end if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit) if iview>1 && ~isempty(TimeUnit) && ~strcmp(TimeUnit,XmlData.Camera.TimeUnit) msgbox_uvmat('WARNING','inconsistent time unit with the first field series'); end TimeUnit=XmlData.Camera.TimeUnit; end end % number of slices if isfield(XmlData,'GeometryCalib') check_calib=1; if isfield(XmlData.GeometryCalib,'SliceCoord') siz=size(XmlData.GeometryCalib.SliceCoord); if siz(1)>1 if iview>1 && ~isempty(NbSlice) && ~strcmp(NbSlice,siz(1)) msgbox_uvmat('WARNING','inconsistent number of Z indices with the first field series'); end NbSlice=siz(1); end end end set(handles.num_NbSlice,'String',num2str(NbSlice)) end %% read timing and total frame number from the current file (movie files) if not already set by the xml file (prioritary) InputTable=get(handles.InputTable,'Data'); % case of movies if isempty(Time) if ~isempty(VideoObject) imainfo=get(VideoObject); if isempty(j1_series); %frame index along i Time=zeros(imainfo.NumberOfFrames+1,2); Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)'; else Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate); end TimeSource='video'; end end %% update time table if ~isempty(Time) TimeTable=get(handles.TimeTable,'Data'); TimeTable{iview,1}=Time(MinIndex_i+1,MinIndex_j+1); if size(Time)>=[first_i+1 first_j+1] TimeTable{iview,2}=Time(first_i+1,first_j+1); end if size(Time)>=[last_i+1 last_j+1] TimeTable{iview,3}=Time(last_i+1,last_j+1); end if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1]; TimeTable{iview,4}=Time(MaxIndex_i+1,MaxIndex_j+1); end set(handles.TimeTable,'Data',TimeTable) end %% update the series info in 'UserData' SeriesData=get(handles.series,'UserData'); SeriesData.i1_series{iview}=i1_series; SeriesData.i2_series{iview}=i2_series; SeriesData.j1_series{iview}=j1_series; SeriesData.j2_series{iview}=j2_series; SeriesData.FileType{iview}=FileType; SeriesData.FileInfo{iview}=FileInfo; SeriesData.Time{iview}=Time; if ~isempty(TimeSource) SeriesData.TimeSource=TimeSource; end % if ~isempty(TimeUnit) % SeriesData.TimeUnit=TimeUnit; % end if check_calib SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib; end set(handles.series,'UserData',SeriesData) %% update pair menus ListView=get(handles.ListView,'String'); ListView{iview}=num2str(iview); set(handles.ListView,'String',ListView); set(handles.ListView,'Value',iview) update_mode(handles,i1_series,i2_series,j1_series,j2_series,Time) %% enable j index visibility status_j='on';%default if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices status_j='off'; % no j index needed elseif strcmp(get(handles.PairString,'Visible'),'on') PairString=get(handles.PairString,'Data'); check_burst=cellfun(@isempty,regexp(PairString,'^j'));%=0 for burst case, 1 otherwise if isempty(find(check_burst, 1))% if all pair string begins by j (burst) status_j='off'; % no j index needed for bust case end end enable_j(handles,status_j) % no j index needed %% display the set of existing files as an image set(handles.FileStatus,'Units','pixels') Position=get(handles.FileStatus,'Position'); set(handles.FileStatus,'Units','normalized') %xI=0.5:Position(3)-0.5; nbview=numel(SeriesData.i1_series); j_max=cell(1,nbview); MaxIndex_i=ones(1,nbview);%default MinIndex_i=ones(1,nbview);%default for iview=1:nbview pair_max=squeeze(max(SeriesData.i1_series{iview},[],1)); %max on pair index j_max{iview}=max(pair_max,[],1);%max on j index if ~isempty(j_max{iview}) MaxIndex_i(iview)=max(find(j_max{iview}))-1;% max ref index i MinIndex_i(iview)=min(find(j_max{iview}))-1;% min ref index i end end MinIndex_i=min(MinIndex_i); MaxIndex_i=max(MaxIndex_i); range_index=MaxIndex_i-MinIndex_i+1; % scale_y=Position(4)/nbview; % scale_x=Position(3)/range_index; %x=(0.5:range_index-0.5)*Position(3)/range_index;% set of abscissa representing the whole i index range % y=(0.5:nbview-0.5)*Position(4)/nbview; range_y=max(1,floor(Position(4)/nbview)); npx=floor(Position(3)); file_indices=MinIndex_i+floor(((0.5:npx-0.5)/npx)*range_index)+1; CData=zeros(nbview*range_y,npx);% initiate the image representing the existing files for iview=1:nbview ind_y=1+(iview-1)*range_y:iview*range_y; LineData=zeros(size(file_indices)); file_select=file_indices(file_indices<=numel(j_max{iview})); ind_select=find(file_indices<=numel(j_max{iview})); LineData(ind_select)=j_max{iview}(file_select)~=0; CData(ind_y,:)=ones(size(ind_y'))*LineData; end CData=cat(3,zeros(size(CData)),CData,zeros(size(CData)));%make color images r=0,g,b=0 set(handles.FileStatus,'CData',CData); %% check for pair display check_pairs=0; for iview=1:numel(SeriesData.i2_series) if ~isempty(SeriesData.i2_series{iview})||~isempty(SeriesData.j2_series{iview}) check_pairs=1; end end if check_pairs set(handles.Pairs,'Visible','on') set(handles.PairString,'Visible','on') else set(handles.Pairs,'Visible','off') set(handles.PairString,'Visible','off') end %% enable field and veltype menus, in accordance with the current action ActionName_Callback([],[], handles) %% set length of waitbar displ_time(handles) %% set default options in menu 'Fields' switch FileType case {'civx','civdata'} [FieldList,ColorList]=set_field_list('U','V','C'); set(handles.FieldName,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data set(handles.FieldName,'Value',2) % set menu to 'velocity set(handles.Coord_x,'Value',1); set(handles.Coord_x,'String',{'X'}); set(handles.Coord_y,'Value',1); set(handles.Coord_y,'String',{'Y'}); case 'netcdf' set(handles.FieldName,'Value',1) set(handles.FieldName,'String',{'get_field...'}) if isempty(i2_series) i2=[]; else i2=i2_series(1,ref_j+1,ref_i+1); end if isempty(j1_series) j1=[];j2=[]; else j1=j1_series(1,ref_j+1,ref_i+1); if isempty(j2_series) j2=[]; else j2=j2_series(1,ref_j+1,ref_i+1); end end FieldName_Callback([], [], handles) % FileName=fullfile_uvmat(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5},InputTable{iview,4},i1_series(1,ref_j+1,ref_i+1),i2,j1,j2); % hget_field=get_field(FileName); % hhget_field=guidata(hget_field); % get_field('RUN_Callback',hhget_field.RUN,[],hhget_field); otherwise set(handles.FieldName,'Value',1) % set menu to 'image' set(handles.FieldName,'String',{'image'}) set(handles.Coord_x,'Value',1); set(handles.Coord_x,'String',{'AX'}); set(handles.Coord_y,'Value',1); set(handles.Coord_y,'String',{'AY'}); end %------------------------------------------------------------------------ function num_first_i_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ num_last_i_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ function num_last_i_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ SeriesData=get(handles.series,'UserData'); if ~isfield(SeriesData,'Time') SeriesData.Time{1}=[]; end displ_time(handles); %------------------------------------------------------------------------ function num_first_j_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ num_last_j_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ function num_last_j_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ first_j=str2num(get(handles.num_first_j,'String')); last_j=str2num(get(handles.num_last_j,'String')); ref_j=ceil((first_j+last_j)/2); set(handles.num_ref_j,'String', num2str(ref_j)) num_ref_j_Callback(hObject, eventdata, handles) SeriesData=get(handles.series,'UserData'); if ~isfield(SeriesData,'Time') SeriesData.Time{1}=[]; end displ_time(handles); %------------------------------------------------------------------------ % ---- find the times corresponding to the first and last indices of a series function displ_time(handles) %------------------------------------------------------------------------ SeriesData=get(handles.series,'UserData');% PairString=get(handles.PairString,'Data'); ref_i_1=str2num(get(handles.num_first_i,'String'));%first reference index ref_i_2=str2num(get(handles.num_last_i,'String'));%last reference index ref_j_1=[];ref_j_2=[]; if strcmp(get(handles.num_first_j,'Visible'),'on') ref_j_1=str2num(get(handles.num_first_j,'String')); ref_j_2=str2num(get(handles.num_last_j,'String')); end [i1_1,i2_1,j1_1,j2_1] = get_file_index(ref_i_1,ref_j_1,PairString); [i1_2,i2_2,j1_2,j2_2] = get_file_index(ref_i_2,ref_j_2,PairString); TimeTable=get(handles.TimeTable,'Data'); %Pairs=get(handles.PairString,'Data'); for iview=1:size(TimeTable,1) if size(SeriesData.Time,1)=i2_2+1 && (isempty(ref_j_1)||size(SeriesData.Time{iview},2)>=j2_2+1) if isempty(ref_j_1) time_first=(SeriesData.Time{iview}(i1_1+1,2)+SeriesData.Time{iview}(i2_1+1,2))/2; time_last=(SeriesData.Time{iview}(i1_2+1,2)+SeriesData.Time{iview}(i2_2+1,2))/2; else time_first=(SeriesData.Time{iview}(i1_1+1,j1_1+1)+SeriesData.Time{iview}(i2_1+1,j2_1+1))/2; time_last=(SeriesData.Time{iview}(i1_2+1,j1_2+1)+SeriesData.Time{iview}(i2_2+1,j2_1+1))/2; end TimeTable{iview,2}=time_first; %TODO: take into account pairs TimeTable{iview,3}=time_last; %TODO: take into account pairs end end set(handles.TimeTable,'Data',TimeTable) %% set the waitbar position with respect to the min and max in the series MinIndex_i=min(get(handles.MinIndex_i,'Data')); MaxIndex_i=max(get(handles.MaxIndex_i,'Data')); pos_first=(ref_i_1-MinIndex_i)/(MaxIndex_i-MinIndex_i+1); pos_last=(ref_i_2-MinIndex_i+1)/(MaxIndex_i-MinIndex_i+1); if isempty(pos_first), pos_first=0; end if isempty(pos_last), pos_last=1; end Position=get(handles.Waitbar,'Position');% position of the waitbar:= [ x,y, width, height] Position_status=get(handles.FileStatus,'Position'); Position(1)=Position_status(1)+Position_status(3)*pos_first; Position(3)=max(Position_status(3)*(pos_last-pos_first),0.001);% width must remain positive set(handles.Waitbar,'Position',Position) update_waitbar(handles.Waitbar,0) %------------------------------------------------------------------------ % --- Executes when selected cell(s) is changed in PairString. function PairString_CellSelectionCallback(hObject, eventdata, handles) %------------------------------------------------------------------------ if numel(eventdata.Indices)>=1 set(handles.ListView,'Value',eventdata.Indices(1))% detect the selected raw index ListView_Callback ([],[],handles) % update the list of available pairs end %------------------------------------------------------------------------ %------------------------------------------------------------------------ % III - FUNCTIONS ASSOCIATED TO THE FRAME SET PAIRS %------------------------------------------------------------------------ %------------------------------------------------------------------------ % --- Executes on selection change in ListView. function ListView_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ SeriesData=get(handles.series,'UserData'); i2_series=[]; j2_series=[]; iview=get(handles.ListView,'Value'); if ~isempty(SeriesData.i2_series{iview}) i2_series=SeriesData.i2_series{iview}; end if ~isempty(SeriesData.j2_series{iview}) j2_series=SeriesData.j2_series{iview}; end update_mode(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},... SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview}) %------------------------------------------------------------------------ % --- Executes on button press in mode. function mode_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ SeriesData=get(handles.series,'UserData'); iview=get(handles.ListView,'Value'); mode_list=get(handles.mode,'String'); mode=mode_list{get(handles.mode,'Value')}; if isequal(mode,'bursts') enable_i(handles,'On') enable_j(handles,'Off') %do not display j index scanning in burst mode (j is fixed by the burst choice) else enable_i(handles,'On') enable_j(handles,'Off') end fill_ListPair(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},... SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview}) ListPairs_Callback([],[],handles) %------------------------------------------------------------- % --- Executes on selection in ListPairs. function ListPairs_Callback(hObject,eventdata,handles) %------------------------------------------------------------ list_pair=get(handles.ListPairs,'String');%get the menu of image pairs if isempty(list_pair) string=''; else string=list_pair{get(handles.ListPairs,'Value')}; string=regexprep(string,',.*','');%removes time indication (after ',') end PairString=get(handles.PairString,'Data'); iview=get(handles.ListView,'Value'); PairString{iview,1}=string; % report the selected pair string to the table PairString set(handles.PairString,'Data',PairString) %------------------------------------------------------------------------ function num_ref_i_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ mode_list=get(handles.mode,'String'); mode=mode_list{get(handles.mode,'Value')}; SeriesData=get(handles.series,'UserData'); iview=get(handles.ListView,'Value'); fill_ListPair(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},... SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview});% update the menu of pairs depending on the available netcdf files ListPairs_Callback([],[],handles) %------------------------------------------------------------------------ function num_ref_j_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ num_ref_i_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ function update_mode(handles,i1_series,i2_series,j1_series,j2_series,time) %------------------------------------------------------------------------ % check_burst=0; if isempty(j2_series)% no j pair if isempty(i2_series) set(handles.mode,'Value',1) set(handles.mode,'String',{''})% no pair menu to display else set(handles.mode,'Value',1) set(handles.mode,'String',{'series(Di)'}) % pair menu with only option Di end else %existence of j pairs pair_max=squeeze(max(i1_series,[],1)); %max on pair index j_max=max(pair_max,[],1); MaxIndex_i=max(find(j_max))-1;% max ref index i MinIndex_i=min(find(j_max))-1;% min ref index i i_max=max(pair_max,[],2); MaxIndex_j=max(find(i_max))-1;% max ref index i MinIndex_j=min(find(i_max))-1;% min ref index i if MaxIndex_j==MinIndex_j set(handles.mode,'Value',1); set(handles.mode,'String',{'bursts'}) % check_burst=1; elseif MaxIndex_i==MinIndex_i set(handles.mode,'Value',1); set(handles.mode,'String',{'series(Dj)'}) else set(handles.mode,'String',{'bursts';'series(Dj)'}) if (MaxIndex_j-MinIndex_j)>10 set(handles.mode,'Value',2);%set mode to series(Dj) if more than 10 j values else set(handles.mode,'Value',1); % check_burst=1; end end end fill_ListPair(handles,i1_series,i2_series,j1_series,j2_series,time) ListPairs_Callback([],[],handles) %-------------------------------------------------------------- % determine the menu for pairstring depending on existing netcdf files % with the reference indices num_ref_i and num_ref_j %---------------------------------------------------------------- function fill_ListPair(handles,i1_series,i2_series,j1_series,j2_series,time) mode_list=get(handles.mode,'String'); mode=mode_list{get(handles.mode,'Value')}; ref_i=str2num(get(handles.num_ref_i,'String')); if isempty(ref_i) ref_i=1; end if strcmp(get(handles.num_ref_j,'Visible'),'on') ref_j=str2num(get(handles.num_ref_j,'String')); if isempty(ref_j) ref_j=1; end else ref_j=1; end TimeUnit=get(handles.TimeUnit,'String'); if length(TimeUnit)>=1 dtunit=['m' TimeUnit]; else dtunit='e-03'; end displ_pair={}; if strcmp(mode,'series(Di)') if isempty(i2_series) msgbox_uvmat('ERROR','no i1-i2 pair available') return end diff_i=i2_series-i1_series; min_diff=min(diff_i(diff_i>0)); max_diff=max(diff_i(diff_i>0)); for ipair=min_diff:max_diff if numel(diff_i(diff_i==ipair))>0 pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ]; if ~isempty(time) if ref_i<=floor(ipair/2) ref_i=floor(ipair/2)+1;% shift ref_i to get the first pair end Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j); pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit]; end displ_pair=[displ_pair;{pair_string}]; end end if ~isempty(displ_pair) displ_pair=[displ_pair;{'Di=*|*'}]; end elseif strcmp(mode,'series(Dj)') if isempty(j2_series) msgbox_uvmat('ERROR','no j1-j2 pair available') return end diff_j=j2_series-j1_series; min_diff=min(diff_j(diff_j>0)); max_diff=max(diff_j(diff_j>0)); for ipair=min_diff:max_diff if numel(diff_j(diff_j==ipair))>0 pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ]; if ~isempty(time) if ref_j<=floor(ipair/2) ref_j=floor(ipair/2)+1;% shift ref_i to get the first pair end Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2)); pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit]; end displ_pair=[displ_pair;{pair_string}]; end end if ~isempty(displ_pair) displ_pair=[displ_pair;{'Dj=*|*'}]; end elseif strcmp(mode,'bursts') if isempty(j2_series) msgbox_uvmat('ERROR','no j1-j2 pair available') return end diff_j=j2_series-j1_series; min_j1=min(j1_series(j1_series>0)); max_j1=max(j1_series(j1_series>0)); min_j2=min(j2_series(j2_series>0)); max_j2=max(j2_series(j2_series>0)); for pair1=min_j1:min(max_j1,min_j1+20) for pair2=min_j2:min(max_j2,min_j2+20) if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0 displ_pair=[displ_pair;{['j= ' num2str(pair1) '-' num2str(pair2)]}]; end end end if ~isempty(displ_pair) displ_pair=[displ_pair;{'j=*-*'}]; end end set(handles.num_ref_i,'String',num2str(ref_i)) % update ref_i and ref_j set(handles.num_ref_j,'String',num2str(ref_j)) %% display list of pairstring displ_pair_list=get(handles.ListPairs,'String'); NewVal=[]; if ~isempty(displ_pair_list) Val=get(handles.ListPairs,'Value'); NewVal=find(strcmp(displ_pair_list{Val},displ_pair),1);% look at the previous display in the new menu displ_p�ir end if ~isempty(NewVal) set(handles.ListPairs,'Value',NewVal) else set(handles.ListPairs,'Value',1) end set(handles.ListPairs,'String',displ_pair) %------------------------------------- function enable_i(handles,state) set(handles.i_txt,'Visible',state) set(handles.num_first_i,'Visible',state) set(handles.num_last_i,'Visible',state) set(handles.num_incr_i,'Visible',state) set(handles.num_ref_i,'Visible',state) set(handles.ref_i_text,'Visible',state) %----------------------------------- function enable_j(handles,state) set(handles.j_txt,'Visible',state) set(handles.num_first_j,'Visible',state) set(handles.num_last_j,'Visible',state) set(handles.num_incr_j,'Visible',state) set(handles.num_ref_j,'Visible',state) set(handles.ref_j_text,'Visible',state) set(handles.MinIndex_j,'Visible',state) set(handles.MaxIndex_j,'Visible',state) %%%%%%%%%%%%%%%%%%%% %% MAIN ActionName FUNCTIONS %%%%%%%%%%%%%%%%%%%% %------------------------------------------------------------------------ % --- Executes on button press in RUN. %------------------------------------------------------------------------ function RUN_Callback(hObject, eventdata, handles) %% settings of the button RUN set(handles.RUN,'BusyAction','queue');% activation of STOP button will set BusyAction to 'cancel' set(handles.RUN, 'Enable','Off')% avoid further RUN action until the current one is finished set(handles.RUN,'BackgroundColor',[1 1 0])%show activation of RUN by yellow color drawnow set(handles.status,'Value',0)% desable status display if relevant status_Callback(hObject, eventdata, handles) %% read the data on the GUI series Param=read_GUI_series(handles);%displayed parameters SeriesData=get(handles.series,'UserData');%hidden parameters %% create the output data directory if needed if isfield(Param,'OutputSubDir') SubDirOut=[get(handles.OutputSubDir,'String') Param.OutputDirExt]; SubDirOutNew=SubDirOut; detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir');% test if the dir already exist check_create=1; %need to create the result directory by default while detect answer=msgbox_uvmat('INPUT_Y-N',['use existing ouput directory: ' fullfile(Param.InputTable{1,1},SubDirOutNew) ', possibly delete previous data']); if strcmp(answer,'Cancel') errormsg='Cancel'; return elseif strcmp(answer,'Yes') detect=0; check_create=0; else r=regexp(SubDirOutNew,'(?.*\D)(?\d+)$','names');%detect whether name ends by a number if isempty(r) r(1).root=[SubDirOutNew '_']; r(1).num1='0'; end SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1 detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir');% test if the dir already exists check_create=1; end end Param.OutputDirExt=regexprep(SubDirOutNew,Param.OutputSubDir,''); Param.OutputRootFile=Param.InputTable{1,3};% the first sorted RootFile taken for output set(handles.OutputDirExt,'String',Param.OutputDirExt) OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]);% full name (with path) of output directory if check_create % create output directory if it does not exist [tild,msg1]=mkdir(OutputDir); if ~strcmp(msg1,'') msgbox_uvmat('ERROR',['cannot create ' OutputDir ': ' msg1]);%error message for directory creation return end [success,msg] = fileattrib(OutputDir,'+w','g','s');% allow writing access for the group of users, recursively in the folder if success==0 msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg1});%error message for directory creation return end end OutputNomType=nomtype2pair(Param.InputTable{1,4});% nomenclature for output files DirXml=fullfile(OutputDir,'0_XML'); if ~exist(DirXml,'dir') [tild,msg1]=mkdir(DirXml); if ~strcmp(msg1,'') msgbox_uvmat('ERROR',['cannot create ' DirXml ': ' msg1]);%error message for directory creation return end [success,msg] = fileattrib(DirXml,'+w','g','s');% allow writing access for the group of users, recursively in the folder if success==0 msgbox_uvmat('WARNING',{['unable to set group write access to ' DirXml ':']; msg1});%error message for directory creation return end end end %% select the Action mode, 'local', 'background' or 'cluster' (if available) RunMode='local';%default (needed for first opening of the GUI series) if isfield(Param.Action,'RunMode') RunMode=Param.Action.RunMode; end ActionExt='.m';%default if isfield(Param.Action,'ActionExt') ActionExt=Param.Action.ActionExt;% '.m' or '.sh' (compiled) end ActionName=Param.Action.ActionName; ActionPath=Param.Action.ActionPath; path_series=fileparts(which('series')); %% create the Action fct handle if RunMode option = 'local' if strcmp(RunMode,'local') if ~isequal(ActionPath,path_series) eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION if ~exist(ActionPath,'dir') msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']); return end if ~isequal(spath,ActionPath) addpath(ActionPath)% add the prescribed path if not the current one end end eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION if ~isequal(ActionPath,path_series) rmpath(ActionPath)% add the prescribed path if not the current one end end %% Get RunTime code from the file PARAM.xml (needed to run compiled functions) errormsg='';%default error message xmlfile=fullfile(path_series,'PARAM.xml'); test_batch=0;%default: ,no batch mode available if ~exist(xmlfile,'file') [success,message]=copyfile(fullfile(path_series,'PARAM.xml.default'),xmlfile); end RunTime=''; if strcmp(ActionExt,'.sh') if exist(xmlfile,'file') s=xml2struct(xmlfile); if strcmp(RunMode,'cluster_oar') && isfield(s,'BatchParam') if isfield(s.BatchParam,'RunTime') RunTime=s.BatchParam.RunTime; end if isfield(s.BatchParam,'NbCore') NbCore=s.BatchParam.NbCore; end elseif (strcmp(RunMode,'background')||strcmp(RunMode,'local')) && isfield(s,'RunParam') if isfield(s.RunParam,'RunTime') RunTime=s.RunParam.RunTime; end if isfield(s.RunParam,'NbCore') NbCore=s.RunParam.NbCore; end end end if isempty(RunTime) && strcmp(RunMode,'cluster_oar') msgbox_uvmat('ERROR','RunTime name not found in PARAM.xml, compiled version .sh cannot run on cluster') return end end %% set nbre of cluster cores and processes switch RunMode case {'local','background'} NbCore=1;% no need to split the calculation case 'cluster_oar' if strcmp(Param.Action.ActionExt,'.m')% case of Matlab function (uncompiled) NbCore=1;% one core used only (limitation of Matlab licences) msgbox_uvmat('WARNING','Number of cores =1: select the compiled version civ_matlab.sh for multi-core processing'); extra_oar=''; else answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''}); NbCore=str2double(answer{1}); extra_oar=answer{2}; end end if ~isfield(Param.IndexRange,'NbSlice') Param.IndexRange.NbSlice=[]; end if isempty(Param.IndexRange.NbSlice) NbProcess=NbCore;% choose one process per core else NbProcess=Param.IndexRange.NbSlice;% the nbre of run processes is equal to the number of slices NbCore=min(NbCore,NbProcess);% at least one process per core end %% get the set of reference field indices first_i=1; last_i=1; incr_i=1; first_j=1; last_j=1; incr_j=1; if isfield(Param.IndexRange,'first_i') first_i=Param.IndexRange.first_i; incr_i=Param.IndexRange.incr_i; last_i=Param.IndexRange.last_i; end if isfield(Param.IndexRange,'first_j') first_j=Param.IndexRange.first_j; last_j=Param.IndexRange.last_j; incr_j=Param.IndexRange.incr_j; end if last_i < first_i || last_j < first_j msgbox_uvmat('ERROR', 'series/Run_Callback:last field index must be larger or equal to the first one') set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]) return end %incr_i must be defined, =1 by default, if NbSlice is active if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice) incr_i=1; set(handles.num_incr_i,'String','1') end if isempty(incr_i) if isempty(incr_j) [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:))); ref_j=ref_j(ref_j>=first_j & ref_j<=last_j); ref_i=ref_i(ref_i>=first_i & ref_i<=last_i); ref_j=ref_j-1; ref_i=ref_i-1; else ref_j=first_j:incr_j:last_j; [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:))); ref_i=ref_i-1; ref_i=ref_i(ref_i>=first_i & ref_i<=last_i); end else ref_i=first_i:incr_i:last_i; if isempty(incr_j) [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:))); ref_j=ref_j-1; ref_j=ref_j(ref_j>=first_j & ref_j<=last_j); else ref_j=first_j:incr_j:last_j; end end BlockLength=ceil(numel(ref_i)/NbProcess); nbfield_j=numel(ref_j); %% record nbre of output files and starting time for computation for status StatusData=get(handles.status,'UserData'); if isfield(StatusData,'OutputFileMode') switch StatusData.OutputFileMode case 'NbInput' StatusData.NbOutputFile=numel(ref_i)*nbfield_j; case 'NbInput_i' StatusData.NbOutputFile=numel(ref_i); case 'NbSlice' StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String')); end end StatusData.TimeStart=now; set(handles.status,'UserData',StatusData) %% direct processing on the current Matlab session if strcmp (RunMode,'local') for iprocess=1:NbProcess if isempty(Param.IndexRange.NbSlice) %Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i; Param.IndexRange.first_i=ref_i(1+(iprocess-1)*BlockLength); if Param.IndexRange.first_i>last_i break end Param.IndexRange.last_i=min(ref_i(iprocess*BlockLength),last_i); %Param.IndexRange.last_i=min(first_i+(iprocess)*BlockLength*incr_i-1,last_i); else %multislices (then incr_i is not empty) Param.IndexRange.first_i= first_i+incr_i*(iprocess-1); Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice; end if isfield(Param,'OutputSubDir') t=struct2xml(Param); t=set(t,1,'name','Series'); filexml=fullfile_uvmat(DirXml,'',Param.InputTable{1,3},'.xml',OutputNomType,... Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j); save(t,filexml); end switch ActionExt case '.m' h_fun(Param); case '.sh' switch computer case {'PCWIN','PCWIN64'} %Windows system filexml=regexprep(filexml,'\\','\\\\');% add '\' so that '\' are left as characters system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]);% TODO: adapt to DOS system case {'GLNX86','GLNXA64','MACI64'}%Linux system system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]); end end end elseif strcmp(get(handles.OutputDirExt,'Visible'),'off') msgbox_uvmat('ERROR',['no output file for Action ' ActionName ', use run mode = local']);% a output dir is needed for background option return else %% processing on a different session of the same computer (background) or cluster, create executable files batch_file_list=cell(NbProcess,1);% initiate the list of executable files DirBat=fullfile(OutputDir,'0_EXE'); switch computer case {'PCWIN','PCWIN64'} %Windows system ExeExt='.bat'; case {'GLNX86','GLNXA64','MACI64'}%Linux system ExeExt='.sh'; end %create subdirectory for executable files if ~exist(DirBat,'dir') [tild,msg1]=mkdir(DirBat); if ~strcmp(msg1,'') msgbox_uvmat('ERROR',['cannot create ' DirBat ': ' msg1]);%error message for directory creation return end end %create subdirectory for log files DirLog=fullfile(OutputDir,'0_LOG'); if ~exist(DirLog,'dir') [tild,msg1]=mkdir(DirLog); if ~strcmp(msg1,'') msgbox_uvmat('ERROR',['cannot create ' DirLog ': ' msg1]);%error message for directory creation return end end for iprocess=1:NbProcess if isempty(Param.IndexRange.NbSlice)% process by blocks of i index Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i; if Param.IndexRange.first_i>last_i NbProcess=iprocess-1; break% leave the loop, we are at the end of the calculation end Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1); else% process by slices of i index if NbSlice is defined, computation in a single process if NbSlice =1 Param.IndexRange.first_i= first_i+iprocess-1; Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice; end % create, fill and save the xml parameter file t=struct2xml(Param); t=set(t,1,'name','Series'); filexml=fullfile_uvmat(DirXml,'',Param.InputTable{1,3},'.xml',OutputNomType,... Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j); save(t,filexml);% save the parameter file %create the executable file filebat=fullfile_uvmat(DirBat,'',Param.InputTable{1,3},ExeExt,OutputNomType,... Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j); batch_file_list{iprocess}=filebat; [fid,message]=fopen(filebat,'w');% create the executable file if isequal(fid,-1) msgbox_uvmat('ERROR', ['creation of .bat file: ' message]); return end % set the log file name filelog=fullfile_uvmat(DirLog,'',Param.InputTable{1,3},'.log',OutputNomType,... Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j); % fill and save the executable file switch ActionExt case '.m'% Matlab function switch computer case {'GLNX86','GLNXA64','MACI64'} cmd=[... '#!/bin/bash \n'... '. /etc/sysprofile \n'... 'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog ''' <','.stderr') ' '... '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '... extra_oar ' '... '"oar-parexec -s -f ' filename_joblist ' '... '-l ' filename_joblist '.log"\n']; filename_oarcommand=fullfile(DirOAR,'oar_command'); fid=fopen(filename_oarcommand,'w'); fprintf(fid,oar_command); fclose(fid); fprintf(oar_command);% display in command line system(oar_command); msgbox_uvmat('CONFIRMATION',[ActionName ' launched in cluster: press STATUS to see results']) end %% reset the GUI series update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate launching is finished set(handles.RUN, 'Enable','On') set(handles.RUN,'BackgroundColor',[1 0 0]) set(handles.RUN, 'Value',0) %------------------------------------------------------------------------ function STOP_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.RUN, 'BusyAction','cancel') set(handles.RUN,'BackgroundColor',[1 0 0]) set(handles.RUN,'enable','on') set(handles.RUN, 'Value',0) %------------------------------------------------------------------------ % --- read parameters from the GUI series %------------------------------------------------------------------------ function Param=read_GUI_series(handles) %% read raw parameters from the GUI series Param=read_GUI(handles.series); %% clean the output structure by removing unused information if isfield(Param,'Pairs') Param=rmfield(Param,'Pairs'); %info Pairs not needed for output end Param.IndexRange=rmfield(Param.IndexRange,'TimeTable'); empty_line=false(size(Param.InputTable,1),1); for iline=1:size(Param.InputTable,1) empty_line(iline)=isempty(cell2mat(Param.InputTable(iline,1:3))); end Param.InputTable(empty_line,:)=[]; %------------------------------------------------------------------------ % --- Executes on selection change in ActionName. function ActionName_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ %% stop any ongoing series processing if isequal(get(handles.RUN,'Value'),1) answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?'); if strcmp(answer,'Yes') STOP_Callback(hObject, eventdata, handles) else return end end set(handles.ActionName,'BackgroundColor',[1 1 0]) huigetfile=findobj(allchild(0),'tag','status_display'); if ~isempty(huigetfile) delete(huigetfile) end drawnow %% get Action name and path nb_builtin_ACTION=4; %nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series) ActionList=get(handles.ActionName,'String');% list menu fields ActionIndex=get(handles.ActionName,'Value'); if ~isequal(ActionIndex,1)% if we are not just opening series InputTable=get(handles.InputTable,'Data'); if isempty(InputTable{1,4}) msgbox_uvmat('ERROR','no input file available: use Open in the menu bar') return end end ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name ActionPathList=get(handles.ActionName,'UserData');%list of recorded paths to functions of the list ActionName %% add a new function to the menu if 'more...' has been selected in the menu ActionName if isequal(ActionName,'more...') [FileName, PathName] = uigetfile( ... {'*.m', ' (*.m)'; '*.m', '.m files '; ... '*.*', 'All Files (*.*)'}, ... 'Pick a series processing function ',get(handles.ActionPath,'String')); if length(FileName)<2 return end [ActionPath,ActionName,ActionExt]=fileparts(FileName); % insert the choice in the menu ActionName ActionIndex=find(strcmp(ActionName,ActionList),1);% look for the selected function in the menu Action if isempty(ActionIndex)%the input string does not exist in the menu ActionIndex= length(ActionList); ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)];% the selected function is appended in the menu, before the last item 'more...' set(handles.ActionName,'String',ActionList) end % record the file extension and extend the path list if it is a new extension ActionExtList=get(handles.ActionExt,'String'); ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1); if isempty(ActionExtIndex) set(handles.ActionExt,'String',[ActionExtList;{ActionExt}]) ActionExtIndex=numel(ActionExtList)+1; ActionPathNew=cell(size(ActionPathList,1),1);%new column of ActionPath ActionPathList=[ActionPathList ActionPathNew]; end set(handles.ActionName,'UserData',ActionPathList); % remove old Action options in the menu (keeping a menu length nb_builtin_ACTION+5; %nb_builtin=nbre of functions always remaining in the initial menu nbremove=length(ActionList)-nb_builtin_ACTION-5; ActionList(nb_builtin_ACTION+1:end-5)=[]; ActionPathList(nb_builtin_ACTION+1:end-4,:)=[]; ActionIndex=ActionIndex-nbremove; end % record action menu, choice and path set(handles.ActionName,'Value',ActionIndex) set(handles.ActionName,'String',ActionList) set(handles.ActionExt,'Value',ActionExtIndex) ActionPathList{ActionIndex,ActionExtIndex}=PathName; %record the user defined menu additions in personal file profil_perso dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if nb_builtin_ACTION+1<=numel(ActionList)-1 ActionListUser=ActionList(nb_builtin_ACTION+1:numel(ActionList)-1); ActionPathListUser=ActionPathList(nb_builtin_ACTION+1:numel(ActionList)-1,:); ActionExtListUser={}; if numel(ActionExtList)>2 ActionExtListUser=ActionExtList(3:end); end if exist(profil_perso,'file') save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append') else save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6') end end end %% check the current ActionPath to the selected function ActionPath=ActionPathList{ActionIndex};%current recorded path set(handles.ActionPath,'String',ActionPath); %show the path to the senlected function %% reinitialise the waitbar update_waitbar(handles.Waitbar,0) %% create the function handle for Action path_series=which('series'); if ~isequal(ActionPath,path_series) eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION if ~exist(ActionPath,'dir') errormsg=['The prescribed function path ' ActionPath ' does not exist']; return end if ~isequal(spath,ActionPath) addpath(ActionPath)% add the prescribed path if not the current one end end eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION if ~isequal(ActionPath,path_series) rmpath(ActionPath)% add the prescribed path if not the current one end %% Activate the Action fct Param=read_GUI_series(handles);% read the parameters from the GUI series ParamOut=h_fun(Param);%run the selected Action function to get the relevant input %% Put the first line of the selected Action fct as tooltip help try [fid,errormsg] =fopen([ActionName '.m']); InputText=textscan(fid,'%s',1,'delimiter','\n'); fclose(fid); set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help end %% Detect the types of input files SeriesData=get(handles.series,'UserData');% info on the input file series iview_civ=[];nb_netcdf=0; if ~isempty(SeriesData)&&isfield(SeriesData,'FileType') iview_civ=find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)); nb_netcdf=numel(find(strcmp('netcdf',SeriesData.FileType))); end if numel(iview_civ)>=1 && ~isempty(iview_civ(1)) menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)}); set(handles.VelType,'String',[{'*'};menu]) if numel(iview_civ)>=2 menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)}); set(handles.VelType_1,'String',[{'*'};menu]) end end %% Check whether alphabetical sorting of input Subdir is allowed by the Action fct (for multiples series entries) if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Param.InputTable,1)>1 [tild,iview]=sort(InputTable(:,2)); %subdirectories sorted in alphabetical order set(handles.InputTable,'Data',InputTable(iview,:)); MinIndex_i=get(handles.MinIndex_i,'Data'); MinIndex_j=get(handles.MinIndex_j,'Data'); MaxIndex_i=get(handles.MaxIndex_i,'Data'); MaxIndex_j=get(handles.MaxIndex_j,'Data'); set(handles.MinIndex_i,'Data',MinIndex_i(iview,:)); set(handles.MinIndex_j,'Data',MinIndex_j(iview,:)); set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:)); set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:)); TimeTable=get(handles.TimeTable,'Data'); set(handles.TimeTable,'Data',TimeTable(iview,:)); PairString=get(handles.PairString,'Data'); set(handles.PairString,'Data',PairString(iview,:)); end %% Impose the whole input file index range if requested if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on') MinIndex_i=get(handles.MinIndex_i,'Data'); MinIndex_j=get(handles.MinIndex_j,'Data'); MaxIndex_i=get(handles.MaxIndex_i,'Data'); MaxIndex_j=get(handles.MaxIndex_j,'Data'); set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line) set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line) set(handles.num_incr_i,'String','1') set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line) set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line) set(handles.num_incr_j,'String','1') else % check index ranges first_i=1;last_i=1;first_j=1;last_j=1; if isfield(Param.IndexRange,'first_i') first_i=Param.IndexRange.first_i; % incr_i=Param.IndexRange.incr_i; last_i=Param.IndexRange.last_i; end if isfield(Param.IndexRange,'first_j') first_j=Param.IndexRange.first_j; % incr_j=Param.IndexRange.incr_j; last_j=Param.IndexRange.last_j; end if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),... set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end; end %% desable j index if if set by the civ_input GUI if isfield(ParamOut,'Desable_j_index')&&isequal(ParamOut.Desable_j_index,'on') set(handles.num_first_j,'Enable','off') set(handles.num_last_j,'Enable','off') set(handles.num_incr_j,'Enable','off') set(handles.num_incr_j,'String','') else set(handles.num_first_j,'Enable','on') set(handles.num_last_j,'Enable','on') set(handles.num_incr_j,'Enable','on') end %% NbSlice visibility NbSliceVisible='off';%default if isfield(ParamOut,'NbSlice') && isequal(ParamOut.NbSlice,'on') NbSliceVisible='on'; set(handles.num_NbProcess,'String',get(handles.num_NbSlice,'String'))% the nbre of processes is imposed as the nbre of slices else set(handles.num_NbProcess,'String','')% free nbre of processes end set(handles.num_NbSlice,'Visible',NbSliceVisible) set(handles.NbSlice_title,'Visible',NbSliceVisible) %% Visibility of VelType and VelType_1 menus VelTypeVisible='off'; %hidden by default VelType_1Visible='off'; InputFieldsVisible='off';%visibility of the frame Fields if isfield(ParamOut,'VelType') if strcmp( ParamOut.VelType,'on')||strcmp(ParamOut.VelType,'one')||strcmp( ParamOut.VelType,'two') if numel(iview_civ)>=1 VelTypeVisible='on'; InputFieldsVisible='on'; end end if strcmp( ParamOut.VelType,'two') if numel(iview_civ)>=2 VelType_1Visible='on'; end end end set(handles.VelType,'Visible',VelTypeVisible) set(handles.VelType_text,'Visible',VelTypeVisible); set(handles.VelType_1,'Visible',VelType_1Visible) set(handles.VelType_text_1,'Visible',VelType_1Visible); %% Visibility of FieldName and FieldName_1 menus FieldNameVisible='off'; %hidden by default FieldName_1Visible='off'; %hidden by default if isfield(ParamOut,'FieldName') if strcmp( ParamOut.FieldName,'on') || strcmp(ParamOut.FieldName,'one')||strcmp( ParamOut.FieldName,'two') if (numel(iview_civ)+nb_netcdf)>=1 InputFieldsVisible='on'; FieldNameVisible='on'; end end if strcmp( ParamOut.FieldName,'two') if (numel(iview_civ)+nb_netcdf)>=1 FieldName_1Visible='on'; end end end set(handles.InputFields,'Visible',InputFieldsVisible) set(handles.FieldName,'Visible',FieldNameVisible) % test for MenuBorser set(handles.FieldName_1,'Visible',FieldName_1Visible) %% Visibility of FieldTransform menu FieldTransformVisible='off'; %hidden by default if isfield(ParamOut,'FieldTransform') FieldTransformVisible=ParamOut.FieldTransform; TransformName_Callback([],[], handles) end set(handles.FieldTransform,'Visible',FieldTransformVisible) if isfield(ParamOut,'TransformPath') set(handles.ActionExt,'UserData',ParamOut.TransformPath) else set(handles.ActionExt,'UserData',[]) end %% Visibility of projection object ProjObjectVisible='off'; %hidden by default if isfield(ParamOut,'ProjObject') ProjObjectVisible=ParamOut.ProjObject; end set(handles.CheckObject,'Visible',ProjObjectVisible) if ~get(handles.CheckObject,'Value') ProjObjectVisible='off'; end set(handles.ProjObject,'Visible',ProjObjectVisible) set(handles.DeleteObject,'Visible',ProjObjectVisible) set(handles.ViewObject,'Visible',ProjObjectVisible) set(handles.EditObject,'Visible',ProjObjectVisible) %% Visibility of mask input MaskVisible='off'; %hidden by default if isfield(ParamOut,'Mask') MaskVisible=ParamOut.Mask; end %set(handles.Mask,'Visible',MaskVisible) set(handles.CheckMask,'Visible',MaskVisible); %% definition of the directory containing the output files OutputDirVisible='off'; if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt) OutputSubDirMode='all';%default if isfield(ParamOut,'OutputSubDirMode') OutputSubDirMode=ParamOut.OutputSubDirMode; end set(handles.OutputDirExt,'String',ParamOut.OutputDirExt) OutputDirVisible='on'; SubDir=InputTable(1:end,2); %set of subdirectories sorted in alphabetical order if strcmp(OutputSubDirMode,'last') SubDirOut=SubDir{end}; else SubDirOut=SubDir{1}; if ~strcmp(OutputSubDirMode,'first') && numel(SubDir)>1 for ilist=2:numel(SubDir) SubDirOut=[SubDirOut '-' SubDir{ilist}]; end end end set(handles.OutputSubDir,'String',SubDirOut) end set(handles.OutputDirExt,'Visible',OutputDirVisible) set(handles.OutputSubDir,'Visible',OutputDirVisible) set(handles.OutputDir_title,'Visible',OutputDirVisible) set(handles.RunMode,'Visible',OutputDirVisible) set(handles.ActionExt,'Visible',OutputDirVisible) set(handles.RunMode_title,'Visible',OutputDirVisible) set(handles.ActionExt_title,'Visible',OutputDirVisible) %% Expected nbre of output files if isfield(ParamOut,'OutputFileMode') StatusData.OutputFileMode=ParamOut.OutputFileMode; set(handles.status,'UserData',StatusData) end %% definition of an additional parameter set, determined by an ancillary GUI if isfield(ParamOut,'ActionInput') % set(handles.ActionInput,'Visible','on') % set(handles.ActionInput_title,'Visible','on') set(handles.ActionInput,'Visible','on') % set(handles.ActionInput,'Value',0) % set(handles.ActionInput,'String',ActionName) ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput SeriesData.ActionInput=ParamOut.ActionInput; else % set(handles.ActionInput,'Visible','off') % set(handles.ActionInput_title,'Visible','off') set(handles.ActionInput,'Visible','off') if isfield(SeriesData,'ActionInput') SeriesData=rmfield(SeriesData,'ActionInput'); end end set(handles.series,'UserData',SeriesData) set(handles.ActionName,'BackgroundColor',[1 1 1]) %------------------------------------------------------------------------ % --- Executes on button press in ActionInput. function ActionInput_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ % if get(handles.ActionInput,'Value') ActionName_Callback(hObject, eventdata, handles) % end %------------------------------------------------------------------------ % --- Executes on selection change in FieldName. function FieldName_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ field_str=get(handles.FieldName,'String'); field_index=get(handles.FieldName,'Value'); field=field_str{field_index(1)}; if isequal(field,'get_field...') hget_field=findobj(allchild(0),'name','get_field'); if ~isempty(hget_field) delete(hget_field)%delete opened versions of get_field end Param=read_GUI(handles.series); Param.InputTable=Param.InputTable(1,:); % check the existence of the first file in the series first_j=[]; if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end last_j=[]; if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end PairString=''; if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); % filecell=get_file_series(Param); % if exist(FirstFileName,'file') ParamIn.SeriesInput=1; GetFieldData=get_field(FirstFileName,ParamIn); FieldList={}; switch GetFieldData.FieldOption case 'vectors' UName=GetFieldData.PanelVectors.vector_x; VName=GetFieldData.PanelVectors.vector_y; YName={GetFieldData.Coordinates.Coord_y}; CName=GetFieldData.PanelVectors.vec_color; FieldList={['vec(' UName ',' VName ')'];... ['norm(' UName ',' VName ')'];... UName;VName}; VecColorList={['norm(' UName ',' VName ')'];... UName;VName}; if ~isempty(CName) VecColorList=[{CName};VecColorList]; end case 'scalar' FieldList=GetFieldData.PanelScalar.scalar; YName={GetFieldData.Coordinates.Coord_y}; if ischar(FieldList) FieldList={FieldList}; end case '1D plot' YName=GetFieldData.PanelOrdinate.ordinate; % case 'civdata...'%reinitiate input, return to automatic civ data reading % display_file_name(handles,FileName,1) end if ~strcmp(GetFieldData.FieldOption,'civdata...') XName=GetFieldData.Coordinates.Coord_x; TimeNameStr=GetFieldData.Time.SwitchVarIndexTime; switch TimeNameStr case 'file index' set(handles.TimeName,'String',''); case 'attribute' set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]); case 'variable' set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName]) set(handles.NomType,'String','*') set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!! set(handles.FileIndex,'String','') ParamIn.TimeVarName=GetFieldData.Time.TimeName; case 'matrix_index' set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]); set(handles.NomType,'String','*') set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')]) set(handles.FileIndex,'String','') ParamIn.TimeDimName=GetFieldData.Time.TimeName; end set(handles.Coord_x,'String',{XName}) set(handles.Coord_y,'String',YName) set(handles.FieldName,'Value',1) set(handles.FieldName,'String',[FieldList; {'get_field...'}]); end end end %------------------------------------------------------------------------ % --- Executes on selection change in FieldName_1. function FieldName_1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ field_str=get(handles.FieldName_1,'String'); field_index=get(handles.FieldName_1,'Value'); field=field_str{field_index}; if isequal(field,'get_field...') hget_field=findobj(allchild(0),'name','get_field_1'); if ~isempty(hget_field) delete(hget_field) end SeriesData=get(handles.series,'UserData'); filename=SeriesData.CurrentInputFile_1; if exist(filename,'file') hget_field=get_field(filename); set(hget_field,'name','get_field_1') end % elseif isequal(field,'more...') % str=calc_field; % [ind_answer,v] = listdlg('PromptString','Select a file:',... % 'SelectionMode','single',... % 'ListString',str); % % edit the choice in the fields and actionname menu % scalar=cell2mat(str(ind_answer)); % update_menu(handles.FieldName_1,scalar) end %%%%%%%%%%%%% function [ind_remove]=find_pairs(dirpair,ind_i,last_i) indsel=ind_i; indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds if ~isempty(indiff) indiff2=diff(indiff); indiffp=[indiff2 1]; indiffm=[1 indiff2]; ind_multi_m=find((indiff==0)&(indiffm<0))-1;%indices of first members of multiplets ind_multi_p=find((indiff==0)&(indiffp>0));%indices of last members of multiplets %for each multiplet, select the most recent file ind_remove=[]; for i=1:length(ind_multi_m) ind_pairs=ind_multi_m(i):ind_multi_p(i); for imulti=1:length(ind_pairs) datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date);%dates of creation end [datenew,indsort2]=sort(datepair); %sort the multiplet by creation date ind_s=indsort2(1:end-1);% ind_remove=[ind_remove ind_pairs(ind_s)];%remove these indices, leave the last one end end %------------------------------------------------------------------------ % --- determine the list of index pairstring of processing file function [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) %------------------------------------------------------------------------ num_i1=num_i;% set of first image numbers by default num_i2=num_i; num_j1=num_j; num_j2=num_j; num_i_out=num_i; num_j_out=num_j; % if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2') if isequal(mode,'series(Di)') num_i1_line=num_i+ind_shift(3);% set of first image numbers num_i2_line=num_i+ind_shift(4); % adjust the first and last field number indsel=find(num_i1_line >= 1); num_i_out=num_i(indsel); num_i1_line=num_i1_line(indsel); num_i2_line=num_i2_line(indsel); num_j1=meshgrid(num_j,ones(size(num_i1_line))); num_j2=meshgrid(num_j,ones(size(num_i1_line))); [xx,num_i1]=meshgrid(num_j,num_i1_line); [xx,num_i2]=meshgrid(num_j,num_i2_line); elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts') if isequal(mode,'bursts') %case of bursts (png_old or png_2D) num_j1=ind_shift(1)*ones(size(num_i)); num_j2=ind_shift(2)*ones(size(num_i)); else num_j1_col=num_j+ind_shift(1);% set of first image numbers num_j2_col=num_j+ind_shift(2); % adjust the first field number indsel=find((num_j1_col >= 1)); num_j_out=num_j(indsel); num_j1_col=num_j1_col(indsel); num_j2_col=num_j2_col(indsel); [num_i1,num_j1]=meshgrid(num_i,num_j1_col); [num_i2,num_j2]=meshgrid(num_i,num_j2_col); end end %------------------------------------------------------------------------ % --- Executes on button press in CheckObject. function CheckObject_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ hset_object=findobj(allchild(0),'tag','set_object');%find the set_object interface handle if get(handles.CheckObject,'Value') SeriesData=get(handles.series,'UserData'); if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject) set(handles.ViewObject,'Value',1) ViewObject_Callback(hObject, eventdata, handles) else if ishandle(hset_object) uistack(hset_object,'top')% show the GUI set_object if opened else %get the object file InputTable=get(handles.InputTable,'Data'); defaultname=InputTable{1,1}; if isempty(defaultname) defaultname={''}; end fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml'); if isempty(fileinput)% exit if no object file is selected set(handles.CheckObject,'Value',0) return end %read the file data=xml2struct(fileinput); if ~isfield(data,'Type') msgbox_uvmat('ERROR',[fileinput ' is not an object xml file']) set(handles.CheckObject,'Value',0) return end if ~isfield(data,'ProjMode') data.ProjMode='none'; end hset_object=set_object(data);% call the set_object interface set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat end ProjObject=read_GUI(hset_object); set(handles.ProjObject,'String',ProjObject.Name);%display the object name SeriesData=get(handles.series,'UserData'); SeriesData.ProjObject=ProjObject; set(handles.series,'UserData',SeriesData); end set(handles.EditObject,'Visible','on'); set(handles.DeleteObject,'Visible','on'); set(handles.ViewObject,'Visible','on'); set(handles.ProjObject,'Visible','on'); else set(handles.EditObject,'Visible','off'); set(handles.DeleteObject,'Visible','off'); set(handles.ViewObject,'Visible','off'); if ~ishandle(hset_object) set(handles.ViewObject,'Value',0); end set(handles.ProjObject,'Visible','off'); end %------------------------------------------------------------------------ % --- Executes on button press in ViewObject. %------------------------------------------------------------------------ function ViewObject_Callback(hObject, eventdata, handles) UserData=get(handles.series,'UserData'); hset_object=findobj(allchild(0),'Tag','set_object'); if ~isempty(hset_object) delete(hset_object)% refresh set_object if already opened end hset_object=set_object(UserData.ProjObject); set(hset_object,'Name','view_object_series') %------------------------------------------------------------------------ % --- Executes on button press in EditObject. function EditObject_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ if get(handles.EditObject,'Value') set(handles.ViewObject,'Value',0) UserData=get(handles.series,'UserData'); hset_object=set_object(UserData.ProjObject); set(hset_object,'Name','edit_object_series') set(get(hset_object,'Children'),'Enable','on') else hset_object=findobj(allchild(0),'Tag','set_object'); if ~isempty(hset_object) set(get(hset_object,'Children'),'Enable','off') end end %------------------------------------------------------------------------ % --- Executes on button press in DeleteObject. function DeleteObject_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ SeriesData=get(handles.series,'UserData'); SeriesData.ProjObject=[]; set(handles.series,'UserData',SeriesData) set(handles.ProjObject,'String','') set(handles.ProjObject,'Visible','off') set(handles.CheckObject,'Value',0) set(handles.ViewObject,'Visible','off') set(handles.EditObject,'Visible','off') hset_object=findobj(allchild(0),'name','set_object_series'); if ~isempty(hset_object) delete(hset_object) end set(handles.DeleteObject,'Visible','off') %------------------------------------------------------------------------ % --- Executed when CheckMask is activated %------------------------------------------------------------------------ function CheckMask_Callback(hObject, eventdata, handles) if get(handles.CheckMask,'Value') InputTable=get(handles.InputTable,'Data'); nbview=size(InputTable,1); MaskTable=cell(nbview,1);%default ListMask=cell(nbview,1);%default MaskData=get(handles.MaskTable,'Data'); MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1);%complement if undefined lines for iview=1:nbview ListMask{iview,1}=num2str(iview); RootPath=InputTable{iview,1}; if ~isempty(RootPath) if isempty(MaskData{iview}) SubDir=InputTable{iview,2}; MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']);%take the root part of SubDir, before the first dot '.' if exist(MaskPath,'dir') ListStruct=dir(MaskPath);%look for a mask file ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files ListFiles=ListCells(1,:);%list of file and dri names ListFiles=ListFiles(~check_dir);%list of file names (excluding dir) mdetect=0; if ~isempty(ListFiles) for ifile=1:numel(ListFiles) [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0); if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series) mdetect=1; MaskName=ListFiles{ifile}; end if ~strcmp(MaskFile{ifile},MaskFile{1}) mdetect=0;% cancel detection test in case of multiple masks, use the brower for selection break end end end if mdetect==1 MaskName=fullfile(MaskPath,'mask_1.png'); else MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image'); end else MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image'); end MaskTable{iview,1}=MaskName ; ListMask{iview,1}=num2str(iview); end end end set(handles.MaskTable,'Data',MaskTable) set(handles.MaskTable,'Visible','on') set(handles.MaskBrowse,'Visible','on') set(handles.ListMask,'Visible','on') set(handles.ListMask,'String',ListMask) set(handles.ListMask,'Value',1) else set(handles.MaskTable,'Visible','off') set(handles.MaskBrowse,'Visible','off') set(handles.ListMask,'Visible','off') end %------------------------------------------------------------------------ % --- Executes on button press in MaskBrowse. %------------------------------------------------------------------------ function MaskBrowse_Callback(hObject, eventdata, handles) InputTable=get(handles.InputTable,'Data'); iview=get(handles.ListMask,'Value'); RootPath=InputTable{iview,1}; MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image'); if ~isempty(MaskName) MaskTable=get(handles.MaskTable,'Data'); MaskTable{iview,1}=MaskName ; set(handles.MaskTable,'Data',MaskTable) end %------------------------------------------------------------------------ % --- Executes when selected cell(s) is changed in MaskTable. %------------------------------------------------------------------------ function MaskTable_CellSelectionCallback(hObject, eventdata, handles) if numel(eventdata.Indices)>=1 set(handles.ListMask,'Value',eventdata.Indices(1)) end %------------------------------------------------------------------- function MenuHelp_Callback(hObject, eventdata, handles) %------------------------------------------------------------------- path_to_uvmat=which ('uvmat');% check the path of uvmat pathelp=fileparts(path_to_uvmat); helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html'); 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') else addpath (fullfile(pathelp,'uvmat_doc')) web([helpfile '#series']) end %------------------------------------------------------------------- % --- Executes on selection change in TransformName. function TransformName_Callback(hObject, eventdata, handles) %---------------------------------------------------------------------- TransformList=get(handles.TransformName,'String'); TransformIndex=get(handles.TransformName,'Value'); TransformName=TransformList{TransformIndex}; TransformPathList=get(handles.TransformName,'UserData'); nb_builtin_transform=4; if isequal(TransformName,'more...'); FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m'); if isempty(FileName) return %browser closed without choice end [TransformPath,TransformName,TransformExt]=fileparts(FileName);% removes extension .m if ~strcmp(TransformExt,'.m') msgbox_uvmat('ERROR','a Matlab function .m must be introduced'); return end % insert the choice in the menu TransformIndex=find(strcmp(TransformName,TransformList),1);% look for the selected function in the menu Action if isempty(TransformIndex)%the input string does not exist in the menu TransformIndex= length(TransformList); TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)];% the selected function is appended in the menu, before the last item 'more...' set(handles.TransformName,'String',TransformList) TransformPathList=[TransformPathList;{TransformPath}]; else% the input function already exist, we update its path (possibly new) TransformPathList{TransformIndex}=TransformPath;% set(handles.TransformName,'Value',TransformIndex) end % save the new menu in the personal file 'uvmat_perso.mat' dir_perso=prefdir;%personal Matalb directory profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') for ilist=nb_builtin_transform+1:numel(TransformPathList) TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist}; TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist}; end TransformPathListUser=TransformPathListUser'; TransformListUser=TransformListUser'; save (profil_perso,'TransformPathListUser','TransformListUser','-append'); %store the root name for future opening of uvmat end end %display the current function path set(handles.TransformPath,'String',TransformPathList{TransformIndex}); %show the path to the senlected function set(handles.TransformName,'UserData',TransformPathList); %------------------------------------------------------------------------ % --- fct activated by the upper bar menu ExportConfig %------------------------------------------------------------------------ function MenuExportConfig_Callback(hObject, eventdata, handles) global Param Param=read_GUI_series(handles); evalin('base','global Param')%make CurData global in the workspace display('current series config :') evalin('base','Param') %display CurData in the workspace commandwindow; %brings the Matlab command window to the front %------------------------------------------------------------------------ % --- fct activated by the upper bar menu InportConfig: import % menu settings from an xml file (stored in /0_XML for each run) %------------------------------------------------------------------------ function MenuImportConfig_Callback(hObject, eventdata, handles) % SeriesData=get(handles.series,'UserData'); % if isfield(SeriesData,'RefFile') % oldfile=SeriesData.RefFile{1}; % end %% use a strating file name for browserr InputTable=get(handles.InputTable,'Data'); oldfile=InputTable{1,1}; if isempty(oldfile) % use a file name stored in prefdir dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') h=load (profil_perso); if isfield(h,'RootPath') && ischar(h.RootPath) oldfile=h.RootPath; end end end filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml');% get the xml file containing processing parameters %proceed only if a file has been introduced by the browser if ~isempty(filexml) Param=xml2struct(filexml);% read the input xml file as a Matlab structure % ask to stop current Action if button RUN is in action (another process is already running) if isequal(get(handles.RUN,'Value'),1) answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?'); if strcmp(answer,'Yes') STOP_Callback(hObject, eventdata, handles) else return end end Param.Action.RUN=0; %desactivate the input RUN=1 fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters SeriesData=get(handles.series,'UserData'); if isfield(Param,'ActionInput')% introduce parameters specific to an Action fct, for instance PIV parameters set(handles.ActionInput,'Visible','on') set(handles.ActionInput,'Value',0) SeriesData.ActionInput=Param.ActionInput; end if isfield(Param,'ProjObject') %introduce projection object if relevant SeriesData.ProjObject=Param.ProjObject; end set(handles.series,'UserData',SeriesData) if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1) set(handles.ProjObject,'String',Param.ProjObject.Name) set(handles.ViewObject,'Visible','on') set(handles.EditObject,'Visible','on') set(handles.DeleteObject,'Visible','on') else set(handles.ProjObject,'String','') set(handles.ProjObject,'Visible','off') set(handles.ViewObject,'Visible','off') set(handles.EditObject,'Visible','off') set(handles.DeleteObject,'Visible','off') end set(handles.REFRESH,'BackgroundColor',[1 0 1]); %paint REFRESH button in magenta to indicate that it should be activated end %------------------------------------------------------------------------ % --- Executes when the GUI series is resized. %------------------------------------------------------------------------ function series_ResizeFcn(hObject, eventdata, handles) %% input table set(handles.InputTable,'Unit','pixel') Pos=get(handles.InputTable,'Position'); set(handles.InputTable,'Unit','normalized') ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52)); ColumnWidth=num2cell(ColumnWidth); set(handles.InputTable,'ColumnWidth',ColumnWidth) %% MinIndex_j and MaxIndex_i unit=get(handles.MinIndex_i,'Unit'); set(handles.MinIndex_i,'Unit','pixel') Pos=get(handles.MinIndex_i,'Position'); set(handles.MinIndex_i,'Unit',unit) set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18}) set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18}) set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18}) set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18}) %% TimeTable set(handles.TimeTable,'Unit','pixel') Pos=get(handles.TimeTable,'Position'); set(handles.TimeTable,'Unit','normalized') % ColumnWidth=get(handles.TimeTable,'ColumnWidth'); ColumnWidth=num2cell(floor([0.25 0.25 0.25 0.25]*(Pos(3)-20))); set(handles.TimeTable,'ColumnWidth',ColumnWidth) %% PairString set(handles.PairString,'Unit','pixel') Pos=get(handles.PairString,'Position'); set(handles.PairString,'Unit','normalized') set(handles.PairString,'ColumnWidth',{Pos(3)-5}) %% MaskTable set(handles.MaskTable,'Unit','pixel') Pos=get(handles.MaskTable,'Position'); set(handles.MaskTable,'Unit','normalized') set(handles.MaskTable,'ColumnWidth',{Pos(3)-5}) %------------------------------------------------------------------------ % --- Executes on button press in status. %------------------------------------------------------------------------ function status_Callback(hObject, eventdata, handles) if get(handles.status,'Value') set(handles.status,'BackgroundColor',[1 1 0]) drawnow Param=read_GUI(handles.series); RootPath=Param.InputTable{1,1}; if ~isfield(Param,'OutputSubDir') msgbox_uvmat('ERROR','no directory defined for output files') return end OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files OutputDir=fullfile(RootPath,OutputSubDir); if exist(OutputDir,'dir') uigetfile_uvmat('status_display',OutputDir) else msgbox_uvmat('ERROR','output folder not created yet: calculation did not start') set(handles.status,'BackgroundColor',[0 1 0]) end else %% delete current display fig if selection is off set(handles.status,'BackgroundColor',[0 1 0]) hfig=findobj(allchild(0),'name','status_display'); if ~isempty(hfig) delete(hfig) end return end %------------------------------------------------------------------------ % launched by selecting a file on the list %------------------------------------------------------------------------ function view_file(hObject, eventdata) list=get(hObject,'String'); index=get(hObject,'Value'); rootroot=get(hObject,'UserData'); selectname=list{index}; ind_dot=regexp(selectname,'\.\.\.'); if ~isempty(ind_dot) selectname=selectname(1:ind_dot-1); end FullSelectName=fullfile(rootroot,selectname); if exist(FullSelectName,'dir')% a directory has been selected ListFiles=dir(FullSelectName); ListDisplay=cell(numel(ListFiles),1); for ilist=2:numel(ListDisplay)% suppress the first line '.' ListDisplay{ilist-1}=ListFiles(ilist).name; end set(hObject,'Value',1) set(hObject,'String',ListDisplay) if strcmp(selectname,'..') FullSelectName=fileparts(fileparts(FullSelectName)); end set(hObject,'UserData',FullSelectName) hfig=get(hObject,'parent'); htitlebox=findobj(hfig,'tag','titlebox'); set(htitlebox,'String',FullSelectName) elseif exist(FullSelectName,'file')%visualise the vel field if it exists FileType=get_file_type(FullSelectName); if strcmp(FileType,'txt') edit(FullSelectName) elseif strcmp(FileType,'xml') editxml(FullSelectName) else uvmat(FullSelectName) end set(gcbo,'Value',1) end %------------------------------------------------------------------------ % launched by refreshing the status figure %------------------------------------------------------------------------ function refresh_GUI(hfig) htitlebox=findobj(hfig,'tag','titlebox'); hlist=findobj(hfig,'tag','list'); hseries=findobj(allchild(0),'tag','series'); hstatus=findobj(hseries,'tag','status'); StatusData=get(hstatus,'UserData'); OutputDir=get(htitlebox,'String'); if ischar(OutputDir),OutputDir={OutputDir};end ListFiles=dir(OutputDir{1}); if numel(ListFiles)<1 return end ListFiles(1)=[];%removes the first line ='.' ListDisplay=cell(numel(ListFiles),1); testrecent=0; datnum=zeros(numel(ListDisplay),1); for ilist=1:numel(ListDisplay) ListDisplay{ilist}=ListFiles(ilist).name; if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum') datnum(ilist)=ListFiles(ilist).datenum;%only available in recent matlab versions testrecent=1; end end set(hlist,'String',ListDisplay) %% Look at date of creation ListDisplay=ListDisplay(datnum~=0); datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files NbOutputFile=[]; if isempty(datnum) if testrecent message='no civ result created yet'; else message=''; end else [first,indfirst]=min(datnum); [last,indlast]=max(datnum); NbOutputFile_str='?'; NbOutputFile=[]; if isfield(StatusData,'NbOutputFile') NbOutputFile=StatusData.NbOutputFile; NbOutputFile_str=num2str(NbOutputFile); end message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification: ' ListDisplay{indfirst} ' : ' datestr(first)];... ['latest modification: ' ListDisplay{indlast} ' : ' datestr(last)]}; end set(htitlebox,'String', [OutputDir{1};message]) %% update the waitbar hwaitbar=findobj(hfig,'tag','waitbar'); if ~isempty(NbOutputFile) BarPosition=get(hwaitbar,'Position'); BarPosition(3)=0.9*numel(datnum)/NbOutputFile; set(hwaitbar,'Position',BarPosition) end %------------------------------------------------------------------------ % --- Executes on selection change in ActionExt. %------------------------------------------------------------------------ function ActionExt_Callback(hObject, eventdata, handles) ActionExtList=get(handles.ActionExt,'String'); ActionExt=ActionExtList{get(handles.ActionExt,'Value')}; ActionList=get(handles.ActionName,'String'); ActionName=ActionList{get(handles.ActionName,'Value')}; TransformPath=''; if ~isempty(get(handles.ActionExt,'UserData')) TransformPath=get(handles.ActionExt,'UserData'); end if strcmp(ActionExt,'.sh') set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch' set(handles.ActionExt,'BackgroundColor',[1 1 0]) ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionName '.sh']); if ~exist(ActionFullName,'file') answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?'); if strcmp(answer,'Yes') set(handles.ActionExt,'BackgroundColor',[1 1 0]) path_uvmat=fileparts(which('series')); currentdir=pwd; cd(get(handles.ActionPath,'String'))% go to the directory of Action % addpath(get(handles.TransformPath,'String')) addpath(path_uvmat)% add the path to uvmat to run the fct 'compile' % addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile' compile(ActionName,TransformPath) cd(currentdir) end else sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.sh'])); m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m'])); if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum set(handles.ActionExt,'BackgroundColor',[1 1 0]) drawnow answer=msgbox_uvmat('INPUT_Y-N',[ActionName '.sh needs to be updated: recompile now?']); if strcmp(answer,'Yes') path_uvmat=fileparts(which('series')); currentdir=pwd; cd(get(handles.ActionPath,'String'))% go to the directory of Action % addpath(get(handles.TransformPath,'String')) addpath(path_uvmat)% add the path to uvmat to run the fct 'compile' addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile' compile(ActionName,TransformPath) cd(currentdir) end end end set(handles.ActionExt,'BackgroundColor',[1 1 1]) set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch end function num_NbProcess_Callback(hObject, eventdata, handles) function num_NbSlice_Callback(hObject, eventdata, handles) NbSlice=str2num(get(handles.num_NbSlice,'String')); set(handles.num_NbProcess,'String',num2str(NbSlice)) %------------------------------------------------------------------------ % --- set the visibility of relevant velocity type menus: function menu=set_veltype_display(Civ,FileType) %------------------------------------------------------------------------ if ~exist('FileType','var') FileType='civx'; end switch FileType case 'civx' menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'}; if isequal(Civ,0) imax=0; elseif isequal(Civ,1) || isequal(Civ,2) imax=1; elseif isequal(Civ,3) imax=3; elseif isequal(Civ,4) || isequal(Civ,5) imax=4; elseif isequal(Civ,6) %patch2 imax=6; end case 'civdata' menu={'civ1';'filter1';'civ2';'filter2'}; if isequal(Civ,0) imax=0; elseif isequal(Civ,1) || isequal(Civ,2) imax=1; elseif isequal(Civ,3) imax=2; elseif isequal(Civ,4) || isequal(Civ,5) imax=3; elseif isequal(Civ,6) %patch2 imax=4; end end menu=menu(1:imax); % --- Executes on mouse motion over figure - except title and menu. function series_WindowButtonMotionFcn(hObject, eventdata, handles) set(hObject,'Pointer','arrow');