%'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 % %======================================================================= % Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France % http://www.legi.grenoble-inp.fr % Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr % % 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 (see LICENSE.txt) for more details. %======================================================================= %------------------------------------------------------------------------ %------------------------------------------------------------------------ % 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(hObject,'DeleteFcn',{@closefcn})% % check default input data if ~exist('Param','var') Param=[]; % default end %% Read the parameter file series.xml, or created from series.xml.default if it does not exist SeriesData=[]; [path_series,name,ext]=fileparts(which('series'));% path to the GUI series xmlfile=fullfile(path_series,'series.xml'); if ~exist(xmlfile,'file') [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile); end if exist(xmlfile,'file') SeriesData.SeriesParam=xml2struct(xmlfile); if ~(isfield(SeriesData.SeriesParam,'ClusterParam')&& isfield(SeriesData.SeriesParam.ClusterParam,'LaunchCmdFcn')) [success,message]=copyfile(xmlfile,fullfile(path_series,'series_old.xml'));% update the file series.xml inot correctly documented delete(xmlfile); [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile); end SeriesData.SeriesParam=xml2struct(xmlfile); end %% list of builtin functions in the menu 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); set(handles.Action,'UserData',NbBuiltinAction) path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series' [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' % % command = ['LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "l = x.split('':''); l = [s for s in l if ''matlab'' not in s]; print('':''.join(l))") ' ... % % 'python -c "import fluidimage"']; % % [code, ~] = system(command); % % if code==0 ActionExtList={'.m';'.sh';'.py (in dev.)'}; % default choice of extensions (Matlab fct .m or compiled version .sh % % else % % ActionExtList={'.m';'.sh'}; % python options not installed % % end ActionPathList=cell(NbBuiltinAction,1); % 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(SeriesData.SeriesParam.ClusterParam.ExistenceTest); % look for cluster system presence if isequal(s,0) RunModeList=[RunModeList;{'cluster'}]; set(handles.MonitorCluster,'Visible','on'); % make visible button for access to Monika set(handles.num_CPUTime,'Visible','on'); % make visible button for CPU time estimate for one ref index set(handles.num_CPUTime,'String','')% default CPU time undefined set(handles.CPUTime_txt,'Visible','on'); % make visible button for CPU time title end set(handles.RunMode,'String',RunModeList)% display the menu of available run modes, local, background or cluster manager %% list of builtin transform functions in the menu 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 SeriesData.TransformPath=path_transform_fct;% store the standard path for trqnsform functions (needed for compilation) %% 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 menu of actions if isfield(h,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser) ActionList=[ActionList;h.ActionListUser]; ActionPathList=[ActionPathList;h.ActionPathListUser(:,1)]; 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,'Coordinates') if isfield(Param.Coordinates,'Coord_x') set(handles.Coord_x,'String',Param.Coordinates.Coord_x) end if isfield(Param.Coordinates,'Coord_y') set(handles.Coord_y,'String',Param.Coordinates.Coord_y) end if isfield(Param.Coordinates,'Coord_z') set(handles.Coord_z,'String',Param.Coordinates.Coord_z) end end %% introduce the input file name(s) if defined from input Param, set(handles.series,'UserData',SeriesData)% initiate Userdata if isfield(Param,'InputFile') %% fill the list of input file series InputTable=[{Param.InputFile.RootPath},{Param.InputFile.SubDir},{Param.InputFile.RootFile},{Param.InputFile.NomType},{Param.InputFile.FileExt}]; if isempty(find(cellfun('isempty',InputTable)==0)) % if there is no input file, do not introduce input info set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed return end TimeTable=[{Param.InputFile.TimeName},{[]},{[]},{[]},{[]}]; if isfield(Param.InputFile,'RootPath_1') InputTable=[InputTable;[{Param.InputFile.RootPath_1},{Param.InputFile.SubDir_1},{Param.InputFile.RootFile_1},{Param.InputFile.NomType_1},{Param.InputFile.FileExt_1}]]; TimeTable=[TimeTable; [{Param.InputFile.TimeName_1},{[]},{[]},{[]},{[]}]]; end set(handles.InputTable,'Data',InputTable) %% define the default path for the output files [InputPath,Device,DeviceExt]=fileparts(InputTable{1,1}); [InputPath,Experiment,ExperimentExt]=fileparts(InputPath); set(handles.Device,'String',[Device DeviceExt]) set(handles.Experiment,'String',[Experiment ExperimentExt]) if ~isempty(regexp(InputTable{1,1},'(^http://)|(^https://)')) set(handles.OutputPathBrowse,'Value',1)% an output folder needs to be specified for OpenDAP data end %update the output path if needed if ~(isfield(SeriesData,'InputPath') && strcmp(SeriesData.InputPath,InputPath)) if get(handles.OutputPathBrowse,'Value')==1 % fix the output path in manual mode OutputPathOld=get(handles.OutputPath,'String'); OutputPath=uigetdir(OutputPathOld,'pick a root folder for output data'); set(handles.OutputPath,'String',OutputPath) else %reproduce the input path for output set(handles.OutputPath,'String',InputPath) end end %% determine the selected reference field indices for pair display [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(Param.InputFile.FileIndex); 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)); 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 SeriesData.ref_i=ref_i; SeriesData.ref_j=ref_j; set(handles.series,'UserData',SeriesData) update_rootinfo(handles,Param.HiddenData.i1_series{1},Param.HiddenData.i2_series{1},Param.HiddenData.j1_series{1},Param.HiddenData.j2_series{1},... Param.HiddenData.FileInfo{1},Param.HiddenData.MovieObject{1},1) if isfield(Param,'FileName_1') % display_file_name(handles,Param,2) update_rootinfo(handles,Param.HiddenData.i1_series{2},Param.HiddenData.i2_series{2},Param.HiddenData.j1_series{2},Param.HiddenData.j2_series{2},... Param.HiddenData.FileInfo{2},Param.HiddenData.MovieObject{2},2) end %% enable field and veltype menus, in accordance with the current action ActionName_Callback([],[], handles) %% set length of waitbar displ_time(handles) else set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed end if isfield(Param,'incr_i') set(handles.num_incr_i,'String',num2str(Param.incr_i)) else set(handles.num_incr_i,'String','1') end if isfield(Param,'incr_j') set(handles.num_incr_j,'String',num2str(Param.incr_j)) else set(handles.num_incr_j,'String','1') end %------------------------------------------------------------------------ % --- 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/Browse...' %------------------------------------------------------------------------ function MenuBrowseCampaign_Callback(hObject, eventdata, handles) %% look for the previously opened file 'oldfile' InputTable=get(handles.InputTable,'Data'); if ~isempty(InputTable) oldfile=[InputTable{1,1} InputTable{1,2}]; else % 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,'MenuCampaign') && ~isempty(h.MenuCampaign)&& ischar(h.MenuCampaign{1}) oldfile=h.MenuCampaign{1}; end end end InputTable{1,1}='...'; set(handles.InputTable,'Data',InputTable) browse_data(oldfile,'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device % NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries); % icount=0; % for iexp=1:numel(OutPut.Experiment) % for idevice=1:numel(OutPut.DataSeries) % icount=icount+1; % InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp}); % InputTable{icount,2}=OutPut.DataSeries{idevice}; % if isempty(InputTable{icount,3}) % if icount>1 % InputTable{icount,3}=InputTable{icount-1,3}; % else % InputTable{icount,3}=''; % end % end % if isempty(InputTable{icount,4}) % if icount>1 % InputTable{icount,4}=InputTable{icount-1,4}; % else % InputTable{icount,4}=''; % end % end % if isempty(InputTable{icount,5}) % if icount>1 % InputTable{icount,5}=InputTable{icount-1,5}; % else % InputTable{icount,5}=''; % end % end % end % end % if size(InputTable,1)>icount % InputTable(icount+1:size(InputTable,1),:)=[]; % end %REFRESH_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- % function MenuCampaign_Callback(hObject, eventdata, handles) % % -------------------------------------------------------------------- % % OutPut=browse_data(get(hObject,'Label'),'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device % if ~isfield(OutPut,'Campaign') % return % end % NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries); % icount=0; % InputTable=get(handles.InputTable,'Data'); % for iexp=1:numel(OutPut.Experiment) % for idevice=1:numel(OutPut.DataSeries) % icount=icount+1; % InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp}); % InputTable{icount,2}=OutPut.DataSeries{idevice}; % if isempty(InputTable{icount,3}) % if icount>1 % InputTable{icount,3}=InputTable{icount-1,3}; % else % InputTable{icount,3}=''; % end % end % if isempty(InputTable{icount,4}) % if icount>1 % InputTable{icount,4}=InputTable{icount-1,4}; % else % InputTable{icount,4}=''; % end % end % if isempty(InputTable{icount,5}) % if icount>1 % InputTable{icount,5}=InputTable{icount-1,5}; % else % InputTable{icount,5}=''; % end % end % end % end % if size(InputTable,1)>icount % InputTable(icount+1:size(InputTable,1),:)=[]; % end % set(handles.InputTable,'Data',InputTable) % REFRESH_Callback(hObject, eventdata, handles) % --- Executes when selected cell(s) is changed in InputTable. function InputTable_CellSelectionCallback(hObject, eventdata, handles) iline=[]; if ~isempty(eventdata.Indices) iline=eventdata.Indices(1); end set(handles.InputLine,'String',num2str(iline)); %------------------------------------------------------------------------ % --- 'key_press_fcn:' function activated when a key is pressed on the keyboard %------------------------------------------------------------------------ function InputTable_KeyPressFcn(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.OutputSubDir,'BackgroundColor',[1 0 1])% set edit box OutputSubDir to magenta color to indicate that refresh may be needed xx=double(get(handles.series,'CurrentCharacter')); % get the keyboard character if ~isempty(xx) switch xx case 31 %downward arrow InputTable=get(handles.InputTable,'Data'); iline=str2double(get(handles.InputLine,'String')); if isequal(iline,size(InputTable,1))% arrow downward InputTable=[InputTable;InputTable(iline,:)]; % create a new line as a copy of the last one set(handles.InputTable,'Data',InputTable); end case 127 %key 'Suppress' ClearLine_Callback(hObject, eventdata, handles) end end %------------------------------------------------------------------------ % --- Executes on button press in REFRESH. function REFRESH_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ check_input_file_series(handles) %% enable field and veltype menus, in accordance with the current action ActionInput_Callback([],[], handles) %------------------------------------------------------------------------ % --- check the input file series. function check_input_file_series(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)));%check the empty lines in the input table end if ~isempty(find(empty_line,1)) InputTable(empty_line,:)=[]; % remove empty lines set(handles.InputTable,'Data',InputTable) ListTable={'MinIndex_i','MaxIndex_i','MinIndex_j','MaxIndex_j','PairString','TimeTable'}; for ilist=1:numel(ListTable) Table=get(handles.(ListTable{ilist}),'Data'); Table(empty_line,:)=[]; % remove empty lines set(handles.(ListTable{ilist}),'Data',Table); end set(handles.series,'UserData',[])%refresh the stored info end nbview=size(InputTable,1); for iview=1:nbview RootPath=fullfile(InputTable{iview,1},InputTable{iview,2}); if ~exist(RootPath,'dir') i1_series=[]; RootFile=''; else %scan the input folder InputTable{iview,3}=regexprep(InputTable{iview,3},'^/','');%suppress '/' at the beginning of the input name i1=str2num(get(handles.num_first_i,'String')); j1=str2num(get(handles.num_first_j,'String')); InputFile=fullfile_uvmat('','',InputTable{iview,3},InputTable{iview,5},InputTable{iview,4},i1,[],j1,[]); [RootPath,~,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=... find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),InputFile); end % if no file is found, open a browser if isempty(RootFile)&& 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,FileInfo,MovieObject,iview) end end %% update MinIndex_i and MaxIndex_i if the input table content has been reduced in line nbre MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex set(handles.MinIndex_i,'Data',MinIndex_i_table(1:nbview,:)); MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex set(handles.MinIndex_j,'Data',MinIndex_j_table(1:nbview,:)); MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex set(handles.MaxIndex_i,'Data',MaxIndex_i_table(1:nbview,:)); MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex set(handles.MaxIndex_j,'Data',MaxIndex_j_table(1:nbview,:)); PairString=get(handles.PairString,'Data'); % retrieve the min indices in the table MinIndex set(handles.PairString,'Data',PairString(1:nbview,:)); TimeTable=get(handles.TimeTable,'Data'); % retrieve the min indices in the table MinIndex set(handles.TimeTable,'Data',TimeTable(1:nbview,:)); %% set length of waitbar displ_time(handles) 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 %------------------------------------------------------------------------ % INPUT: % handles: handles of elements in the GUI % Param: structure of input parameters, including input file name and path % iview: line index in the input table % or 'one': refresh the list % 'append': add a new line to the input table function errormsg=display_file_name(handles,Param,iview) set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH button to yellow color (indicate activation) drawnow errormsg=''; % default if ischar(Param) fileinput=Param; else% input set when series is opened (called by the GUI uvmat) fileinput=Param.FileName; end %% get the input root name, indices, file extension and nomenclature NomType if isempty(regexp(fileinput,'^http')) && ~exist(fileinput,'file') errormsg=['input file ' fileinput ' does not exist']; msgbox_uvmat('ERROR',errormsg) set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color (refresh still needed) return end %% detect root name, nomenclature and indices in the input file name: [FilePath,FileName,FileExt]=fileparts(fileinput); %%%%%%%%%%%%%%%%%% %TODO: case of input by uvmat: do not check agai the input series %%%%%%% %%%%%%%%%%%%%%%%%%% % 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,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]); FileType=FileInfo.FileType; if isempty(RootFile)&&isempty(i1_series) errormsg='no input file in the series'; msgbox_uvmat('ERROR',errormsg) set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color (end of activation) return end if strcmp(FileType,'txt') edit(fileinput) set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color (end of activation) return elseif strcmp(FileType,'xml') editxml(fileinput) set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color (end of activation) return elseif strcmp(FileType,'figure') open(fileinput) set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color (end of activation) return end %% enable other menus and uicontrols 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 elseif strcmp(iview,'one') % refresh the list of input file series iview=1; % the first line in InputTable becomes the current line InputTable={'','','','',''}; 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.PairString,'Data',{''}) SeriesData.CheckPair=0; % reset the list of input lines with pairs SeriesData.i1_series={}; SeriesData.i2_series={}; SeriesData.j1_series={}; SeriesData.j2_series={}; SeriesData.FileType={}; SeriesData.FileInfo={}; SeriesData.Time={}; end if isfield(SeriesData,'i1_series') SeriesData.i1_series(iview+1:end)=[]; SeriesData.i2_series(iview+1:end)=[]; SeriesData.j1_series(iview+1:end)=[]; SeriesData.j2_series(iview+1:end)=[]; SeriesData.FileType(iview+1:end)=[]; SeriesData.FileInfo(iview+1:end)=[]; SeriesData.Time(iview+1:end)=[]; end InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}]; if iview >1 set(handles.InputLine,'String',num2str(iview)) end 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)); 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 SeriesData.ref_i=ref_i; SeriesData.ref_j=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; %% define the path for the output files [InputPath,Device,DeviceExt]=fileparts(InputTable{1,1}); [InputPath,Experiment,ExperimentExt]=fileparts(InputPath); set(handles.Device,'String',[Device DeviceExt]) set(handles.Experiment,'String',[Experiment ExperimentExt]) if ~isempty(regexp(InputTable{1,1},'(^http://)|(^https://)')) set(handles.OutputPathBrowse,'Value',1)% an output folder needs to be specified for OpenDAP data end %update the output path if needed if ~(isfield(SeriesData,'InputPath') && strcmp(SeriesData.InputPath,InputPath)) if get(handles.OutputPathBrowse,'Value')==1 % fix the output path in manual mode OutputPathOld=get(handles.OutputPath,'String'); OutputPath=uigetdir(OutputPathOld,'pick a root folder for output data'); set(handles.OutputPath,'String',OutputPath) else %reproduce the input path for output set(handles.OutputPath,'String',InputPath) end SeriesData.InputPath=InputPath; end 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,FileInfo,MovieObject,iview); %% enable field and veltype menus, in accordance with the current action ActionName_Callback([],[], handles) %% set length of waitbar displ_time(handles) 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,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 SeriesData=get(handles.series,'UserData'); %% 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 ref_i=1; if isfield(SeriesData,'ref_i') ref_i=SeriesData.ref_i; end 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=1; if isfield(SeriesData,'ref_j') ref_j=SeriesData.ref_j; end 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=str2double(get(handles.num_NbSlice,'String')); end %% default time settings TimeUnit=''; % read value set by the first series for the append mode (iwiew >1) if iview>1 TimeUnit=get(handles.TimeUnit,'String'); end TimeName=''; Time=[]; % default TimeMin=[]; TimeFirst=[]; TimeLast=[]; TimeMax=[]; %% 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; TimeName='xml'; end if isfield(XmlData,'Camera') 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,'TranslationMotor')&& isfield(XmlData.TranslationMotor,'NbSlice') NbSlice_motor=XmlData.TranslationMotor.NbSlice; if ~isempty(NbSlice) && ~isequal(NbSlice_motor,NbSlice) msgbox_uvmat('WARNING','inconsistent Z numbers of Z indices'); else NbSlice=NbSlice_motor; end end end if ~isempty(NbSlice) set(handles.num_NbSlice,'String',num2str(NbSlice)) set(handles.num_NbSlice,'Visible','on') end %% read timing from the current file (prioritary) if ~isempty(VideoObject)% case of movies imainfo=get(VideoObject); if isfield(imainfo,'NumFrames') imainfo.NumberOfFrames=imainfo.NumFrames; end 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 TimeName='video'; end %% determine the min and max times: case of Netcdf files will be treated later in FieldName_Callback if ~isempty(TimeName) if size(Time)<[MaxIndex_i+1 MaxIndex_j+1] msgbox_uvmat('WARNING',['incomplete time info in ' XmlFileName]); end TimeMin=Time(MinIndex_i+1,MinIndex_j+1); if size(Time)>=[first_i+1 first_j+1] TimeFirst=Time(first_i+1,first_j+1); end if size(Time)>=[last_i+1 last_j+1] TimeLast=Time(last_i+1,last_j+1); end if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1] TimeMax=Time(MaxIndex_i+1,MaxIndex_j+1); end end %% update the time table TimeTable=get(handles.TimeTable,'Data'); TimeTable{iview,1}=TimeName; TimeTable{iview,2}=TimeMin; TimeTable{iview,3}=TimeFirst; TimeTable{iview,4}=TimeLast; TimeTable{iview,5}=TimeMax; set(handles.TimeTable,'Data',TimeTable) %% update the series info in '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}=FileInfo.FileType; SeriesData.FileInfo{iview}=FileInfo; SeriesData.Time{iview}=Time; SeriesData.TimeName=TimeName; if check_calib SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib; end set(handles.series,'UserData',SeriesData) %% update pair menus hset_pair=findobj(allchild(0),'Tag','set_pairs'); if ~isempty(hset_pair), delete(hset_pair); end % delete the GUI set_pair if opened CheckPair= ~isempty(i2_series)||~isempty(j2_series); % check whether index pairs need to be defined PairString=get(handles.PairString,'Data'); if CheckPair% if pairs need to be display for line iview [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series); Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,ModeMenu{ModeValue},Time,TimeUnit,ref_i,ref_j,TimeName,InputTable(iview,:),FileInfo); PairString{iview,1}=Menu{1}; else PairString{iview,1}=''; % no pair for #iview end set(handles.PairString,'Data',PairString) if isempty(find(cellfun('isempty',get(handles.PairString,'Data'))==0, 1))% if all lines of pairs are empty set(handles.PairString,'Visible','off') set(handles.SetPairs,'Visible','off') else set(handles.PairString,'Visible','on') set(handles.SetPairs,'Visible','on') end %% 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 iline=1:nbview pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); % max on pair index j_max{iline}=max(pair_max,[],1); % max on j index if ~isempty(j_max{iline}) MaxIndex_i(iline)=find(j_max{iline}, 1, 'last' )-1; % max ref index i MinIndex_i(iline)=find(j_max{iline}, 1 )-1; % min ref index i end end MinIndex_i=min(MinIndex_i); MaxIndex_i=max(MaxIndex_i); range_index=MaxIndex_i-MinIndex_i+1; 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 iline=1:nbview ind_y=1+(iline-1)*range_y:iline*range_y; LineData=zeros(size(file_indices)); file_select=file_indices(file_indices<=numel(j_max{iline})); ind_select=file_indices<=numel(j_max{iline}); LineData(ind_select)=j_max{iline}(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); %-----------------------------------------------------------guide ------------- %------------------------------------------------------------------------ % III - FUNCTIONS ASSOCIATED TO THE FRAME IndexRange %------------------------------------------------------------------------ % ---- determine the menu to put in mode and advice a default choice %------------------------------------------------------------------------ function [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series) %------------------------------------------------------------------------ ModeMenu={''}; if isempty(j2_series)% no j pair ModeValue=1; if ~isempty(i2_series) ModeMenu={'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=find(j_max, 1, 'last' )-1; % max ref index i MinIndex_i=find(j_max, 1 )-1; % min ref index i i_max=max(pair_max,[],2); MaxIndex_j=find(i_max, 1, 'last' )-1; % max ref index i MinIndex_j=find(i_max, 1 )-1; % min ref index i if MaxIndex_j==MinIndex_j ModeValue=1; ModeMenu={'bursts'}; elseif MaxIndex_i==MinIndex_i ModeValue=1; ModeMenu={'series(Dj)'}; else ModeMenu={'bursts';'series(Dj)'}; if (MaxIndex_j-MinIndex_j)>10 ModeValue=2; % set mode to series(Dj) if more than 10 j values else ModeValue=1; end end end %------------------------------------------------------------------------ %fill the menu of possible pairs as input function displ_pair=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo) %------------------------------------------------------------------------ displ_pair={}; if isempty(TimeUnit) dtunit='e-03'; else dtunit=['m' TimeUnit]; end switch mode case 'series(Di)' 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 ~isempty(find(diff_i==ipair,1))% if the considered difference exists as input pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ]; if size(time,1)>=ref_i+ceil(ipair/2) 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 case '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 case '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 pair_string=['j= ' num2str(pair1) '-' num2str(pair2)]; [TimeValue,DtValue]=get_time(ref_i,[],pair_string,InputTable,FileInfo,TimeName,'Dt'); %Dt=time(ref_i,pair2+1)-time(ref_i,pair1+1); pair_string=[pair_string ', Dt=' num2str(DtValue) ' ' dtunit]; displ_pair=[displ_pair;{pair_string}]; end end end if ~isempty(displ_pair) displ_pair=[displ_pair;{'j=*-*'}]; end 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'); % if ~isfield(SeriesData,'Time') return end 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'); %%%%%% %TODO: read time in netcdf file, see ActionName_Callback %%%%%%% %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,3}=time_first; % TODO: take into account pairs TimeTable{iview,4}=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 PairString=get(hObject,'Data'); if ~isempty(PairString{eventdata.Indices(1)}) SetPairs_Callback(hObject, eventdata.Indices(1), handles) end end %------------------------------------- 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) %----------------------------------- 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.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 if ~isequal(get(handles.ActionInput,'BackgroundColor'),[1 0 0]) msgbox_uvmat('ERROR','first activate the button ActionInput') return end 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([], eventdata, handles) %% launch action errormsg=launch_action(handles); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) 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) %------------------------------------------------------------------------ % --- called by RUN_Callback %------------------------------------------------------------------------ % The calculations are launched in three different ways: % RunMode='local': calculation on the local Matlab session, will prevent other actions during that time. % RunMode='background': calculation on the local computer, but in a new Matlab session (with no graphic output). % RunMode='cluster': calculations dispatched in a cluster, using a managing system, 'oar, 'sge, or 'sgb'. % In the latter case, the calculation is split in 'packets' of i index (all j indices are contained in a single packet). % This splitting is possible only if the different calculations in the series are independent. Otherwise the action % function imposes a number of processes NbSlice in input, for instance NbSlice=1 for a time series. % If NbSlice is not imposed, the splitting in packets (jobs) is determined % so that a job is optimum length AdvisedJobCPUTime), and the total job number in any case smaller % than MaxJobNumber (these parameters are defined in the file series.xml in % accordance with the management strategy for the cluster). The jobs are % dispatched in parallel into NbCore processors by the cluster managing system. function errormsg=launch_action(handles) errormsg=''; % default %% read the data on the GUI series Param=read_GUI_series(handles); % displayed parameters SeriesData=get(handles.series,'UserData'); % hidden parameters if isfield(SeriesData,'TransformInput') Param.TransformInput=SeriesData.TransformInput; end if isfield(SeriesData,'ProjObject') Param.ProjObject=SeriesData.ProjObject; end if ~isfield(SeriesData,'i1_series') errormsg='The input field series needs to be refreshed: press REFRESH'; return end if isfield(Param,'InputFields')&& isfield(Param.InputFields,'FieldName')&& isequal(Param.InputFields.FieldName,'add_field...') errormsg='input field name(s) not defined, select add_field...'; return 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; Param.Action=rmfield(Param.Action,'RunMode'); % remove from the recorded xml file to avoid interference during ImportConfig Param.RunMode=RunMode; % keep track of the mode end ActionExt='.m'; % default if isfield(Param.Action,'ActionExt') ActionExt=Param.Action.ActionExt; % '.m', '.sh' (compiled) or '.py' (Python) Param.Action=rmfield(Param.Action,'ActionExt'); % remove from the recorded xml file to avoid interference during ImportConfig 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') 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 end %% Get parameters from series.xml errormsg=''; % default error message ActionFullName=fullfile(get(handles.ActionPath,'String'),ActionName); %% If a compiled version has been selected (ext .sh) check wether it needs to be recompiled if strcmp(ActionExt,'.sh') TransformPath=''; if isfield(SeriesData,'TransformPath') TransformPath=SeriesData.TransformPath; if isfield(SeriesData,'TransformList') TransformList=get(handles.TransformName,'String'); TransformIndex=get(handles.TransformName,'Value'); TransformName=TransformList{TransformIndex}; if ~ismember(TransformName,SeriesData.TransformList) TransformPath=''; end end end if ~isempty(TransformPath)&&... ~strcmp(TransformPath,get(handles.TransformPath,'String'))% if the transform is not in paths set for compilation msgbox_uvmat('ERROR', 'compilation not available for this transform function, select .m') return end set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch' set(handles.ActionExt,'BackgroundColor',[1 1 0]) [mcrmajor, mcrminor] = mcrversion; MCRROOT = ['MCRROOT',int2str(mcrmajor),int2str(mcrminor)]; RunTime = getenv('MCRROOT'); % Just variable MCRROOT with no version in it's name if strcmp(RunTime,'') RunTime = getenv(MCRROOT); % Use specialize MCRROOT with version end ActionNameVersion=[ActionName '_' MCRROOT]; ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']); % compile the .m file if the .sh file does not exist yet 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(path_uvmat)% add the path to uvmat to run the fct 'compile' compile(ActionName,TransformPath) cd(currentdir) else errormsg='Action launch interrupted'; return end else sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.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',[ActionNameVersion '.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(path_uvmat)% add the path to uvmat to run the fct 'compile' addpath(fullfile(path_uvmat,'transform_field'))% add the path to transform functions 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 %% set nbre of cluster cores and processes: % NbCore is the number of computer processors used % NbProcess is the number of independent processes in which the required calculation is split. % switch RunMode % case {'local','background'} % NbCore=1; % no need to split the calculation % case 'cluster' % %proposed number of cores to reserve in the cluster % NbCoreAdvised=SeriesData.SeriesParam.ClusterParam.NbCoreAdvised; % NbCoreMax=min(NbProcess,SeriesData.SeriesParam.ClusterParam.NbCoreMax); % if NbCoreMax~=1 % if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled) % warning_string=', preferably use .sh option to save Matlab licences'; % else % warning_string=')'; % end % answer=msgbox_uvmat('INPUT_TXT',['Number of cores (max ' num2str(NbCoreMax) ', ' warning_string],num2str(NbCoreAdvised)); % if isempty(answer) % errormsg='Action launch interrupted by user'; % return % end % NbCore=str2double(answer); % if NbCore > NbCoreMax % NbCore=NbCoreMax; % end % else % NbCore=1; % end % end if ~isfield(Param.IndexRange,'NbSlice') Param.IndexRange.NbSlice=[]; end OutputPath=get(handles.OutputPath,'String'); %% Look for processing on multiple experiments set by the GUI browse_data NbExp=1;% initiate the number of experiments set by the GUI browse_data, =1 otherwise if get(handles.Replicate,'Value') hh=findobj(allchild(0),'Tag','browse_data'); if isempty(hh) set(handles.Replicate,'Value',0) else set(handles.Replicate,'BackgroundColor',[1 1 0])%paint Relicate button in yellow BrowseData=guidata(hh); SourceDir=get(BrowseData.SourceDir,'String'); ListExp=get(BrowseData.ListExperiments,'String'); ExpIndices=get(BrowseData.ListExperiments,'Value'); ListExp=ListExp(ExpIndices); ListDevices=get(BrowseData.ListDevices,'String'); DeviceIndices=get(BrowseData.ListDevices,'Value'); ListDevices=ListDevices(DeviceIndices); ListDataSeries=get(BrowseData.DataSeries,'String'); DataSeriesIndices=get(BrowseData.DataSeries,'Value'); ListDataSeries=ListDataSeries(DataSeriesIndices); NbExp=0; % counter of the number of experiments set by the GUI browse_data for iexp=1:numel(ListExp) if ~isempty(regexp(ListExp{iexp},'^\+/'))% if it is a folder %if strcmp(get(BrowseData.DataSeries,'enable'),'off') %case of a multiple input line for series % NbExp=NbExp+1; % ExpIndex{NbExp}=iexp; % for idevice=1:numel(ListDevices) % lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),... % regexprep(ListDevices{idevice},'^\+/','')); % lpathout=fullfile(OutputPath,regexprep(ListExp{iexp},'^\+/',''),... % regexprep(ListDevices{idevice},'^\+/','')); % ldir=regexprep(ListDataSeries{idevice},'^\+/',''); % ListPath{idevice,NbExp}=lpath; % ListPathOut{idevice,NbExp}=lpathout; % ListSubdir{idevice,NbExp}=ldir; % end %else for idevice=1:numel(ListDevices) if ~isempty(regexp(ListDevices{idevice},'^\+/'))% if it is a folder for isubdir=1:numel(ListDataSeries) if ~isempty(regexp(ListDataSeries{isubdir},'^\+/'))% if it is a folder lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),... regexprep(ListDevices{idevice},'^\+/','')); lpathout= fullfile(OutputPath,regexprep(ListExp{iexp},'^\+/',''),... regexprep(ListDevices{idevice},'^\+/','')); ldir= regexprep(ListDataSeries{isubdir},'^\+/',''); if exist(fullfile(lpath,ldir),'dir') NbExp=NbExp+1; ExpIndex(NbExp)=ExpIndices(iexp); DeviceIndex(NbExp)=DeviceIndices(idevice); ListPath{NbExp}=lpath; ListPathOut{NbExp}=lpathout; ListDeviceOut{NbExp}=regexprep(ListDevices{idevice},'^\+/',''); ListExpOut{NbExp}=regexprep(ListExp{iexp},'^\+/',''); ListSubdir{NbExp}=ldir; end end end end end % end end end answer=msgbox_uvmat('INPUT_Y-N-Cancel',['replicate the processing on ' num2str(NbExp) ' data series']); if strcmp(answer,'Cancel')||strcmp(answer,'No') return end end end %%%%%%%%%%%%%%%%%%% LOOP ON EXPERIMENTS POSSIBLY SET BY THE GUI browse_data, NbExp=1 otherwise %%%%%%%%% for iexp=1:NbExp if get(handles.Replicate,'Value') if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action disp('program stopped by user') return end set(BrowseData.ListExperiments,'Value',ExpIndex(iexp)) set(BrowseData.ListDevices,'Value',DeviceIndex(iexp)) Param.InputTable(:,1)=ListPath(:,iexp); Param.InputTable(:,2)=ListSubdir(:,iexp); OutputSubDir=unique(ListSubdir(:,iexp)); Param.OutputSubDir=OutputSubDir{1}; if numel(OutputSubDir)>1% case for iout=2:numel(OutputSubDir) Param.OutputSubDir=[Param.OutputSubDir '-' OutputSubDir{iout}]; end end end [xx,ExpName]=fileparts(Param.InputTable{1,1}); Param.IndexRange.first_i=str2num(get(handles.num_first_i,'String'));%reset the firrst_i and last_i for multiple experiments, modified by the splitting into NbProcess Param.IndexRange.last_i=str2num(get(handles.num_last_i,'String')); %% create the output data directory if needed, after checking its existence OutputDir=''; answer=''; if isfield(Param,'OutputSubDir')&& isfield(Param,'OutputDirExt')% possibly update the output dir if it already exists PathOut=get(handles.OutputPath,'String'); if ~exist(PathOut,'dir') % test if the dir already exist PathOut=uigetdir(PathOut,'pick the output root path'); set(handles.OutputPath,'String',PathOut); end if get(handles.Replicate,'Value') PathExpOut=fileparts(ListPath{iexp}); PathExpDeviceOut=ListPath{iexp}; else PathExpOut=fullfile(PathOut,get(handles.Experiment,'String')); PathExpDeviceOut=fullfile(PathExpOut,get(handles.Device,'String')) end if ~exist(PathExpOut,'dir') [tild,msg1]=mkdir(PathExpOut); if ~strcmp(msg1,'') errormsg=['cannot create ' PathExpOut ': ' msg1]; % error message for directory creation return end end if ~exist(PathExpDeviceOut,'dir') [tild,msg1]=mkdir(PathExpDeviceOut); if ~strcmp(msg1,'') errormsg=['cannot create ' PathExpDeviceOut ': ' msg1]; % error message for directory creation return end end SubDirOut=[Param.OutputSubDir Param.OutputDirExt]; SubDirOutNew=SubDirOut; detect=exist(fullfile(PathExpDeviceOut,SubDirOutNew),'dir'); % test if the dir already exist check_create=1; % need to create the result directory by default CheckOverwrite=1; if isfield(Param,'CheckOverwrite') CheckOverwrite=Param.CheckOverwrite;% will overwrite previous data if it is equal to 1 end while detect if CheckOverwrite comment=', possibly overwrite previous data'; else comment=', will complement existing result files (no overwriting)'; end answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(PathExpDeviceOut,SubDirOutNew) comment]); if strcmp(answer,'Cancel') break 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(PathExpDeviceOut,SubDirOutNew),'dir'); % test if the dir already exists check_create=1; end end if strcmp(answer,'Cancel') continue end Param.OutputDirExt=regexprep(SubDirOutNew,['^' Param.OutputSubDir],''); Param.OutputRootFile=Param.InputTable{1,3}; % the first sorted RootFile taken for output OutputDir=fullfile(PathExpDeviceOut,[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,'') errormsg=['cannot create ' OutputDir ': ' msg1]; % error message for directory creation return end end elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir OutputDir=Param.ActionInput.LogPath; end if isfield(Param,'OutputSubDir')&& isfield(Param,'OutputDirExt') set(handles.OutputSubDir,'String',Param.OutputSubDir) set(handles.OutputDirExt,'String',Param.OutputDirExt) drawnow end if get(handles.Replicate,'Value') set(handles.InputTable,'Data',Param.InputTable) set(handles.OutputPath,'String',OutputPath) set(handles.Experiment,'String',ListExpOut{iexp}) set(handles.Device,'String',ListDeviceOut{iexp}) Param.Experiment=ListExpOut{iexp}; Param.Device=ListDeviceOut{iexp}; check_input_file_series(handles) end DirXml=fullfile(OutputDir,'0_XML'); if ~exist(DirXml,'dir') [~,msg1]=mkdir(DirXml); if ~strcmp(msg1,'') errormsg=['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 ':']; msg}); % error message for directory creation end end OutputNomType=nomtype2pair(Param.InputTable{1,4}); % nomenclature for output files %% get the set of reference input field indices first_i=1; % first i index to process last_i=1; % last i index to process incr_i=1; % increment step in i index first_j=1; % first j index to process last_j=1; % last j index to process incr_j=1; % increment step in j index 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,'incr_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 errormsg= 'series/Run_Callback:last field index must be larger or equal to the first one'; 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 % case of no increment i defined: processing is done on the available files found in i1_series 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 % increment i is defined: processing is done on first_i:incr_i:last_i; else ref_i=first_i:incr_i:last_i; if isempty(incr_j)% automatic finding of the existing j indices [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 nbfield_j=numel(ref_j); % number of j indices BlockLength=numel(ref_i); % by default, job involves the full set of i field indicesNbProcess NbProcess=1; NbCore=1; switch RunMode case 'cluster' if (isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime) && isnumeric(Param.Action.CPUTime)) CPUTime=Param.Action.CPUTime; % Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j else answer=msgbox_uvmat('INPUT_TXT','estimate the CPU time(in minutes) for each value of index i:' ,''); CPUTime=str2num(answer); set(handles.num_CPUTime,'String',answer) Param.Action.CPUTime=CPUTime; end JobNumberMax=SeriesData.SeriesParam.ClusterParam.JobNumberMax; JobCPUTimeAdvised=SeriesData.SeriesParam.ClusterParam.JobCPUTimeAdvised; if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined BlockLength= ceil(JobCPUTimeAdvised/(CPUTime*nbfield_j)); % iterations are grouped in sets with length BlockLength such that the typical CPU time of a job is JobCPUTimeAdvised. BlockLength=max(BlockLength,ceil(numel(ref_i)*NbExp/JobNumberMax)); % possibly increase the BlockLength to have less than MaxJobNumber jobs NbProcess=ceil(numel(ref_i)/BlockLength) ; % nbre of processes sent to oar else NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes end % %proposed number of cores to reserve in the cluster NbCoreAdvised=SeriesData.SeriesParam.ClusterParam.NbCoreAdvised; NbCoreMax=min(NbProcess,SeriesData.SeriesParam.ClusterParam.NbCoreMax);% reduces the number of cores if it exceeds the number of processes if NbCoreMax~=1 if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled) warning_string=', preferably use .sh option to save Matlab licences'; else warning_string=')'; end answer=msgbox_uvmat('INPUT_TXT',['Number of cores (max ' num2str(NbCoreMax) ', ' warning_string],num2str(NbCoreAdvised)); if isempty(answer) errormsg='Action launch interrupted by user'; return end NbCore=str2double(answer); if NbCore > NbCoreMax NbCore=NbCoreMax; end end otherwise if ~isempty(Param.IndexRange.NbSlice) NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes end end %% 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) %% case of a function in Python if strcmp(ActionExt, '.py (in dev.)') fprintf([ '\n' ... '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ... 'The option .py is used. It is still in development.\n' ... 'To try it, first install pyper and the most recent version of fluidimage\n' ... '(see https://bitbucket.org/fluiddyn/fluidimage).\n' ... 'Warning: there is no direct correspondance between UVMAT and fluidimage parameters\n' ... '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n']) RunMode = 'python'; end %% direct processing on the current Matlab session or creation of command files filexml=cell(1,NbProcess); % initialisation of the names of the files containing the processing parameters extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process for iprocess=1:NbProcess extxml{iprocess}='.xml'; end for iprocess=1:NbProcess if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action disp('program stopped by user') return end Param.IndexRange.incr_slice=incr_i; if isempty(Param.IndexRange.NbSlice) Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i; if Param.IndexRange.first_i>last_i NbProcess=iprocess-1; % leave the loop, we are at the end of the calculation break end Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1); else %multislices (then incr_i is not empty) Param.IndexRange.first_i= first_i+iprocess-1; Param.IndexRange.incr_slice=incr_i*Param.IndexRange.NbSlice; end for ilist=1:size(Param.InputTable,1) Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/'); % correct path name for PCWIN system end if isfield(Param,'OutputSubDir') t=struct2xml(Param); t=set(t,1,'name','Series'); extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,... Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j); filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess}); try save(t, filexml{iprocess}); % save the xml file containing the processing parameters catch ME if ~strcmp (RunMode,'local') errormsg=['error writting ' filexml{iprocess} ': ' ME.message]; return end end end if strcmp (RunMode,'local') switch ActionExt case '.m' h_fun(Param); % direct launching case '.sh' switch computer case {'PCWIN','PCWIN64'} %Windows system filexml=regexprep(filexml,'\\','\\\\'); % add '\' so that '\' are left as characters system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); % TODO: adapt to DOS system case {'GLNX86','GLNXA64','MACI64'}%Linux system system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); end end end end if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python') %% 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 DirExe=fullfile(OutputDir,'0_EXE'); % directory name for executable files 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(DirExe,'dir') [tild,msg1]=mkdir(DirExe); if ~strcmp(msg1,'') errormsg=['cannot create ' DirExe ': ' msg1]; % error message for directory creation return end [success,msg] = fileattrib(DirExe,'+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 ' DirExe ':']; msg}); % error message for directory creation end end %create subdirectory for log files DirLog=fullfile(OutputDir,'0_LOG'); if ~exist(DirLog,'dir') [tild,msg1]=mkdir(DirLog); if ~strcmp(msg1,'') errormsg=['cannot create ' DirLog ': ' msg1]; % error message for directory creation return end [success,msg] = fileattrib(DirLog,'+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 ' DirLog ':']; msg}); % error message for directory creation end end %create the executable and log file names file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,... first_i,last_i,first_j,last_j); file_exe_global=fullfile(OutputDir,'0_EXE',file_exe_global); filelog_global=fullfile_uvmat('','',Param.InputTable{1,3},'.log',OutputNomType,... first_i,last_i,first_j,last_j); filelog_global=fullfile(OutputDir,'0_LOG',filelog_global); for iprocess=1:NbProcess batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt)); % executable file names filelog{iprocess}=fullfile(OutputDir,'0_LOG',regexprep(extxml{iprocess},'.xml$','.log'));% corresponding log file names end end %% launch the executable files for background or cluster processing switch RunMode case 'background' [fid,message]=fopen(file_exe_global,'w'); if isequal(fid,-1) errormsg=['creation of ' file_exe_global ':' message]; return end switch ActionExt case '.m'% Matlab function switch computer case {'GLNX86','GLNXA64','MACI64'} cmd=command_launch_matlab(filelog_global,path_series,Param.Action.ActionPath,Param.Action.ActionName,filexml,'background'); fprintf(fid,cmd); % fill the executable file with the char string cmd fclose(fid); % close the executable filefilelog_global system(['chmod +x ' file_exe_global]); % set the file to executable case {'PCWIN','PCWIN64'} cmd=['matlab -automation -logfile ' regexprep(filelog{iprocess},'\\','\\\\')... ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'... 'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');']; for iprocess=1:NbProcess cmd=[cmd '' Param.Action.ActionName '( ''' regexprep(filexml{iprocess},'\\','\\\\') ''');'] end cmd=[cmd ';exit"']; fprintf(fid,cmd); % fill the executable file with the char string cmd fclose(fid); % close the executable file end system([file_exe_global ' &'])% directly execute the command file case '.sh' % compiled Matlab function for iprocess=1:NbProcess switch computer case {'GLNX86','GLNXA64','MACI64'} [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file if isequal(fid,-1) errormsg=['creation of .bat file: ' message]; return end cmd=['#!/bin/bash \n '... '#$ -cwd \n '... 'hostname && date \n '... 'umask 002 \n'... ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group fprintf(fid,cmd); % fill the executable file with the char string cmd fclose(fid); % close the executable file system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable system([batch_file_list{iprocess} ' &'])% directly execute the command file case {'PCWIN','PCWIN64'} msgbox_uvmat('ERROR','option for compiled Matlab functions not implemented for Windows system') return end end msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched in background for ' ExpName ': press STATUS to see results']) end case 'cluster' % option 'oar-parexec' used %create subdirectory for oar commands for iprocess=1:NbProcess [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file if isequal(fid,-1) errormsg=['creation of .bat file: ' message]; return end if strcmp(ActionExt,'.sh') cmd=['#!/bin/bash \n '... '#$ -cwd \n '... 'hostname && date \n '... 'umask 002 \n'... ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group else cmd=command_launch_matlab(filelog_global,path_series,Param.Action.ActionPath,Param.Action.ActionName,filexml{iprocess},'cluster'); % matlab_ver = ver('MATLAB'); % matlab_version = matlab_ver.Version; % cmd=[... % '#!/bin/bash\n'... % 'source /etc/profile\n'... % 'module purge\n'... % 'module load matlab/' matlab_version '\n'...% CHOICE OF CURRENT MATLAB VERSION % 'matlab -nodisplay -nosplash -nojvm -singleCompThread -logfile ''' filelog{iprocess} ''' <','.stderr') ' '... % '-O ' regexprep(ListProcess,'\.txt\>','.log') ' '... % extra_qstat ' '... % '"oar-parexec -s -f ' ListProcess ' '... % '-l ' ListProcess '.log"']; % filename_oarcommand=fullfile(DirPBS,'pbs_command'); % fid=fopen(filename_oarcommand,'w'); % fprintf(fid,pbs_command); % fclose(fid); % fprintf(pbs_command); % display in command line % %system(pbs_command); % msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster']) case 'cluster_sge' % for PSMN % TODO: use the standard 'cluster' config with an external fct % Au PSMN, on ne cr??e pas 1 job avec plusieurs c??urs, mais N jobs de 1 c??urs % o?? N < 1000. %create subdirectory for pbs command and log files DirSGE=fullfile(OutputDir,'0_SGE'); if exist(DirSGE,'dir')% delete the content of the dir 0_LOG to allow new input curdir=pwd; cd(DirSGE) delete('*') cd(curdir) else [tild,msg1]=mkdir(DirSGE); if ~strcmp(msg1,'') errormsg=['cannot create ' DirSGE ': ' msg1]; % error message for directory creation return end end maxImgsPerJob = ceil(length(batch_file_list)/NbCore); disp(['Max number of jobs: ' num2str(NbCore)]) disp(['Images per job: ' num2str(maxImgsPerJob)]) iprocess = 1; imgsInJob = []; currJobIndex = 1; done = 0; while(~done) if(iprocess <= length(batch_file_list)) imgsInJob = [imgsInJob, iprocess]; end if((numel(imgsInJob) >= maxImgsPerJob) || (iprocess == length(batch_file_list))) cmd=['#!/bin/sh \n'... '#$ -cwd \n'... 'hostname && date\n'] for ii=1:numel(imgsInJob) cmd=[cmd ActionFullName ' /softs/matlab ' filexml{imgsInJob(ii)} '\n']; end [fid, message] = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w'); fprintf(fid, cmd); fclose(fid); system(['chmod +x ' DirSGE '/job' num2str(currJobIndex) '.sh']) sge_command=['qsub -N civ_' num2str(currJobIndex) ' '... '-q ' qstat_Queue ' '... '-e ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '... '-o ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '... fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])]; fprintf(sge_command); % display in command line [status, result] = system(sge_command); fprintf(result); currJobIndex = currJobIndex + 1; imgsInJob = []; end if(iprocess == length(batch_file_list)) done = 1; end iprocess = iprocess + 1; end msgbox_uvmat('CONFIRMATION',[num2str(currJobIndex-1) ' jobs launched on queue ' qstat_Queue '.']) case 'python' ActionName='fluidimage.run_from_xml';% name of the function to launch command = command_launch_python('','',ActionName,filexml{iprocess}); % ['LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "l = x.split('':''); l = [s for s in l if ''matlab'' not in s]; print('':''.join(l))") ' ... % 'python -m fluidimage.run_from_xml ' filexml{iprocess}]; fprintf(['command:\n' command '\n\n']) errorcheck=system(command, '-echo') end if exist(OutputDir,'dir') [SUCCESS,MESSAGE,MESSAGEID] = fileattrib (OutputDir); if MESSAGE.GroupWrite~=1 [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 ':']; msg}); % error message for directory creation end end end end set(handles.Replicate,'BackgroundColor',[0 1 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 if isfield(Param,'InputLine') Param=rmfield(Param,'InputLine'); end if isfield(Param,'EditObject') Param=rmfield(Param,'EditObject'); end Param.IndexRange.TimeSource=Param.IndexRange.TimeTable{end,1}; 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, ActionPath, 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, [], 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 NbBuiltinAction=get(handles.Action,'UserData'); % 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...') if ~ischar(ActionPath) ActionPath=get(handles.ActionPath,'String'); end [FileName, PathName] = uigetfile( ... {'*.m', ' (*.m)'; '*.m', '.m files '; ... '*.*', 'All Files (*.*)'}, ... 'Pick a series processing function ',ActionPath); if length(FileName)<2 return end [tild,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 PathName=regexprep(PathName,'/$',''); if ~isempty(ActionIndex) && ~strcmp(ActionPathList{ActionIndex},PathName)%compare the path to the existing fct ActionIndex=[]; % the selected path is different than the recorded one end if isempty(ActionIndex)%the qselected fct (with selected path) 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...' ActionPathList=[ActionPathList; PathName]; 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}]) end % remove old Action options in the menu (keeping a menu length NbBuiltinAction+5; % nb_builtin_ACTION=nbre of functions always remaining in the initial menu nbremove=length(ActionList)-NbBuiltinAction-5; ActionList(NbBuiltinAction+1:end-5)=[]; ActionPathList(NbBuiltinAction+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.ActionName,'UserData',ActionPathList); set(handles.ActionExt,'Value',ActionExtIndex) %record the user defined menu additions in personal file profil_perso dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if NbBuiltinAction+1<=numel(ActionList)-1 ActionListUser=ActionList(NbBuiltinAction+1:numel(ActionList)-1); ActionPathListUser=ActionPathList(NbBuiltinAction+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) %% 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 set(handles.ActionName,'BackgroundColor',[1 1 1]) set(handles.ActionInput,'BackgroundColor',[1 0 1])% set ActionInput button to magenta color to indicate that input refr set(handles.num_CPUTime,'String','') % --- Executes on button press in ActionInput. function ActionInput_Callback(hObject, eventdata, handles) set(handles.ActionInput,'BackgroundColor',[1 1 0]) SeriesData=get(handles.series,'UserData'); % info on the input file series %% create the function handle for Action ActionPath=get(handles.ActionPath,'String'); ActionList=get(handles.ActionName,'String'); ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name if ~exist(ActionPath,'dir') ActionName_Callback(handles.ActionName, ActionPath, handles)% update the function return end current_dir=pwd; % current working dir cd(ActionPath) h_fun=str2func(ActionName);% create the function handle for the function ActionName cd(current_dir) %% Activate the Action fct to adapt the configuration of the GUI series and bring specific parameters in SeriesData Param=read_GUI_series(handles); % read the parameters from the GUI series Param.Action.RUN=0; Param.SeriesData=SeriesData; ParamOut=h_fun(Param); % run the selected Action function to get the relevant input %% Visibility of VelType and VelType_1 menus asked by ActionName VelTypeRequest=1; % VelType requested by default VelTypeRequest_1=1; % VelType requested by default if isfield(ParamOut,'VelType') VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'}); VelTypeRequest_1=strcmp( ParamOut.VelType,'two'); end FieldNameRequest=0; %hidden by default FieldNameRequest_1=0; %hidden by default if isfield(ParamOut,'FieldName') FieldNameRequest=ismember(ParamOut.FieldName,{'on','one','two'}); FieldNameRequest_1=strcmp( ParamOut.FieldName,'two'); end %% Detect the types of input files and set menus and default options in 'VelType' if ~isfield(SeriesData,'FileType') SeriesData.FileType={'none'}; end iview_civ=find( strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)); iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)); % all nc files, icluding civ FieldList=get(handles.FieldName,'String'); % previous list as default if ~iscell(FieldList),FieldList={FieldList};end FieldList_1=get(handles.FieldName_1,'String'); % previous list as default if ~iscell(FieldList_1),FieldList_1={FieldList_1};end CheckPivData_1=0; % indicate whether FieldName_1 has been updated with civ data, 0 by default handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title]; if VelTypeRequest && numel(iview_civ)>=1 menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)}); set(handles.VelType,'Value',1)% set first choice by default set(handles.VelType,'String',[{'*'};menu]) set(handles.VelType,'Visible','on') set(handles.VelType_title,'Visible','on') FieldList=set_field_list('U','V'); % standard menu for civx data if max(get(handles.FieldName,'Value'))>numel(FieldList) set(handles.FieldName,'Value',1); % velocity vector choice by default end if VelTypeRequest_1 && numel(iview_civ)>=2 menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)}); set(handles.VelType_1,'Value',1)% set first choice by default set(handles.VelType_1,'String',[{'*'};menu]) set(handles.VelType_1,'Visible','on') set(handles.VelType_title_1,'Visible','on') FieldList_1=[set_field_list('U','V');{'C'};{'add_field...'}]; % standard menu for civx data CheckPivData_1=1; set(handles.FieldName_1,'Value',1); % velocity vector choice by default else set(handles.VelType_1,'Visible','off') set(handles.VelType_title_1,'Visible','off') end else set(handles.VelType,'Visible','off') set(handles.VelType_title,'Visible','off') end %% Detect the types of input files and set menus and default options in 'FieldName' if (FieldNameRequest || VelTypeRequest) && numel(iview_netcdf)>=1 set(handles.InputFields,'Visible','on')% set the frame InputFields visible if FieldNameRequest && isfield(SeriesData.FileInfo{iview_netcdf(1)},'ListVarName') set(handles.FieldName,'Visible','on') set(handles.Field_text,'Visible','on') ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName; ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables for ilist=1:numel(ind_var) if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName))) FieldList={}; % previous choice not consistent with new input field set(handles.FieldName,'Value',1) break end end if ~isempty(FieldList)iview_netcdf if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||... isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName))) FieldList={}; set(handles.Coord_x,'String','') set(handles.Coord_y,'String','') end Coord_z=get(handles.Coord_z,'String'); if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))REFRESH FieldList={}; set(handles.Coord_z,'String','') end end else set(handles.FieldName,'Visible','off') set(handles.Field_text,'Visible','off') end set(handles_coord,'Visible','on') if isempty(find(strcmp('add_field...',FieldList))) FieldList=[FieldList;{'add_field...'}];%add 'add_field...' to the menu FieldName if it is not already end if FieldNameRequest_1 && numel(iview_netcdf)>=2 set(handles.FieldName_1,'Visible','on') set(handles.Field_text_1,'Visible','on') if CheckPivData_1==0 % not civ input made FieldList_1={'add_field...'} ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName; ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables for ilist=1:numel(ind_var) if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName))) %FieldList_1={}; % previous choice not consistent with new input field set(handles.FieldName_1,'Value',1) break end end warn_coord=0; if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||... isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName))) warn_coord=1; end if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName))) FieldList_1={'add_field...'}; warn_coord=1; end if warn_coord msgbox_uvmat('WARNING','coordinate names do not exist in the second netcdf input file') end set(handles.FieldName_1,'Visible','on') set(handles.FieldName_1,'Value',1) set(handles.FieldName_1,'String',FieldList_1) end else set(handles.FieldName_1,'Visible','off') end if isempty(FieldList) set(handles.Field_text,'Visible','off') set(handles.FieldName,'Visible','off') else set(handles.Field_text,'Visible','on') set(handles.FieldName,'Visible','on') set(handles.FieldName,'String',FieldList) end else set(handles.InputFields,'Visible','off') end %% Introduce visibility of file overwrite option if isfield(ParamOut,'CheckOverwriteVisible')&& strcmp(ParamOut.CheckOverwriteVisible,'on') set(handles.CheckOverwrite,'Visible','on') else set(handles.CheckOverwrite,'Visible','off') 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(Param.InputTable(:,2)); % subdirectories sorted in alphabetical order set(handles.InputTable,'Data',Param.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'); if size(TimeTable,1)1 for ilist=2:numel(SubDir) SubDirOut=[SubDirOut '-' regexprep(SubDir{ilist},'^/','')]; end end case 'one' OutputDirVisible='on'; SubDirOut=InputTable{1,2}; % use the first subdir name (+OutputDirExt) as output subdirectory case 'two' OutputDirVisible='on'; SubDir=InputTable(1:2,2); % set of subdirectories SubDirOut=SubDir{1}; if numel(SubDir)>1 SubDirOut=[SubDirOut '-' regexprep(SubDir{2},'^/','')]; end case 'last' OutputDirVisible='on'; SubDirOut=InputTable{end,2}; % use the last subdir name (+OutputDirExt) as output subdirectory end set(handles.OutputSubDir,'String',SubDirOut) set(handles.OutputSubDir,'BackgroundColor',[1 1 1])% set edit box to white color to indicate refreshment set(handles.OutputDirExt,'Visible',OutputDirVisible) set(handles.OutputSubDir,'Visible',OutputDirVisible) % set(handles.OutputDir_title,'Visible',OutputDirVisible) SeriesData.ActionName=ActionName; % record ActionName for next use %% visibility of the run mode (local or background or cluster) if strcmp(OutputSubDirMode,'none') RunModeVisible='off'; % only local mode available if no output file is produced else RunModeVisible='on'; end set(handles.RunMode,'Visible',RunModeVisible) set(handles.ActionExt,'Visible',RunModeVisible) set(handles.RunMode_title,'Visible',RunModeVisible) set(handles.ActionExt_title,'Visible',RunModeVisible) %% 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') ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput SeriesData.ActionInput=ParamOut.ActionInput; else % set(handles.ActionInput,'Visible','off') if isfield(SeriesData,'ActionInput') SeriesData=rmfield(SeriesData,'ActionInput'); end end set(handles.series,'UserData',SeriesData) set(handles.ActionInput,'BackgroundColor',[1 0 0]) %------------------------------------------------------------------------ % --- Executes on button press in RefreshField. function RefreshField_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.FieldName,'String',{'add_field...'}); set(handles.FieldName,'Value',1); FieldName_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ % --- Executes on selection change in FieldName. function FieldName_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ FieldListInit=get(handles.FieldName,'String'); field_index=get(handles.FieldName,'Value'); field=FieldListInit{field_index(1)}; if isequal(field,'add_field...') FieldListInit(field_index(1))=[]; SeriesData=get(handles.series,'UserData'); % input line for which the field choice is relevant iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ 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); InputTable=Param.InputTable(iview,:); % check the existence of the first file in the series first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1; % default setting for index j if isfield(Param.IndexRange,'first_j') % if index j is used first_j=Param.IndexRange.first_j; last_j=Param.IndexRange.last_j; MinIndex_j=Param.IndexRange.MinIndex_j(iview); MaxIndex_j=Param.IndexRange.MaxIndex_j(iview); end PairString=''; if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); LineIndex=iview(1); if numel(iview)>1 answer=msgbox_uvmat('INPUT_TXT',['select the line of the input table:' num2str(iview)] ,num2str(iview(1))); LineIndex=str2num(answer); end FirstFileName=fullfile_uvmat(InputTable{LineIndex,1},InputTable{LineIndex,2},InputTable{LineIndex,3},... InputTable{LineIndex,5},InputTable{LineIndex,4},i1,i2,j1,j2); if exist(FirstFileName,'file') || ~isempty(regexp(InputTable{LineIndex,1},'^http')) ParamIn.Title='get_field: pick input variables and coordinates for series processing'; ParamIn.SeriesInput=1; GetFieldData=get_field(FirstFileName,ParamIn); FieldList={}; if isfield(GetFieldData,'FieldOption')% if a field has been selected switch GetFieldData.FieldOption case 'vectors' UName=GetFieldData.PanelVectors.vector_x; VName=GetFieldData.PanelVectors.vector_y; YName={GetFieldData.Coordinates.Coord_y}; FieldList={['vec(' UName ',' VName ')'];... ['norm(' UName ',' VName ')'];... UName;VName}; set(handles.VelType,'Visible','off') case {'scalar'} FieldList=GetFieldData.PanelScalar.scalar; YName={GetFieldData.Coordinates.Coord_y}; if ischar(FieldList) FieldList={FieldList}; end set(handles.VelType,'Visible','off') case 'civdata...' FieldList=[set_field_list('U','V') ;{'C'}]; set(handles.FieldName,'Value',1) % set menu to 'velocity XName='X'; YName='y'; set(handles.VelType,'Visible','on') end set(handles.FieldName,'Value',1) set(handles.FieldName,'String',[FieldListInit; FieldList; {'add_field...'}]); if ~strcmp(GetFieldData.FieldOption,'civdata...') if ~isempty(regexp(FieldList{1},'^vec')) set(handles.FieldName,'Value',1) else set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default end XName=GetFieldData.Coordinates.Coord_x; YName=GetFieldData.Coordinates.Coord_y; TimeNameStr=GetFieldData.Time.SwitchVarIndexTime; % get the time info TimeTable=get(handles.TimeTable,'Data'); switch TimeNameStr case 'file index' TimeName=''; case 'attribute' TimeName=['att:' GetFieldData.Time.TimeName]; % update the time table TimeTable{LineIndex,2}=get_time(Param.IndexRange.MinIndex_i(LineIndex),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName); % Min time TimeTable{LineIndex,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName); % first time TimeTable{LineIndex,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName); % last time TimeTable{LineIndex,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName); % Max time 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' TimeName=['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 TimeTable{LineIndex,1}=TimeName; set(handles.TimeTable,'Data',TimeTable); end set(handles.Coord_x,'String',XName) set(handles.Coord_y,'String',YName) set(handles.Coord_x,'Visible','on') set(handles.Coord_y,'Visible','on') end else msgbox_uvmat('ERROR',[FirstFileName ' does not exist']) end end function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName) [i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString); FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2); %Data=nc2struct(FileName,[]); TimeValue=[]; DtValue=[]; switch FileInfo.FileType case 'civdata' Data=nc2struct(FileName,[]); if ismember(TimeName,{'civ1','filter1'}) if isfield(Data,'Civ1_Time') TimeValue=Data.Civ1_Time; end if isfield(Data,'Civ1_Dt') DtValue=Data.Civ1_Dt; end else if isfield(Data,'Civ2_Time') TimeValue=Data.Civ2_Time; end if isfield(Data,'Civ2_Dt') DtValue=Data.Civ2_Dt; end end case 'pivdata_fluidimage' TimeValue=ref_i;%default DtValue=1;%default case 'netcdf' Data=nc2struct(FileName,[]); if ~isempty(TimeName)&& isfield(Data,TimeName) TimeValue=Data.(TimeName); end if exist('DtName','var') && isfield(Data,DtName) DtValue=Data.(DtName); 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(1)}; if strcmp(field,'add_field...') %iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ 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); InputTable=Param.InputTable(2,:); % 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 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{2,1},Param.InputTable{2,2},Param.InputTable{2,3},... Param.InputTable{2,5},Param.InputTable{2,4},i1,i2,j1,j2); 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; FieldList={['vec(' UName ',' VName ')'];... ['norm(' UName ',' VName ')'];... UName;VName}; case {'scalar','pick variables'} FieldList=GetFieldData.PanelScalar.scalar; if ischar(FieldList) FieldList={FieldList}; end case '1D plot' case 'civdata...' FieldList=set_field_list('U','V','C'); set(handles.FieldName,'Value',2) % set menu to 'velocity end % if ~strcmp(GetFieldData.FieldOption,'civdata...') % 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 % end set(handles.FieldName_1,'Value',1) set(handles.FieldName_1,'String',[FieldList; {'add_field...'}]); end 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)% a projection object is already loaded in the GUI series set(handles.ViewObject,'Value',1) ViewObject_Callback(hObject, eventdata, handles) else if ishandle(hset_object)% a projection object is already displayed in a GUI set_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.ProjObjectName,'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.ProjObjectName,'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.ProjObjectName,'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'); if isfield(UserData,'ProjObject') hset_object=set_object(UserData.ProjObject); set(hset_object,'Name','edit_object_series') set(get(hset_object,'Children'),'Enable','on') else msgbox_uvmat('ERROR','no projection object available'); end 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.ProjObjectName,'String','') set(handles.ProjObjectName,'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; %% browse transform functions with the input menu option more... if isequal(TransformName,'more...')% browse transform functions 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); %% create the function handle of the selected fct if ~isempty(TransformName) if ~exist(TransformPathList{TransformIndex},'dir') msgbox_uvmat('ERROR',['The prescribed transform function path ' TransformPathList{TransformIndex} ' does not exist']); return end current_dir=pwd; % current working dir cd(TransformPathList{TransformIndex}) transform_handle=str2func(TransformName); cd(current_dir) Field.Action.RUN=0;% indicate that the transform fct is called only to get input param SeriesData=get(handles.series,'UserData'); ParamIn=[]; if isfield(SeriesData,'TransformInput') ParamIn.TransformInput=SeriesData.TransformInput; end DataOut=feval(transform_handle,Field,ParamIn);% execute the transform fct to get its input parameters if isfield(DataOut,'TransformInput')% used to add transform parameters at selection of the transform fct SeriesData.TransformInput=DataOut.TransformInput; set(handles.series,'UserData',SeriesData) end end %------------------------------------------------------------------------ % --- fct activated by the upper bar menu ExportConfig %------------------------------------------------------------------------ function MenuDisplayConfig_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) %% use a browser to choose the xml file containing the processing config InputTable=get(handles.InputTable,'Data'); oldfile=InputTable{1,1}; % current path in InputTable 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 if isempty(filexml), return, end % quit function if an xml file has not been opened %% fill the GUI series with the content of the xml file [Param,RootTag,errormsg]=xml2struct(filexml); % read the input xml file as a Matlab structure if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg); return end % 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,'InputFields') ListField=Param.InputFields.FieldName; if ischar(ListField),ListField={ListField}; end set(handles.FieldName,'String',[ListField;{'add_field...'}]) set(handles.FieldName,'Value',1:numel(ListField)) set(handles.FieldName,'Visible','on') end 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) Param.ActionInput.ConfigSource=filexml; % record the source of config for future info SeriesData.ActionInput=Param.ActionInput; end if isfield(Param,'TransformInput')% introduce parameters specific to a transform fct SeriesData.TransformInput=Param.TransformInput; 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.ProjObjectName,'String',Param.ProjObject.Name) set(handles.ViewObject,'Visible','on') set(handles.EditObject,'Visible','on') set(handles.DeleteObject,'Visible','on') else set(handles.ProjObjectName,'String','') set(handles.ProjObjectName,'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 %------------------------------------------------------------------------ % --- 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([0.2 0.2 0.2 0.2 0.2]*(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=fullfile(Param.OutputPath,Param.Experiment,Param.Device); if ~isfield(Param,'OutputSubDir') msgbox_uvmat('ERROR','no standard sub-directory definition for output files, use a browser to check the output') set(handles.status,'BackgroundColor',[0 1 0]) 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 FileInfo=get_file_info(FullSelectName); if strcmp(FileInfo.FileType,'txt') edit(FullSelectName) elseif strcmp(FileInfo.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')}; if strcmp(ActionExt,'.py (in dev.)') set(handles.RunMode,'Value',2) end function num_NbSlice_Callback(hObject, eventdata, handles) NbSlice=str2num(get(handles.num_NbSlice,'String')); %------------------------------------------------------------------------ % --- 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; else%if 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'); % --- Executes on button press in SetPairs. function SetPairs_Callback(hObject, eventdata, handles) %% delete previous occurrence of 'set_pairs' hfig=findobj(allchild(0),'Tag','set_pairs'); if ~isempty(hfig) delete(hfig) end %% create the GUI set_pairs set(0,'Unit','points') ScreenSize=get(0,'ScreenSize'); % get the size of the screen, to put the fig on the upper right Width=220; % fig width in points (1/72 inch) Height=min(0.8*ScreenSize(4),300); Left=ScreenSize(3)- Width-40; % right edge close to the right, with margin=40 Bottom=ScreenSize(4)-Height-40; % put fig at top right hfig=findobj(allchild(0),'Tag','set_slice'); if ~isempty(hfig),delete(hfig), end; % delete existing version of the GUI hfig=figure('name','set_pairs','tag','set_pairs','MenuBar','none','NumberTitle','off','Unit','points','Position',[Left,Bottom,Width,Height]); BackgroundColor=get(hfig,'Color'); SeriesData=get(handles.series,'UserData'); TimeUnit=get(handles.TimeUnit,'String'); PairString=get(handles.PairString,'Data'); ListViewLines=find(cellfun('isempty',PairString)==0); % find list of non empty pairs ListViewMenu=cell(numel(ListViewLines),1); %iview=get(handles.PairString,'Value'); iview=[]; for ilist=1:numel(ListViewLines) ListViewMenu{ilist}=num2str(ListViewLines(ilist)); end if isempty(iview) ListViewValue=numel(ListViewLines); % we work by default on the pair option for the last line which requires pairs iview=ListViewLines(end); else ListViewValue=find(ListViewLines==iview); end ref_i=str2num(get(handles.num_first_i,'String')); ref_j=1; % default if strcmp(get(handles.num_first_j,'String'),'Visible') ref_j=str2num(get(handles.num_first_j,'String')); end [ModeMenu,ModeValue]=update_mode(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j2_series{1}); InputTable=get(handles.InputTable,'Data'); displ_pair=update_listpair(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j1_series{1},SeriesData.j2_series{1},ModeMenu{ModeValue},... SeriesData.Time{1},TimeUnit,ref_i,ref_j,SeriesData.TimeName,InputTable,SeriesData.FileInfo{1}); for iline=1:size(InputTable,1) viewcell{iline}=num2str(iline); end viewcell=viewcell'; ModeMenu={'bursts';'series(Dj)'}; ModeValue=1; %i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo % first raw of the GUI uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,... 'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right'); % title uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.54 0.8 0.3 0.2],'BackgroundColor',[1 1 1],... 'Callback',@(hObject,eventdata)ListView_Callback(hObject,eventdata),'String',viewcell,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',... 'Tag','ListView','TooltipString','''ListView'':choice of the file series w for pair display'); % second raw of the GUI uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.79 0.7 0.1],'BackgroundColor',BackgroundColor,... 'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.05 0.62 0.9 0.2],'BackgroundColor',[1 1 1],... 'Callback',@(hObject,eventdata)Mode_Callback(hObject,eventdata),'String',ModeMenu,'Value',ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold',... 'Tag','Mode','TooltipString','''Mode'': choice of the image pair mode'); % third raw uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.6 0.7 0.1],'BackgroundColor',BackgroundColor,... 'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title uicontrol('Style','listbox','Units','normalized', 'Position', [0.05 0.42 0.9 0.2],'BackgroundColor',[1 1 1],... 'Callback',@(hObject,eventdata)ListPair_Callback(hObject,eventdata),'String',displ_pair,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',... 'Tag','ListPair','TooltipString','''ListPair'': menu for selecting the image pair'); uicontrol('Style','text','Units','normalized', 'Position', [0.1 0.22 0.8 0.1],'BackgroundColor',BackgroundColor,... 'String','ref_i ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center'); % title uicontrol('Style','edit','Units','normalized', 'Position', [0.15 0.17 0.3 0.08],'BackgroundColor',[1 1 1],... 'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),'String',num2str(ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold',... 'Tag','num_ref_i','TooltipString','''num_ref_i'': reference field index i used to display dt in ''list_pair_civ'''); uicontrol('Style','edit','Units','normalized', 'Position', [0.55 0.17 0.3 0.08],'BackgroundColor',[1 1 1],... 'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),'String',num2str(ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold',... 'Tag','num_ref_j','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ'''); uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.01 0.01 0.3 0.12],'BackgroundColor',[0 1 0],... 'Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),'String','OK','FontUnits','points','FontSize',12,'FontWeight','bold',... 'Tag','OK','TooltipString','''OK'': validate the choice'); % last raw of the GUI: pushbuttons % uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.35 0.01 0.3 0.15],'BackgroundColor',[0 1 0],'String','OK','Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),... % 'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''OK'': apply the output to the current field series in uvmat'); drawnow %------------------------------------------------------------------------ function ListView_Callback(hObject,eventdata) Mode_Callback(hObject,eventdata) %------------------------------------------------------------------------ function Mode_Callback(hObject,eventdata) %% get input info hseries=findobj(allchild(0),'tag','series'); % handles of the GUI series hhseries=guidata(hseries); % handles of the elements in the GUI series TimeUnit=get(hhseries.TimeUnit,'String'); SeriesData=get(hseries,'UserData'); mode_list=get(hObject,'String'); mode=mode_list{get(hObject,'Value')}; hListView=findobj(get(hObject,'parent'),'Tag','ListView'); iview=get(hListView,'Value'); i1_series=SeriesData.i1_series{iview}; i2_series=SeriesData.i2_series{iview}; j1_series=SeriesData.j1_series{iview}; j2_series=SeriesData.j2_series{iview}; %% enable j index visibility after the new choice if strcmp(mode,'series(Dj)') status_j='on'; % default else status_j='off'; % no j index needed for bust case end enable_j(hhseries,status_j) % no j index needed %% get the reference indices for the time interval Dt href_i=findobj(get(hObject,'parent'),'Tag','ref_i'); ref_i=[];ref_j=[]; if strcmp(get(href_i,'Visible'),'on') ref_i=str2num(get(href_i,'String')); end if isempty(ref_i) ref_i=1; end if isempty(ref_j) ref_j=1; end %% update the menu ListPair Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo); hlist_pairs=findobj(get(hObject,'parent'),'Tag','ListPair'); set(hlist_pairs,'Value',1)% set the first choice by default in ListPair set(hlist_pairs,'String',Menu)% set the menu in ListPair ListPair_Callback(hlist_pairs,[])% apply the default choice in ListPair %------------------------------------------------------------- % --- Executes on selection in ListPair. function ListPair_Callback(hObject,eventdata) %------------------------------------------------------------ list_pair=get(hObject,'String'); % get the menu of image pairs if isempty(list_pair) string=''; else string=list_pair{get(hObject,'Value')}; % string=regexprep(string,',.*',''); % removes time indication (after ',') end hseries=findobj(allchild(0),'tag','series'); hPairString=findobj(hseries,'tag','PairString'); PairString=get(hPairString,'Data'); hListView=findobj(get(hObject,'parent'),'Tag','ListView'); iview=get(hListView,'Value'); PairString{iview,1}=string; % report the selected pair string to the table PairString set(hPairString,'Data',PairString) %------------------------------------------------------------------------ function num_ref_i_Callback(hObject, eventdata) %------------------------------------------------------------------------ Mode_Callback([],[]) %------------------------------------------------------------------------ function num_ref_j_Callback(hObject, eventdata) %------------------------------------------------------------------------ Mode_Callback([],[]) %------------------------------------------------------------------------ function OK_Callback(hObject, eventdata) %------------------------------------------------------------------------ delete(get(hObject,'parent')) %------------------------------------------------------------------------ % --- Executes on button press in ClearLine. %------------------------------------------------------------------------ function ClearLine_Callback(hObject, eventdata, handles) InputTable=get(handles.InputTable,'Data'); iline=str2double(get(handles.InputLine,'String')); if size(InputTable,1)>1 InputTable(iline,:)=[]; % suppress the current line if not the first set(handles.InputTable,'Data',InputTable); end set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refr % --- Executes on button press in MonitorCluster. function MonitorCluster_Callback(hObject, eventdata, handles) [rr,ss]=system('oarstat |grep N=UVmat');% check the list of jobs launched with uvmat if isempty(ss) disp( 'no job presently submitted with uvmat') else disp('format: R/W=run/wait, time lapsed, R=nbre of cores,W=walltime') disp(ss) end function OutputSubDir_Callback(hObject, eventdata, handles) set(handles.OutputSubDir,'BackgroundColor',[1 1 1]) % --- Executes on button press in CheckOverwrite. function CheckOverwrite_Callback(hObject, eventdata, handles) % --- Executes on button press in TestCPUTime. function TestCPUTime_Callback(hObject, eventdata, handles) % hObject handle to TestCPUTime (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % --- Executes on button press in DiskQuota. function DiskQuota_Callback(hObject, eventdata, handles) SeriesData=get(handles.series,'UserData'); system(SeriesData.SeriesParam.DiskQuotaCmd) % --- Executes on button press in Replicate. function Replicate_Callback(hObject, eventdata, handles) if get(handles.Replicate,'Value') InputTable=get(handles.InputTable,'Data'); for ilist=1:size(InputTable,1) InputDir{ilist}=fullfile(InputTable{ilist,1},InputTable{ilist,2}); end browse_data(InputDir) else hh=findobj(allchild(0),'Tag','browse_data'); if ~isempty(hh) delete(hh) end end function OutputPath_Callback(hObject, eventdata, handles) function Experiment_Callback(hObject, eventdata, handles) function Device_Callback(hObject, eventdata, handles) % --- Executes on button press in OutputPathBrowse. function OutputPathBrowse_Callback(hObject, eventdata, handles) CheckValue=get(handles.OutputPathBrowse,'Value'); if CheckValue OutputPath=uigetdir(get(handles.OutputPath,'String')); set(handles.OutputPath,'String',OutputPath) else InputTable=get(handles.InputTable,'Data'); set(handles.OutputPath,'String',InputTable{1,1}) end function Mask_Callback(hObject, eventdata, handles) % hObject handle to Mask (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % Hints: get(hObject,'String') returns contents of Mask as text % str2double(get(hObject,'String')) returns contents of Mask as a double