%'series': master function associated to the GUI series.m for analysis field series %------------------------------------------------------------------------ % function varargout = series(varargin) % associated with the GUI series.fig % %INPUT % param: structure with input parameters (link with the GUI uvmat) % .menu_coord_str: string for the TransformName (menu for coordinate transforms) % .menu_coord_val: value for TransformName (menu for coordinate transforms) % .FileName: input file name % .FileName_1: second input file name % .list_field: menu of input fields % .index_fields: chosen index % .civ1=0 or 1, .interp1, ... : input civ field type % %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA % Copyright 2008-2014, LEGI / CNRS UJF G-INP, Joel.Sommeria@legi.grenoble-inp.fr %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA % This file is part of the toolbox UVMAT. % % UVMAT is free software; you can redistribute it and/or modify % it under the terms of the GNU General Public License as published by % the Free Software Foundation; either version 2 of the License, or % (at your option) any later version. % % UVMAT is distributed in the hope that it will be useful, % but WITHOUT ANY WARRANTY; without even the implied warranty of % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the % GNU General Public License (file UVMAT/COPYING.txt) for more details. %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA %------------------------------------------------------------------------ %------------------------------------------------------------------------ % I - MAIN FUNCTION series %------------------------------------------------------------------------ %------------------------------------------------------------------------ function varargout = series(varargin) % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name', mfilename, ... 'gui_Singleton', gui_Singleton, ... 'gui_OpeningFcn', @series_OpeningFcn, ... 'gui_OutputFcn', @series_OutputFcn, ... 'gui_LayoutFcn', [] , ... 'gui_Callback', []); if nargin && ischar(varargin{1}) gui_State.gui_Callback = str2func(varargin{1}); end if nargout [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); else gui_mainfcn(gui_State, varargin{:}); end % End initialization code - DO NOT EDIT %-------------------------------------------------------------------------- % --- Executes just before series is made visible. %-------------------------------------------------------------------------- function series_OpeningFcn(hObject, eventdata, handles,Param) % Choose default command line output for series handles.output = hObject; % Update handles structure guidata(hObject, handles); %% initial settings % position and size of the GUI at opening set(0,'Unit','points') ScreenSize=get(0,'ScreenSize');%size of the current screen, in points (1/72 inch) Width=900;% prefered width of the GUI in points (1/72 inch) Height=624;% prefered height of the GUI in points (1/72 inch) %adjust to screen size (reduced by a min margin) RescaleFactor=min((ScreenSize(3)-80)/Width,(ScreenSize(4)-80)/Height); if RescaleFactor>1 RescaleFactor=min(RescaleFactor,1); end Width=Width*RescaleFactor; Height=Height*RescaleFactor; LeftX=80*RescaleFactor;%position of the left fig side, in pixels (put to the left side, with some margin) LowY=round(ScreenSize(4)/2-Height/2); % put at the middle height on the screen set(hObject,'Units','points') set(hObject,'Position',[LeftX LowY Width Height])% position and size of the GUI at opening % settings of table MinIndex_j set(handles.MinIndex_i,'ColumnFormat',{'numeric'}) set(handles.MinIndex_i,'ColumnEditable',false) set(handles.MinIndex_i,'ColumnName',{'i min'}) set(handles.MinIndex_i,'Data',[])% initiate Data to double (not cell) % settings of table MinIndex_j set(handles.MinIndex_j,'ColumnFormat',{'numeric'}) set(handles.MinIndex_j,'ColumnEditable',false) set(handles.MinIndex_j,'ColumnName',{'j min'}) set(handles.MinIndex_j,'Data',[])% initiate Data to double (not cell) % settings of table MaxIndex_i set(handles.MaxIndex_i,'ColumnFormat',{'numeric'}) set(handles.MaxIndex_i,'ColumnEditable',false) set(handles.MaxIndex_i,'ColumnName',{'i max'}) set(handles.MaxIndex_i,'Data',[])% initiate Data to double (not cell) % settings of table MaxIndex_j set(handles.MaxIndex_j,'ColumnFormat',{'numeric'}) set(handles.MaxIndex_j,'ColumnEditable',false) set(handles.MaxIndex_j,'ColumnName',{'j max'}) set(handles.MaxIndex_j,'Data',[])% initiate Data to double (not cell) % settings of table PairString set(handles.PairString,'ColumnName',{'pairs'}) set(handles.PairString,'ColumnEditable',false) set(handles.PairString,'ColumnFormat',{'char'}) set(handles.PairString,'Data',{''}) % settings of table MaskTable set(handles.MaskTable,'ColumnName',{'mask name'}) set(handles.PairString,'ColumnEditable',false) set(handles.PairString,'ColumnFormat',{'char'}) set(handles.PairString,'Data',{''}) series_ResizeFcn(hObject, eventdata, handles)%resize table according to series GUI size set(hObject,'WindowButtonDownFcn',{'mouse_down'})%allows mouse action with right button (zoom for uicontrol display) set(hObject,'DeleteFcn',{@closefcn})% % check default input data if ~exist('Param','var') Param=[]; %default end %% list of builtin functions in the mebu ActionName ActionList={'check_data_files';'aver_stat';'time_series';'civ_series';'merge_proj'};% WARNING: fits with nb_builtin_ACTION=4 in ActionName_callback NbBuiltinAction=numel(ActionList); set(handles.Action,'UserData',NbBuiltinAction) [path_series,name,ext]=fileparts(which('series'));% path to the GUI series path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series' ActionExtList={'.m';'.sh';'.py (in dev.)'};% default choice of extensions (Matlab fct .m or compiled version .sh 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('oarstat');% look for cluster system 'oar' if isequal(s,0) RunModeList=[RunModeList;{'cluster_oar'}]; end [s,w]=system('qstat');% look for cluster system 'sge' if isequal(s,0) RunModeList=[RunModeList;{'cluster_sge'}]; end set(handles.RunMode,'String',RunModeList) %% list of builtin transform functions in the 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 %% get the user defined functions stored in the personal file uvmat_perso.mat dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') h=load (profil_perso); %get the list of previous input files in the upper bar menu Open if isfield(h,'MenuFile') for ifile=1:min(length(h.MenuFile),5) set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile}); set(handles.(['MenuFile_' num2str(ifile+5)]),'Label',h.MenuFile{ifile}); end end %get the list of previous campaigns in the upper bar menu Open campaign if isfield(h,'MenuCampaign') for ifile=1:min(length(h.MenuCampaign),5) set(handles.(['MenuCampaign_' num2str(ifile)]),'Label',h.MenuCampaign{ifile}); end end %get the menu of actions if isfield(h,'ActionExtListUser') && iscell(h.ActionExtListUser) ActionExtList=[ActionExtList; h.ActionExtListUser]; end if isfield(h,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser) ActionList=[ActionList;h.ActionListUser]; ActionPathList=[ActionPathList;h.ActionPathListUser(:,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,'Coord_x_str') && ischar(Param.Coord_x_str) set(handles.Coord_x,'String',Param.Coord_x_str);% list menu fields end if isfield(Param,'Coord_y_str')&& ischar(Param.Coord_y_str) set(handles.Coord_y,'String',Param.Coord_y_str);% list menu fields end %% introduce the input file name(s) if defined from input Param, if isfield(Param,'InputFile') %% fill the list of file series InputTable=[{Param.InputFile.RootPath},{Param.InputFile.SubDir},{Param.InputFile.RootFile},{Param.InputFile.NomType},{Param.InputFile.FileExt}]; 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) %% 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'); RootPathCell=InputTable(:,1); SubDirCell=InputTable(:,2); oldfile=fullfile(RootPathCell{1},SubDirCell{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 append='one'; set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0]) drawnow browse_campaign(handles,append); %------------------------------------------------------------------------ % --- fct activated by the browser under 'Open campaign/Browse...' %------------------------------------------------------------------------ function MenuBrowseCampaignAppend_Callback(hObject, eventdata, handles) append='append'; browse_campaign(handles,append); %------------------------------------------------------------------------ function browse_campaign(handles,append); %% look for the previously opened file 'oldfile' % % % InputTable=get(handles.InputTable,'Data'); % RootPath=InputTable{1,1}; % CampaignPath=fileparts(fileparts(RootPath)); % DirFull=uigetfile_uvmat('define this path as the Campaign folder:',CampaignPath,'uigetdir'); % if ~ischar(DirFull)|| ~exist(DirFull,'dir') % return % end OutPut=browse_data(oldfile);% open the GUI browse_data to get select a campaign dir, experiment and device if ~isfield(OutPut,'Campaign') return end DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1}); ListStruct=dir(DirName); %list files and the dir DataSeries % select the first appropriate file in the dir FileName=''; for ilist=1:numel(ListStruct) if ~isequal(ListStruct(ilist).isdir,1)%look for files, not dir FileName=ListStruct(ilist).name; FileInfo=get_file_info(fullfile(DirName,FileName)); switch FileInfo.FileType case {'image','multimage','civx','civdata','netcdf'} break end end end if isempty(FileName) msgbox_uvmat('ERROR',['no appropriate input file in the DataSeries folder ' fullfile(DirName)]) return end %% update the list of campaigns in the menubar MenuCampaign=[{get(handles.MenuCampaign_1,'Label')};{get(handles.MenuCampaign_2,'Label')};... {get(handles.MenuCampaign_3,'Label')};{get(handles.MenuCampaign_4,'Label')};{get(handles.MenuCampaign_5,'Label')}]; check_dir=isempty(find(strcmp(DirName,MenuCampaign))); if check_dir %insert the new campaign in the list if it is not found MenuCampaign(end)=[]; %suppress the last item MenuCampaign=[{DirName};MenuCampaign];%insert the new campaign for ilist=1:numel(MenuCampaign) set(handles.(['MenuCampaign_' num2str(ilist)]),'Label',MenuCampaign{ilist}) end % save the list for future opening: dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') save (profil_perso,'MenuCampaign','-append'); %store the file names for future opening of uvmat else save (profil_perso,'MenuCampaign','-V6'); %store the file names for future opening of uvmat end end %% display the selected field and related information if get(handles.CheckAppend,'Value') display_file_name(handles,fullfile(DirName,FileName),'append') else display_file_name(handles,fullfile(DirName,FileName),'one') end set(handles.MenuOpenCampaign,'ForegroundColor',[0 0 0]) % -------------------------------------------------------------------- function MenuCampaign_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0]) OutPut=browse_data(get(hObject,'Label'));% open the GUI browse_data to get select a campaign dir, experiment and device if ~isfield(OutPut,'Campaign') return end DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1}); hdir=dir(DirName); %list files and dirs for ilist=1:numel(hdir) if ~isequal(hdir(ilist).isdir,1)%look for files, not dir FileName=hdir(ilist).name; FileInfo=get_file_info(fullfile(DirName,FileName)); switch FileInfo.FileType case {'image','multimage','civx','civdata','netcdf'} break end end end if get(handles.CheckAppend,'Value') display_file_name(handles,fullfile(DirName,FileName),'append') else display_file_name(handles,fullfile(DirName,FileName),'one') end set(handles.MenuOpenCampaign,'ForegroundColor',[0 0 0]) % --- Executes when 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)); % set(handles.InputTable,'UserData',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 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) %------------------------------------------------------------------------ InputTable=get(handles.InputTable,'Data'); set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch' set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH button to yellow color (indicate activation) drawnow empty_line=false(size(InputTable,1),1); for iline=1:size(InputTable,1) empty_line(iline)= isempty(cell2mat(InputTable(iline,1:3))); end if ~isempty(find(empty_line)); 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 for iview=1:size(InputTable,1) RootPath=fullfile(InputTable{iview,1},InputTable{iview,2}); if ~exist(RootPath,'dir') i1_series=[]; %RootPath=fileparts(RootPath); %will try the upper folder RootFile=''; else %scan the input folder [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=... find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]); end % if no file is found, open a browser if isempty(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 %% 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 (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 ~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 seies %%%%%%% %%%%%%%%%%%%%%%%%%% % 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.MenuOpenCampaign,'Enable','on') set(handles.MenuCampaign_1,'Enable','on') set(handles.MenuCampaign_2,'Enable','on') set(handles.MenuCampaign_3,'Enable','on') set(handles.MenuCampaign_4,'Enable','on') set(handles.MenuCampaign_5,'Enable','on') set(handles.RUN, 'Enable','On') set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box to yellow drawnow %% fill the list of file series InputTable=get(handles.InputTable,'Data'); SeriesData=get(handles.series,'UserData'); if strcmp(iview,'append') % display the input data as a new line in the table iview=size(InputTable,1)+1;% the next line in InputTable becomes the current line % InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}]; elseif strcmp(iview,'one') % refresh the list of input file series iview=1; %the first line in InputTable becomes the current line InputTable={'','','','',''}; % InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}]; set(handles.TimeTable,'Data',[{''},{[]},{[]},{[]},{[]}]) set(handles.MinIndex_i,'Data',[]) set(handles.MaxIndex_i,'Data',[]) set(handles.MinIndex_j,'Data',[]) set(handles.MaxIndex_j,'Data',[]) set(handles.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 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)=[]; 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; 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=str2num(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,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice) if iview>1 && ~isempty(NbSlice) && ~strcmp(NbSlice,XmlData.Camera.NbSlice) msgbox_uvmat('WARNING','inconsistent number of slices with the first field series'); end NbSlice=XmlData.Camera.NbSlice;% Nbre of slices from camera end if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit) if iview>1 && ~isempty(TimeUnit) && ~strcmp(TimeUnit,XmlData.Camera.TimeUnit) msgbox_uvmat('WARNING','inconsistent time unit with the first field series'); end TimeUnit=XmlData.Camera.TimeUnit; end end % number of slices if isfield(XmlData,'GeometryCalib') check_calib=1; if isfield(XmlData.GeometryCalib,'SliceCoord') siz=size(XmlData.GeometryCalib.SliceCoord); if siz(1)>1 if iview>1 && ~isempty(NbSlice) && ~strcmp(NbSlice,siz(1)) msgbox_uvmat('WARNING','inconsistent number of Z indices with the first field series'); end NbSlice=siz(1); end end end set(handles.num_NbSlice,'String',num2str(NbSlice)) end %% read timing from the current file (prioritary) if ~isempty(VideoObject)% case of movies imainfo=get(VideoObject); if isempty(j1_series); %frame index along i Time=zeros(imainfo.NumberOfFrames+1,2); Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)'; else Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate); end TimeName='video'; end %% determine the min and max times: case of Netcdf files will be treated later in FieldName_Callback if ~isempty(TimeName) 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; % if ~isempty(TimeName) % SeriesData.TimeSource=TimeSource; % end 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)=max(find(j_max{iline}))-1;% max ref index i MinIndex_i(iline)=min(find(j_max{iline}))-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=find(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 %------------------------------------------------------------------------ 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 numel(diff_i(diff_i==ipair))>0 pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ]; if ~isempty(time) if ref_i<=floor(ipair/2) ref_i=floor(ipair/2)+1;% shift ref_i to get the first pair end Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j); pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit]; end displ_pair=[displ_pair;{pair_string}]; end end if ~isempty(displ_pair) displ_pair=[displ_pair;{'Di=*|*'}]; end 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 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 %------------------------------------------------------------------------ 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,'i1_series') errormsg='The input field series needs to be refreshed: press REFRESH'; return end if isfield(Param,'InputFields')&& isequal(Param.InputFields.FieldName,'get_field...') errormsg='input field name(s) not defined, select get_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 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 RunTime code from the file PARAM.xml (needed to run compiled functions) errormsg='';%default error message xmlfile=fullfile(path_series,'PARAM.xml'); test_batch=0;%default: ,no batch mode available if ~exist(xmlfile,'file') [success,message]=copyfile(fullfile(path_series,'PARAM.xml.default'),xmlfile); end RunTime=''; if strcmp(ActionExt,'.sh') if exist(xmlfile,'file') s=xml2struct(xmlfile); if strcmp(RunMode,'cluster_oar') && isfield(s,'BatchParam') if isfield(s.BatchParam,'RunTime') RunTime=s.BatchParam.RunTime; end if isfield(s.BatchParam,'NbCore') NbCore=s.BatchParam.NbCore; end elseif (strcmp(RunMode,'background')||strcmp(RunMode,'local')) && isfield(s,'RunParam') if isfield(s.RunParam,'RunTime') RunTime=s.RunParam.RunTime; end if isfield(s.RunParam,'NbCore') NbCore=s.RunParam.NbCore; end end end if isempty(RunTime) && strcmp(RunMode,'cluster_oar') errormsg='RunTime name not found in PARAM.xml, compiled version .sh cannot run on cluster'; return end end %% If a compiled version has been selected (ext .sh) check weather it needs to be recompiled if strcmp(ActionExt,'.sh') TransformPath=''; if ~isempty(get(handles.ActionExt,'UserData')) TransformPath=get(handles.ActionExt,'UserData'); end set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch' set(handles.ActionExt,'BackgroundColor',[1 1 0]) ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionName '.sh']); if ~exist(ActionFullName,'file') answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?'); if strcmp(answer,'Yes') set(handles.ActionExt,'BackgroundColor',[1 1 0]) path_uvmat=fileparts(which('series')); currentdir=pwd; cd(get(handles.ActionPath,'String'))% go to the directory of Action addpath(path_uvmat)% add the path to uvmat to run the fct 'compile' compile(ActionName,TransformPath) cd(currentdir) end else sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.sh'])); m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m'])); if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum set(handles.ActionExt,'BackgroundColor',[1 1 0]) drawnow answer=msgbox_uvmat('INPUT_Y-N',[ActionName '.sh needs to be updated: recompile now?']); if strcmp(answer,'Yes') path_uvmat=fileparts(which('series')); currentdir=pwd; cd(get(handles.ActionPath,'String'))% go to the directory of Action addpath(path_uvmat)% add the path to uvmat to run the fct 'compile' addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile' compile(ActionName,TransformPath) cd(currentdir) end end end set(handles.ActionExt,'BackgroundColor',[1 1 1]) set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch end %% set nbre of cluster cores and processes switch RunMode case {'local','background'} NbCore=1;% no need to split the calculation case 'cluster_oar' if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled) NbCore=1;% one core used only (limitation of Matlab licences) msgbox_uvmat('WARNING','Number of cores =1: select the compiled version .sh for multi-core processing'); extra_oar=''; else answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''}); NbCore=str2double(answer{1}); extra_oar=answer{2}; end end if ~isfield(Param.IndexRange,'NbSlice') Param.IndexRange.NbSlice=[]; end if isempty(Param.IndexRange.NbSlice) NbProcess=NbCore;% choose one process per core else NbProcess=Param.IndexRange.NbSlice;% the nbre of run processes is equal to the number of slices NbCore=min(NbCore,NbProcess);% at least one process per core end %% create the output data directory if needed OutputDir=''; if isfield(Param,'OutputSubDir') SubDirOut=[get(handles.OutputSubDir,'String') Param.OutputDirExt]; SubDirOutNew=SubDirOut; detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir');% test if the dir already exist check_create=1; %need to create the result directory by default while detect answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(Param.InputTable{1,1},SubDirOutNew) ', possibly delete previous data']); if strcmp(answer,'Cancel') set(handles.RUN,'backgroundcolor',[1 0 0]) return elseif strcmp(answer,'Yes') detect=0; check_create=0; else r=regexp(SubDirOutNew,'(?.*\D)(?\d+)$','names');%detect whether name ends by a number if isempty(r) r(1).root=[SubDirOutNew '_']; r(1).num1='0'; end SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1 detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir');% test if the dir already exists check_create=1; end end Param.OutputDirExt=regexprep(SubDirOutNew,Param.OutputSubDir,''); Param.OutputRootFile=Param.InputTable{1,3};% the first sorted RootFile taken for output set(handles.OutputDirExt,'String',Param.OutputDirExt) OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]);% full name (with path) of output directory if check_create % create output directory if it does not exist [tild,msg1]=mkdir(OutputDir); if ~strcmp(msg1,'') errormsg=['cannot create ' OutputDir ': ' msg1];%error message for directory creation return end [success,msg] = fileattrib(OutputDir,'+w','g','s');% allow writing access for the group of users, recursively in the folder if success==0 msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg1});%error message for directory creation end end elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir OutputDir=Param.ActionInput.LogPath; end DirXml=fullfile(OutputDir,'0_XML'); if ~exist(DirXml,'dir') [tild,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 field indices first_i=1; last_i=1; incr_i=1; first_j=1; last_j=1; incr_j=1; if isfield(Param.IndexRange,'first_i') first_i=Param.IndexRange.first_i; incr_i=Param.IndexRange.incr_i; last_i=Param.IndexRange.last_i; end if isfield(Param.IndexRange,'first_j') first_j=Param.IndexRange.first_j; last_j=Param.IndexRange.last_j; incr_j=Param.IndexRange.incr_j; end if last_i < first_i || last_j < first_j 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 if isempty(incr_i) if isempty(incr_j) [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:))); ref_j=ref_j(ref_j>=first_j & ref_j<=last_j); ref_i=ref_i(ref_i>=first_i & ref_i<=last_i); ref_j=ref_j-1; ref_i=ref_i-1; else ref_j=first_j:incr_j:last_j; [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:))); ref_i=ref_i-1; ref_i=ref_i(ref_i>=first_i & ref_i<=last_i); end else ref_i=first_i:incr_i:last_i; if isempty(incr_j) [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:))); ref_j=ref_j-1; ref_j=ref_j(ref_j>=first_j & ref_j<=last_j); else ref_j=first_j:incr_j:last_j; end end BlockLength=ceil(numel(ref_i)/NbProcess); nbfield_j=numel(ref_j); %% record nbre of output files and starting time for computation for status StatusData=get(handles.status,'UserData'); if isfield(StatusData,'OutputFileMode') switch StatusData.OutputFileMode case 'NbInput' StatusData.NbOutputFile=numel(ref_i)*nbfield_j; case 'NbInput_i' StatusData.NbOutputFile=numel(ref_i); case 'NbSlice' StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String')); end end StatusData.TimeStart=now; set(handles.status,'UserData',StatusData) if strcmp(ActionExt, '.py (in dev.)') fprintf([ '\n' ... '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ... 'The option .py is used. It is still in development.\n' ... 'Do not use it unless you really know what you do!\n' ... 'To try it, first install Pyp and the most recent version of FluidDyn.\n' ... '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n']) RunMode = 'python'; t = struct2xml(Param); t = set(t, 1, 'name', 'Series'); filexml = fullfile_uvmat(DirXml, '', Param.InputTable{1,3}, '.xml', OutputNomType,... Param.IndexRange.first_i, Param.IndexRange.last_i, first_j, last_j); save(t, filexml); end %% direct processing on the current Matlab session if strcmp (RunMode,'local') for iprocess=1:NbProcess if isempty(Param.IndexRange.NbSlice) %Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i; Param.IndexRange.first_i=ref_i(1+(iprocess-1)*BlockLength); if Param.IndexRange.first_i>last_i break end Param.IndexRange.last_i=min(ref_i(iprocess*BlockLength),last_i); %Param.IndexRange.last_i=min(first_i+(iprocess)*BlockLength*incr_i-1,last_i); else %multislices (then incr_i is not empty) Param.IndexRange.first_i= first_i+incr_i*(iprocess-1); Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice; end if isfield(Param,'OutputSubDir') t=struct2xml(Param); t=set(t,1,'name','Series'); filexml=fullfile_uvmat(DirXml,'',Param.InputTable{1,3},'.xml',OutputNomType,... Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j); save(t,filexml); end switch ActionExt case '.m' h_fun(Param); case '.sh' switch computer case {'PCWIN','PCWIN64'} %Windows system filexml=regexprep(filexml,'\\','\\\\');% add '\' so that '\' are left as characters system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]);% TODO: adapt to DOS system case {'GLNX86','GLNXA64','MACI64'}%Linux system system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]); end end end elseif ~strcmp(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 DirBat=fullfile(OutputDir,'0_EXE'); switch computer case {'PCWIN','PCWIN64'} %Windows system ExeExt='.bat'; case {'GLNX86','GLNXA64','MACI64'}%Linux system ExeExt='.sh'; end %create subdirectory for executable files if ~exist(DirBat,'dir') [tild,msg1]=mkdir(DirBat); if ~strcmp(msg1,'') errormsg=['cannot create ' DirBat ': ' msg1];%error message for directory creation return end end %create subdirectory for log files DirLog=fullfile(OutputDir,'0_LOG'); if ~exist(DirLog,'dir') [tild,msg1]=mkdir(DirLog); if ~strcmp(msg1,'') errormsg=['cannot create ' DirLog ': ' msg1];%error message for directory creation return end end for iprocess=1:NbProcess if isempty(Param.IndexRange.NbSlice)% process by blocks of i index Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i; if Param.IndexRange.first_i>last_i NbProcess=iprocess-1; break% leave the loop, we are at the end of the calculation end Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1); else% process by slices of i index if NbSlice is defined, computation in a single process if NbSlice =1 Param.IndexRange.first_i= first_i+iprocess-1; Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice; end for ilist=1:size(Param.InputTable,1) Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/');%correct path name for PCWIN system end % create, fill and save the xml parameter file t=struct2xml(Param); t=set(t,1,'name','Series'); filexml=fullfile_uvmat(DirXml,'',Param.InputTable{1,3},'.xml',OutputNomType,... Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j); save(t,filexml);% save the parameter file %create the executable file filebat=fullfile_uvmat(DirBat,'',Param.InputTable{1,3},ExeExt,OutputNomType,... Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j); batch_file_list{iprocess}=filebat; [fid,message]=fopen(filebat,'w');% create the executable file if isequal(fid,-1) errormsg=['creation of .bat file: ' message]; return end % set the log file name filelog=fullfile_uvmat(DirLog,'',Param.InputTable{1,3},'.log',OutputNomType,... Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j); % fill and save the executable file switch ActionExt case '.m'% Matlab function switch computer case {'GLNX86','GLNXA64','MACI64'} cmd=[... '#!/bin/bash \n'... '. /etc/sysprofile \n'... 'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog ''' <','.stderr') ' '... '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '... extra_oar ' '... '"oar-parexec -s -f ' filename_joblist ' '... '-l ' filename_joblist '.log"\n']; filename_oarcommand=fullfile(DirOAR,'oar_command'); fid=fopen(filename_oarcommand,'w'); fprintf(fid,oar_command); fclose(fid); fprintf(oar_command);% display in command line system(oar_command); msgbox_uvmat('CONFIRMATION',[ActionName ' launched in cluster: press STATUS to see results']) case 'python' command = [ 'LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "p.split('':'') | [s for s in p if ''matlab'' not in s] | '':''.join(p)") ' ... 'python -m fluiddyn.postproc.uvmat ' filexml]; % fprintf(['command:\n' command '\n\n']) system(command, '-echo'); end %------------------------------------------------------------------------ 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, eventdata, handles) %------------------------------------------------------------------------ %% stop any ongoing series processing if isequal(get(handles.RUN,'Value'),1) answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?'); if strcmp(answer,'Yes') STOP_Callback(hObject, eventdata, handles) else return end end set(handles.ActionName,'BackgroundColor',[1 1 0]) huigetfile=findobj(allchild(0),'tag','status_display'); if ~isempty(huigetfile) delete(huigetfile) end drawnow %% check whether the input file(s) need to be refreshed % SeriesData=get(handles.series,'UserData');%hidden parameters % if ~isfield(SeriesData,'i1_series') % msgbox_uvmat('ERROR','The input field series needs to be refreshed: press REFRESH'); % return % end %% 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...') [FileName, PathName] = uigetfile( ... {'*.m', ' (*.m)'; '*.m', '.m files '; ... '*.*', 'All Files (*.*)'}, ... 'Pick a series processing function ',get(handles.ActionPath,'String')); if length(FileName)<2 return end [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) % ActionPathList{ActionIndex,ActionExtIndex}=PathName; %record the user defined menu additions in personal file profil_perso dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if 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) %% create the function handle for Action path_series=which('series'); if ~isequal(ActionPath,path_series) eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION if ~exist(ActionPath,'dir') errormsg=['The prescribed function path ' ActionPath ' does not exist']; return end if ~isequal(spath,ActionPath) addpath(ActionPath)% add the prescribed path if not the current one end end eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION if ~isequal(ActionPath,path_series) rmpath(ActionPath)% add the prescribed path if not the current one end %% Activate the Action fct 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 ParamOut=h_fun(Param);%run the selected Action function to get the relevant input %% Put the first line of the selected Action fct as tooltip help try [fid,errormsg] =fopen([ActionName '.m']); InputText=textscan(fid,'%s',1,'delimiter','\n'); fclose(fid); set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help end %% 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' SeriesData=get(handles.series,'UserData');% info on the input file series 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 CheckList=0;% indicate whether FieldName has been updated CheckList_1=1;% indicate whether FieldName_1 has been updated 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');{'C'};{'get_field...'}];%standard menu for civx data CheckList=1; set(handles.FieldName,'Value',1); %velocity vector choice by default 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'};{'get_field...'}];%standard menu for civx data CheckList_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 && numel(iview_netcdf)>=1 set(handles.InputFields,'Visible','on') if CheckList==0 % not civ input made if isfield(SeriesData.FileInfo{iview_netcdf(1)},'ListVarName') 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) 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))) FieldList={}; set(handles.Coord_z,'String','') end end set(handles_coord,'Visible','on') FieldList=[FieldList;{'get_field...'}]; if FieldNameRequest_1 && numel(iview_netcdf)>=2 set(handles.FieldName_1,'Visible','on') if CheckList_1==0 % not civ input made 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={}; warn_coord=1; end if warn_coord msgbox_uvmat('WARNING','coordiante names do not exist in the second netcdf input file') end set(handles.FieldName,'String',[FieldList;{'get_field...'}]) 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 end else set(handles_coord,'Visible','off')% no coord display for civ data end set(handles.FieldName,'String',FieldList) else set(handles.InputFields,'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(InputTable(:,2)); %subdirectories sorted in alphabetical order set(handles.InputTable,'Data',InputTable(iview,:)); MinIndex_i=get(handles.MinIndex_i,'Data'); MinIndex_j=get(handles.MinIndex_j,'Data'); MaxIndex_i=get(handles.MaxIndex_i,'Data'); MaxIndex_j=get(handles.MaxIndex_j,'Data'); set(handles.MinIndex_i,'Data',MinIndex_i(iview,:)); set(handles.MinIndex_j,'Data',MinIndex_j(iview,:)); set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:)); set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:)); TimeTable=get(handles.TimeTable,'Data'); set(handles.TimeTable,'Data',TimeTable(iview,:)); PairString=get(handles.PairString,'Data'); set(handles.PairString,'Data',PairString(iview,:)); end %% Impose the whole input file index range if requested if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on') MinIndex_i=get(handles.MinIndex_i,'Data'); MinIndex_j=get(handles.MinIndex_j,'Data'); MaxIndex_i=get(handles.MaxIndex_i,'Data'); MaxIndex_j=get(handles.MaxIndex_j,'Data'); set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line) set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line) set(handles.num_incr_i,'String','1') set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line) set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line) set(handles.num_incr_j,'String','1') else % check index ranges first_i=1;last_i=1;first_j=1;last_j=1; if isfield(Param.IndexRange,'first_i') first_i=Param.IndexRange.first_i; last_i=Param.IndexRange.last_i; end if isfield(Param.IndexRange,'first_j') first_j=Param.IndexRange.first_j; last_j=Param.IndexRange.last_j; end if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),... set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end; end %% enable or desable j index visibility status_j='on';%default if isfield(ParamOut,'Desable_j_index')&&isequal(ParamOut.Desable_j_index,'on') status_j='off'; end if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices status_j='off'; % no j index needed elseif strcmp(get(handles.PairString,'Visible'),'on') check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j'));%=0 for burst case, 1 otherwise if isempty(find(check_burst, 1))% if all pair string begins by j (burst) status_j='off'; % no j index needed for bust case end end enable_j(handles,status_j) % no j index needed %% NbSlice visibility NbSliceVisible='off';%default if isfield(ParamOut,'NbSlice') && isequal(ParamOut.NbSlice,'on') NbSliceVisible='on'; set(handles.num_NbProcess,'String',get(handles.num_NbSlice,'String'))% the nbre of processes is imposed as the nbre of slices else set(handles.num_NbProcess,'String','')% free nbre of processes end set(handles.num_NbSlice,'Visible',NbSliceVisible) set(handles.NbSlice_title,'Visible',NbSliceVisible) %% Visibility of FieldTransform menu FieldTransformVisible='off'; %hidden by default if isfield(ParamOut,'FieldTransform') FieldTransformVisible=ParamOut.FieldTransform; TransformName_Callback([],[], handles) end set(handles.FieldTransform,'Visible',FieldTransformVisible) if isfield(ParamOut,'TransformPath') set(handles.ActionExt,'UserData',ParamOut.TransformPath) else set(handles.ActionExt,'UserData',[]) end %% Visibility of projection object ProjObjectVisible='off'; %hidden by default if isfield(ParamOut,'ProjObject') ProjObjectVisible=ParamOut.ProjObject; end set(handles.CheckObject,'Visible',ProjObjectVisible) if ~get(handles.CheckObject,'Value') ProjObjectVisible='off'; end set(handles.ProjObject,'Visible',ProjObjectVisible) set(handles.DeleteObject,'Visible',ProjObjectVisible) set(handles.ViewObject,'Visible',ProjObjectVisible) set(handles.EditObject,'Visible',ProjObjectVisible) %% Visibility of mask input MaskVisible='off'; %hidden by default if isfield(ParamOut,'Mask') MaskVisible=ParamOut.Mask; end set(handles.CheckMask,'Visible',MaskVisible); %% definition of the directory containing the output files if ~(isfield(SeriesData,'ActionName') && strcmp(ActionName,SeriesData.ActionName)) OutputDirExt='.series'; %default if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt) OutputDirExt=ParamOut.OutputDirExt; end set(handles.OutputDirExt,'String',OutputDirExt) end OutputDirVisible='off'; OutputSubDirMode='auto';%default SubDirOut=''; if isfield(ParamOut,'OutputSubDirMode') OutputSubDirMode=ParamOut.OutputSubDirMode; end switch OutputSubDirMode case 'auto';%default OutputDirVisible='on'; SubDir=InputTable(1:end,2); %set of subdirectories SubDirOut=SubDir{1}; if numel(SubDir)>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.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.ActionName,'BackgroundColor',[1 1 1]) %------------------------------------------------------------------------ % --- Executes on selection change in FieldName. function FieldName_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ field_str=get(handles.FieldName,'String'); field_index=get(handles.FieldName,'Value'); field=field_str{field_index(1)}; if isequal(field,'get_field...') 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); % InputLine=str2num(get(handles.InputLine,'String')); % if ismember(InputLine,iview) % LineIndex=InputLine; % end 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') ParamIn.Title='get_field: pick input variables and coordinates for series processing'; ParamIn.SeriesInput=1; GetFieldData=get_field(FirstFileName,ParamIn); FieldList={}; switch GetFieldData.FieldOption case 'vectors' UName=GetFieldData.PanelVectors.vector_x; VName=GetFieldData.PanelVectors.vector_y; YName={GetFieldData.Coordinates.Coord_y}; FieldList={['vec(' UName ',' VName ')'];... ['norm(' UName ',' VName ')'];... UName;VName}; case {'scalar'} FieldList=GetFieldData.PanelScalar.scalar; YName={GetFieldData.Coordinates.Coord_y}; if ischar(FieldList) FieldList={FieldList}; end case 'civdata...' FieldList=[set_field_list('U','V') ;{'C'}]; set(handles.FieldName,'Value',1) % set menu to 'velocity XName='X'; YName='y'; end set(handles.FieldName,'Value',1) set(handles.FieldName,'String',[FieldList; {'get_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') 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=[]; if isequal(FileInfo.FileType,'civdata') if ismember(TimeName,{'civ1','filter1'}) TimeValue=Data.Civ1_Time; DtValue=Data.Civ1_Dt; else TimeValue=Data.Civ2_Time; DtValue=Data.Civ2_Dt; end else 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 isequal(field,'get_field...') hget_field=findobj(allchild(0),'name','get_field'); if ~isempty(hget_field) delete(hget_field)%delete opened versions of get_field end Param=read_GUI(handles.series); Param.InputTable=Param.InputTable(1,:); % check the existence of the first file in the series first_j=[]; if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end 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') 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; {'get_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) set(handles.ViewObject,'Value',1) ViewObject_Callback(hObject, eventdata, handles) else if ishandle(hset_object) uistack(hset_object,'top')% show the GUI set_object if opened else %get the object file InputTable=get(handles.InputTable,'Data'); defaultname=InputTable{1,1}; if isempty(defaultname) defaultname={''}; end fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml'); if isempty(fileinput)% exit if no object file is selected set(handles.CheckObject,'Value',0) return end %read the file data=xml2struct(fileinput); if ~isfield(data,'Type') msgbox_uvmat('ERROR',[fileinput ' is not an object xml file']) set(handles.CheckObject,'Value',0) return end if ~isfield(data,'ProjMode') data.ProjMode='none'; end hset_object=set_object(data);% call the set_object interface set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat end ProjObject=read_GUI(hset_object); set(handles.ProjObject,'String',ProjObject.Name);%display the object name SeriesData=get(handles.series,'UserData'); SeriesData.ProjObject=ProjObject; set(handles.series,'UserData',SeriesData); end set(handles.EditObject,'Visible','on'); set(handles.DeleteObject,'Visible','on'); set(handles.ViewObject,'Visible','on'); set(handles.ProjObject,'Visible','on'); else set(handles.EditObject,'Visible','off'); set(handles.DeleteObject,'Visible','off'); set(handles.ViewObject,'Visible','off'); if ~ishandle(hset_object) set(handles.ViewObject,'Value',0); end set(handles.ProjObject,'Visible','off'); end %------------------------------------------------------------------------ % --- Executes on button press in ViewObject. %------------------------------------------------------------------------ function ViewObject_Callback(hObject, eventdata, handles) UserData=get(handles.series,'UserData'); hset_object=findobj(allchild(0),'Tag','set_object'); if ~isempty(hset_object) delete(hset_object)% refresh set_object if already opened end hset_object=set_object(UserData.ProjObject); set(hset_object,'Name','view_object_series') %------------------------------------------------------------------------ % --- Executes on button press in EditObject. function EditObject_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ if get(handles.EditObject,'Value') set(handles.ViewObject,'Value',0) UserData=get(handles.series,'UserData'); hset_object=set_object(UserData.ProjObject); set(hset_object,'Name','edit_object_series') set(get(hset_object,'Children'),'Enable','on') else hset_object=findobj(allchild(0),'Tag','set_object'); if ~isempty(hset_object) set(get(hset_object,'Children'),'Enable','off') end end %------------------------------------------------------------------------ % --- Executes on button press in DeleteObject. function DeleteObject_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ SeriesData=get(handles.series,'UserData'); SeriesData.ProjObject=[]; set(handles.series,'UserData',SeriesData) set(handles.ProjObject,'String','') set(handles.ProjObject,'Visible','off') set(handles.CheckObject,'Value',0) set(handles.ViewObject,'Visible','off') set(handles.EditObject,'Visible','off') hset_object=findobj(allchild(0),'name','set_object_series'); if ~isempty(hset_object) delete(hset_object) end set(handles.DeleteObject,'Visible','off') %------------------------------------------------------------------------ % --- Executed when CheckMask is activated %------------------------------------------------------------------------ function CheckMask_Callback(hObject, eventdata, handles) if get(handles.CheckMask,'Value') InputTable=get(handles.InputTable,'Data'); nbview=size(InputTable,1); MaskTable=cell(nbview,1);%default ListMask=cell(nbview,1);%default MaskData=get(handles.MaskTable,'Data'); MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1);%complement if undefined lines for iview=1:nbview ListMask{iview,1}=num2str(iview); RootPath=InputTable{iview,1}; if ~isempty(RootPath) if isempty(MaskData{iview}) SubDir=InputTable{iview,2}; MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']);%take the root part of SubDir, before the first dot '.' if exist(MaskPath,'dir') ListStruct=dir(MaskPath);%look for a mask file ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files ListFiles=ListCells(1,:);%list of file and dri names ListFiles=ListFiles(~check_dir);%list of file names (excluding dir) mdetect=0; if ~isempty(ListFiles) for ifile=1:numel(ListFiles) [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0); if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series) mdetect=1; MaskName=ListFiles{ifile}; end if ~strcmp(MaskFile{ifile},MaskFile{1}) mdetect=0;% cancel detection test in case of multiple masks, use the brower for selection break end end end if mdetect==1 MaskName=fullfile(MaskPath,'mask_1.png'); else MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image'); end else MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image'); end MaskTable{iview,1}=MaskName ; ListMask{iview,1}=num2str(iview); end end end set(handles.MaskTable,'Data',MaskTable) set(handles.MaskTable,'Visible','on') set(handles.MaskBrowse,'Visible','on') set(handles.ListMask,'Visible','on') set(handles.ListMask,'String',ListMask) set(handles.ListMask,'Value',1) else set(handles.MaskTable,'Visible','off') set(handles.MaskBrowse,'Visible','off') set(handles.ListMask,'Visible','off') end %------------------------------------------------------------------------ % --- Executes on button press in MaskBrowse. %------------------------------------------------------------------------ function MaskBrowse_Callback(hObject, eventdata, handles) InputTable=get(handles.InputTable,'Data'); iview=get(handles.ListMask,'Value'); RootPath=InputTable{iview,1}; MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image'); if ~isempty(MaskName) MaskTable=get(handles.MaskTable,'Data'); MaskTable{iview,1}=MaskName ; set(handles.MaskTable,'Data',MaskTable) end %------------------------------------------------------------------------ % --- Executes when selected cell(s) is changed in MaskTable. %------------------------------------------------------------------------ function MaskTable_CellSelectionCallback(hObject, eventdata, handles) if numel(eventdata.Indices)>=1 set(handles.ListMask,'Value',eventdata.Indices(1)) end %------------------------------------------------------------------- function MenuHelp_Callback(hObject, eventdata, handles) %------------------------------------------------------------------- % path_to_uvmat=which ('uvmat');% check the path of uvmat % pathelp=fileparts(path_to_uvmat); % helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html'); % if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package') % else % addpath (fullfile(pathelp,'uvmat_doc')) % web([helpfile '#series']) % end %------------------------------------------------------------------- % --- Executes on selection change in TransformName. function TransformName_Callback(hObject, eventdata, handles) %---------------------------------------------------------------------- TransformList=get(handles.TransformName,'String'); TransformIndex=get(handles.TransformName,'Value'); TransformName=TransformList{TransformIndex}; TransformPathList=get(handles.TransformName,'UserData'); nb_builtin_transform=4; if isequal(TransformName,'more...'); FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m'); if isempty(FileName) return %browser closed without choice end [TransformPath,TransformName,TransformExt]=fileparts(FileName);% removes extension .m if ~strcmp(TransformExt,'.m') msgbox_uvmat('ERROR','a Matlab function .m must be introduced'); return end % insert the choice in the menu TransformIndex=find(strcmp(TransformName,TransformList),1);% look for the selected function in the menu Action if isempty(TransformIndex)%the input string does not exist in the menu TransformIndex= length(TransformList); TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)];% the selected function is appended in the menu, before the last item 'more...' set(handles.TransformName,'String',TransformList) TransformPathList=[TransformPathList;{TransformPath}]; else% the input function already exist, we update its path (possibly new) TransformPathList{TransformIndex}=TransformPath;% set(handles.TransformName,'Value',TransformIndex) end % save the new menu in the personal file 'uvmat_perso.mat' dir_perso=prefdir;%personal Matalb directory profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') for ilist=nb_builtin_transform+1:numel(TransformPathList) TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist}; TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist}; end TransformPathListUser=TransformPathListUser'; TransformListUser=TransformListUser'; save (profil_perso,'TransformPathListUser','TransformListUser','-append'); %store the root name for future opening of uvmat end end %display the current function path set(handles.TransformPath,'String',TransformPathList{TransformIndex}); %show the path to the senlected function set(handles.TransformName,'UserData',TransformPathList); %------------------------------------------------------------------------ % --- fct activated by the upper bar menu ExportConfig %------------------------------------------------------------------------ function 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=xml2struct(filexml);% read the input xml file as a Matlab structure % ask to stop current Action if button RUN is in action (another process is already running) if isequal(get(handles.RUN,'Value'),1) answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?'); if strcmp(answer,'Yes') STOP_Callback(hObject, eventdata, handles) else return end end Param.Action.RUN=0; %desactivate the input RUN=1 fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters SeriesData=get(handles.series,'UserData'); if isfield(Param,'InputFields') ListField=Param.InputFields.FieldName; if ischar(ListField),ListField={ListField}; end set(handles.FieldName,'String',[ListField;{'get-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,'ProjObject') %introduce projection object if relevant SeriesData.ProjObject=Param.ProjObject; end set(handles.series,'UserData',SeriesData) if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1) set(handles.ProjObject,'String',Param.ProjObject.Name) set(handles.ViewObject,'Visible','on') set(handles.EditObject,'Visible','on') set(handles.DeleteObject,'Visible','on') else set(handles.ProjObject,'String','') set(handles.ProjObject,'Visible','off') set(handles.ViewObject,'Visible','off') set(handles.EditObject,'Visible','off') set(handles.DeleteObject,'Visible','off') end set(handles.REFRESH,'BackgroundColor',[1 0 1]); %paint REFRESH button in magenta to indicate that it should be activated %------------------------------------------------------------------------ % --- 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=Param.InputTable{1,1}; 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 % ActionList=get(handles.ActionName,'String'); % ActionName=ActionList{get(handles.ActionName,'Value')}; function num_NbProcess_Callback(hObject, eventdata, handles) function num_NbSlice_Callback(hObject, eventdata, handles) NbSlice=str2num(get(handles.num_NbSlice,'String')); set(handles.num_NbProcess,'String',num2str(NbSlice)) %------------------------------------------------------------------------ % --- set the visibility of relevant velocity type menus: function menu=set_veltype_display(Civ,FileType) %------------------------------------------------------------------------ if ~exist('FileType','var') FileType='civx'; end switch FileType case 'civx' menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'}; if isequal(Civ,0) imax=0; elseif isequal(Civ,1) || isequal(Civ,2) imax=1; elseif isequal(Civ,3) imax=3; elseif isequal(Civ,4) || isequal(Civ,5) imax=4; elseif isequal(Civ,6) %patch2 imax=6; end case 'civdata' menu={'civ1';'filter1';'civ2';'filter2'}; if isequal(Civ,0) imax=0; elseif isequal(Civ,1) || isequal(Civ,2) imax=1; elseif isequal(Civ,3) imax=2; elseif isequal(Civ,4) || isequal(Civ,5) imax=3; elseif isequal(Civ,6) %patch2 imax=4; end end menu=menu(1:imax); % --- Executes on mouse motion over figure - except title and menu. function series_WindowButtonMotionFcn(hObject, eventdata, handles) set(hObject,'Pointer','arrow'); % --- Executes on button press in SetPairs. function SetPairs_Callback(hObject, iview, 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); 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{iview},SeriesData.i2_series{iview},SeriesData.j2_series{iview}); displ_pair=update_listpair(SeriesData.i1_series{iview},SeriesData.i2_series{iview},SeriesData.j1_series{iview},SeriesData.j2_series{iview},ModeMenu{ModeValue},... SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo{iview}); % 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',ListViewMenu,'Value',ListViewValue,'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'''); % 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 status_j='on';%default if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices status_j='off'; % no j index needed elseif strcmp(get(handles.PairString,'Visible'),'on') check_burst=cellfun(@isempty,regexp(PairString,'^j'));%=0 for burst case, 1 otherwise if isempty(find(check_burst, 1))% if all pair string begins by j (burst) status_j='off'; % no j index needed for bust case end end enable_j(handles,status_j) % no j index needed %% 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,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([],[]) %------------------------------------------------------------------------ % --- 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