%'series': master function associated to the GUI series.m for analysis field series %------------------------------------------------------------------------ % function varargout = series(varargin) % associated with the GUI series.fig % %INPUT % param: structure with input parameters (link with the GUI uvmat) % .menu_coord_str: string for the TransformName (menu for coordinate transforms) % .menu_coord_val: value for TransformName (menu for coordinate transforms) % .FileName: input file name % .FileName_1: second input file name % .list_field: menu of input fields % .index_fields: chosen index % .civ1=0 or 1, .interp1, ... : input civ field type % %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA % Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA % This file is part of the toolbox UVMAT. % % UVMAT is free software; you can redistribute it and/or modify % it under the terms of the GNU General Public License as published by % the Free Software Foundation; either version 2 of the License, or % (at your option) any later version. % % UVMAT is distributed in the hope that it will be useful, % but WITHOUT ANY WARRANTY; without even the implied warranty of % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the % GNU General Public License (file UVMAT/COPYING.txt) for more details. %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA %------------------------------------------------------------------------ %------------------------------------------------------------------------ % I - MAIN FUNCTION series %------------------------------------------------------------------------ %------------------------------------------------------------------------ function varargout = series(varargin) % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name', mfilename, ... 'gui_Singleton', gui_Singleton, ... 'gui_OpeningFcn', @series_OpeningFcn, ... 'gui_OutputFcn', @series_OutputFcn, ... 'gui_LayoutFcn', [] , ... 'gui_Callback', []); if nargin && ischar(varargin{1}) gui_State.gui_Callback = str2func(varargin{1}); end if nargout [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); else gui_mainfcn(gui_State, varargin{:}); end % End initialization code - DO NOT EDIT %-------------------------------------------------------------------------- % --- Executes just before series is made visible. %-------------------------------------------------------------------------- function series_OpeningFcn(hObject, eventdata, handles,param) global nb_builtin_ACTION nb_builtin_transform % Choose default command line output for series handles.output = hObject; % Update handles structure guidata(hObject, handles); %default initial parameters drawnow set(hObject,'Units','pixels') set(handles.PairString,'ColumnName',{'pairs'}) set(handles.PairString,'ColumnEditable',logical(0)) 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) dir_perso=prefdir; test_profil_perso=0; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') h=load (profil_perso); if isfield(h,'MenuFile') for ifile=1:min(length(h.MenuFile),5) eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});']) end end test_profil_perso=1; end %check default input data if ~exist('param','var') param=[]; %default end %% file name and browser initialisation if isfield(param,'transform_str') set(handles.TransformName,'String',param.transform_str) end if isfield(param,'transform_val') set(handles.TransformName,'Value',param.transform_val); else set(handles.TransformName,'Value',1);%default end if isfield(param,'FileName') InputTable={'','','','',''}; set(handles.InputTable,'Data',InputTable) if isfield(param,'FileName_1') display_file_name(handles,param.FileName_1,0) display_file_name(handles,param.FileName,1) else display_file_name(handles,param.FileName,0) end end if isfield(param,'incr_i') set(handles.num_incr_i,'String',num2str(param.incr_i)) end if isfield(param,'incr_j') set(handles.num_incr_j,'String',num2str(param.incr_j)) end %% fields input initialisation if isfield(param,'list_fields')&& isfield(param,'index_fields') &&~isempty(param.list_fields) &&~isempty(param.index_fields) set(handles.FieldName,'String',param.list_fields);% list menu fields set(handles.FieldName,'Value',param.index_fields);% selected string index end if isfield(param,'Coord_x_str')&& isfield(param,'Coord_x_val') set(handles.Coord_x,'String',param.Coord_x_str);% list menu fields set(handles.Coord_x,'Value',param.Coord_x_val);% selected string index end if isfield(param,'Coord_y_str')&& isfield(param,'Coord_y_val') set(handles.Coord_y,'String',param.Coord_y_str);% list menu fields set(handles.Coord_y,'Value',param.Coord_y_val);% selected string index end %loads the information stored in prefdir to initiate the list of ActionName functions fct_menu={'check_data_files';'aver_stat';'time_series';'merge_proj';'clean_civ_cmx'}; transform_menu={'';'phys';'px';'phys_polar'}; nb_builtin_ACTION=numel(fct_menu); %number of functions nb_transform=numel(transform_menu); [path_series,name,ext]=fileparts(which('series')); path_series=fullfile(path_series,'series');%path of the function 'series' addpath (path_series) ; %add the path to UVMAT, (useful in case of change of working directory after civ has been s opened in the working directory) path_transform=fullfile(path_series,'transform_field');%path to the field transform functions for ilist=1:length(fct_menu) fct_path{ilist,1}=path_series;%paths of the fuctions buil-in in 'series.m' end %% TRANSFORM menu: loads the information stored in prefdir to initiate the list of field transform functions menu_str={'';'sub_field';'phys';'phys_polar'}; nb_builtin_transform=numel(menu_str); %number of functions [path_uvmat,name,ext]=fileparts(which('uvmat')); addpath(fullfile(path_uvmat,'transform_field')) fct_handle{1,1}=[]; testexist(1)=1; for ilist=2:length(menu_str) if exist(menu_str{ilist},'file') fct_handle{ilist,1}=str2func(menu_str{ilist}); testexist(ilist)=1; else testexist(ilist)=0; end end rmpath(fullfile(path_uvmat,'transform_field')) %% read the list of transform functions stored in the personal file 'uvmat_perso.mat' in prefdir if test_profil_perso if isfield(h,'series_fct') && iscell(h.series_fct) for ilist=1:length(h.series_fct) [path,file]=fileparts(h.series_fct{ilist}); fct_path=[fct_path; {path}];%concatene the list of paths fct_menu=[fct_menu; {file}]; end end if isfield(h,'transform_fct') && iscell(h.transform_fct) for ilist=1:length(h.transform_fct); [path,file]=fileparts(h.transform_fct{ilist}); addpath(path) if exist(file,'file') h_func=str2func(file); testexist=[testexist 1]; else h_func=[]; testexist=[testexist 0]; end fct_handle=[fct_handle; {h_func}];%concatene the list of paths rmpath(path) menu_str=[menu_str; {file}]; end end end fct_menu=[fct_menu;{'more...'}]; set(handles.ActionName,'String',fct_menu) set(handles.ActionName,'UserData',fct_path)% store the list of path in UserData of ACTION menu_str=menu_str(find(testexist)); fct_handle=fct_handle(find(testexist)); menu_str=[menu_str;{'more...'}]; set(handles.TransformName,'String',menu_str) set(handles.TransformName,'UserData',fct_handle)% store the list of path in UserData of ACTION %% Adjust the GUI according to the binaries available in PARAM.xml path_uvmat=fileparts(which('uvmat')); %path to civ addpath (path_uvmat) ; %add the path to civ, (useful in case of change of working directory after civ has been s opened in the working directory) errormsg=[];%default error message xmlfile='PARAM.xml'; if exist(xmlfile,'file') try t=xmltree(xmlfile); sparam=convert(t); catch ME errormsg={' Unable to read the file PARAM.xml defining the civx binaries:';ME.message}; end else errormsg=[xmlfile ' not found: path to civx binaries undefined']; end if ~isempty(errormsg) msgbox_uvmat('WARNING',errormsg); end test_batch=0;%default: ,no batch mode available if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode') test_batch=strcmp(sparam.BatchParam.BatchMode,'sge'); %sge is currently the only implemented batch mod end RUNVal=get(handles.RunMode,'Value'); if test_batch==0 if RUNVal>2 set(handles.RunMode,'Value',1) end set(handles.RunMode,'String',{'local';'background'}) else set(handles.RunMode,'String',{'local';'background';'cluster'}) end %------------------------------------------------------------------------ % --- Outputs from this function are returned to the command line. function varargout = series_OutputFcn(hObject, eventdata, handles) %------------------------------------------------------------------------ % varargout cell array for returning output args (see VARARGOUT); % hObject handle to figure % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % Get default command line output from handles structure varargout{1} = handles.output; %------------------------------------------------------------------------ %------------------------------------------------------------------------ % 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 %------------------------------------------------------------------------ %------------------------------------------------------------------------ function MenuBrowse_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ InputTable=get(handles.InputTable,'Data'); if isempty(InputTable) RootPathCell={}; else RootPathCell=InputTable(:,1); end oldfile=''; %default if isempty(RootPathCell)||isequal(RootPathCell,{''})%loads the previously stored file name and set it as default in the file_input box dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') h=load (profil_perso); if isfield(h,'filebase')&&ischar(h.filebase) oldfile=h.filebase; end if isfield(h,'RootPath')&&ischar(h.RootPath) oldfile=h.RootPath; end end else SubDirCell=InputTable(:,2); RootFileCell=InputTable(:,3); oldfile=fullfile(RootPathCell{1},SubDirCell{1},RootFileCell{1}); end [FileName, PathName, filterindex] = uigetfile( ... {'*.xml;*.xls;*.png;*.tif;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png,*.tif, *.avi,*.nc)'; '*.xml', '.xml files '; ... '*.xls', '.xls files '; ... '*.png','.png image files'; ... '*.tif','.tif image files'; ... '*.avi;*.AVI','.avi movie files'; ... '*.nc','.netcdf files'; ... '*.*', 'All Files (*.*)'}, ... 'Pick a file',oldfile); fileinput=[PathName FileName];%complete file name if isempty(fileinput),return;end %abandon if no file is introduced by the browser [path,name,ext]=fileparts(fileinput); if isequal(ext,'.xml') [Param,Heading]=xml2struct(fileinput); if ~strcmp(Heading,'Series') msg_box_uvmat('ERROR','xml file heading is not ') else fill_GUI(Param,handles);%fill the GUI with the parameters retrieved from the xml file if isfield(Param,'CheckObject')&& Param.CheckObject set_object(Param.ProjObject) end set(handles.REFRESH,'UserData',[1:size(Param.InputTable,1)]) REFRESH_Callback([],[], handles) return end elseif isequal(ext,'.xls') msg_box_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer else display_file_name(handles,fileinput,0) end % -------------------------------------------------------------------- function MenuFile_1_Callback(hObject, eventdata, handles) fileinput=get(handles.MenuFile_1,'Label'); display_file_name(handles,fileinput,0) % -------------------------------------------------------------------- function MenuFile_2_Callback(hObject, eventdata, handles) fileinput=get(handles.MenuFile_2,'Label'); display_file_name(handles,fileinput,0) % -------------------------------------------------------------------- function MenuFile_3_Callback(hObject, eventdata, handles) fileinput=get(handles.MenuFile_3,'Label'); display_file_name( handles,fileinput,0) % -------------------------------------------------------------------- function MenuFile_4_Callback(hObject, eventdata, handles) fileinput=get(handles.MenuFile_4,'Label'); display_file_name(handles,fileinput,0) % -------------------------------------------------------------------- function MenuFile_5_Callback(hObject, eventdata, handles) fileinput=get(handles.MenuFile_5,'Label'); display_file_name(handles,fileinput,0) % -------------------------------------------------------------------- function MenuBrowse_insert_Callback(hObject, eventdata, handles) InputTable=get(handles.InputTable,'Data'); RootPathCell=InputTable(:,1); SubDirCell=InputTable(:,3); RootFileCell=InputTable(:,2); oldfile=''; %default if isempty(RootPathCell)||isequal(RootPathCell,{''})%loads the previously stored file name and set it as default in the file_input box dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') h=load (profil_perso); if isfield(h,'filebase')&ischar(h.filebase) oldfile=h.filebase; end if isfield(h,'RootPath')&ischar(h.RootPath) oldfile=h.RootPath; end end else oldfile=fullfile(RootPathCell{1},RootFileCell{1}); end [FileName, PathName, filterindex] = uigetfile( ... {'*.xml;*.xls;*.png;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png, *.avi,*.nc)'; '*.xml', '.xml files '; ... '*.xls', '.xls files '; ... '*.png','.png image files'; ... '*.avi;*.AVI','.avi movie files'; ... '*.nc','.netcdf files'; ... '*.*', 'All Files (*.*)'}, ... 'Pick a file',oldfile); fileinput=[PathName FileName];%complete file name sizf=size(fileinput); if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end [path,name,ext]=fileparts(fileinput); if isequal(ext,'.xml') msgbox_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer elseif isequal(ext,'.xls') msgbox_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer else display_file_name(handles,fileinput,'append') end % -------------------------------------------------------------------- function MenuFile_insert_1_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- fileinput=get(handles.MenuFile_insert_1,'Label'); display_file_name(handles,fileinput,'append') % -------------------------------------------------------------------- function MenuFile_insert_2_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- fileinput=get(handles.MenuFile_insert_2,'Label'); display_file_name(handles,fileinput,'append') % -------------------------------------------------------------------- function MenuFile_insert_3_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- fileinput=get(handles.MenuFile_insert_3,'Label'); display_file_name( handles,fileinput,'append') % -------------------------------------------------------------------- function MenuFile_insert_4_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- fileinput=get(handles.MenuFile_insert_4,'Label'); display_file_name( handles,fileinput,'append') % -------------------------------------------------------------------- function MenuFile_insert_5_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- fileinput=get(handles.MenuFile_insert_5,'Label'); display_file_name(handles,fileinput,'append') %------------------------------------------------------------------------ % --- Executes when entered data in editable cell(s) in InputTable. function InputTable_CellEditCallback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.REFRESH,'Visible','on') iview=eventdata.Indices(1); view_set=get(handles.REFRESH,'UserData'); if isempty(find(view_set==iview)) set(handles.REFRESH,'UserData',[view_set iview]) end %% enable other menus and uicontrols set(handles.MenuOpen_insert,'Enable','on') set(handles.MenuFile_insert_1,'Enable','on') set(handles.MenuFile_insert_2,'Enable','on') set(handles.MenuFile_insert_3,'Enable','on') set(handles.MenuFile_insert_4,'Enable','on') set(handles.MenuFile_insert_5,'Enable','on') set(handles.RUN, 'Enable','On') set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red %update the output dir % SubDir=sort(InputTable(:,2)); %set of subdirectories sorted in alphabetical order % SubDirOut=SubDir{1}; % if numel(SubDir)>1 % for ilist=2:numel(SubDir) % SubDirOut=[SubDirOut '-' SubDir{ilist}]; % end % end % set(handles.OutputSubDir,'String',SubDirOut) %------------------------------------------------------------------------ % --- Executes on button press in REFRESH. function REFRESH_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ InputTable=get(handles.InputTable,'Data'); view_set=get(handles.REFRESH,'UserData'); set(handles.REFRESH,'BackgroundColor',[0.7 0.7 0.7])% set REFRESH button to grey color drawnow for iview=view_set RootPath=fullfile(InputTable{iview,1},InputTable{iview,2}); if ~exist(RootPath,'dir') i1_series=[]; RootPath=fileparts(RootPath); %will try the upped forldr else [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=... find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]); end if isempty(i1_series) [FileName, PathName, filterindex] = uigetfile( ... {'*.xml;*.xls;*.png;*.tif;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png,*.tif, *.avi,*.nc)'; '*.xml', '.xml files '; ... '*.xls', '.xls files '; ... '*.png','.png image files'; ... '*.tif','.tif image files'; ... '*.avi;*.AVI','.avi movie files'; ... '*.nc','.netcdf files'; ... '*.*', 'All Files (*.*)'}, ... ['unvalid entry at line ' num2str(iview) ', pick a file'],RootPath); fileinput=[PathName FileName];%complete file name if isempty(fileinput),return;end %abandon if the operation has been cancelled: no input from browser [path,name,ext]=fileparts(fileinput); display_file_name(handles,fileinput,iview) else update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,iview) end end set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH button to grey color set(handles.REFRESH,'Visible','off') set(handles.REFRESH,'UserData',[]) %------------------------------------------------------------------------ % --- Function called when a new file is opened, either by series_OpeningFcn or by the browser function display_file_name(handles,fileinput,iview) %------------------------------------------------------------------------ % % INPUT: % handles: handles of elements in the GUI % fielinput: input file name, including path % append =0 (refresh the Input table with the new file), ='append' append a new line in the table %% get the input root name, indices, file extension and nomenclature NomType if ~exist(fileinput,'file') msgbox_uvmat('ERROR',['input file ' fileinput ' does not exist']) return end %% enable other menus and uicontrols set(handles.MenuOpen_insert,'Enable','on') set(handles.MenuFile_insert_1,'Enable','on') set(handles.MenuFile_insert_2,'Enable','on') set(handles.MenuFile_insert_3,'Enable','on') set(handles.MenuFile_insert_4,'Enable','on') set(handles.MenuFile_insert_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 %% detect root name, nomenclature and indices in the input file name: [FilePath,FileName,FileExt]=fileparts(fileinput); % detect the file type, get the movie object if relevant, and look for the corresponding file series: % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]); if isempty(RootFile)&&isempty(i1_series) errormsg='no input file in the series'; return end %% fill the list of file series InputTable=get(handles.InputTable,'Data'); if strcmp(iview,'append') % display the input data as a new line in the table iview=size(InputTable,1); InputTable(iview+1,:)={'','','','',''}; InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}]; elseif iview==0 % or re-initialise the list of input file series iview=1; InputTable=[{'','','','',''};{'','','','',''}]; InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}]; set(handles.TimeTable,'Data',[{[]},{[]},{[]},{[]}]) set(handles.MinIndex,'Data',[{[]},{[]}]) set(handles.MaxIndex,'Data',[{[]},{[]}]) set(handles.ListView,'Value',1) set(handles.ListView,'String',{'1'}) end nbview=size(InputTable,1); set(handles.ListView,'String',mat2cell((1:nbview)',ones(nbview,1))) set(handles.ListView,'Value',iview) set(handles.InputTable,'Data',InputTable) %% determine the selected reference field indices for pair display ref_i=1; %default ref_i is a reference frame index used to find existing pairs from PIV if ~isempty(i1) ref_i=i1; if ~isempty(i2) ref_i=floor((ref_i+i2)/2);% reference image number corresponding to the file end end set(handles.num_ref_i,'String',num2str(ref_i)); ref_j=1; %default ref_j is a reference frame index used to find existing pairs from PIV if ~isempty(j1) ref_j=j1; if ~isempty(j2) ref_j=floor((j1+j2)/2); end end set(handles.num_ref_j,'String',num2str(ref_j)); %% 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});']) eval(['set(handles.MenuFile_insert_' 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 set(handles.InputTable,'BackgroundColor',[1 1 1]) %% initiate input file series and refresh the current field view: update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,iview); %------------------------------------------------------------------------ % --- Update information about a new field series (indices to scan, timing, % calibration from an xml file function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,VideoObject,iview) %------------------------------------------------------------------------ %% update the output dir InputTable=get(handles.InputTable,'Data'); SubDir=sort(InputTable(1:end-1,2)); %set of subdirectories sorted in alphabetical order SubDirOut=SubDir{1}; if numel(SubDir)>1 for ilist=2:numel(SubDir) SubDirOut=[SubDirOut '-' SubDir{ilist}]; end end set(handles.OutputSubDir,'String',SubDirOut) %% display the min and max indices for the file series if size(i1_series,2)==1 MinIndex_j=1; MaxIndex_j=1; MinIndex_i=min(find(i1_series)); MaxIndex_i=max(find(i1_series)); else pair_max=squeeze(max(i1_series,[],1)); %max on pair index j_max=max(pair_max,[],1); %i_sum=sum(sum(i1_series,2),1);%sum of i1_series on the last index MaxIndex_i=max(find(j_max))-1;% max ref index i MinIndex_i=min(find(j_max))-1;% min ref index i diff_i_max=diff(j_max); if isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max))) set(handles.num_incr_i,'String',num2str(diff_i_max(1))) end i_max=max(pair_max,[],2); MaxIndex_j=max(find(i_max))-1;% max ref index i MinIndex_j=min(find(i_max))-1;% min ref index i diff_j_max=diff(i_max); if 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 MinIndex=get(handles.MinIndex,'Data');%retrieve the min indices in the table MinIndex MaxIndex=get(handles.MaxIndex,'Data');%retrieve the max indices in the table MaxIndex MinIndex{iview,1}=MinIndex_i; MinIndex{iview,2}=MinIndex_j; MaxIndex{iview,1}=MaxIndex_i; MaxIndex{iview,2}=MaxIndex_j; set(handles.MinIndex,'Data',MinIndex)%display the min indices in the table MinIndex set(handles.MaxIndex,'Data',MaxIndex)%display the max indices in the table MaxIndex %% adjust the first and last indices if requested by the bounds first_i=str2num(get(handles.num_first_i,'String')); ref_i=str2num(get(handles.num_ref_i,'String')); ref_j=str2num(get(handles.num_ref_j,'String')); if isempty(first_i) first_i=ref_i; elseif first_i < MinIndex_i first_i=MinIndex_i; elseif first_i >MaxIndex_i first_i=MinIndex_i; end first_j=str2num(get(handles.num_first_j,'String')); if isempty(first_j) first_j=ref_j; elseif first_jMaxIndex_j first_j=MinIndex_j; end 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_i1 %case of image with multiple frames nbfield=length(imainfo); nbfield_j=1; end end end %% read image documentation file if found%%%%%%%%%%%%%%%%%%%%%%%%%%% XmlData=[]; NbSlice_calib={}; XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5}); if ~isempty(XmlFileName) [XmlData,warntext]=imadoc2struct(XmlFileName); if isfield(XmlData,'Heading') && isfield(XmlData.Heading,'ImageName') && ischar(XmlData.Heading.ImageName) [PP,FF,ext_ima_read]=fileparts(XmlData.Heading.ImageName); end if isfield(XmlData,'Time') time=XmlData.Time; end if isfield(XmlData,'Camera') if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice) NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); end end if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit) TimeUnit=XmlData.Camera.TimeUnit; end end if ~isempty(warntext) msgbox_uvmat('WARNING',warntext) end end %% update time table if ~isempty(time) TimeTable=get(handles.TimeTable,'Data'); first_i=str2num(get(handles.num_first_i,'String')); last_i=str2num(get(handles.num_last_i,'String')); first_j=str2num(get(handles.num_first_j,'String')); last_j=str2num(get(handles.num_last_j,'String')); MinIndexTable=get(handles.MinIndex,'Data'); MinIndex_i=MinIndexTable{iview,1}; MinIndex_j=MinIndexTable{iview,2}; MaxIndexTable=get(handles.MaxIndex,'Data'); MaxIndex_i=MaxIndexTable{iview,1}; MaxIndex_j=MaxIndexTable{iview,2}; if isempty(MinIndex_j)% only i index if MinIndex_i>0 TimeTable{iview,1}=time(MinIndex_i); end TimeTable{iview,2}=time(first_i); TimeTable{iview,3}=time(last_i); TimeTable{iview,4}=time(MaxIndex_i); elseif ~isempty(time) if MinIndex_i>0 TimeTable{iview,1}=time(MinIndex_i,MinIndex_j); end TimeTable{iview,2}=time(first_i,first_j); TimeTable{iview,3}=time(last_i,last_j); if size(time)>=[MaxIndex_i MaxIndex_j]; TimeTable{iview,4}=time(MaxIndex_i,MaxIndex_j); end end set(handles.TimeTable,'Data',TimeTable) end %% number of slices NbSlice=1;%default if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord') siz=size(XmlData.GeometryCalib.SliceCoord); if siz(1)>1 NbSlice=siz(1); end end set(handles.num_NbSlice,'String',num2str(NbSlice)) %% update pair menus set(handles.Pairs,'Visible','on') set(handles.PairString,'Visible','on') ListView=get(handles.ListView,'String'); ListView{iview}=num2str(iview); set(handles.ListView,'String',ListView); set(handles.ListView,'Value',iview) update_mode(handles,i1_series,i2_series,j1_series,j2_series,time) %% update the series info in 'UserData' SeriesData=get(handles.series,'UserData'); SeriesData.i1_series{iview}=i1_series; SeriesData.i2_series{iview}=i2_series; SeriesData.j1_series{iview}=j1_series; SeriesData.j2_series{iview}=j2_series; SeriesData.FileType{iview}=FileType; SeriesData.Time{iview}=time; set(handles.series,'UserData',SeriesData) %% enable j index visibilitycellfun(@isempty,regexp(PairString,'^j')) % state='off'; check_jindex=~cellfun(@isempty,SeriesData.j1_series); %look for non empty j indices if isempty(find(check_jindex)) enable_j(handles,'off') % no j index needed else PairString=get(handles.PairString,'Data'); if isempty(find(cellfun(@isempty,regexp(PairString,'^j'))))% if all pair string begins by j (burst) enable_j(handles,'off') % no j index needed else enable_j(handles,'on') end 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); pair_max=cell(1,nbview); for iview=1:nbview pair_max{iview}=squeeze(max(SeriesData.i1_series{iview},[],1)); %max on pair index if (strcmp(get(handles.num_first_j,'Visible'),'off')&& size(pair_max{iview},2)~=1) pair_max{iview}=squeeze(max(pair_max{iview},[],1)); % consider only the i index end index_min(iview)=find(pair_max{iview}>0, 1 ); index_max(iview)=find(pair_max{iview}>0, 1, 'last' ); end index_min=min(index_min); index_max=max(index_max); range_index=index_max-index_min+1; scale_y=Position(4)/nbview; scale_x=Position(3)/range_index; x=(0.5:range_index-0.5)*Position(3)/range_index; % y=(0.5:nbview-0.5)*Position(4)/nbview; range_y=max(1,floor(Position(4)/nbview)); CData=zeros(nbview*range_y,Position(3)); for iview=1:nbview ind_y=1+(iview-1)*range_y:iview*range_y; LineData=zeros(1,range_index); x_index=find(pair_max{iview}>0)-index_min+1; LineData(x_index)=1; LineData=interp1(x,LineData,xI,'nearest'); CData(ind_y,:)=ones(size(ind_y'))*LineData; end CData=cat(3,zeros(size(CData)),CData,zeros(size(CData))); set(handles.FileStatus,'CData',CData); %% enable field and veltype menus, in accordance with the current action ActionName_Callback([],[], handles) %% check for pair display check_pairs=0; for iview=1:numel(SeriesData.i2_series) if ~isempty(SeriesData.i2_series{iview})||~isempty(SeriesData.j2_series{iview}) check_pairs=1; end end if check_pairs set(handles.Pairs,'Visible','on') set(handles.PairString,'Visible','on') else set(handles.Pairs,'Visible','off') set(handles.PairString,'Visible','off') end %% set length of waitbar displ_time(handles) %% set default options in menu 'Fields' switch FileType case {'civx','civdata'} [FieldList,ColorList]=calc_field; set(handles.FieldName,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data set(handles.FieldName,'Value',2) % set menu to 'velocity set(handles.Coord_x,'Value',1); set(handles.Coord_x,'String',{'X'}); set(handles.Coord_y,'Value',1); set(handles.Coord_y,'String',{'Y'}); case 'netcdf' set(handles.FieldName,'Value',1) set(handles.FieldName,'String',{'get_field...'}) if isempty(i2_series) i2=[]; else i2=i2_series(1,ref_j+1,ref_i+1); end if isempty(j1_series) j1=[];j2=[]; else j1=j1_series(1,ref_j+1,ref_i+1); if isempty(j2_series) j2=[]; else j2=j2_series(1,ref_j+1,ref_i+1); end end FileName=fullfile_uvmat(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5},InputTable{iview,4},i1_series(1,ref_j+1,ref_i+1),i2,j1,j2); hget_field=get_field(FileName); hhget_field=guidata(hget_field); get_field('RUN_Callback',hhget_field.RUN,[],hhget_field); otherwise set(handles.FieldName,'Value',1) % set menu to 'image' set(handles.FieldName,'String',{'image'}) set(handles.Coord_x,'Value',1); set(handles.Coord_x,'String',{'AX'}); set(handles.Coord_y,'Value',1); set(handles.Coord_y,'String',{'AY'}); end %------------------------------------------------------------------------ function num_first_i_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ num_last_i_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ function num_last_i_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ SeriesData=get(handles.series,'UserData'); if ~isfield(SeriesData,'Time') SeriesData.Time{1}=[]; end displ_time(handles); %------------------------------------------------------------------------ function num_first_j_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ num_last_j_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ function num_last_j_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ first_j=str2num(get(handles.num_first_j,'String')); last_j=str2num(get(handles.num_last_j,'String')); ref_j=ceil((first_j+last_j)/2); set(handles.num_ref_j,'String', num2str(ref_j)) num_ref_j_Callback(hObject, eventdata, handles) SeriesData=get(handles.series,'UserData'); if ~isfield(SeriesData,'Time') SeriesData.Time{1}=[]; end displ_time(handles); %------------------------------------------------------------------------ % ---- find the times corresponding to the first and last indices of a series function displ_time(handles) %------------------------------------------------------------------------ SeriesData=get(handles.series,'UserData');% ref_i=[str2num(get(handles.num_first_i,'String')) str2num(get(handles.num_last_i,'String'))]; ref_j=[str2num(get(handles.num_first_j,'String')) str2num(get(handles.num_last_j,'String'))]; TimeTable=get(handles.TimeTable,'Data'); Pairs=get(handles.PairString,'Data'); for iview=1:size(TimeTable,1) if size(SeriesData.Time,1)(Di=)|(Dj=)) -*(?\d+)\|(?\d+)','names'); if isempty(r) r=regexp(Pairs{iview,1},'(?\d+)(?-)(?\d+)','names'); end switch r.mode case 'Di=' % case 'series(Di)') i1=ref_i-str2num(r.num1); i2=ref_i+str2num(r.num2); case 'Dj=' % case 'series(Dj)' j1=ref_j-str2num(r.num1); j2=ref_j+str2num(r.num2); case '-' % case 'bursts' j1=str2num(r.num1)*ones(size(ref_i)); j2=str2num(r.num2)*ones(size(ref_i)); end end TimeTable{iview,2}=[]; TimeTable{iview,3}=[]; if size(SeriesData.Time{iview},1)>=i2(2)&&size(SeriesData.Time{iview},1)>=j2(2) if isempty(ref_j) time_first=(SeriesData.Time{iview}(i1(1))+SeriesData.Time{iview}(i2(1)))/2; time_last=(SeriesData.Time{iview}(i1(2))+SeriesData.Time{iview}(i2(2)))/2; else time_first=(SeriesData.Time{iview}(i1(1),j1(1))+SeriesData.Time{iview}(i2(1),j2(1)))/2; time_last=(SeriesData.Time{iview}(i1(2),j1(2))+SeriesData.Time{iview}(i2(2),j2(2)))/2; end TimeTable{iview,2}=time_first; %TODO: take into account pairs TimeTable{iview,3}=time_last; %TODO: take into account pairs end end set(handles.TimeTable,'Data',TimeTable) %% set the waitbar position with respect to the min and max in the series for iview=1:numel(SeriesData.i1_series) pair_max{iview}=squeeze(max(SeriesData.i1_series{iview},[],1)); %max on pair index if (strcmp(get(handles.num_first_j,'Visible'),'off')&& size(pair_max{iview},2)~=1) pair_max{iview}=squeeze(max(pair_max{iview},[],1)); % consider only the i index end pair_max{iview}=reshape(pair_max{iview},1,[]); index_min(iview)=find(pair_max{iview}>0, 1 ); index_max(iview)=find(pair_max{iview}>0, 1, 'last' ); end [index_min,iview_min]=min(index_min); [index_max,iview_max]=min(index_max); if size(SeriesData.i1_series{iview_min},2)==1% movie index_first=ref_i(1); index_last=ref_i(2); else index_first=(ref_i(1)-1)*(size(SeriesData.i1_series{iview_min},1))+ref_j(1)+1; index_last=(ref_i(2)-1)*(size(SeriesData.i1_series{iview_max},1))+ref_j(2)+1; end range=index_max-index_min+1; coeff_min=(index_first-index_min)/range; coeff_max=(index_last-index_min+1)/range; Position=get(handles.Waitbar,'Position');% position of the waitbar:= [ x,y, width, height] Position_status=get(handles.FileStatus,'Position'); Position(1)=coeff_min*Position_status(3)+Position_status(1); Position(3)=Position_status(3)*(coeff_max-coeff_min); 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) %------------------------------------------------------------------------ set(handles.ListView,'Value',eventdata.Indices(1))% detect the selected raw index ListView_Callback ([],[],handles) % update the list of available pairs %------------------------------------------------------------------------ %------------------------------------------------------------------------ % III - FUNCTIONS ASSOCIATED TO THE FRAME SET PAIRS %------------------------------------------------------------------------ %------------------------------------------------------------------------ % --- Executes on selection change in ListView. function ListView_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ SeriesData=get(handles.series,'UserData'); i2_series=[]; j2_series=[]; iview=get(handles.ListView,'Value'); if ~isempty(SeriesData.i2_series{iview}) i2_series=SeriesData.i2_series{iview}; end if ~isempty(SeriesData.j2_series{iview}) j2_series=SeriesData.j2_series{iview}; end update_mode(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},... SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview}) %------------------------------------------------------------------------ % --- Executes on button press in mode. function mode_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ SeriesData=get(handles.series,'UserData'); iview=get(handles.ListView,'Value'); mode_list=get(handles.mode,'String'); mode=mode_list{get(handles.mode,'Value')}; if isequal(mode,'bursts') enable_i(handles,'On') enable_j(handles,'Off') %do not display j index scanning in burst mode (j is fixed by the burst choice) else enable_i(handles,'On') enable_j(handles,'Off') end fill_ListPair(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},... SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview}) ListPairs_Callback([],[],handles) %------------------------------------------------------------- % --- Executes on selection in ListPairs. function ListPairs_Callback(hObject,eventdata,handles) %------------------------------------------------------------ list_pair=get(handles.ListPairs,'String');%get the menu of image pairs if isempty(list_pair) string=''; else string=list_pair{get(handles.ListPairs,'Value')}; string=regexprep(string,',.*','');%removes time indication (after ',') end PairString=get(handles.PairString,'Data'); iview=get(handles.ListView,'Value'); PairString{iview,1}=string; % report the selected pair string to the table PairString set(handles.PairString,'Data',PairString) %------------------------------------------------------------------------ function num_ref_i_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ mode_list=get(handles.mode,'String'); mode=mode_list{get(handles.mode,'Value')}; SeriesData=get(handles.series,'UserData'); iview=get(handles.ListView,'Value'); fill_ListPair(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},... SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview});% update the menu of pairs depending on the available netcdf files ListPairs_Callback([],[],handles) %------------------------------------------------------------------------ function num_ref_j_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ num_ref_i_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ function update_mode(handles,i1_series,i2_series,j1_series,j2_series,time) %------------------------------------------------------------------------ % check_burst=0; if isempty(j2_series)% no j pair if isempty(i2_series) set(handles.mode,'Value',1) set(handles.mode,'String',{''})% no pair menu to display else set(handles.mode,'Value',1) set(handles.mode,'String',{'series(Di)'}) % pair menu with only option Di end else %existence of j pairs pair_max=squeeze(max(i1_series,[],1)); %max on pair index j_max=max(pair_max,[],1); MaxIndex_i=max(find(j_max))-1;% max ref index i MinIndex_i=min(find(j_max))-1;% min ref index i i_max=max(pair_max,[],2); MaxIndex_j=max(find(i_max))-1;% max ref index i MinIndex_j=min(find(i_max))-1;% min ref index i if MaxIndex_j==MinIndex_j set(handles.mode,'Value',1); set(handles.mode,'String',{'bursts'}) % check_burst=1; elseif MaxIndex_i==MinIndex_i set(handles.mode,'Value',1); set(handles.mode,'String',{'series(Dj)'}) else set(handles.mode,'String',{'bursts';'series(Dj)'}) if (MaxIndex_j-MinIndex_j)>10 set(handles.mode,'Value',2);%set mode to series(Dj) if more than 10 j values else set(handles.mode,'Value',1); % check_burst=1; end end end % if check_burst % enable_i(handles,'On') % enable_j(handles,'Off') %do not display j index scanning in burst mode (j is fixed by the burst choice) % else % enable_i(handles,'On') % if isempty(j1_series) % enable_j(handles,'Off') % else % enable_j(handles,'On') % end % end fill_ListPair(handles,i1_series,i2_series,j1_series,j2_series,time) ListPairs_Callback([],[],handles) %-------------------------------------------------------------- % determine the menu for civ1 pairstring depending on existing netcdf files % with the reference indices num_ref_i and num_ref_j %---------------------------------------------------------------- function fill_ListPair(handles,i1_series,i2_series,j1_series,j2_series,time) mode_list=get(handles.mode,'String'); mode=mode_list{get(handles.mode,'Value')}; ref_i=str2num(get(handles.num_ref_i,'String')); if isempty(ref_i) ref_i=1; end if strcmp(get(handles.num_ref_j,'Visible'),'on') ref_j=str2num(get(handles.num_ref_j,'String')); if isempty(ref_j) ref_j=1; end else ref_j=1; end TimeUnit=get(handles.TimeUnit,'String'); if length(TimeUnit)>=1 dtunit=['m' TimeUnit]; else dtunit='e-03'; end displ_pair={}; if strcmp(mode,'series(Di)') if isempty(i2_series) msgbox_uvmat('ERROR','no i1-i2 pair available') return end diff_i=i2_series-i1_series; min_diff=min(diff_i(diff_i>0)); max_diff=max(diff_i(diff_i>0)); for ipair=min_diff:max_diff if numel(diff_i(diff_i==ipair))>0 pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ]; if ~isempty(time) if ref_i<=floor(ipair/2) ref_i=floor(ipair/2)+1;% shift ref_i to get the first pair end Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j); pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit]; end displ_pair=[displ_pair;{pair_string}]; end end if ~isempty(displ_pair) displ_pair=[displ_pair;{'Di=*|*'}]; end elseif strcmp(mode,'series(Dj)') if isempty(j2_series) msgbox_uvmat('ERROR','no j1-j2 pair available') return end diff_j=j2_series-j1_series; min_diff=min(diff_j(diff_j>0)); max_diff=max(diff_j(diff_j>0)); for ipair=min_diff:max_diff if numel(diff_j(diff_j==ipair))>0 pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ]; if ~isempty(time) if ref_j<=floor(ipair/2) ref_j=floor(ipair/2)+1;% shift ref_i to get the first pair end Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2)); pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit]; end displ_pair=[displ_pair;{pair_string}]; end end if ~isempty(displ_pair) displ_pair=[displ_pair;{'Dj=*|*'}]; end elseif strcmp(mode,'bursts') if isempty(j2_series) msgbox_uvmat('ERROR','no j1-j2 pair available') return end diff_j=j2_series-j1_series; min_j1=min(j1_series(j1_series>0)); max_j1=max(j1_series(j1_series>0)); min_j2=min(j2_series(j2_series>0)); max_j2=max(j2_series(j2_series>0)); for pair1=min_j1:min(max_j1,min_j1+20) for pair2=min_j2:min(max_j2,min_j2+20) if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0 displ_pair=[displ_pair;{['j= ' num2str(pair1) '-' num2str(pair2)]}]; end end end if ~isempty(displ_pair) displ_pair=[displ_pair;{'j=*-*'}]; end end set(handles.num_ref_i,'String',num2str(ref_i)) % update ref_i and ref_j set(handles.num_ref_j,'String',num2str(ref_j)) %% display list of pairstring displ_pair_list=get(handles.ListPairs,'String'); NewVal=[]; if ~isempty(displ_pair_list) Val=get(handles.ListPairs,'Value'); NewVal=find(strcmp(displ_pair_list{Val},displ_pair),1);% look at the previous display in the new menu displ_p�ir end if ~isempty(NewVal) set(handles.ListPairs,'Value',NewVal) else set(handles.ListPairs,'Value',1) end set(handles.ListPairs,'String',displ_pair) %------------------------------------- function enable_i(handles,state) set(handles.i_txt,'Visible',state) set(handles.num_first_i,'Visible',state) set(handles.num_last_i,'Visible',state) set(handles.num_incr_i,'Visible',state) % set(handles.num_MaxIndex_i,'Visible',state) set(handles.num_ref_i,'Visible',state) set(handles.ref_i_text,'Visible',state) %----------------------------------- function enable_j(handles,state) set(handles.j_txt,'Visible',state) set(handles.num_first_j,'Visible',state) set(handles.num_last_j,'Visible',state) set(handles.num_incr_j,'Visible',state) set(handles.num_ref_j,'Visible',state) set(handles.ref_j_text,'Visible',state) % if strcmp(state,'off') % set(handles.MinIndex,'ColumnName',{'imax'}) % set(handles.MinIndex,'ColumnEditable',logical(0)) % else % set(handles.MinIndex,'ColumnName',{'imax','jmax'}) % end %%%%%%%%%%%%%%%%%%%% %% MAIN ActionName FUNCTIONS %%%%%%%%%%%%%%%%%%%% %------------------------------------------------------------------------ % --- Executes on button press in RUN. function RUN_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.RUN,'BusyAction','queue'); set(0,'CurrentFigure',handles.series) set(handles.RUN, 'Enable','Off') set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784]) drawnow [h_fun,Series,filexml,errormsg]=prepare_jobs(handles); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) return end RunModeList=get(handles.RunMode,'String'); RunMode=RunModeList{get(handles.RunMode,'Value')}; switch RunMode case 'local' Series=h_fun(Series); if ~isempty(filexml) t=struct2xml(Series); t=set(t,1,'name','Series'); save(t,filexml); end case 'background' if isempty(filexml) Series=h_fun(Series);% no background in the absence of output file else % update the xml file after interactive input with the function Series.Specific='?'; Series=h_fun(Series); t=struct2xml(Series); t=set(t,1,'name','Series'); save(t,filexml); path_uvmat=fileparts(which('uvmat')); filename_bat=regexprep(filexml,'.xml$','.bat'); [fid,message]=fopen(filename_bat,'w'); if isequal(fid,-1) msgbox_uvmat('ERROR', ['creation of .bat file: ' message]); return end path_fct=get(handles.ActionPath,'String'); filelog=regexprep(filexml,'.xml$','.log'); switch computer case {'GLNX86','GLNXA64','MACI64'} text_matlabscript=[... '#!/bin/bash \n'... '. /etc/sysprofile \n'... 'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog ''' <1 && isfield(SeriesData,'AllowInputSort') && isfield(SeriesData.AllowInputSort) [tild,iview]=sort(Series.InputTable(:,2)); %subdirectories sorted in alphabetical order Series.InputTable=Series.InputTable(iview,:); end detect=exist(fullfile(Series.InputTable{1,1},SubDirOutNew),'dir');% test if the dir already exist check_create=1; %need to create the result directory by default while detect answer=msgbox_uvmat('INPUT_Y-N',['use existing ouput directory: ' fullfile(Series.InputTable{1,1},SubDirOutNew) ', possibly delete previous data']); if isequal(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(Series.InputTable{1,1},SubDirOutNew),'dir');% test if the dir already exists check_create=1; end end Series.OutputDirExt=regexprep(SubDirOutNew,Series.OutputSubDir,''); % Series.OutputSubDir=SubDirOutNew; % Series.OutputDir=fullfile(Series.InputTable{1,1},Series.OutputSubDir);%directory set for output results Series.OutputRootFile=Series.InputTable{1,3};% the first sorted RootFile taken for output set(handles.OutputDirExt,'String',Series.OutputDirExt) % create output directory OutputDir=fullfile(Series.InputTable{1,1},[Series.OutputSubDir Series.OutputDirExt]); if check_create [tild,msg1]=mkdir(OutputDir); if ~strcmp(msg1,'') errormsg=['cannot create ' OutputDir ': ' msg1];%error message for directory creation return end end filexml=fullfile(OutputDir,[Series.InputTable{1,3} '.xml']);% name of the parameter xml file set in this directory end %removes redondant information Series.IndexRange=rmfield(Series.IndexRange,'TimeTable'); Series.IndexRange=rmfield(Series.IndexRange,'MinIndex'); Series.IndexRange=rmfield(Series.IndexRange,'MaxIndex'); %removes empty lines of InputTable empty_line=zeros(size(Series.InputTable,1),1); for iline=1:size(Series.InputTable,1) empty_line(iline)=isequal(Series.InputTable(iline,1:3),{'','',''}); end Series.InputTable(find(empty_line),:)=[]; %------------------------------------------------------------------------ % --- Executes on selection change in ActionName. function ActionName_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ global nb_builtin_ACTION list_ACTION=get(handles.ActionName,'String');% list menu fields index_ACTION=get(handles.ActionName,'Value');% selected string index ACTION= list_ACTION{index_ACTION}; % selected function name path_series=which('series');%path to series.m list_path=get(handles.ActionName,'UserData');%list of recorded paths to functions of the list ACTION default_file=fullfile(list_path{end},ACTION); % add a new function to the menu if the selected item is 'more...' if isequal(ACTION,'more...') pathfct=fileparts(path_series); [FileName, PathName, filterindex] = uigetfile( ... {'*.m', ' (*.m)'; '*.m', '.m files '; ... '*.*', 'All Files (*.*)'}, ... 'Pick a file',default_file); if length(FileName)<2 return end [pp,ACTION,ext_fct]=fileparts(FileName);%(end-1:end); if ~isequal(ext_fct,'.m') msgbox_uvmat('ERROR','a Matlab function .m must be introduced'); return end % insert the choice in the actionname menu menu_str=update_menu(handles.ActionName,ACTION);%new action menu in which the new item has been appended if needed index_ACTION=get(handles.ActionName,'Value');% currently selected index in the list list_path{index_ACTION}=PathName; if length(menu_str)>nb_builtin_ACTION+5; %nb_builtin=nbre of functions always remaining in the initial menu nbremove=length(menu_str)-nb_builtin_ACTION-5; menu_str(nb_builtin_ACTION+1:end-5)=[]; list_path(nb_builtin_ACTION+1:end-4)=[]; index_ACTION=index_ACTION-nbremove; set(handles.ActionName,'Value',index_ACTION) set(handles.ActionName,'String',menu_str) end list_path{index_ACTION}=PathName; set(handles.ActionName,'UserData',list_path); set(handles.ActionPath,'enable','inactive')% indicate that the current path is accessible (not 'off') %record the current menu in personal file profil_perso dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); for ilist=nb_builtin_ACTION+1:length(menu_str)-1 series_fct{ilist-nb_builtin_ACTION}=fullfile(list_path{ilist},[menu_str{ilist} '.m']); end if nb_builtin_ACTION+1<=length(menu_str)-1 if exist(profil_perso,'file')% && nb_builtin_ACTION+1>=length(menu_str)-1 save(profil_perso,'series_fct','-append') else txt=ver('MATLAB'); Release=txt.Release; relnumb=str2num(Release(3:4)); if relnumb >= 14%recent relaese of Matlab save(profil_perso,'series_fct','-V6') else save(profil_perso, 'series_fct') end end end end %check the current ActionPath to the selected function PathName=list_path{index_ACTION};%current recorded path set(handles.ActionPath,'String',PathName); %show the path to the senlected function %reinitialise the waitbar update_waitbar(handles.Waitbar,0) %default setting for the visibility of the GUI elements set(handles.num_NbSlice,'Visible','off') set(handles.NbSlice_title,'Visible','off') set(handles.VelType,'Visible','off'); set(handles.VelType_text,'Visible','off'); set(handles.VelType_1,'Visible','off'); set(handles.VelType_text_1,'Visible','off'); set(handles.InputFields,'Visible','off') set(handles.FieldName_1,'Visible','off') %view_FieldMenu_1(handles,'off') set(handles.FieldTransform,'Visible','off') set(handles.CheckObject,'Visible','off'); set(handles.ProjObject,'Visible','off'); set(handles.CheckMask,'Visible','off') set(handles.Mask,'Visible','off') set(handles.OutputDirExt,'Visible','off') set(handles.OutputSubDir,'Visible','off') set(handles.OutputDir_title,'Visible','off') %set the displayed GUI item needed for input parameters if ~isequal(path_series,PathName) addpath(PathName) end eval(['h_function=@' ACTION ';']); try [fid,errormsg] =fopen([ACTION '.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 if ~isequal(path_series,PathName) rmpath(PathName) end varargout=h_function(); Param_list={}; InputTable=get(handles.InputTable,'Data'); nbview=size(InputTable,1); SeriesData=get(handles.series,'UserData'); nb_civ=numel(find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType))); nb_netcdf=numel(find(strcmp('netcdf',SeriesData.FileType))); for ilist=1:length(varargout)-1 switch varargout{ilist} case 'AllowInputSort' if isequal(lower(varargout{ilist+1}),'on')% sort the input table by alphabetical order of the SubDir SeriesData.AllowInputSort=1; set(handles.series,'UserData',SeriesData) end case 'WholeIndexRange' if isequal(lower(varargout{ilist+1}),'on')% set by default the input index range from min to max MinIndex=get(handles.MinIndex,'Data'); MaxIndex=get(handles.MaxIndex,'Data'); if ~isempty(MinIndex) set(handles.num_first_i,'String',num2str(MinIndex{1})) set(handles.num_last_i,'String',num2str(MaxIndex{1})) set(handles.num_incr_i,'String','1') if size(MinIndex,2)>=2 set(handles.num_first_j,'String',num2str(MinIndex{1,2})) set(handles.num_last_j,'String',num2str(MaxIndex{1,2})) set(handles.num_incr_j,'String','1') end end end case 'NbSlice' %hidden by default if isequal(lower(varargout{ilist+1}),'on') set(handles.num_NbSlice,'Visible','on') set(handles.NbSlice_title,'Visible','on') end case 'VelType' %hidden by default if isequal(lower(varargout{ilist+1}),'one') || isequal(lower(varargout{ilist+1}),'two') if nb_civ>=1 set(handles.VelType,'Visible','on') set(handles.VelType_text,'Visible','on'); end end if isequal(lower(varargout{ilist+1}),'two') if nb_civ>=2 set(handles.VelType_1,'Visible','on') set(handles.VelType_text_1,'Visible','on'); end end case 'FieldName' %hidden by default if isequal(lower(varargout{ilist+1}),'one')||isequal(lower(varargout{ilist+1}),'two') if (nb_civ+nb_netcdf)>=1 set(handles.FieldName,'Visible','on') % test for MenuBorser set(handles.InputFields,'Visible','on') end end if isequal(lower(varargout{ilist+1}),'two') if (nb_civ+nb_netcdf)>=1 set(handles.FieldName_1,'Visible','on') end end case 'FieldTransform' %hidden by default if isequal(lower(varargout{ilist+1}),'on') set(handles.TransformName,'Enable','on') set(handles.FieldTransform,'Visible','on') TransformName_Callback([],[], handles) end case 'ProjObject' %hidden by default if isequal(lower(varargout{ilist+1}),'on') set(handles.CheckObject,'Visible','on') set(handles.ProjObject,'Visible','on') end case 'Mask' %hidden by default if isequal(lower(varargout{ilist+1}),'on') set(handles.Mask,'Visible','on') set(handles.CheckMask,'Visible','on'); end case 'OutputDirExt' if ~isempty(varargout{ilist+1}) set(handles.OutputDirExt,'String',varargout{ilist+1}) set(handles.OutputDirExt,'Visible','on') set(handles.OutputSubDir,'Visible','on') set(handles.OutputDir_title,'Visible','on') end end end if ~isempty(Param_list) set(handles.ParamKey,'String',Param_list) set(handles.ParamVal,'Visible','on') end %------------------------------------------------------------------------ % --- Executes on selection change in FieldName. function FieldName_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ field_str=get(handles.FieldName,'String'); field_index=get(handles.FieldName,'Value'); field=field_str{field_index(1)}; if isequal(field,'get_field...') hget_field=findobj(allchild(0),'name','get_field'); if ~isempty(hget_field) delete(hget_field)%delete opened versions of get_field end filecell=get_file_series(read_GUI(handles.series)); if exist(filecell{1,1},'file') get_field(filecell{1,1}) end elseif isequal(field,'more...') str=calc_field; [ind_answer,v] = listdlg('PromptString','Select a file:',... 'SelectionMode','single',... 'ListString',str); % edit the choice in the fields and actionname menu scalar=cell2mat(str(ind_answer)); update_menu(handles.FieldName,scalar) end %------------------------------------------------------------------------ % --- Executes on selection change in FieldName_1. function FieldName_1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ field_str=get(handles.FieldName_1,'String'); field_index=get(handles.FieldName_1,'Value'); field=field_str{field_index}; if isequal(field,'get_field...') hget_field=findobj(allchild(0),'name','get_field_1'); if ~isempty(hget_field) delete(hget_field) end SeriesData=get(handles.series,'UserData'); filename=SeriesData.CurrentInputFile_1; if exist(filename,'file') hget_field=get_field(filename); set(hget_field,'name','get_field_1') end elseif isequal(field,'more...') str=calc_field; [ind_answer,v] = listdlg('PromptString','Select a file:',... 'SelectionMode','single',... 'ListString',str); % edit the choice in the fields and actionname menu scalar=cell2mat(str(ind_answer)); update_menu(handles.FieldName_1,scalar) end %%%%%%%%%%%%% function [ind_remove]=find_pairs(dirpair,ind_i,last_i) indsel=ind_i; indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds if ~isempty(indiff) indiff2=diff(indiff); indiffp=[indiff2 1]; indiffm=[1 indiff2]; ind_multi_m=find((indiff==0)&(indiffm<0))-1;%indices of first members of multiplets ind_multi_p=find((indiff==0)&(indiffp>0));%indices of last members of multiplets %for each multiplet, select the most recent file ind_remove=[]; for i=1:length(ind_multi_m) ind_pairs=ind_multi_m(i):ind_multi_p(i); for imulti=1:length(ind_pairs) datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date);%dates of creation end [datenew,indsort2]=sort(datepair); %sort the multiplet by creation date ind_s=indsort2(1:end-1);% ind_remove=[ind_remove ind_pairs(ind_s)];%remove these indices, leave the last one end end %------------------------------------------------------------------------ % --- determine the list of index pairstring of processing file function [num_i1,num_i2,num_j1,num_j2,num_i_out,num_j_out]=find_file_indices(num_i,num_j,ind_shift,NomType,mode) %------------------------------------------------------------------------ num_i1=num_i;% set of first image numbers by default num_i2=num_i; num_j1=num_j; num_j2=num_j; num_i_out=num_i; num_j_out=num_j; % if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2') if isequal(mode,'series(Di)') num_i1_line=num_i+ind_shift(3);% set of first image numbers num_i2_line=num_i+ind_shift(4); % adjust the first and last field number indsel=find(num_i1_line >= 1); num_i_out=num_i(indsel); num_i1_line=num_i1_line(indsel); num_i2_line=num_i2_line(indsel); num_j1=meshgrid(num_j,ones(size(num_i1_line))); num_j2=meshgrid(num_j,ones(size(num_i1_line))); [xx,num_i1]=meshgrid(num_j,num_i1_line); [xx,num_i2]=meshgrid(num_j,num_i2_line); elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts') if isequal(mode,'bursts') %case of bursts (png_old or png_2D) num_j1=ind_shift(1)*ones(size(num_i)); num_j2=ind_shift(2)*ones(size(num_i)); else num_j1_col=num_j+ind_shift(1);% set of first image numbers num_j2_col=num_j+ind_shift(2); % adjust the first field number indsel=find((num_j1_col >= 1)); num_j_out=num_j(indsel); num_j1_col=num_j1_col(indsel); num_j2_col=num_j2_col(indsel); [num_i1,num_j1]=meshgrid(num_i,num_j1_col); [num_i2,num_j2]=meshgrid(num_i,num_j2_col); end end %------------------------------------------------------------------------ % --- Executes on button press in CheckObject. function CheckObject_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ value=get(handles.CheckObject,'Value'); if value set(handles.CheckObject,'BackgroundColor',[1 1 0])%put unactivated buttons to yellow hset_object=findobj(allchild(0),'tag','set_object');%find the set_object interface handle 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 [FileName, PathName, filterindex] = uigetfile( ... {'*.xml;*.mat', ' (*.xml,*.mat)'; '*.xml', '.xml files '; ... '*.mat', '.mat matlab files '}, ... 'Pick an xml object file (or use uvmat to create it)',defaultname); fileinput=[PathName FileName];%complete file name sizf=size(fileinput); if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %read the file data=xml2struct(fileinput); if ~isfield(data,'Type') msgbox_uvmat('ERROR',[fileinput ' is not an object xml file']) return end if ~isfield(data,'ProjMode') data.ProjMode='none'; end hset_object=set_object(data);% call the set_object interface end Object=read_GUI(hset_object); set(handles.ProjObject,'String',Object.Name);%display the object name else set(handles.CheckObject,'BackgroundColor',[0.7 0.7 0.7])%put activated buttons to green end %set(handles.series,'UserData',SeriesData) %-------------------------------------------------------------- function CheckMask_Callback(hObject, eventdata, handles) value=get(handles.CheckMask,'Value'); if value msgbox_uvmat('ERROR','not implemented yet') end %-------------------------------------------------------------- %------------------------------------------------------------------- %'uv_ncbrowser': interactively calls the netcdf file browser 'get_field.m' function ncbrowser_uvmat(hObject, eventdata) %------------------------------------------------------------------- bla=get(gcbo,'String'); ind=get(gcbo,'Value'); filename=cell2mat(bla(ind)); blank=find(filename==' '); filename=filename(1:blank-1); get_field(filename) % ------------------------------------------------------------------ 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) %------------------------------------------------------------------- global nb_transform menu=get(handles.TransformName,'String'); ind_coord=get(handles.TransformName,'Value'); coord_option=menu{ind_coord}; list_transform=get(handles.TransformName,'UserData'); ff=functions(list_transform{end}); if isequal(coord_option,'more...'); coord_fct=''; prompt = {'Enter the name of the transform function'}; dlg_title = 'user defined transform'; num_lines= 1; [FileName, PathName, filterindex] = uigetfile( ... {'*.m', ' (*.m)'; '*.m', '.m files '; ... '*.*', 'All Files (*.*)'}, ... 'Pick a file', ff.file); if isequal(PathName(end),'/')||isequal(PathName(end),'\') PathName(end)=[]; end transform_selected =fullfile(PathName,FileName); if ~exist(transform_selected,'file') return end [ppp,transform,xt_fct]=fileparts(FileName);% removes extension .m if ~isequal(ext_fct,'.m') msgbox_uvmat('ERROR','a Matlab function .m must be introduced'); return end menu=update_menu(handles.TransformName,transform);%add the selected fct to the menu ind_coord=get(handles.TransformName,'Value'); addpath(PathName) list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function set(handles.TransformName,'UserData',list_transform) rmpath(PathName) % 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_transform+1:numel(list_transform) ff=functions(list_transform{ilist}); transform_fct{ilist-nb_transform}=ff.file; end save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat end end %check the current ActionPath to the selected function if ~isempty(list_transform{ind_coord}) func=functions(list_transform{ind_coord}); set(handles.TransformPath,'String',fileparts(func.file)); %show the path to the senlected function else set(handles.TransformPath,'String',''); %show the path to the senlected function end % -------------------------------------------------------------------- function MenuExportConfig_Callback(hObject, eventdata, handles) global Series [tild,Series,errormsg]=prepare_jobs(handles,0); % Series=read_GUI(handles.series); evalin('base','global Series')%make CurData global in the workspace display('current series config :') evalin('base','Series') %display CurData in the workspace commandwindow; %brings the Matlab command window to the front % --- Executes on selection change in RunMode. function RunMode_Callback(hObject, eventdata, handles) % --- Executes on selection change in Coord_x. function Coord_x_Callback(hObject, eventdata, handles) % --- Executes on selection change in Coord_y. function Coord_y_Callback(hObject, eventdata, handles) % --- Executes when 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 and MaxIndex set(handles.MinIndex,'Unit','pixel') Pos=get(handles.MinIndex,'Position'); set(handles.MinIndex,'Unit','normalized') ColumnWidth=get(handles.MinIndex,'ColumnWidth'); if numel(ColumnWidth)==2 ColumnWidth=num2cell(floor([0.5 0.5]*(Pos(3)-20))); else ColumnWidth={Pos(3)-5}; end set(handles.MinIndex,'ColumnWidth',ColumnWidth) set(handles.MaxIndex,'ColumnWidth',ColumnWidth) %% TimeTable set(handles.TimeTable,'Unit','pixel') Pos=get(handles.TimeTable,'Position'); set(handles.TimeTable,'Unit','normalized') ColumnWidth=get(handles.TimeTable,'ColumnWidth'); ColumnWidth=num2cell(floor([0.25 0.25 0.25 0.25]*(Pos(3)-20))); set(handles.TimeTable,'ColumnWidth',ColumnWidth) %% PairString set(handles.PairString,'Unit','pixel') Pos=get(handles.PairString,'Position'); set(handles.PairString,'Unit','normalized') set(handles.PairString,'ColumnWidth',{Pos(3)-5})