%'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 transform_fct (menu for coordinate transforms) % .menu_coord_val: value for transform_fct (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,'ColumnEditable',logical(0)) set(handles.PairString,'ColumnFormat',{'char'}) set(handles.PairString,'ColumnWidth',{60}) set(handles.PairString,'Data',{''}) % set(0,'Units','pixels') % screensize=get(0,'ScreenSize'); %screen size in pixels set(hObject,'WindowButtonDownFcn',{'mouse_down'})%allows mouse action with right button (zoom for uicontrol display) %set(hObject,'Position',[150 100 1000 600] );%position and size in pixels (get adjusted to the screen size in case of excess) %load the list of previously browsed files in menus Open and Open_1 dir_perso=prefdir; test_profil_perso=0; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') h=load (profil_perso); test_profil_perso=1; if isfield(h,'MenuFile_1') set(handles.MenuFile_1,'Label',h.MenuFile_1); set(handles.MenuFile_insert_1,'Label',h.MenuFile_1); end if isfield(h,'MenuFile_1') set(handles.MenuFile_2,'Label',h.MenuFile_2); set(handles.MenuFile_insert_2,'Label',h.MenuFile_2); end if isfield(h,'MenuFile_1') set(handles.MenuFile_3,'Label',h.MenuFile_3); set(handles.MenuFile_insert_3,'Label',h.MenuFile_3); end if isfield(h,'MenuFile_1') set(handles.MenuFile_4,'Label',h.MenuFile_4); set(handles.MenuFile_insert_4,'Label',h.MenuFile_4); end if isfield(h,'MenuFile_1') set(handles.MenuFile_5,'Label',h.MenuFile_5); set(handles.MenuFile_insert_5,'Label',h.MenuFile_5); end end %check default input data if ~exist('param','var') param=[]; %default end %% file name and browser initialisation if isfield(param,'menu_coord_str') set(handles.transform_fct,'String',param.menu_coord_str) end if isfield(param,'menu_coord_val') set(handles.transform_fct,'Value',param.menu_coord_val); else set(handles.transform_fct,'Value',1);%default end if isfield(param,'FileName') 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 %% fields input initialisation if isfield(param,'list_fields')&& isfield(param,'index_fields') &&~isempty(param.list_fields) &&~isempty(param.index_fields) set(handles.FieldMenu,'String',param.list_fields);% list menu fields set(handles.FieldMenu,'Value',param.index_fields);% selected string index FieldCell{1}=param.list_fields{param.index_fields}; end %loads the information stored in prefdir to initiate the list of ACTION 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={'';'phys';'px';'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 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.ACTION,'String',fct_menu) set(handles.ACTION,'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.transform_fct,'String',menu_str) set(handles.transform_fct,'UserData',fct_handle)% store the list of path in UserData of ACTION % display the GUI for the default action 'check_data_files' ACTION_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ % --- 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 action 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'); RootPathCell=InputTable(:,1); SubDirCell=InputTable(:,2); RootFileCell=InputTable(:,3); 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},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 sizf=size(fileinput); if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end [path,name,ext]=fileparts(fileinput); SeriesData=[];%dfault if isequal(ext,'.xml') msgbox_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer 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) %update list of recent files in the menubar MenuFile_1=fileinput; MenuFile_2=get(handles.MenuFile_1,'Label'); MenuFile_3=get(handles.MenuFile_2,'Label'); MenuFile_4=get(handles.MenuFile_3,'Label'); MenuFile_5=get(handles.MenuFile_4,'Label'); set(handles.MenuFile_1,'Label',MenuFile_1) set(handles.MenuFile_2,'Label',MenuFile_2) set(handles.MenuFile_3,'Label',MenuFile_3) set(handles.MenuFile_4,'Label',MenuFile_4) set(handles.MenuFile_5,'Label',MenuFile_5) set(handles.MenuFile_insert_1,'Label',MenuFile_1) set(handles.MenuFile_insert_2,'Label',MenuFile_2) set(handles.MenuFile_insert_3,'Label',MenuFile_3) set(handles.MenuFile_insert_4,'Label',MenuFile_4) set(handles.MenuFile_insert_5,'Label',MenuFile_5) dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat else txt=ver('MATLAB'); Release=txt.Release; relnumb=str2num(Release(3:4)); if relnumb >= 14 save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat else save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat end end 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); % RootPathCell=get(handles.RootPath,'String'); % RootFileCell=get(handles.RootFile,'String'); 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,1) end % -------------------------------------------------------------------- function MenuFile_insert_1_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- fileinput=get(handles.MenuFile_insert_1,'Label'); display_file_name(handles,fileinput,1) % -------------------------------------------------------------------- function MenuFile_insert_2_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- fileinput=get(handles.MenuFile_insert_2,'Label'); display_file_name(handles,fileinput,1) % -------------------------------------------------------------------- function MenuFile_insert_3_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- fileinput=get(handles.MenuFile_insert_3,'Label'); display_file_name( handles,fileinput,1) % -------------------------------------------------------------------- function MenuFile_insert_4_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- fileinput=get(handles.MenuFile_insert_4,'Label'); display_file_name( handles,fileinput,1) % -------------------------------------------------------------------- function MenuFile_insert_5_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- fileinput=get(handles.MenuFile_insert_5,'Label'); display_file_name(handles,fileinput,1) %------------------------------------------------------------------------ % --- Executes when entered data in editable cell(s) in InputTable. function InputTable_CellEditCallback(hObject, eventdata, handles) %------------------------------------------------------------------------ iview=eventdata.Indices(1); InputTable=get(handles.InputTable,'Data'); filename=fullfile(InputTable{iview,1},InputTable{iview,2},[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]) display_file_name(handles,fileinput,0) % hObject handle to InputTable (see GCBO) % eventdata structure with the following fields (see UITABLE) % Indices: row and column indices of the cell(s) edited % PreviousData: previous data for the cell(s) edited % EditData: string(s) entered by the user % NewData: EditData or its converted form set on the Data property. Empty if Data was not changed % Error: error string when failed to convert EditData to appropriate value for Data % handles structure with handles and user data (see GUIDATA) % check_lines=get(handles.REFRESH_INDICES,'UserData'); % check_lines(eventdata.Indices(1))=1; %select the edited line for refresh % set(handles.REFRESH_INDICES,'UserData',check_lines); % set(handles.REFRESH_INDICES,'Visible','on') %InputTable=get(handles.InputTable,'Data') %------------------------------------------------------------------------ % --- refresh the GUI data after introduction of a new file % INPUT: % handles: handles of the elements in the GUI series % fileinput: name of the input file % append: =0 to refresh the list of file series, =1 to append a new series to the list (from the menu bar option 'Open_insert') function display_file_name(handles,fileinput,append) %------------------------------------------------------------------------ %% 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.RootPath,'BackgroundColor',[1 1 0]) % set RootPath edit box to yellow 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 append % display the input data as a new line in the table lastview=size(InputTable,1)+1; InputTable(lastview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}]; set(handles.ListView,'String',[get(handles.ListView,'String');{num2str(lastview)}]) set(handles.ListView,'Value',lastview) % check_lines=get(handles.REFRESH_INDICES,'UserData'); else % or re-initialise the list of input file series lastview=1; InputTable=[{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 set(handles.InputTable,'Data',InputTable) % check_lines(lastview)=1; %select the edited line for refresh % set(handles.REFRESH_INDICES,'UserData',check_lines); %% refresh menus with info from the new series: TODO:check %REFRESH_INDICES_Callback([],[], handles) %% 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 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(FileName,MenuFile); if isempty(find(str_find,1)) MenuFile=[{FileName};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,lastview); %------------------------------------------------------------------------ % --- Update information about a new field series (indices to scan, timing, % calibration from an xml file, then refresh current plots function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,VideoObject,iview) %------------------------------------------------------------------------ %% enable j index visibility if isempty(j1_series) state='off'; else state='on'; end enable_j(handles,state) %% display the min and max indices for all the file series 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_i=min(i1_series(i1_series>0)); % if ~isempty(i2_series) % MaxIndex_i=max(i2_series(i2_series>0)); % else % MaxIndex_i=max(i1_series(i1_series>0)); % end % MinIndex_j=min(j1_series(j1_series>0)); % if ~isempty(j2_series) % MaxIndex_j=max(j2_series(j2_series>0)); % else % MaxIndex_j=max(j1_series(j1_series>0)); % end i_sum=sum(sum(i1_series,2),3); MaxIndex_i=max(find(i_sum>0))-1; MinIndex_i=min(find(i_sum>0))-1; j_sum=sum(sum(i1_series,1),3); MaxIndex_j=max(find(j_sum>0))-1; MinIndex_j=min(find(j_sum>0))-1; 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; end first_j=str2num(get(handles.num_first_j,'String')); if isempty(first_j) first_j=ref_j; elseif first_j MaxIndex_i last_i=MaxIndex_i; end last_j=str2num(get(handles.num_first_j,'String')); if isempty(last_j) last_j=ref_j; elseif last_j>MaxIndex_j last_j=MaxIndex_j; end set(handles.num_first_i,'String',num2str(first_i)); set(handles.num_first_j,'String',num2str(first_j)); set(handles.num_last_i,'String',num2str(last_i)); set(handles.num_last_j,'String',num2str(last_j)); %% read timing and total frame number from the current file (movie files) !! may be overrid by xml file InputTable=get(handles.InputTable,'Data'); FileBase=fullfile(InputTable{iview,1},InputTable{iview,3}); time=[];%default % case of movies if strcmp(InputTable{iview,4},'*') if ~isempty(VideoObject) imainfo=get(VideoObject); time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames-1)/imainfo.FrameRate)'; set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec ColorType='truecolor'; elseif ~isempty(imformats(regexprep(InputTable{iview,5},'^.',''))) || isequal(InputTable{iview,5},'.vol')%&& isequal(NomType,'*')% multi-frame image if ~isempty(InputTable{iview,2}) imainfo=imfinfo(fullfile(InputTable{iview,1},InputTable{iview,2},[InputTable{iview,3} InputTable{iview,5}])); else imainfo=imfinfo([FileBase InputTable{iview,5}]); end ColorType=imainfo.ColorType;%='truecolor' for color images if length(imainfo) >1 %case of image with multiple frames nbfield=length(imainfo); nbfield_j=1; end end end %% read image documentation file if found%%%%%%%%%%%%%%%%%%%%%%%%%%% ext_imadoc=''; if exist([FileBase '.xml'],'file') ext_imadoc='.xml'; elseif exist([FileBase '.civ'],'file') ext_imadoc='.civ'; end %read the ImaDoc file XmlData=[]; NbSlice_calib={}; if isequal(ext_imadoc,'.xml') [XmlData,warntext]=imadoc2struct([FileBase '.xml']); 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 elseif isequal(ext_imadoc,'.civ') [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']); time=XmlData.Time; if error==2, warntext=['no file ' FileBase '.civ']; elseif error==1, warntext='inconsistent number of fields in the .civ file'; end end %% update time table TimeTable=get(handles.TimeTable,'Data'); if isempty(MinIndex_j) TimeTable{iview,1}=time(MinIndex_i); TimeTable{iview,2}=time(first_i); TimeTable{iview,3}=time(last_i); TimeTable{iview,4}=time(MaxIndex_i); elseif ~isempty(time) TimeTable{iview,1}=time(MinIndex_i,MinIndex_j); TimeTable{iview,2}=time(first_i,first_j); TimeTable{iview,3}=time(last_i,last_j); TimeTable{iview,4}=time(MaxIndex_i,MaxIndex_j); end set(handles.TimeTable,'Data',TimeTable) %% number of slices if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord') siz=size(XmlData.GeometryCalib.SliceCoord); if siz(1)>1 NbSlice=siz(1); else NbSlice=1; end set(handles.num_NbSlice,'String',num2str(NbSlice)) end %% update pair menus ListView=get(handles.ListView,'String'); ListView{iview}=num2str(iview); set(handles.ListView,'String'); set(handles.ListView,'Value',iview) update_mode(handles,i1_series,i2_series,j1_series,j2_series,time) %% display the set of existing files as an image set(handles.waitbar_frame,'Units','pixels') pos=get(handles.waitbar_frame,'Position'); xima=0.5:pos(3)-0.5;% pixel positions on the image representing the existing file indices yima=0.5:pos(4)-0.5; [XIma,YIma]=meshgrid(xima,yima); nb_i=size(i1_series,1); nb_j=size(i1_series,2); ind_i=(0.5:nb_i-0.5)*pos(3)/nb_i; ind_j=(0.5:nb_j-0.5)*pos(4)/nb_j; [Ind_i,Ind_j]=meshgrid(ind_i,ind_j); CData=zeros([size(XIma) 3]); file_ima=double((i1_series(:,:,1)>0)'); if numel(file_ima)>=2 if size(file_ima,1)==1 CLine=interp1(ind_i,file_ima,xima,'nearest'); CData(:,:,2)=ones(size(yima'))*CLine; else CData(:,:,2)=interp2(Ind_i,Ind_j,file_ima,XIma,YIma,'nearest'); end set(handles.waitbar_frame,'CData',CData) end set(handles.waitbar_frame,'Units','normalized') %% enable field and veltype menus SeriesData=get(handles.series,'UserData'); SeriesData.FileType{iview}=FileType; check_civ=0; check_netcdf=0; for iview=1:length(SeriesData.FileType) switch SeriesData.FileType{iview} case {'civx','civdata'} check_civ=check_civ+1; case 'netcdf' check_netcdf=check_netcdf+1; end end if check_civ enable='on'; else enable='off'; end set(handles.VelTypeMenu,'Visible',enable) set(handles.VelType_text,'Visible',enable) if check_civ>=2 enable='on'; else enable='off'; end set(handles.VelTypeMenu_1,'Visible',enable) set(handles.VelType_text_1,'Visible',enable) if check_civ || check_netcdf enable='on'; else enable='off'; end set(handles.FieldMenu,'Visible',enable) set(handles.Field_text,'Visible',enable) if check_civ+ check_netcdf>=2 enable='on'; else enable='off'; end set(handles.FieldMenu_1,'Visible',enable) set(handles.Field_text_1,'Visible',enable) FieldString={''}; if check_civ FieldString=[calc_field;{'get_field...'}]; elseif check_netcdf FieldString={'get_field...'}; end set(handles.FieldMenu,'String',FieldString) FieldString={''}; if check_civ>=2 FieldString=[calc_field;{'get_field...'}]; elseif check_civ+check_netcdf>=2 FieldString={'get_field...'}; end set(handles.FieldMenu_1,'String',{'get_field...'}) % testfield=isequal(get(handles.FieldMenu,'enable'),'on'); % testfield_1=isequal(get(handles.FieldMenu_1,'enable'),'on'); % testveltype=isequal(get(handles.VelTypeMenu,'enable'),'on'); % testveltype_1=isequal(get(handles.VelTypeMenu_1,'enable'),'on'); % testtransform=isequal(get(handles.transform_fct,'Enable'),'on'); % testnc=0; % testnc_1=0; % testcivx=0; % testcivx_1=0; % testima=0; %test for image input % if isequal(lower(FileExt),'.avi') %.avi file % testima=1; % elseif ~isempty(imformats(FileExt(2:end))) % testima=1; % elseif isequal(FileExt,'.vol') % testima=1; % end %TODO: update % if length(FileExtCell)==1 || length(FileExtCell)>2 % for iview=1:length(FileExtCell) % if isequal(FileExtCell{iview},'.nc') % testnc=1; % end % if isequal(FileTypeCell{iview},'civx') % testcivx=1; % end % end % elseif length(FileExtCell)==2 % testnc=isequal(FileExtCell{1},'.nc'); % testnc_1=isequal(FileExtCell{2},'.nc'); % testcivx=isequal(FileTypeCell{1},'civx'); % testcivx_1=isequal(FileTypeCell{2},'civx'); % end % switch FileType % case {'civx','civdata'} % view_FieldMenu(handles,'on') % menustr=get(handles.FieldMenu,'String'); % if isequal(menustr,{'get_field...'}) % set(handles.FieldMenu,'String',{'get_field...';'velocity';'vort';'div';'more...'}) % end % set(handles.VelTypeMenu,'Visible','on') % set(handles.FieldTransform,'Visible','on') % % view_TRANSFORM(handles,'on') % % TODO: second menu % % view_FieldMenu_1(handles,'on') % % if testcivx_1 % % menustr=get(handles.FieldMenu_1,'String'); % % if isequal(menustr,{'get_field...'}) % % set(handles.FieldMenu_1,'String',{'get_field...';'velocity';'vort';'div';'more...'}) % % end % % else % % set(handles.FieldMenu_1,'Value',1) % % set(handles.FieldMenu_1,'String',{'get_field...'}) % % set(handles.VelTypeMenu_1,'Visible','on') % % set(handles.VelType_text_1,'Visible','on'); % % end % % view_FieldMenu_1(handles,'off') % case 'netcdf' % view_FieldMenu(handles,'on') % set(handles.FieldMenu,'Value',1) % set(handles.FieldMenu,'String',{'get_field...'}) % set(handles.FieldTransform,'Visible','off') % % view_TRANSFORM(handles,'off') % case {'image','multimage','video'} % view_FieldMenu(handles,'off') % view_FieldMenu_1(handles,'off') % set(handles.VelTypeMenu,'Visible','off') % set(handles.VelType_text,'Visible','off'); % end %% store 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}=FileType; SeriesData.Time{iview}=time; set(handles.series,'UserData',SeriesData) return %% set default options in menu 'Fields'%% TODO: check VelType if ~testima testcivx=0; if isfield(UvData,'FieldsString') && isequal(UvData.FieldsString,{'get_field...'})% field menu defined as input (from get_field) set(handles_Fields,'Value',1) set(handles_Fields,'String',{'get_field...'}) UvData=rmfield(UvData,'FieldsString'); else Data=nc2struct(FileName,'ListGlobalAttribute','Conventions','absolut_time_T0','civ'); if strcmp(Data.Conventions,'uvmat/civdata') ||( ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0))%if the new input is Civx FieldList=calc_field; set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data set(handles_Fields,'Value',2) % set menu to 'velocity' col_vec=FieldList; col_vec(1)=[];%remove 'velocity' option for vector color (must be a scalar) testcivx=1; end if ~testcivx set(handles_Fields,'Value',1) % set menu to 'get_field... set(handles_Fields,'String',{'get_field...'}) col_vec={'get_field...'}; end set(handles.ColorScalar,'String',col_vec) end end set(handles.uvmat,'UserData',UvData) %% set index navigation options and refresh plots scan_option='i';%default state_j='off'; %default if index==2 if get(handles.scan_j,'Value') scan_option='j'; %keep the scan option for the second fiel series end if strcmp(get(handles.j1,'Visible'),'on') state_j='on'; end end if ~isempty(j1_series) state_j='on'; if isequal(nbfield,1) &&index==1 scan_option='j'; %scan j index by default if nbfield=1 end end if isequal(scan_option,'i') set(handles.scan_i,'Value',1) scan_i_Callback([],[], handles); else set(handles.scan_j,'Value',1) scan_j_Callback([],[], handles); end set(handles.scan_j,'Visible',state_j) set(handles.j1,'Visible',state_j) set(handles.j2,'Visible',state_j) set(handles.last_j,'Visible',state_j); set(handles.frame_j,'Visible',state_j); set(handles.j_text,'Visible',state_j); if ~isempty(i2_series)||~isempty(j2_series) set(handles.CheckFixPair,'Visible','on') elseif index==1 set(handles.CheckFixPair,'Visible','off') end mode_Callback(hObject, eventdata, handles) set(handles.REFRESH_INDICES,'BackgroundColor',[0.7 0.7 0.7]) InputTable=get(handles.InputTable,'Data'); check_lines=get(handles.REFRESH_INDICES,'UserData'); %% check the indices and FileTypes for each series (limited to the new ones to save time) for ind_list=1:length(check_lines) if check_lines(ind_list) InputLine=InputTable(ind_list,:); detect_idem=strcmp('"',InputLine);% look for '" (repeat of previous data) detect_idem=detect_idem(detect_idem>0); if ~isempty (detect_idem) InputLine(detect_idem)=InputTable(ind_list-1,detect_idem); set(handles.InputTable,'Data',InputTable) end fileinput=fullfile_uvmat(InputLine{1},InputLine{2},InputLine{3},InputLine{5},InputLine{4},1,2,1,2); %fileinput=name_generator(fullfile(InputLine{1},InputLine{3}),1,1,InputLine{5},InputLine{4},1,2,2,InputLine{2}) %update file series defined by the selected line [InputTable{ind_list,3},InputTable{(ind_list),4},errormsg]=update_indices(handles,fileinput,ind_list); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) return end end end set(handles.InputTable,'Data',InputTable) SeriesData=get(handles.series,'UserData'); state_j='off'; state_Pairs='off'; state_InputFields='off'; val=get(handles.ListView,'Value'); ListViewString={''}; if ~isempty(SeriesData) % ListViewString={}; for iview=1:size(InputTable,1) if ~isempty(SeriesData.j1_series{iview}) state_j='on'; end if ~isempty(SeriesData.i2_series{iview})||~isempty(SeriesData.j2_series{iview}) state_Pairs='on'; ListViewString{iview}=num2str(iview); if check_lines(iview) val=iview;%select the last pair if it is a new entry end end if strcmp(SeriesData.FileType{iview},'civx')||strcmp(SeriesData.FileType{iview},'civdata') state_InputFields='on'; end end end set(handles.ListView,'Value',val) set(handles.ListView,'String',ListViewString) if strcmp(state_Pairs,'on') ListView_Callback(hObject,eventdata,handles) end set(handles.PairString,'Visible',state_Pairs) enable_j(handles,state_j) %------------------------------------------------------------------------ % --- 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 string=list_pair{get(handles.ListPairs,'Value')}; string=regexprep(string,',.*','');%removes time indication (after ',') 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 pair menu to display if isempty(i2_series) set(handles.mode,'String',{''}) else set(handles.mode,'Value',1) set(handles.mode,'String',{'series(Di)'}) end else nbfield=size(j2_series,1); nbfield2=size(j2_series,2); set(handles.mode,'String',{'bursts';'series(Dj)'}) if nbfield2>10 || nbfield==1 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 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') enable_j(handles,'On') 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')); ref_j=str2num(get(handles.num_ref_j,'String')); if isempty(ref_i) ref_i=1; end if isempty(ref_j) 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) 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) 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 %% 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) if isempty(displ_pair) msgbox_uvmat('ERROR',['no file available for the selected subdirectory ' SubDir]) end % return % %%%%%%%% % %update num_first_i and num_last_i according to the chosen image pairstring % testupdate=0; % % SeriesData=get(handles.series,'UserData'); % NomType=SeriesData.NomType{Val}; % list_pair=get(handles.ListPairs,'String');%get the menu of image pairs % index_pair=get(handles.ListPairs,'Value'); % str_pair=list_pair{index_pair}; % ind_equ=strfind(str_pair,'=');%find '=' % ind_sep=strfind(str_pair,'|');%find pair separator '|' % ind_com=strfind(str_pair,':');%find ':' % test_bursts=0; % if isempty(ind_sep) % ind_sep=strfind(str_pair,'-');%find pair separator if it is not '|' % test_bursts=1;% we are in the case of bursts % end % displ_num=[0 0 0 0]; %default % if ~isempty(ind_sep)&& ~strcmp(str_pair(ind_sep-1),'*')% if there is a pair separator ('|' or '-') % num1_str=str_pair(ind_equ(1)+1:ind_sep-1); % num2_str=str_pair(ind_sep+1:ind_com-1); % num1=str2double(num1_str); % num2=str2double(num2_str); % if isequal(num1_str(1),' ') % num1_str(1)=[]; % end % if isequal(num2_str(end),' ') % num2_str(end)=[]; % end % switch NomType % case {'_1-2_1'} % if isequal(num1_str(1),'0') % IndexCell{Val}=['_(i-(i+' num2_str ')_j']; % else % IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')_j']; % end % displ_num(3)=num1; % displ_num(4)=num2; % case {'_1-2'} % if isequal(num1_str(1),'0') % IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')']; % else % IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')']; % end % displ_num(3)=num1; % displ_num(4)=num2; % case '_1_1-2' % if test_bursts % IndexCell{Val}=['_i_' num1_str '-' num2_str ]; % else % if isequal(num1_str(1),'0') % IndexCell{Val}=['_i_j-(j+' num2_str ')']; % else % IndexCell{Val}=['_i_(j' num1_str ')-(j+' num2_str ')']; % end % end % displ_num(1)=num1; % displ_num(2)=num2; % case {'#_ab'} %TO COMPLETE % IndexCell{Val}=['_i_' num1_str '-' num2_str ]; % % end % end % set(handles.NomType,'String',IndexCell) % SeriesData.displ_num(Val,:)=displ_num; % set(handles.series,'UserData',SeriesData) % % set(handles.NomType,'Value',Val) % % if ~isequal(str_pair,'Dj=*|*')&~isequal(str_pair,'Di=*|*') % mode_list=get(handles.mode,'String'); % mode_value=get(handles.mode,'Value'); % mode=mode_list{mode_value}; % if isequal(mode,'series(Di)') % first_i=str2num(get(handles.num_first_i,'String')); % last_i=str2num(get(handles.num_last_i,'String')); % incr_i=str2num(get(handles.num_incr_i,'String')); % num1=first_i:incr_i:last_i; % lastfieldCell=get(handles.num_MaxIndex_i,'String'); % lastfield=str2num(lastfieldCell{1}); % if ~isempty(lastfield) % ind=find((num1-floor(index_pair/2)*ones(size(num1))>0)& (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield)); % num1=num1(ind); % end % if ~isempty(num1) % set(handles.num_first_i,'String',num2str(num1(1))); % set(handles.num_last_i,'String',num2str(num1(end))); % end % testupdate=1; % elseif isequal(mode,'series(Dj)') % first_j=str2num(get(handles.num_first_j,'String')); % last_j=str2num(get(handles.num_last_j,'String')); % incr_j=str2num(get(handles.num_incr_j,'String')); % num_j=first_j:incr_j:last_j; % lastfieldCell=get(handles.num_MaxIndex_j,'String'); % if ~isempty(lastfieldCell) % lastfield2=lastfieldCell{1}; % ind=find((num_j-floor(index_pair/2)*ones(size(num_j))>0)& ... % (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2)); % end % testupdate=1; % end % % %update the first and last times of the series % if testupdate && isfield(SeriesData,'Time') % if ~isempty(SeriesData.Time{1}) % displ_time(handles); % end % 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) % 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_MinIndex_j,'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_MaxIndex_j,'Visible',state) set(handles.num_ref_j,'Visible',state) set(handles.ref_j_text,'Visible',state) %----------------------------------- function view_FieldMenu(handles,state) % set(handles.FieldMenu,'Visible',state) % set(handles.Field_text,'Visible',state) set(handles.InputFields,'Visible',state) %----------------------------------- function view_FieldMenu_1(handles,state) set(handles.FieldMenu_1,'Visible',state) set(handles.Field_text_1,'Visible',state) % %----------------------------------- % function view_TRANSFORM(handles,state) % set(handles.TRANSFORM_frame,'Visible',state) % set(handles.transform_fct,'Visible',state); % set(handles.TRANSFORM_title,'Visible',state) %list_pair_civ_Callback([],[],handles) %------------------------------------------------------------------------ % --- Executes on button press in RUN. function RUN_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ %% Read parameters from series Series=read_GUI(handles.series);%TODO: extend to all input param Series.hseries=handles.series; % handles to the series GUI %% read root name and field type set(handles.RUN,'BusyAction','queue'); set(0,'CurrentFigure',handles.series) if isequal(get(handles.GetObject,'Visible'),'on') && isequal(get(handles.GetObject,'Value'),1) Series.GetObject=1; GetObject_Callback(hObject, eventdata, handles) else Series.GetObject=0; end % SeriesData=get(handles.series,'UserData'); % Series.hseries=handles.series; % handles to the series GUI first_i=1; last_i=1; incr_i=1; first_j=1; last_j=1; incr_j=1; if isfield(Series.IndexRange,'first_i') first_i=Series.IndexRange.first_i; incr_i=Series.IndexRange.incr_i; last_i=Series.IndexRange.last_i; end if isfield(Series.IndexRange,'first_j') first_j=Series.IndexRange.first_j; incr_j=Series.IndexRange.incr_j; last_j=Series.IndexRange.last_j; end %% read input file parameters and set menus Series.PathProject=get(handles.PathCampaign,'String'); % InputTable=get(handles.InputTable,'Data'); % RootPath=Series.InputTable(:,1); % SubDir=Series.InputTable(:,2); % RootFile=Series.InputTable(:,3); % NomType=Series.InputTable(:,4); % FileExt=Series.InputTable(:,5); % if isempty(SeriesData) % msgbox_uvmat('ERROR','no input file series') % return % end % NomType=SeriesData.NomType; % if length(RootPath)==1 %string character input for user fct % Series.RootPath=RootPath{1}; % Series.RootFile=RootFile{1}; % Series.SubDir=SubDir{1}; % Series.FileExt=FileExt{1}; % Series.NomType=NomType{1}; % else %cell input for user fct % Series.RootPath=RootPath; % Series.RootFile=RootFile; % Series.SubDir=SubDir; % Series.FileExt=FileExt; % Series.NomType=NomType; % end % if isequal(get(handles.FieldMenu,'Visible'),'on') % FieldMenu=get(handles.FieldMenu,'String'); % FieldValue=get(handles.FieldMenu,'Value'); % Series.Field=FieldMenu(FieldValue); % end menu_coord_state=get(handles.transform_fct,'Visible'); Series.CoordType='';%default if isequal(menu_coord_state,'on') % menu_coord=get(handles.transform_fct,'String'); menu_index=get(handles.transform_fct,'Value'); transform_list=get(handles.transform_fct,'UserData'); Series.FieldTransform.fct_handle=transform_list{menu_index};% transform function handles end %reinitiate waitbar position Series.WaitbarPos=get(handles.waitbar_frame,'Position');%TO SUPPRESS waitbarpos=Series.WaitbarPos; waitbarpos(4)=0.005;%reinitialize waitbar to zero height waitbarpos(2)=Series.WaitbarPos(2)+Series.WaitbarPos(4)-0.005; % set(handles.waitbar,'Position',waitbarpos) if isfield(Series.IndexRange,'NbSlice') Series.NbSlice=Series.IndexRange.NbSlice; 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; num_i=first_i:incr_i:last_i; num_j=first_j:incr_j:last_j; % nbfield_cell=get(handles.num_MaxIndex_i,'String'); nbfield=cell2mat(Series.IndexRange.MaxIndex); nb=min(nbfield,1); % nbfield=nb(1); % nbfield2=nb(2); %get complementary information from the 'series' interface list_action=get(handles.ACTION,'String');% list menu action index_action=get(handles.ACTION,'Value');% selected string index action= list_action{index_action}; % selected string mode_list=get(handles.mode,'String'); index_mode=get(handles.mode,'Value'); mode=mode_list{index_mode}; ind_shift=0;%default %% defining the ACTION function handle path_series=which('series'); list_path=get(handles.ACTION,'UserData'); index=get(handles.ACTION,'Value'); fct_path=list_path{index}; %path stored for the function ACTION if ~isequal(fct_path,path_series) eval(['spath=which(''' action ''');']) %spath = current path of the selected function ACTION if ~exist(fct_path,'dir') msgbox_uvmat('ERROR',['The prescibed function path ' fct_path ' does not exist']) return end if ~isequal(spath,fct_path) addpath(fct_path)% add the prescribed path if not the current one end end eval(['h_fun=@' action ';'])%create a function handle for ACTION if ~isequal(fct_path,path_series) rmpath(fct_path)% add the prescribed path if not the current one end %% RUN ACTION Series.Action=action;%name of the processing programme set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784]) h_fun(Series); % if length(RootPath)>1 % h_fun(i1_series_cell,i2_series_cell,j1_series_cell,j2_series_cell,Series); % else % h_fun(i1_series,i2_series,j1_series,j2_series,Series); % end set(handles.RUN,'BackgroundColor',[1 0 0]) % %save the current interface setting as figure namefig, append .0 to the name if it already exists % detect=1; % while detect==1 % namefigfull=[namedoc '.fig']; % hh=dir(namefigfull); % if ~isempty(hh) % detect=1; % namedoc=[namedoc '.0']; % else % detect=0; % end % end % saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER .xml) %------------------------------------------------------------------------ function STOP_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.RUN, 'BusyAction','cancel') set(handles.RUN,'BackgroundColor',[1 0 0]) %------------------------------------------------------------------------ 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)) ref_j_Callback(hObject, eventdata, handles) SeriesData=get(handles.series,'UserData'); if ~isfield(SeriesData,'Time') SeriesData.Time{1}=[]; end displ_time(handles); % NomTypeCell=SeriesData.NomType; % if ~isempty(NomTypeCell) % Val=get(handles.NomType,'Value'); % NomType=NomTypeCell{Val}; % if isequal(NomType,'_1_1-2')|| isequal(NomType,'_1-2_1')|| isequal(NomType,'_1-2') % if isequal(mode,'series(Dj)') % fill_ListPair(handles,Val);% update the menu of pairstring depending on the available netcdf files % end % end % end %------------------------------------------------------------------------ % ---- 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'))]; % last_i=str2num(get(handles.num_last_i,'String')); % last_j=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.list_pair_civ,'(?\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) % % NomType=InputTable(:,4); % mode_list=get(handles.mode,'String'); % index_mode=get(handles.mode,'Value'); % % mode=mode_list{index_mode}; % % time_first=[]; % time_last=[]; % if ~isfield(SeriesData,'Time') % SeriesData.Time{1}=[]; % end % TimeTable=get(handles.TimeTable,'Data'); % for iview=1:size(TimeTable,1) % time_first_cell{iview}='?'; % time_last_cell{iview}='?';%default % time=SeriesData.Time{iview}; % if isequal(NomType{iview},'_1-2_1')|isequal(NomType{iview},'_1_1-2')|isequal(NomType{iview},'#_ab')|isequal(NomType{iview},'_1-2') % if isfield(SeriesData,'displ_num')& ~isempty(SeriesData.displ_num) % ind_shift=SeriesData.displ_num(iview,:); % if isequal(mode,'bursts') % first_j=0; % last_j=0; % end % first_i1=first_i +ind_shift(3); % first_i2 =first_i +ind_shift(4); % first_j1 =first_j +ind_shift(1); % first_j2 =first_j +ind_shift(2); % last_i1=last_i +ind_shift(3); % last_i2 =last_i +ind_shift(4); % last_j1 =last_j +ind_shift(1); % last_j2 =last_j +ind_shift(2); % siz=size(SeriesData.Time{1}); % if first_i1>=1 && first_j1>=1 && siz(1)>=last_i2 && siz(2)>=last_j2 % time_first=(time(first_i1,first_j1)+time(first_i2,first_j2))/2; % time_last=(time(last_i1,last_j1)+time(last_i2,last_j2))/2; % else%read the time in the nc files % RootPath=get(handles.RootPath,'String'); % RootFile=get(handles.RootFile,'String'); % SubDir=get(handles.SubDir,'String'); % %VelType=get(handles.VelType,'String'); % VelType_str=get(handles.VelTypeMenu,'String'); % VelType_val=get(handles.VelTypeMenu,'Value'); % VelType=VelType_str{VelType_val}; % filebase=fullfile(RootPath{1},RootFile{1}); % [filefirst]=name_generator(filebase,first_i1,first_j1,'.nc',NomType{iview},1,first_i2,first_j2,SubDir{iview}); % if exist(filefirst,'file') % Attrib=nc2struct(filefirst,[]); % if isfield(Attrib,'Time') % time_first=Attrib.Time; % else % if isfield(Attrib,'absolut_time_T0') % time_first=Attrib.absolut_time_T0; % end % if isfield(Attrib,'absolut_time_T0_2')&&~(isequal(VelType,'civ1')||isequal(VelType,'interp1')||isequal(VelType,'filter1')) % time_first=Attrib.absolut_time_T0_2; % end % end % end % [filelast]=name_generator(filebase,last_i1,last_j1,'.nc',NomType{iview},1,last_i2,last_j2,SubDir{iview}); % if exist(filelast,'file') % Attrib=nc2struct(filelast,[]); % if isfield(Attrib,'Time') % time_last=Attrib.Time; % else % if isfield(Attrib,'absolut_time_T0') % time_last=Attrib.absolut_time_T0; % end % if isfield(Attrib,'absolut_time_T0_2')&&~(isequal(VelType,'civ1')||isequal(VelType,'interp1')||isequal(VelType,'filter1')) % time_last=Attrib.absolut_time_T0_2; % end % end % end % end % end % else % siz=size(time); % if siz(1)>=last_i && siz(2)>=last_j && first_i>=1 && first_j>=1 % time_first=times(first_i,first_j); % time_last=times(last_i,last_j); % end % end % time_first_cell{iview}=num2str(time_first,4); % time_last_cell{iview}=num2str(time_last,4); % end % %------------------------------------------------------------------------ % --- Executes on selection change in ACTION. function ACTION_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ global nb_builtin_ACTION list_ACTION=get(handles.ACTION,'String');% list menu fields index_ACTION=get(handles.ACTION,'Value');% selected string index ACTION= list_ACTION{index_ACTION}; % selected function name path_series=which('series');%path to series.m list_path=get(handles.ACTION,'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 action menu menu_str=update_menu(handles.ACTION,ACTION);%new action menu in which the new item has been appended if needed index_ACTION=get(handles.ACTION,'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.ACTION,'Value',index_ACTION) set(handles.ACTION,'String',menu_str) end list_path{index_ACTION}=PathName; set(handles.ACTION,'UserData',list_path); set(handles.path,'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 path to the selected function PathName=list_path{index_ACTION};%current recorded path set(handles.path,'String',PathName); %show the path to the senlected function %default setting for the visibility of the GUI elements % set(handles.RootPath,'UserData','many') % set(handles.SubDir,'Visible','on') % set(handles.RootFile,'Visible','on') % set(handles.NomType,'Visible','on') % set(handles.FileExt,'Visible','on') set(handles.num_NbSlice,'Visible','off') set(handles.NbSlice_title,'Visible','off') set(handles.VelTypeMenu,'Visible','off'); set(handles.VelType_text,'Visible','off'); set(handles.VelTypeMenu_1,'Visible','off'); set(handles.VelType_text_1,'Visible','off'); view_FieldMenu(handles,'off') view_FieldMenu_1(handles,'off') set(handles.FieldTransform,'Visible','off') % view_TRANSFORM(handles,'off')Visible','off') set(handles.Objects,'Visible','off'); set(handles.GetMask,'Visible','off') set(handles.Mask,'Visible','off') % set(handles.GetObject,'Visible','off'); set(handles.OutputDir,'Visible','off'); % set(handles.PARAMETERS_frame,'Visible','off'); % set(handles.PARAMETERS_title,'Visible','off'); set(handles.ParamKey,'Visible','off') set(handles.ParamVal,'Visible','off') ParamKey={}; set(handles.FieldMenu,'Enable','off') set(handles.VelTypeMenu,'Enable','off') set(handles.FieldMenu_1,'Enable','off') set(handles.VelTypeMenu_1,'Enable','off') set(handles.transform_fct,'Enable','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.ACTION,'ToolTipString',InputText{1}{1}) end if ~isequal(path_series,PathName) rmpath(PathName) end varargout=h_function(); Param_list={}; %nb_series=length(RootFile); % FileExt=get(handles.FileExt,'String'); % nb_series=length(FileExt); InputTable=get(handles.InputTable,'Data'); nb_series=size(InputTable,1); % if ~isempty(checkcell) % nb_series=checkcell(end); % end % nb_series=size(InputFiles,1) testima_series=1; %test for a list of images only testima=1; testima_1=1; testciv_series=1; for iview=1:nb_series ext=InputTable{iview,5}; if length(ext)<2 ext='.none'; end testimaview=~isempty(imformats(ext(2:end))) || isequal(lower(ext),'.avi'); if ~testimaview if iview==1 testima=0; end if iview==2 testima_1=0; end testima_series=0; end end for ilist=1:length(varargout)-1 switch varargout{ilist} %RootFile always visible % case 'RootPath' %visible by default % value=lower(varargout{ilist+1}); % if isequal(value,'one')||isequal(value,'two')||isequal(value,'many') % set(handles.RootFile,'UserData',value)% for use in menu Open_insert % end % case 'SubDir' %visible by default % if isequal(lower(varargout{ilist+1}),'off') % set(handles.SubDir,'Visible','off') % end % case 'RootFile' %visible by default % value=lower(varargout{ilist+1}); % if isequal(value,'off') % set(handles.RootFile,'Visible','off') % elseif isequal(value,'one')||isequal(value,'two')||isequal(value,'many') % set(handles.RootFile,'Visible','on') % set(handles.RootFile,'UserData',value)% for use in menu Open_insert % end % case 'NomType' %visible by default % if isequal(lower(varargout{ilist+1}),'off') % set(handles.NomType,'Visible','off') % end % case 'FileExt' %visible by default % if isequal(lower(varargout{ilist+1}),'off') % set(handles.FileExt,'Visible','off') % 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 'VelTypeMenu' %hidden by default if isequal(lower(varargout{ilist+1}),'one') || isequal(lower(varargout{ilist+1}),'two') set(handles.VelTypeMenu,'Enable','on') if nb_series >=1 && ~testima_series set(handles.VelTypeMenu,'Visible','on') set(handles.VelType_text,'Visible','on'); % set(handles.Field_frame,'Visible','on') end end if isequal(lower(varargout{ilist+1}),'two') set(handles.VelTypeMenu_1,'Enable','on') if nb_series >=2 && ~testima_series set(handles.VelTypeMenu_1,'Visible','on') set(handles.VelType_text_1,'Visible','on'); end end case 'FieldMenu' %hidden by default if isequal(lower(varargout{ilist+1}),'one')||isequal(lower(varargout{ilist+1}),'two') set(handles.FieldMenu,'Enable','on') % test for MenuBorser if nb_series >=1 && ~testima_series view_FieldMenu(handles,'on') end end if isequal(lower(varargout{ilist+1}),'two') set(handles.FieldMenu_1,'Enable','on') if nb_series >=2 && ~testima_1 view_FieldMenu_1(handles,'on') end end case 'CoordType' %hidden by default if isequal(lower(varargout{ilist+1}),'on') set(handles.transform_fct,'Enable','on') set(handles.FieldTransform,'Visible','on') % view_TRANSFORM(handles,'on') end case 'GetObject' %hidden by default if isequal(lower(varargout{ilist+1}),'on') set(handles.Objects,'Visible','on') % set(handles.GetObject,'Visible','on'); end case 'Mask' %hidden by default if isequal(lower(varargout{ilist+1}),'on') set(handles.Objects,'Visible','on') % set(handles.GetMask,'Visible','on'); end case 'PARAMETER' set(handles.PARAMETERS_frame,'Visible','on') set(handles.PARAMETERS_title,'Visible','on') set(handles.ParamKey,'Visible','on') %set(handles.ParamVal,'Visible','on') Param_str=varargout{ilist+1}; Param_list=[Param_list; {Param_str}]; end end if ~isempty(Param_list) set(handles.ParamKey,'String',Param_list) set(handles.ParamVal,'Visible','on') end %------------------------------------------------------------------------ % --- Executes on selection change in FieldMenu. function FieldMenu_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ field_str=get(handles.FieldMenu,'String'); field_index=get(handles.FieldMenu,'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,i1_series,i2_series,j1_series,j2_series]=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 action menu scalar=cell2mat(str(ind_answer)); update_menu(handles.FieldMenu,scalar) end %------------------------------------------------------------------------ % --- Executes on selection change in FieldMenu_1. function FieldMenu_1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ field_str=get(handles.FieldMenu_1,'String'); field_index=get(handles.FieldMenu_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 action menu scalar=cell2mat(str(ind_answer)); update_menu(handles.FieldMenu_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 % set(handles.time_first,'Value',1) % set(handles.time_last,'Value',1) % set(handles.time_first,'String',time_first_cell); % set(handles.time_last,'String',time_last_cell); %------------------------------------------------------------------------ % --- Executes on button press in GetObject. function GetObject_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ SeriesData=get(handles.series,'UserData'); value=get(handles.GetObject,'Value'); if value set(handles.GetObject,'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); % t=xmltree(fileinput); % data=convert(t); if ~isfield(data,'Style') data.Style='points'; end if ~isfield(data,'ProjMode') data.ProjMode='projection'; end % data.desable_plot=1; [SeriesData.hset_object,SeriesData.sethandles]=set_object(data);% call the set_object interface end else set(handles.GetObject,'BackgroundColor',[0.7 0.7 0.7])%put activated buttons to green end set(handles.series,'UserData',SeriesData) %-------------------------------------------------------------- function GetMask_Callback(hObject, eventdata, handles) value=get(handles.GetMask,'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 transform_fct. function transform_fct_Callback(hObject, eventdata, handles) %------------------------------------------------------------------- global nb_transform menu=get(handles.transform_fct,'String'); ind_coord=get(handles.transform_fct,'Value'); coord_option=menu{ind_coord}; list_transform=get(handles.transform_fct,'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.transform_fct,transform);%add the selected fct to the menu ind_coord=get(handles.transform_fct,'Value'); addpath(PathName) list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function set(handles.transform_fct,'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 path to the selected function if ~isempty(list_transform{ind_coord}) func=functions(list_transform{ind_coord}); set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function else set(handles.path_transform,'String',''); %show the path to the senlected function end %------------------------------------------------------------------------ % --- Executes on button press in REFRESH_INDICES. function REFRESH_INDICES_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ % hObject handle to REFRESH_INDICES (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) set(handles.REFRESH_INDICES,'BackgroundColor',[0.7 0.7 0.7]) InputTable=get(handles.InputTable,'Data'); check_lines=get(handles.REFRESH_INDICES,'UserData'); %% check the indices and FileTypes for each series (limited to the new ones to save time) for ind_list=1:length(check_lines) if check_lines(ind_list) InputLine=InputTable(ind_list,:); detect_idem=strcmp('"',InputLine);% look for '" (repeat of previous data) detect_idem=detect_idem(detect_idem>0); if ~isempty (detect_idem) InputLine(detect_idem)=InputTable(ind_list-1,detect_idem); set(handles.InputTable,'Data',InputTable) end fileinput=fullfile_uvmat(InputLine{1},InputLine{2},InputLine{3},InputLine{5},InputLine{4},1,2,1,2); %fileinput=name_generator(fullfile(InputLine{1},InputLine{3}),1,1,InputLine{5},InputLine{4},1,2,2,InputLine{2}) %update file series defined by the selected line [InputTable{ind_list,3},InputTable{(ind_list),4},errormsg]=update_indices(handles,fileinput,ind_list); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) return end end end set(handles.InputTable,'Data',InputTable) SeriesData=get(handles.series,'UserData'); state_j='off'; state_Pairs='off'; state_InputFields='off'; val=get(handles.ListView,'Value'); ListViewString={''}; if ~isempty(SeriesData) % ListViewString={}; for iview=1:size(InputTable,1) if ~isempty(SeriesData.j1_series{iview}) state_j='on'; end if ~isempty(SeriesData.i2_series{iview})||~isempty(SeriesData.j2_series{iview}) state_Pairs='on'; ListViewString{iview}=num2str(iview); if check_lines(iview) val=iview;%select the last pair if it is a new entry end end if strcmp(SeriesData.FileType{iview},'civx')||strcmp(SeriesData.FileType{iview},'civdata') state_InputFields='on'; end end end set(handles.ListView,'Value',val) set(handles.ListView,'String',ListViewString) if strcmp(state_Pairs,'on') ListView_Callback(hObject,eventdata,handles) end set(handles.PairString,'Visible',state_Pairs) enable_j(handles,state_j) set(handles.REFRESH_INDICES,'BackgroundColor',[1 0 0]) set(handles.REFRESH_INDICES,'visible','off') % ----------------------------------------------------------------------- % --- Update min and max indices of a file series by scanning with find_file_series % --- which also changes the root file and NomType in case of movie. Also adjust the string representation of indices (e.g; % --- 1 or 001 by the function find_file_series % --- This function also dispaly the set of availbale files in the series % --- and the menus appropriate to the file type as well as timing possibly set % --- by an xml image documentation file function [RootFile,NomType,errormsg]=update_indices(handles,fileinput,iview) % ----------------------------------------------------------------------- %% look for min and max indices existing in the file series and update SeriesData errormsg=''; [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,Object,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 %% adjust the min and max indices common to all the file series MinIndex=get(handles.MinIndex,'Data'); MaxIndex=get(handles.MaxIndex,'Data'); MinIndex_i=min(i1_series(i1_series>0)); if ~isempty(i2_series) MaxIndex_i=max(i2_series(i2_series>0)); else MaxIndex_i=max(i1_series(i1_series>0)); end MinIndex_j=min(j1_series(j1_series>0)); if ~isempty(j2_series) MaxIndex_j=max(j2_series(j2_series>0)); else MaxIndex_j=max(j1_series(j1_series>0)); end 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) set(handles.MaxIndex,'Data',MaxIndex) 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; %% display the set of existing files as an image set(handles.waitbar_frame,'Units','pixels') pos=get(handles.waitbar_frame,'Position'); xima=0.5:pos(3)-0.5;% pixel positions on the image representing the existing file indices yima=0.5:pos(4)-0.5; [XIma,YIma]=meshgrid(xima,yima); nb_i=size(i1_series,1); nb_j=size(i1_series,2); ind_i=(0.5:nb_i-0.5)*pos(3)/nb_i; ind_j=(0.5:nb_j-0.5)*pos(4)/nb_j; [Ind_i,Ind_j]=meshgrid(ind_i,ind_j); CData=zeros([size(XIma) 3]); file_ima=double((i1_series(:,:,1)>0)'); if numel(file_ima)>=2 if size(file_ima,1)==1 CLine=interp1(ind_i,file_ima,xima,'nearest'); CData(:,:,2)=ones(size(yima'))*CLine; else CData(:,:,2)=interp2(Ind_i,Ind_j,file_ima,XIma,YIma,'nearest'); end set(handles.waitbar_frame,'CData',CData) end set(handles.waitbar_frame,'Units','normalized') %% enable field and veltype menus testfield=isequal(get(handles.FieldMenu,'enable'),'on'); testfield_1=isequal(get(handles.FieldMenu_1,'enable'),'on'); testveltype=isequal(get(handles.VelTypeMenu,'enable'),'on'); testveltype_1=isequal(get(handles.VelTypeMenu_1,'enable'),'on'); testtransform=isequal(get(handles.transform_fct,'Enable'),'on'); % testnc=0; % testnc_1=0; % testcivx=0; % testcivx_1=0; % testima=0; %test for image input % if isequal(lower(FileExt),'.avi') %.avi file % testima=1; % elseif ~isempty(imformats(FileExt(2:end))) % testima=1; % elseif isequal(FileExt,'.vol') % testima=1; % end %TODO: update % if length(FileExtCell)==1 || length(FileExtCell)>2 % for iview=1:length(FileExtCell) % if isequal(FileExtCell{iview},'.nc') % testnc=1; % end % if isequal(FileTypeCell{iview},'civx') % testcivx=1; % end % end % elseif length(FileExtCell)==2 % testnc=isequal(FileExtCell{1},'.nc'); % testnc_1=isequal(FileExtCell{2},'.nc'); % testcivx=isequal(FileTypeCell{1},'civx'); % testcivx_1=isequal(FileTypeCell{2},'civx'); % end switch FileType case {'civx','civdata'} view_FieldMenu(handles,'on') menustr=get(handles.FieldMenu,'String'); if isequal(menustr,{'get_field...'}) set(handles.FieldMenu,'String',{'get_field...';'velocity';'vort';'div';'more...'}) end set(handles.VelTypeMenu,'Visible','on') set(handles.FieldTransform,'Visible','on') % view_TRANSFORM(handles,'on') % TODO: second menu % view_FieldMenu_1(handles,'on') % if testcivx_1 % menustr=get(handles.FieldMenu_1,'String'); % if isequal(menustr,{'get_field...'}) % set(handles.FieldMenu_1,'String',{'get_field...';'velocity';'vort';'div';'more...'}) % end % else % set(handles.FieldMenu_1,'Value',1) % set(handles.FieldMenu_1,'String',{'get_field...'}) % set(handles.VelTypeMenu_1,'Visible','on') % set(handles.VelType_text_1,'Visible','on'); % end % view_FieldMenu_1(handles,'off') case 'netcdf' view_FieldMenu(handles,'on') set(handles.FieldMenu,'Value',1) set(handles.FieldMenu,'String',{'get_field...'}) set(handles.FieldTransform,'Visible','off') % view_TRANSFORM(handles,'off') case {'image','multimage','video'} view_FieldMenu(handles,'off') view_FieldMenu_1(handles,'off') set(handles.VelTypeMenu,'Visible','off') set(handles.VelType_text,'Visible','off'); end %TODO:update % if ~isequal(FileExt,'.nc') && ~isequal(FileExt,'.cdf') && ~testima % msgbox_uvmat('ERROR',['invalid input file extension ' FileExt]) % return % end %% read image documentation file if found%%%%%%%%%%%%%%%%%%%%%%%%%%% ext_imadoc=''; FileBase=fullfile(RootPath,RootFile); if isequal(FileExt,'.xml')||isequal(FileExt,'.civ') ext_imadoc=FileExt; elseif exist([FileBase '.xml'],'file') ext_imadoc='.xml'; elseif exist([FileBase '.civ'],'file') ext_imadoc='.civ'; end %read the ImaDoc file XmlData=[]; NbSlice_calib={}; if isequal(ext_imadoc,'.xml') [XmlData,warntext]=imadoc2struct([FileBase '.xml']); 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{iview}=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 elseif isequal(ext_imadoc,'.civ') [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']); time{iview}=XmlData.Time; if error==2, warntext=['no file ' FileBase '.civ']; elseif error==1, warntext='inconsistent number of fields in the .civ file'; end end %% update time table TimeTable=get(handles.TimeTable,'Data') TimeTable{iview,1}=time(MinIndex_i,MinIndex_j); TimeTable{iview,4}=time(MaxIndex_i,MaxIndex_j); set(handles.TimeTable,'Data',TimeTable) %% number of slices if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord') siz=size(XmlData.GeometryCalib.SliceCoord); if siz(1)>1 NbSlice=siz(1); else NbSlice=1; end set(handles.num_NbSlice,'String',num2str(NbSlice)) end % set(handles.mode,'Visible','off') % do not show index pairstring by default set(handles.PairString,'Visible','off') % set(handles.num_ref_i,'Visible','off') % set(handles.ref_i_text,'Visible','off') testpair=0; %set the menus of image pairstring and default selection for series %list pairstring if relevant % Val=get(handles.NomType,'Value'); % synchronise_view(handles,Val) % if ~isfield(SeriesData,'j1_series')||isempty(SeriesData.j1_series{index}) % state_j='off'; %no need for j index % else % state_j='on'; %case of j index % end % show index pairstring if files exist set(handles.series,'UserData',SeriesData) % --- Executes on button press in BATCH. function BATCH_Callback(hObject, eventdata, handles) % hObject handle to BATCH (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) Series=read_GUI(handles.series); t=struct2xml(Series); save(t); %TODO: determine a xml file name % list_action=get(handles.ACTION,'String');% list menu action % index_action=get(handles.ACTION,'Value');% selected string index % action= list_action{index_action}; % selected string %% defining the ACTION function handle path_series=which('series'); list_path=get(handles.ACTION,'UserData'); index=get(handles.ACTION,'Value'); fct_path=list_path{index}; %path stored for the function ACTION if ~isequal(fct_path,path_series) eval(['spath=which(''' action ''');']) %spath = current path of the selected function ACTION if ~exist(fct_path,'dir') msgbox_uvmat('ERROR',['The prescibed function path ' fct_path ' does not exist']) return end if ~isequal(spath,fct_path) addpath(fct_path)% add the prescribed path if not the current one end end eval(['h_fun=@' action ';'])%create a function handle for ACTION if ~isequal(fct_path,path_series) rmpath(fct_path)% add the prescribed path if not the current one end h_fun('BATCH');% TODO modify the called function to read the xml file as input parameter