%'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,'ColumnEditable',logical(0)) set(handles.PairString,'ColumnFormat',{'char'}) set(handles.PairString,'ColumnWidth',{60}) set(handles.PairString,'Data',{''}) 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});']) % eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',h.MenuFile{ifile});']) end end % if isfield(h,'MenuFile') % for ifile=1:min(length(h.MenuFile),5) % eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});']) % eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',h.MenuFile{ifile});']) % end % end test_profil_perso=1; % if isfield(h,'MenuFile_1') && exist(h.MenuFile_1,'file') % set(handles.MenuFile_1,'Label',h.MenuFile_1); % set(handles.MenuFile_insert_1,'Label',h.MenuFile_1); % end % if isfield(h,'MenuFile_2')&& exist(h.MenuFile_2,'file') % set(handles.MenuFile_2,'Label',h.MenuFile_2); % set(handles.MenuFile_insert_2,'Label',h.MenuFile_2); % end % if isfield(h,'MenuFile_3')&& exist(h.MenuFile_3,'file') % set(handles.MenuFile_3,'Label',h.MenuFile_3); % set(handles.MenuFile_insert_3,'Label',h.MenuFile_3); % end % if isfield(h,'MenuFile_4')&& exist(h.MenuFile_4,'file') % set(handles.MenuFile_4,'Label',h.MenuFile_4); % set(handles.MenuFile_insert_4,'Label',h.MenuFile_4); % end % if isfield(h,'MenuFile_5')&& exist(h.MenuFile_5,'file') % 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.TransformName,'String',param.menu_coord_str) end if isfield(param,'menu_coord_val') set(handles.TransformName,'Value',param.menu_coord_val); else set(handles.TransformName,'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.FieldName,'String',param.list_fields);% list menu fields set(handles.FieldName,'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 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={'';'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.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 % display the GUI for the default actionname 'check_data_files' ActionName_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 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'); 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') Param=xml2struct(fileinput); fill_GUI(Param,handles);%fill the GUI with the parameters retrieved from the xml file return 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); 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'); fileinput=fullfile(InputTable{iview,1},InputTable{iview,2},[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]); display_file_name(handles,fileinput,0) %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) %------------------------------------------------------------------------ % --- 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.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) 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) %% display the min and max indices for all the file series i_sum=sum(sum(i1_series,2),3);%sum of i1_series on the last index MaxIndex_i=max(find(i_sum>0))-1; MinIndex_i=min(find(i_sum>0))-1; i2_min=[]; if ~isempty(i2_series) i2_min=i2_series(1,2); end j1_min=[]; if ~isempty(j1_series) j1_min=j1_series(1,2); end j2_min=[]; if ~isempty(j2_series) j2_min=j2_series(1,2); end if isequal(MinIndex_i,1) && exist (fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,0,i2_min, j1_min,j2_min),'file') MinIndex_i=0; end j_sum=sum(sum(j1_series,1),3); MaxIndex_j=max(find(j_sum>0))-1; MinIndex_j=min(find(j_sum>0))-1; 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{lastview,1}=MinIndex_i; MinIndex{lastview,2}=MinIndex_j; MaxIndex{lastview,1}=MaxIndex_i; MaxIndex{lastview,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)); %% 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) %% 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,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) %% 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 if ~isempty(time) TimeTable=get(handles.TimeTable,'Data'); if isempty(MinIndex_j) 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); TimeTable{iview,4}=time(MaxIndex_i,MaxIndex_j); 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'); 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.VelType,'Visible',enable) set(handles.VelType_text,'Visible',enable) if check_civ>=2 enable='on'; else enable='off'; end set(handles.VelType_1,'Visible',enable) set(handles.VelType_text_1,'Visible',enable) if check_civ || check_netcdf enable='on'; else enable='off'; end set(handles.FieldName,'Visible',enable) set(handles.Field_text,'Visible',enable) if check_civ+ check_netcdf>=2 enable='on'; else enable='off'; end set(handles.FieldName_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.FieldName,'String',FieldString) FieldString={''}; if check_civ>=2 FieldString=[calc_field;{'get_field...'}]; elseif check_civ+check_netcdf>=2 FieldString={'get_field...'}; end set(handles.FieldName_1,'String',{'get_field...'}) %% 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) %% 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 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) %------------------------------------------------------------------------ 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'))]; % 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{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) %------------------------------------------------------------------------ % --- 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 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') 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')); 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) %------------------------------------- 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.FieldName,'Visible',state) % set(handles.Field_text,'Visible',state) set(handles.InputFields,'Visible',state) %----------------------------------- function view_FieldMenu_1(handles,state) set(handles.FieldName_1,'Visible',state) set(handles.Field_text_1,'Visible',state) %%%%%%%%%%%%%%%%%%%% %% 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) else %Series.Specific=h_fun(Series); Series=h_fun(Series); if ~isempty(filexml) t=struct2xml(Series); t=set(t,1,'name','Series'); save(t,filexml); end % h_fun(Series); end set(handles.RUN, 'Enable','On') set(handles.RUN,'BackgroundColor',[1 0 0]) %------------------------------------------------------------------------ function STOP_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.RUN, 'BusyAction','cancel') set(handles.RUN,'BackgroundColor',[1 0 0]) set(handles.RUN,'enable','on') set(handles.BATCH,'BackgroundColor',[1 0 0]) set(handles.BATCH,'enable','on') %------------------------------------------------------------------------ % --- Executes on button press in BATCH. function BATCH_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.BATCH, 'Enable','Off') set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784]) [h_fun,Series,filexml,errormsg]=prepare_jobs(handles); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) return end % 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_series=fileparts(which('series')); filename_xml=fullfile(Series.OutputDir,[Series.OutputRootFile '.xml']); filename_bat=fullfile(Series.OutputDir,[Series.OutputRootFile '.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'); text_matlabscript=[... '#!/bin/bash \n'... '. /etc/sysprofile \n'... 'matlab -nodisplay -nosplash -nojvm <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) %removes redondant information Series=rmfield(Series,'OutputDirExt'); Series.IndexRange=rmfield(Series.IndexRange,'TimeTable'); Series.IndexRange=rmfield(Series.IndexRange,'MinIndex'); Series.IndexRange=rmfield(Series.IndexRange,'MaxIndex'); % create output directory if check_create [tild,msg1]=mkdir(Series.OutputDir); if ~strcmp(msg1,'') errormsg=['cannot create ' Series.OutputDir ': ' msg1];%error message for directory creation return end end filexml=fullfile(Series.OutputDir,[Series.InputTable{1,3} '.xml']);% name of the parameter xml file set in this directory % t=struct2xml(Series); % t=set(t,1,'name','Series'); % save(t,filexml); end %------------------------------------------------------------------------ % --- 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 %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'); view_FieldMenu(handles,'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.ParamKey,'Visible','off') set(handles.ParamVal,'Visible','off') ParamKey={}; set(handles.FieldName,'Enable','off') set(handles.VelType,'Enable','off') set(handles.FieldName_1,'Enable','off') set(handles.VelType_1,'Enable','off') set(handles.TransformName,'Enable','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'); nb_series=size(InputTable,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} case 'NbViewMax' if ~isempty (varargout{ilist+1}) if size(InputTable,1)>varargout{ilist+1} InputTable=InputTable(1:varargout{ilist+1},:); set(handles.InputTable,'Data',InputTable) end end case 'AllowInputSort' if isequal(lower(varargout{ilist+1}),'on')% sort the input table by alphabetical order of the SubDir SeriesData=get(handles.series,'UserData'); SeriesData.AllowInputSort=1; set(handles.series,'UserData',SeriesData) end case 'WholeIndexRange' if isequal(lower(varargout{ilist+1}),'on')% sort the input table by alphabetical order of the SubDir 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') set(handles.VelType,'Enable','on') if nb_series >=1 && ~testima_series set(handles.VelType,'Visible','on') set(handles.VelType_text,'Visible','on'); end end if isequal(lower(varargout{ilist+1}),'two') set(handles.VelType_1,'Enable','on') if nb_series >=2 && ~testima_series 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') set(handles.FieldName,'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.FieldName_1,'Enable','on') if nb_series >=2 && ~testima_1 view_FieldMenu_1(handles,'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') 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 'PARAMETER' % NOT USED 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}]; 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) %------------------------------------------------------------------------ % SeriesData=get(handles.series,'UserData'); 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 % %------------------------------------------------------------------------ % % --- 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.FieldName,'enable'),'on'); testfield_1=isequal(get(handles.FieldName_1,'enable'),'on'); testveltype=isequal(get(handles.VelType,'enable'),'on'); testveltype_1=isequal(get(handles.VelType_1,'enable'),'on'); testtransform=isequal(get(handles.TransformName,'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.FieldName,'String'); if isequal(menustr,{'get_field...'}) set(handles.FieldName,'String',{'get_field...';'velocity';'vort';'div';'more...'}) end set(handles.VelType,'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.FieldName_1,'String'); % if isequal(menustr,{'get_field...'}) % set(handles.FieldName_1,'String',{'get_field...';'velocity';'vort';'div';'more...'}) % end % else % set(handles.FieldName_1,'Value',1) % set(handles.FieldName_1,'String',{'get_field...'}) % set(handles.VelType_1,'Visible','on') % set(handles.VelType_text_1,'Visible','on'); % end % view_FieldMenu_1(handles,'off') case 'netcdf' view_FieldMenu(handles,'on') set(handles.FieldName,'Value',1) set(handles.FieldName,'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.VelType,'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) % -------------------------------------------------------------------- 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