%'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 CoordType (menu for coordinate transforms) % .menu_coord_val: value for CoordType (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 function varargout = series(varargin) % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name', mfilename, ... 'gui_Singleton', gui_Singleton, ... 'gui_OpeningFcn', @series_OpeningFcn, ... 'gui_OutputFcn', @series_OutputFcn, ... 'gui_LayoutFcn', [] , ... 'gui_Callback', []); if nargin && ischar(varargin{1}) gui_State.gui_Callback = str2func(varargin{1}); end if nargout [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); else gui_mainfcn(gui_State, varargin{:}); end % End initialization code - DO NOT EDIT %-------------------------------------------------------------------------- % --- Executes just before series is made visible. %-------------------------------------------------------------------------- function series_OpeningFcn(hObject, eventdata, handles,param) % Choose default command line output for series handles.output = hObject; % Update handles structure guidata(hObject, handles); %default initial parameters %load the list of previously browsed files in menus Open and Open_1 dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') h=load (profil_perso); 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.CoordType,'String',param.menu_coord_str) end if isfield(param,'menu_coord_val') set(handles.CoordType,'Value',param.menu_coord_val); else set(handles.CoordType,'Value',1);%default end if isfield(param,'FileName') if isfield(param,'FileName_1') update_file(hObject, eventdata, handles,param.FileName_1,0) update_file(hObject, eventdata, handles,param.FileName,1) else update_file(hObject, eventdata, 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 if isfield(param,'civ1')&& islogical(param.civ1) && isfield(param,'civ2')&& islogical(param.civ2)&... isfield(param,'interp1')&& islogical(param.interp1)&&isfield(param,'interp2')&& islogical(param.interp2)&... isfield(param,'filter1')&& islogical(param.filter1)&&isfield(param,'filter2')&& islogical(param.filter2) set(handles.civ1,'Value',param.civ1); set(handles.civ2,'Value',param.civ1); set(handles.interp1,'Value',param.interp1); set(handles.interp2,'Value',param.interp2); set(handles.filter1,'Value',param.filter1); set(handles.filter2,'Value',param.filter2); end %set(hObject,'UserData', SeriesData) set(hObject,'WindowButtonUpFcn',{@mouse_up_gui,handles}) NomType_Callback(hObject, eventdata, handles) %mode_Callback(hObject, eventdata, handles) %loads the information stored in prefdir to initiate the browser and the list of functions menu_str={'check_files';'aver_stat';'time_series';'merge_proj';'clean_civ_cmx'}; % menu_str=get(handles.ACTION,'String');%list of functions included in 'series.m' %remove from the list the last option 'more...' [path_series,name,ext]=fileparts(which('series')); path_series=fullfile(path_series,'/series');%path of the function 'series' for ilist=1:length(menu_str) fct_path{ilist,1}=path_series;%paths of the fuctions buil-in in 'series.m' end dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') h=load (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 menu_str=[menu_str; {file}]; end end end menu_str=[menu_str;{'more...'}]; set(handles.ACTION,'String',menu_str) set(handles.ACTION,'UserData',fct_path)% store the list of path in UserData of ACTION % display the GUI for the default action 'check_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; % -------------------------------------------------------------------- function MenuBrowse_Callback(hObject, eventdata, handles) RootPathCell=get(handles.RootPath,'String'); SubDirCell=get(handles.SubDir,'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},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 testblank=findstr(fileinput,' ');%look for blanks if ~isempty(testblank) errordlg('forbidden input file name: contain blanks') return end sizf=size(fileinput); if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end [path,name,ext]=fileparts(fileinput); SeriesData=[];%dfault if isequal(ext,'.xml') errordlg('input file type not implemented')%A Faire: ouvrir le fichier pour naviguer elseif isequal(ext,'.xls') errordlg('input file type not implemented')%A Faire: ouvrir le fichier pour naviguer else update_file(hObject, eventdata, 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; Release=txt(1).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 % set(hseries,'UserData',SeriesData); % RootFile_Callback(hObject, eventdata, handles); % FileExt_Callback(hObject, eventdata, handles); % NomType_Callback(hObject, eventdata, handles) % mode_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- function MenuFile_1_Callback(hObject, eventdata, handles) fileinput=get(handles.MenuFile_1,'Label'); update_file(hObject, eventdata, handles,fileinput,0) % -------------------------------------------------------------------- function MenuFile_2_Callback(hObject, eventdata, handles) fileinput=get(handles.MenuFile_2,'Label'); update_file(hObject, eventdata, handles,fileinput,0) % -------------------------------------------------------------------- function MenuFile_3_Callback(hObject, eventdata, handles) fileinput=get(handles.MenuFile_3,'Label'); update_file(hObject, eventdata, handles,fileinput,0) % -------------------------------------------------------------------- function MenuFile_4_Callback(hObject, eventdata, handles) fileinput=get(handles.MenuFile_4,'Label'); update_file(hObject, eventdata, handles,fileinput,0) % -------------------------------------------------------------------- function MenuFile_5_Callback(hObject, eventdata, handles) fileinput=get(handles.MenuFile_5,'Label'); update_file(hObject, eventdata, handles,fileinput,0) % -------------------------------------------------------------------- function MenuBrowse_insert_Callback(hObject, eventdata, handles) %hseries=get(handles.browse_root,'parent'); RootPathCell=get(handles.RootPath,'String'); % SubDirCell=get(handles.SubDir,'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 testblank=findstr(fileinput,' ');%look for blanks if ~isempty(testblank) errordlg('forbidden input file name: contain blanks') return end sizf=size(fileinput); if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end [path,name,ext]=fileparts(fileinput); SeriesData=[];%dfault if isequal(ext,'.xml') errordlg('input file type not implemented')%A Faire: ouvrir le fichier pour naviguer elseif isequal(ext,'.xls') errordlg('input file type not implemented')%A Faire: ouvrir le fichier pour naviguer else update_file(hObject, eventdata, handles,fileinput,1) %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; Release=txt(1).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_insert_1_Callback(hObject, eventdata, handles) fileinput=get(handles.MenuFile_insert_1,'Label'); update_file(hObject, eventdata, handles,fileinput,1) % -------------------------------------------------------------------- function MenuFile_insert_2_Callback(hObject, eventdata, handles) fileinput=get(handles.MenuFile_insert_2,'Label'); update_file(hObject, eventdata, handles,fileinput,1) % -------------------------------------------------------------------- function MenuFile_insert_3_Callback(hObject, eventdata, handles) fileinput=get(handles.MenuFile_insert_3,'Label'); update_file(hObject, eventdata, handles,fileinput,1) % -------------------------------------------------------------------- function MenuFile_insert_4_Callback(hObject, eventdata, handles) fileinput=get(handles.MenuFile_insert_4,'Label'); update_file(hObject, eventdata, handles,fileinput,1) % -------------------------------------------------------------------- function MenuFile_insert_5_Callback(hObject, eventdata, handles) fileinput=get(handles.MenuFile_insert_5,'Label'); update_file(hObject, eventdata, handles,fileinput,1) % -------------------------------------------------------------------- % refresh the GUI data after introduction of a new file series function update_file(hObject, eventdata, handles,fileinput,addtest) hseries=get(handles.RootPath,'parent'); % refresh input root name, indices, file extension and nomenclature [RootPath,RootFile,field_count,str2,str_a,str_b,FileExt,NomType,SubDir]=name2display(fileinput); %check for movie image files if ~isempty(imformats(FileExt(2:end))) imainfo=imfinfo(fileinput); if length(imainfo) >1 %case of image with multiple frames NomType='*'; [RootPath,RootFile]=fileparts(fileinput); end end NcType='none';%default if isequal(FileExt,'.nc') Data=nc2struct(fileinput,[]); if isfield(Data,'absolut_time_T0') NcType='civx'; % test for civx velocity fields end end set(handles.RootPath,'Value',1) set(handles.SubDir,'Value',1) set(handles.RootFile,'Value',1) set(handles.NomType,'Value',1) set(handles.FileExt,'Value',1) set(handles.nb_field,'Value',1) set(handles.nb_field2,'Value',1) if addtest SeriesData=get(hseries,'UserData'); SeriesData.displ_num=[0 0 0 0;SeriesData.displ_num]; SeriesData.CurrentInputFile_1=SeriesData.CurrentInputFile; RootPathCell=[{RootPath}; get(handles.RootPath,'String')] ; SubDirCell=[{SubDir}; get(handles.SubDir,'String')]; RootFileCell=[{RootFile}; get(handles.RootFile,'String')]; NomTypeCell=[{NomType}; SeriesData.NomType]; FileExtCell=[{FileExt}; get(handles.FileExt,'String')]; NcTypeCell=[{NcType};SeriesData.NcType]; set(handles.NomType,'String',[{};get(handles.NomType,'String')]) else SeriesData=[];%re-initialisation SeriesData.displ_num=[0 0 0 0]; RootPathCell={RootPath}; SubDirCell={SubDir}; RootFileCell={RootFile}; NomTypeCell={NomType}; FileExtCell={FileExt}; NcTypeCell={NcType}; end SeriesData.NomType=NomTypeCell; SeriesData.NcType=NcTypeCell; SeriesData.CurrentInputFile=fileinput; set(handles.RootPath,'String',RootPathCell); set(handles.SubDir,'String',SubDirCell); set(handles.RootFile,'String',RootFileCell); set(handles.NomType,'String',NomTypeCell); set(handles.FileExt,'String',FileExtCell); %determine field indices ref_i=1; %default ref_i is a reference frame index used to find existing pairs from PIV if ~isempty(str2num(field_count)) ref_i=str2num(field_count); if ~isempty(str2num(str2)) ref_i=floor((ref_i+str2num(str2))/2);% reference image number corresponding to the file SeriesData.browse_Di=str2num(str2)-str2num(field_count); end end set(handles.ref_i,'String',num2str(ref_i)); set(handles.first_i,'String',num2str(ref_i)); set(handles.last_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(str2num(str_a)) ref_j=str2num(str_a); if ~isempty(str2num(str_b)) ref_j=floor((str2num(str_a)+str2num(str_b))/2); SeriesData.browse_Dj=str2num(str_b)-str2num(str_a); end end set(handles.ref_j,'String',num2str(ref_j)); set(handles.first_j,'String',num2str(ref_j)) set(handles.last_j,'String',num2str(ref_j)); %set(hseries,'UserData',SeriesData); %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 drawnow % hseries=get(handles.RootFile,'parent'); % SeriesData=get(hseries,'UserData');%read information set by the browser % ext_ima_read=[]; % field_count=1;%default % pxcmx=1; % pxcmy=1; TimeUnit=''; %default % CoordUnit='';%default time=[];%default GeometryCalib=[];%default nb_field=[];%default nb_field2=[];%default % Heading=[]; % [PD,Device]=fileparts(RootPathCell{1}); SeriesData.PathCampaign=get(handles.PathCampaign,'String'); % read timing and total frame number from the current file (movie files) !! may be overrid by xml file %icell=length(RootPathCell); FileBase=fullfile(RootPath,RootFile); % nb_field{icell,1}='?';%default % nb_field2{icell,1}='?';%default testima=0; %test for image input if isequal(lower(FileExt),'.avi') %.avi file testima=1; info=aviinfo([FileBase FileExt]); time=[0:1/info.FramesPerSecond:(info.NumFrames-1)/info.FramesPerSecond]'; nb_field=info.NumFrames; nb_field2=1; elseif ~isempty(imformats(FileExt(2:end))) testima=1; if isequal(NomType,'*')% multi-frame image imainfo=imfinfo([FileBase FileExt]); if length(imainfo) >1 %case of image with multiple frames nb_field=length(imainfo); nb_field2=1; end end elseif isequal(FileExt,'.vol') testima=1; end % 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.CoordType,'Enable'),'on'); testnc=0; testnc_1=0; testcivx=0; testcivx_1=0; if length(FileExtCell)==1 || length(FileExtCell)>2 for iview=1:length(FileExtCell) if isequal(FileExtCell{iview},'.nc') testnc=1; end if isequal(NcTypeCell{iview},'civx') testcivx=1; end end elseif length(FileExtCell)==2 testnc=isequal(FileExtCell{1},'.nc'); testnc_1=isequal(FileExtCell{2},'.nc'); testcivx=isequal(NcTypeCell{1},'civx'); testcivx_1=isequal(NcTypeCell{2},'civx'); end if testfield && testnc view_FieldMenu(handles,'on') if testcivx menustr=get(handles.FieldMenu,'String'); if isequal(menustr,{'get_field...'}) set(handles.FieldMenu,'String',{'get_field...';'velocity';'vort';'div';'more...'}) end else set(handles.FieldMenu,'Value',1) set(handles.FieldMenu,'String',{'get_field...'}) end else view_FieldMenu(handles,'off') end if testfield_1 && testnc_1 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...'}) end else view_FieldMenu_1(handles,'off') end if testveltype && testcivx set(handles.VelTypeMenu,'Visible','on') set(handles.VelType_text,'Visible','on'); else set(handles.VelTypeMenu,'Visible','off') set(handles.VelType_text,'Visible','off'); end if testveltype_1 && testcivx_1 set(handles.VelTypeMenu_1,'Visible','on') set(handles.VelType_text_1,'Visible','on'); else set(handles.VelTypeMenu_1,'Visible','off') set(handles.VelType_text_1,'Visible','off'); end if testtransform && (testcivx || testima) view_TRANSFORM(handles,'on') else view_TRANSFORM(handles,'off') end if ~isequal(FileExt,'.nc') && ~isequal(FileExt,'.cdf') && ~testima msgbox_uvmat('ERROR',['invalid input file extension ' FileExt]) return end %%%%%%%% read image documentation file if found%%%%%%%%%%%%%%%%%%%%%%%%%%% %look for the file existence ext_imadoc=''; 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 % mode=''; %default % testheading=0; XmlData=[]; NbSlice_calib={}; if isequal(ext_imadoc,'.xml') [XmlData,warntext]=imadoc2struct([FileBase '.xml']); if isfield(XmlData,'Heading') && isfield(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; size(time) GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0]; GeometryCalib.Tx=0; GeometryCalib.Ty=0; GeometryCalib.Tz=1; GeometryCalib.dpx=1; GeometryCalib.dpy=1; GeometryCalib.sx=1; GeometryCalib.Cx=0; GeometryCalib.Cy=0; GeometryCalib.f=1; GeometryCalib.kappa1=0; GeometryCalib.CoordUnit='cm'; XmlData.GeometryCalib=GeometryCalib; if error==2, warntext=['no file ' FileBase '.civ']; elseif error==1, warntext='inconsistent number of fields in the .civ file'; end % set(handles.npx,'String',num2str(npx));%fills nbre of pixels x box % set(handles.npy,'String',num2str(npy));%fills nbre of pixels y box % set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box % set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box % set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box % set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box % set(handles.view_xml,'Visible','on') % set(handles.view_xml,'String','view .civ') end if addtest SeriesData.Time=[{time} SeriesData.Time]; else SeriesData.Time={time}; end if ~isempty(time) siztime=size(time); nb_field=siztime(1); nb_field2=siztime(2); end set(handles.TimeUnit,'String',TimeUnit) if isempty(nb_field) nb_field_str='?'; nb_field_str2='?'; else nb_field_str=num2str(nb_field); nb_field_str2=num2str(nb_field2); end if addtest nb_field_cell=[{nb_field_str} ;get(handles.nb_field,'String')]; nb_field2_cell=[{nb_field_str2} ;get(handles.nb_field2,'String')]; else nb_field_cell={nb_field_str}; nb_field2_cell={nb_field_str2}; end set(handles.nb_field,'String',nb_field_cell); set(handles.nb_field2,'String',nb_field2_cell); set(hseries,'UserData',SeriesData); %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.NbSlice,'String',num2str(NbSlice)) end % set menus of index pairs NomType_Callback(hObject, eventdata, handles) dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); % save(profil_perso, 'FileBase'); %store the root name for future opening of uvmat if exist(profil_perso,'file') save (profil_perso,'RootPath','SubDir','RootFile','NomType', '-append'); %store the root name for future opening of uvmat else txt=ver; Release=txt(1).Release; relnumb=str2num(Release(3:4)); if relnumb >= 14 save (profil_perso,'RootPath','SubDir','RootFile','NomType','-V6') %store the root name for future opening of uvmat else save(profil_perso,'RootPath','SubDir','RootFile','NomType') end end set(handles.RootPath,'BackgroundColor',[1 1 1]) set(handles.PathCampaign,'String',SeriesData.PathCampaign) last_j_Callback(hObject, eventdata, handles) last_i_Callback(hObject, eventdata, handles) %------------------------------------------------------------ function RootPath_Callback(hObject, eventdata, handles) Val=get(handles.RootPath,'Value'); synchronise_view(handles,Val) NomType_Callback(hObject, eventdata, handles) %------------------------------------------------------------ function synchronise_view(handles,Val) set(handles.RootPath,'Value',Val) set(handles.SubDir,'Value',Val) set(handles.RootFile,'Value',Val) set(handles.NomType,'Value',Val) set(handles.FileExt,'Value',Val) set(handles.nb_field,'Value',Val) set(handles.nb_field2,'Value',Val) set(handles.time_first,'Value',Val) set(handles.time_last,'Value',Val) %--------------------------------------------------------- % Executes on carriage return on the subdir civ1 edit window %-------------------------------------------------------- function SubDir_Callback(hObject, eventdata, handles) Val=get(handles.SubDir,'Value'); synchronise_view(handles,Val) NomType_Callback(hObject, eventdata, handles) %-------------------------------------------------------------- %function activated when a new filebase (image series) is introduced %------------------------------------------------------------ function RootFile_Callback(hObject, eventdata, handles) Val=get(handles.RootFile,'Value'); synchronise_view(handles,Val) NomType_Callback(hObject, eventdata, handles) %-------------------------------------------------------------- %function activated when a new filebase (image series) is introduced %------------------------------------------------------------ function FileExt_Callback(hObject, eventdata, handles) Val=get(handles.FileExt,'Value'); synchronise_view(handles,Val) %-------------------------------------------------------------- %function activated when a new filebase (image series) is introduced %------------------------------------------------------------ function nb_field_Callback(hObject, eventdata, handles) Val=get(handles.nb_field,'Value'); synchronise_view(handles,Val) %-------------------------------------------------------------- %function activated when a new filebase (image series) is introduced %------------------------------------------------------------ function nb_field2_Callback(hObject, eventdata, handles) Val=get(handles.nb_field2,'Value'); synchronise_view(handles,Val) %-------------------------------------------------------------- %function activated when a new filebase (image series) is introduced %------------------------------------------------------------ function time_first_Callback(hObject, eventdata, handles) Val=get(handles.time_first,'Value'); synchronise_view(handles,Val) %-------------------------------------------------------------- %function activated when a new filebase (image series) is introduced %------------------------------------------------------------ function time_last_Callback(hObject, eventdata, handles) Val=get(handles.time_last,'Value'); synchronise_view(handles,Val) %-------------------------------------------------------------- %function activated by NomType %------------------------------------------------------------ NomType_Callback(hObject, eventdata, handles) function NomType_Callback(hObject, eventdata, handles) hseries=get(handles.ProjObject,'Parent'); SeriesData=get(hseries,'UserData'); if isfield(SeriesData,'NomType') NomTypeCell=SeriesData.NomType; else NomTypeCell={}; end nbfield2_cell=get(handles.nb_field2,'String'); val=get(handles.nb_field2,'Value'); if iscell(nbfield2_cell) nbfield2=str2num(nbfield2_cell{val}); else nbfield2=str2num(nbfield2_cell); end nbfield_cell=get(handles.nb_field,'String'); if iscell(nbfield_cell) nbfield=str2num(nbfield_cell{val}); else nbfield=str2num(nbfield_cell); end set(handles.mode,'Visible','off') % do not show index pairs by default set(handles.list_pair_civ,'Visible','off') set(handles.ref_i,'Visible','off') set(handles.ref_i_text,'Visible','off') testpair=0; state_j='off'; %set the menus of image pairs and default selection for series %list pairs if relevant Val=get(handles.NomType,'Value'); synchronise_view(handles,Val) if ~isempty(NomTypeCell) NomType=NomTypeCell{Val}; switch NomType case {'_i1-i2_j', '_i1-i2'} set(handles.mode,'String',{'series(Di)'}) set(handles.mode,'Value',1); set(handles.mode,'Visible','on') testpair=1; case {'#_ab'} set(handles.mode,'String',{'bursts'}) set(handles.mode,'Value',1); testpair=1; case '_i_j1-j2' set(handles.mode,'String',{'bursts';'series(Dj)'})%multiple choice if ~isempty(nbfield) && ~isempty(nbfield2) && ((nbfield2>10) || (nbfield==1)) set(handles.mode,'Value',2); else set(handles.mode,'Value',1);% advice 'bursts' for small bursts end set(handles.mode,'Visible','on') testpair=1; end switch NomType case {'_i_j','_i_j1-j2','_i1-i2_j','#_ab'},% two navigation indices state_j='on'; end end if testpair mode_Callback(hObject, eventdata, handles) else set(handles.NomType,'String',NomTypeCell) end set(handles.first_j,'Visible',state_j) set(handles.incr_j,'Visible',state_j) set(handles.last_j,'Visible',state_j) set(handles.nb_field2,'Visible',state_j) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%???????????? % --- Executes on button press in mode. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% function mode_Callback(hObject, eventdata, handles) hseries=get(handles.mode,'parent'); SeriesData=get(hseries,'UserData'); mode_list=get(handles.mode,'String'); mode_value=get(handles.mode,'Value'); mode=mode_list{mode_value}; NomType=[]; test_find_pair=0; if isfield(SeriesData,'NomType') NomTypeCell=SeriesData.NomType; Val=get(handles.NomType,'Value'); NomType=NomTypeCell{Val}; test_find_pair=isequal(NomType,'_i_j1-j2')|| isequal(NomType,'_i1-i2_j')|| isequal(NomType,'_i1-i2')|| isequal(NomType,'#_ab'); end % displ_num=[];%default % first_i=str2num(get(handles.first_i,'String')); % last_i=str2num(get(handles.last_i,'String')); time=[]; if isfield(SeriesData,'Time') time=SeriesData.Time{1}; %get the set of times end siztime=size(time); nbfield=siztime(1); nbfield2=siztime(2); indchosen=1; %%first pair selected by default if isequal(mode,'bursts') enable_i(handles,'On') enable_j(handles,'Off') elseif isequal(NomType,'_i_j1-j2')|| isequal(NomType,'_i1-i2_j') enable_i(handles,'On') enable_j(handles,'On') else enable_i(handles,'On') enable_j(handles,'Off') end % elseif isequal(mode,'series(Dj)') % enable_j(handles,'On') % if nbfield==1 % enable_i(handles,'Off') % else % enable_i(handles,'On') % end % elseif isequal(mode,'series(Di)') % if nbfield2 > 1 % enable_j(handles,'On') % else % enable_j(handles,'Off') % end % end set(handles.list_pair_civ,'Value',indchosen);%set the default choice of image pairs for civ1 % SetSeries.displ_num=displ_num; set(hseries,'UserData',SeriesData) %list pairs if relevant if test_find_pair find_netcpair_civ(hObject, eventdata, handles,Val) end %------------------------------------- function enable_i(handles,state) set(handles.i_txt,'Visible',state) set(handles.first_i,'Visible',state) set(handles.last_i,'Visible',state) set(handles.incr_i,'Visible',state) set(handles.nb_field,'Visible',state) set(handles.ref_i,'Visible',state) set(handles.ref_i_text,'Visible',state) %----------------------------------- function enable_j(handles,state) set(handles.j_txt,'Visible',state) set(handles.first_j,'Visible',state) set(handles.last_j,'Visible',state) set(handles.incr_j,'Visible',state) set(handles.nb_field2,'Visible',state) set(handles.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.Field_frame,'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.CoordType,'Visible',state); set(handles.TRANSFORM_title,'Visible',state) %-------------------------------------------------------------- % determine the menu for civ1 pairs depending on existing netcdf file at the middle of % the field series set by first_i, incr, last_i %---------------------------------------------------------------- function find_netcpair_civ(hObject, eventdata, handles,Val) hseries=get(handles.list_pair_civ,'parent'); SeriesData=get(hseries,'UserData'); % NomTypeCell=get(handles.NomType,'String'); NomTypeCell=SeriesData.NomType; NomType=NomTypeCell{Val}; set(handles.list_pair_civ,'Visible','on') %nomenclature types RootPathCell=get(handles.RootPath,'String'); filepath=RootPathCell{Val}; RootFileCell=get(handles.RootFile,'String'); filename=RootFileCell{Val}; filebase=fullfile(filepath,filename); SubDirCell=get(handles.SubDir,'String'); subdir=SubDirCell{Val}; if ~exist(fullfile(filepath,subdir),'dir') msgbox_uvmat('ERROR',['no civ file available: subdirectory ' subdir ' does not exist']) set(handles.list_pair_civ,'String',{''}); return end mode_list=get(handles.mode,'String'); mode_value=get(handles.mode,'Value'); mode=mode_list{mode_value}; %reads image numbers from the interface ref_i=str2num(get(handles.ref_i,'String')); ref_j=str2num(get(handles.ref_j,'String')); % time=[]; % ref_time=[]; ref_time=0; if isfield(SeriesData,'Time')&~isempty(SeriesData.Time{Val})&~isequal(SeriesData.Time{Val},0) time=SeriesData.Time{Val}; %get the set of times siztime=size(time); nbfield=siztime(1); nbfield2=siztime(2); % test_imadoc=1; else % test_imadoc=0;%no image documentation file nbfield=50; nbfield2=50;%default max number of pairs end %look for existing processed pairs involving the field at the middle of the series if civ1 will not % be performed, while the result is needed for next steps. displ_pair={''}; displ_num=[]; ind_exist=0; TimeUnit=get(handles.TimeUnit,'String'); if length(TimeUnit)>=1 dtunit=['m' TimeUnit]; else dtunit='e-03'; end if isequal(mode,'series(Di)') for index=1:min(nbfield-1,50) filename=name_generator(filebase,ref_i-floor(index/2),ref_j,'.nc',NomType,1,ref_i+ceil(index/2),ref_j,subdir); select=(exist(filename,'file')==2); if select==1 ind_exist=ind_exist+1; displ_num(1,ind_exist)=0; displ_num(2,ind_exist)=0; displ_num(3,ind_exist)=-floor(index/2); displ_num(4,ind_exist)=ceil(index/2); %[cte_detect,vdt,cte_read]=read_netcdf(filename,{'dt','dt2','absolut_time_T0','absolute_time_TO_2'}); [Cte,var_detect,ichoice]=nc2struct(filename,{}); if isfield(Cte,'dt2') dt=Cte.dt2; elseif isfield(Cte,'dt') dt=Cte.dt; end if isfield(Cte,'absolut_time_TO_2') ref_time(ind_exist)=Cte.absolut_time_TO_2;%civ2 data used in priority elseif isfield(Cte,'absolut_time_TO') ref_time(ind_exist)=Cte.absolut_time_TO;%civ2 data used in priorit elseif isfield(Cte,'Time') ref_time(ind_exist)=Cte.Time; end displ_pair{ind_exist}=['Di= ' num2str(-floor(index/2)) '|' num2str(ceil(index/2)) ' :dt= ' num2str(dt*1000) dtunit]; end end set(handles.list_pair_civ,'String',[displ_pair';{'Di=*|*'}]); elseif isequal(mode,'series(Dj)')% series on the j index for index=1:min(nbfield2-1,50) filename=name_generator(filebase,ref_i,ref_j-floor(index/2),'.nc',NomType,1,ref_i,ref_j+ceil(index/2),subdir); select=(exist(filename,'file')==2); if select==1 ind_exist=ind_exist+1; displ_num(1,ind_exist)=-floor(index/2); displ_num(2,ind_exist)=ceil(index/2); displ_num(3,ind_exist)=0; displ_num(4,ind_exist)=0; %[cte_detect,vdt,cte_read]=read_netcdf(filename,{'dt','dt2','absolut_time_T0','absolute_time_TO_2'}); [Cte,var_detect,ichoice]=nc2struct(nc,{}); if isfield(Cte,'dt2') dt=Cte.dt2; elseif isfield(Cte,'dt') dt=Cte.dt; end if isfield(Cte,'absolut_time_TO_2') ref_time(ind_exist)=Cte.absolut_time_TO_2;%civ2 data used in priority elseif isfield(Cte,'absolut_time_TO') ref_time(ind_exist)=Cte.absolut_time_TO;%civ2 data used in priorit elseif isfield(Cte,'Time') ref_time(ind_exist)=Cte.Time; end % if cte_detect(2)==1; % dt=cte_read(2); % ref_time(ind_exist)=cte_read(4);%civ2 data used in priority % else % dt=cte_read(1); % ref_time(ind_exist)=cte_read(3); % end displ_pair{ind_exist}=['Dj= ' num2str(-floor(index/2)) '|' num2str(ceil(index/2)) ' :dt= ' num2str(dt*1000) dtunit]; end end set(handles.list_pair_civ,'String',[displ_pair';{'Dj=*|*'}]); elseif isequal(mode,'bursts') %case of bursts for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'bursts' mode for numod_b=(numod_a+1):nbfield2 [filename]=name_generator(filebase,ref_i,numod_a,'.nc',NomType,1,ref_i,numod_b,subdir); select=(exist(filename,'file')==2); if select==1 ind_exist=ind_exist+1; numlist_a(ind_exist)=numod_a; numlist_b(ind_exist)=numod_b; Attr=nc2struct(filename,[]); isfield(Attr,'absolut_time_T0_2') if isfield(Attr,'dt2') dt(ind_exist)=Attr.dt2; ref_time(ind_exist)=Attr.absolut_time_T0_2; elseif isfield(Attr,'dt')& isfield(Attr,'absolut_time_T0') dt(ind_exist)=Attr.dt; ref_time(ind_exist)=Attr.absolut_time_T0; else dt(ind_exist)=NaN;%no information on dt end %determine nom_type_ima for pair display (used in num2stra.m) switch NomType case {'#ab'} nom_type_ima='#a'; case {'#AB'} nom_type_ima='#A'; otherwise nom_type_ima='_i_j'; end displ_pair{ind_exist}=['j= ' num2stra(numod_a,nom_type_ima,2) '-' num2stra(numod_b,nom_type_ima,2) ... ' :dt= ' num2str(dt(ind_exist)*1000)]; end end set(handles.list_pair_civ,'String',[displ_pair';{'j=*-*'}]); end if exist('dt','var') & ~isempty(dt) [dtsort,indsort]=sort(dt); displ_num(1,:)=numlist_a(indsort); displ_num(2,:)=numlist_b(indsort); displ_num(3,:)=0; displ_num(4,:)=0; displ_pair=displ_pair(indsort); ref_time=ref_time(indsort); end end if ind_exist==0 if isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)') msgbox_uvmat('ERROR',['no .nc file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir]) else msgbox_uvmat('ERROR',['no .nc file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir]) end if isequal(mode,'bursts') %case of bursts set(handles.list_pair_civ,'String',{'j=*-*'}); elseif isequal(mode,'series(Di)') %case of bursts set(handles.list_pair_civ,'String',{'Di=*|*'}); elseif isequal(mode,'series(Dj)') %case of bursts set(handles.list_pair_civ,'String',{'Dj=*|*'}); end end val=get(handles.list_pair_civ,'Value'); if val > length(displ_pair) set(handles.list_pair_civ,'Value',1);% first pair proposed by default in the menu val=1; end iview=get(handles.NomType,'Value'); SeriesData.displ_num(iview,:)=(displ_num(:,val))'; SeriesData.ref_time=ref_time; set(hseries,'UserData',SeriesData) list_pair_civ_Callback(hObject, eventdata, handles) %------------------------------------------------------------- % --- Executes on selection in list_pair_civ. function list_pair_civ_Callback(hObject, eventdata, handles) %------------------------------------------------------------ %update first_i and last_i according to the chosen image pairs testupdate=0; Val=get(handles.RootPath,'Value'); IndexCell=get(handles.NomType,'String'); hseries=get(handles.list_pair_civ,'parent'); SeriesData=get(hseries,'UserData'); NomType=SeriesData.NomType{Val}; list_pair=get(handles.list_pair_civ,'String');%get the menu of image pairs index_pair=get(handles.list_pair_civ,'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 {'_i1-i2_j'} 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 {'_i1-i2'} 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 '_i_j1-j2' 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(hseries,'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.first_i,'String')); last_i=str2num(get(handles.last_i,'String')); incr_i=str2num(get(handles.incr_i,'String')); num1=first_i:incr_i:last_i; lastfieldCell=get(handles.nb_field,'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 set(handles.first_i,'String',num2str(num1(1))); set(handles.last_i,'String',num2str(num1(end))); testupdate=1; elseif isequal(mode,'series(Dj)') first_j=str2num(get(handles.first_j,'String')); last_j=str2num(get(handles.last_j,'String')); incr_j=str2num(get(handles.incr_j,'String')); num_j=first_j:incr_j:last_j; lastfieldCell=get(handles.nb_field2,'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,SeriesData.Time{1}); end end end %--------------------------------------------------- % --- Executes on button press in RUN. %------------------------------------------------------ function RUN_Callback(hObject, eventdata, handles) %read root name and field type set(handles.RUN,'BusyAction','queue'); hseries=get(handles.RUN,'parent'); set(0,'CurrentFigure',hseries) if isequal(get(handles.GetObject,'Value'),1) Series.GetObject=1; GetObject_Callback(hObject, eventdata, handles) else Series.GetObject=0; end SeriesData=get(hseries,'UserData'); if isfield(SeriesData,'sethandles') if iscell(SeriesData.sethandles) Series.sethandles=SeriesData.sethandles{1}; else Series.sethandles=SeriesData.sethandles;%retrieve the handles of the set_object interface (to define projection objects) end 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) % read input file parameters and set menus Series.PathProject=get(handles.PathCampaign,'String'); RootPath=get(handles.RootPath,'String');% path of the root name of the first field series RootFile=get(handles.RootFile,'String');% root name of the first field series SubDir=get(handles.SubDir,'String');% subdirectory for netcdf files FileExt=get(handles.FileExt,'String');%file extension 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.CoordType,'Visible'); Series.CoordType='';%default if isequal(menu_coord_state,'on') menu_coord=get(handles.CoordType,'String'); menu_index=get(handles.CoordType,'Value'); Series.CoordType=menu_coord{menu_index}; end Series.hseries=get(hObject,'Parent'); if isequal(get(handles.ParamVal,'Visible'),'on') ParamKey=get(handles.ParamKey,'String'); if ischar(ParamKey) ParamKey{1}=ParamKey; end ParamString=get(handles.ParamVal,'String'); if ischar(ParamString) for ilist=1:size(ParamString,1) ParamVal{ilist}=ParamString(ilist,:); end else ParamVal=ParamString; end end %read the set of field numbers first_i=str2num(get(handles.first_i,'String')); last_i=str2num(get(handles.last_i,'String')); incr_i=str2num(get(handles.incr_i,'String')); first_j=str2num(get(handles.first_j,'String')); last_j=str2num(get(handles.last_j,'String')); incr_j=str2num(get(handles.incr_j,'String')); if ~isequal(get(handles.first_i,'Visible'),'on') first_i=1; last_i=1; incr_i=1; end if ~isequal(get(handles.first_j,'Visible'),'on') first_j=1; last_j=1; incr_j=1; end Series.NbSlice=str2num(get(handles.NbSlice,'String')); if isequal(first_i,[])|isequal(first_j,[]), msgbox_uvmat('ERROR','first field number not defined'),... set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end; if isequal(last_i,[])| isequal(last_j,[]),msgbox_uvmat('ERROR','last field number not defined'),... set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end; if isequal(incr_i,[])| isequal(incr_j,[]),msgbox_uvmat('ERROR','increment in field number not defined'),... set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,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.nb_field,'String'); nbfield=[]; %default for iview=1:length(nbfield_cell) nb=str2num(nbfield_cell{iview}); if ~isempty(nb) nbfield=[nbfield nb]; end end nbfield=min(nbfield); nbfield2_cell=get(handles.nb_field2,'String'); nbfield2=[]; %default for iview=1:length(nbfield2_cell) nb=str2num(nbfield2_cell{iview}); if ~isempty(nb) nbfield2=[nbfield2 nb]; end end nbfield2=min(nbfield2); %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 %determine the list of input file names nbmissing=0; for iview=1:length(RootPath) %case of pairs (.nc files) if isequal(NomType{iview},'_i_j1-j2')| isequal(NomType{iview},'_i1-i2_j')| isequal(NomType{iview},'_i1-i2')| isequal(NomType{iview},'#_ab') ind_shift=SeriesData.displ_num(iview,:); if isequal(ind_shift,[0 0 0 0]) % undefined pairs if isequal(NomType{iview},'#_ab') mode='#_ab'; end [num_i1,num_i2,num_j1,num_j2,nbmissing]=netseries_generator(fullfile(RootPath{iview},RootFile{iview}),SubDir{iview},mode,first_i,incr_i,last_i,first_j,incr_j,last_j); else [num_i1,num_i2,num_j1,num_j2,num_i,num_j]=find_file_indices(num_i,num_j,ind_shift,NomType{iview},mode); if isempty(num_i) msgbox_uvmat('ERROR','ERROR: empty set of input files chosen') return end if num_i(1)>first_i set(handles.first_i,'String',num2str(num_i(1)))%update the display of first field last_i_Callback(hObject, eventdata, handles) end if num_i(end)first_j set(handles.first_j,'String',num2str(num_j(1)))%update the display of first field last_j_Callback(hObject, eventdata, handles) end if num_j(end)1 num_i1_cell{iview}=num_i1; num_i2_cell{iview}=num_i2; num_j1_cell{iview}=num_j1; num_j2_cell{iview}=num_j2; end end % RUN RUN' 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 ~isequal(spath,fct_path)& exist(fct_path,'dir') addpath(fct_path)% add the prescribed path if not the current one end end % fct_path eval(['h_fun=@' action]) if ~isequal(fct_path,path_series) rmpath(fct_path)% add the prescribed path if not the current one end Series.Action=action;%name of the processing programme set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784]) drawnow if length(RootPath)>1 % feval(action,num_i1_cell,num_i2_cell,num_j1_cell,num_j2_cell,Series); h_fun(num_i1_cell,num_i2_cell,num_j1_cell,num_j2_cell,Series); else h_fun(num_i1,num_i2,num_j1,num_j2,Series); % feval(action,num_i1,num_i2,num_j1,num_j2,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 first_i_Callback(hObject, eventdata, handles) last_i_Callback(hObject, eventdata, handles) %---------------------------------------------- function last_i_Callback(hObject, eventdata, handles) hseries=get(handles.last_i,'parent'); first_i=str2num(get(handles.first_i,'String')); last_i=str2num(get(handles.last_i,'String')); ref_i=ceil((first_i+last_i)/2); set(handles.ref_i,'String', num2str(ref_i)) ref_i_Callback(hObject, eventdata, handles) SeriesData=get(hseries,'UserData'); if ~isfield(SeriesData,'Time') SeriesData.Time{1}=[]; end displ_time(handles,SeriesData.Time{1}); %------------------------------------------------------- function first_j_Callback(hObject, eventdata, handles) last_j_Callback(hObject, eventdata, handles) %------------------------------------------------------- function last_j_Callback(hObject, eventdata, handles) hseries=get(handles.last_i,'parent'); first_j=str2num(get(handles.first_j,'String')); last_j=str2num(get(handles.last_j,'String')); ref_j=ceil((first_j+last_j)/2); set(handles.ref_j,'String', num2str(ref_j)) ref_j_Callback(hObject, eventdata, handles) SeriesData=get(hseries,'UserData'); if ~isfield(SeriesData,'Time') SeriesData.Time{1}=[]; end displ_time(handles,SeriesData.Time{1}); %------------------------------------------------------- function ref_i_Callback(hObject, eventdata, handles) mode_list=get(handles.mode,'String'); mode_value=get(handles.mode,'Value'); mode=mode_list{mode_value}; hseries=get(handles.ref_i,'parent'); SeriesData=get(hseries,'UserData'); %NomTypeCell=get(handles.NomType,'String'); NomTypeCell=SeriesData.NomType; if ~isempty(NomTypeCell) Val=get(handles.NomType,'Value'); NomType=NomTypeCell{Val}; % for ilist=1:length(NomType) if isequal(NomType,'_i_j1-j2')|| isequal(NomType,'_i1-i2_j')|| isequal(NomType,'_i1-i2') if isequal(mode,'series(Di)') find_netcpair_civ(hObject, eventdata, handles,Val);% update the menu of pairs depending on the available netcdf files % break end end end %---------------------------------------------------- function ref_j_Callback(hObject, eventdata, handles) mode_list=get(handles.mode,'String'); mode_value=get(handles.mode,'Value'); mode=mode_list{mode_value}; hseries=get(handles.ref_i,'parent'); SeriesData=get(hseries,'UserData'); %NomTypeCell=get(handles.NomType,'String'); NomTypeCell=SeriesData.NomType; if ~isempty(NomTypeCell) Val=get(handles.NomType,'Value'); NomType=NomTypeCell{Val}; % NomType=get(handles.NomType,'String'); if isequal(NomType,'_i_j1-j2')|| isequal(NomType,'_i1-i2_j')|| isequal(NomType,'_i1-i2') if isequal(mode,'series(Dj)') find_netcpair_civ(hObject, eventdata, handles,Val);% update the menu of pairs depending on the available netcdf files % break end end end %---------------------------------------------------- % --- Executes on selection change in ACTION. function ACTION_Callback(hObject, eventdata, handles) 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 nb_builtin=0; for ilist=1:length(list_path) if isequal(list_path{ilist},path_series) nb_builtin=nb_builtin+1; else break end end if nb_builtin==0% the path of series has been changed, reinitialize % series_OpeningFcn(hObject, eventdata, handles) return end % add a new function to the menu if isequal(ACTION,'more...') pathfct=fileparts(path_series); browse_name=fullfile(path_series,'series');%go to UVMAT/SERIES_FCT by default if length(list_path)>nb_builtin browse_name=list_path{end};% initialize browser with the path of the last introduced function end [FileName, PathName, filterindex] = uigetfile( ... {'*.m', ' (*.m)'; '*.m', '.m files '; ... '*.*', 'All Files (*.*)'}, ... 'Pick a file',browse_name); if length(FileName)<2 return end ext_fct=FileName(end-1:end);% to be replaced by fileparts if ~isequal(ext_fct,'.m') msgbox_uvmat('ERROR','a Matlab function .m must be introduced'); return end ACTION=FileName(1:end-2);% ACTION choice updated by the selected item addpath(PathName) eval(['h_function=@' ACTION]); if ~isequal(path_series,PathName) rmpath(PathName) end functions(h_function) % 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+5; nbremove=length(menu_str)-nb_builtin-5; menu_str(nb_builtin+1:end-5)=[]; list_path(nb_builtin+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+1:length(menu_str)-1 series_fct{ilist-nb_builtin}=fullfile(list_path{ilist},[menu_str{ilist} '.m']); end if exist(profil_perso,'file') save(profil_perso,'series_fct','-append') else txt=ver; Release=txt(1).Release; relnumb=str2num(Release(3:4)); if relnumb >= 14 save(profil_perso,'series_fct','-V6') else save(profil_perso, 'series_fct') end end end %check the current path to the selected function PathName=list_path{index_ACTION};%current recorded path if ~isequal(path_series,PathName) CurrentPath=fileparts(which(ACTION)); if ~isequal(CurrentPath,PathName)&&~isequal(CurrentPath,fullfile(PathName,'private')) addpath(PathName) errormsg=check_functions; msgbox_uvmat('CONFIRMATION',[['path ' PathName ' added to the current Matlab pathes'];errormsg]) end end set(handles.path,'String',PathName); %show the path to the senlected function %default setting for the visibility of the GUI elements %set( handles.Field,'Visible','off')%default 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.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') view_TRANSFORM(handles,'off') set(handles.ProjObject_frame,'Visible','off'); set(handles.GetMask,'Visible','off') set(handles.Mask,'Visible','off') set(handles.GetObject,'Visible','off'); set(handles.ProjObject,'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.CoordType,'Enable','off') %set the displayed GUI item needed for input parameters %list_input=feval(ACTION);% input list asked by the selected function varargout=feval(ACTION);% input list asked by the selected function Param_list={}; % RootPath=get(handles.RootPath,'String'); % RootFile=get(handles.RootFile,'String'); %nb_series=length(RootFile); FileExt=get(handles.FileExt,'String'); nb_series=length(FileExt); testima_series=1; %test for a list of images only testima=1; testima_1=1; testciv_series=1; for iview=1:nb_series ext=FileExt{iview}; 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.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.CoordType,'Enable','on') view_TRANSFORM(handles,'on') end case 'GetObject' %hidden by default if isequal(lower(varargout{ilist+1}),'on') set(handles.ProjObject_frame,'Visible','on') set(handles.GetObject,'Visible','on'); end case 'Mask' %hidden by default if isequal(lower(varargout{ilist+1}),'on') set(handles.ProjObject_frame,'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 hseries=get(handles.FieldMenu,'parent'); SeriesData=get(hseries,'UserData'); filename=SeriesData.CurrentInputFile; if exist(filename,'file') get_field(filename) 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 hseries=get(handles.FieldMenu,'parent'); SeriesData=get(hseries,'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 % %---------------------------------------------------------------------- % % --makes a time averaged velocity field % %---------------------------------------------------------------------- % function aver_vel(num_i1,num_i2,num_j1,num_j2,Series) % %handles of the GUI series % % hseries=guidata(Series.hseries);%handles of the GUI series % WaitbarPos=get(hseries.waitbar_frame,'Position'); % Field_list=get(hseries.FieldMenu,'String'); % val=get(hseries.FieldMenu,'Value'); % FieldName=Field_list{val(1)}; % set(hseries.FieldMenu,'Value',val(1))% select only one input field % if isequal(FieldName,'get_field...') % hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI % end % %root input file and type % RootPath=get(hseries.RootPath,'String'); % SubDir=get(hseries.SubDir,'String'); % RootFile=get(hseries.RootFile,'String'); % %NomType=get(hseries.NomType,'String'); % NomType=Series.NomType; % FileExt=get(hseries.FileExt,'String'); % ext=FileExt{1}; % VelType_str=get(hseries.VelTypeMenu,'String'); % VelType_val=get(hseries.VelTypeMenu,'Value'); % VelType{1}=VelType_str{VelType_val}; % % time=0; %default % % number of slices % NbSlice=str2num(get(hseries.NbSlice,'String')); % if isempty(NbSlice) % NbSlice=1; % end % NbSlice_name=num2str(NbSlice); % filebase=fullfile(RootPath{1},RootFile{1}); % Calib=[]; % if exist([filebase '.xml'],'file') % %[error,Heading,nom_type_read,ext_ima_read,time_imadoc,TimeUnit,mode,NbSlice,npx,npy,Calib]=read_imadoc([filebase '.xml']); % [XmlData,warntext]=imadoc2struct([filebase '.xml']); % end % if NbSlice==1 % filebase_mean=[filebase '_mean']; %root name for the result % else % filebase_mean=[filebase '_' NbSlice_name 'mean']; %root name for the results % answeryes=questdlg({['will make average in ' num2str(NbSlice) ' slices'];['results stored as files ' filebase_mean ' ...']}); % if ~isequal(answeryes,'Yes') % return % end % end % siz=size(num_i1); % nbfield2=siz(1); %nb of consecutive fields at each level(burst) % lengthtot=siz(1)*siz(2); % nbfield=floor(lengthtot/(nbfield2*NbSlice));%total number of i indexes (adjusted to an integer number of slices) % nbfield_slice=nbfield*nbfield2;% number of fields per slice % %projection object % GridX=[]; % GridY=[]; % if isfield(Series,'sethandles') % Series.ProjObject=read_set_object(Series.sethandles); % if isfield(Series.ProjObject,'Style') % answeryes=questdlg({['statistics on field series projected on ' Series.ProjObject.Style]}); % if ~isequal(answeryes,'Yes') % return % end % end % end % % %LOOP ON SLICES % for i_slice=1:NbSlice % %select the series of image indices at the level islice % for ifield=1:nbfield % indselect(:,ifield)=((ifield-1)*NbSlice+(i_slice-1))*nbfield2+[1:nbfield2]';%selected indices on the list of files of a slice % end % %name of result file % [filemean,idetect]=... % name_generator(filebase_mean,num_i1(i_slice),num_j1(1),Series.FileExt{1},'_i1-i2_j1-j2',1,num_i2(i_slice+nbfield_slice*NbSlice-1),num_j2(end),Series.SubDir{1}); % % % field=get(handles.civ1,'UserData');%read current selected field type (civ1,civ2...) % itime=0; % dt=[]; % %LOOP ON FIELDS IN A SLICE % test_interpolate=0;%default % for index=1:nbfield*nbfield2 % ifile=indselect(index); % stopstate=get(hseries.RUN,'BusyAction'); % if isequal(stopstate,'queue')% enable STOP command % update_waitbar(hseries.waitbar,WaitbarPos,ifile/(nbfield*nbfield2)) % %name of the current file % [filename,idetect]=name_generator(filebase,num_i1(ifile),num_j1(ifile),Series.FileExt{1},Series.NomType{1},1,num_i2(ifile),num_j2(ifile),Series.SubDir{1}); % %read input file % itime=itime+1; % if isequal(FieldName,'get_field...') % hhget_field=guidata(hget_field);%handles of GUI elements in get_field % hObject=0; % eventdata=0; % SubField=get_field('read_var_names',hObject,eventdata,hhget_field); %read the names of the variables to plot in the get_field GUI % [Data,var_detect]=nc2struct(filename,SubField.ListVarName); %read input data % time(itime)=itime; % dt=1; % Calib_read=[]; % else % [nb_coord,nb_dim,Civ,CivStage,timeread,Data,VelTypeOut,Calib_read]=read_ncfield(filename,VelType{1});%reading the first file % time(itime)=timeread; % if isequal(Civ,1) % Data.CoordType='px';%test for pixel coordinates % if isequal(itime,1) % dt=Data.dt; % elseif ~isequal(Data.dt,dt) % warndlg_uvmat('series with non constant dt, need phys coordinates','ERROR') % return % end % end % end % %increment the detected fields, skip the others % if idetect==0 % warndlg_uvmat(['input file ' filename ' not found'],'ERROR') % %A FAIRE STOCKER LE RESULT ACTUEL S'IL EXISTE % end % % itime=itime+1; % % time(itime)=timeread; % % %coordinate transform % if isempty(Calib) % Calib=Calib_read;%use Calib from xml file in priority, then Calib from the current file % end % if ~isequal(Series.CoordType,'') % Data=feval(Series.CoordType,Data,Calib); % end % %projection on object if defined % if isfield(Series,'ProjObject'); % Data=proj_field(Data,Series.ProjObject); % if isequal(itime,1)%use the positions on the first field for the whole series, ou utiliser grille % if isfield(Data,'Txt')%display error message % warndlg(Data.Txt,'ERROR') % return % end % end % else%remove false vectors and interpolate on the positions of the first field % Data=document_field(Data); % Data.Style='plane'; % end % %%%%%%%%% initiate the average at the first iteration: check list and structure of variables % if ifile==i_slice%first field in the slice % testfalse=0; % ListIndex={}; % testnewcell=1; % %group the variables (fields of 'Data') in cells of variables with the same dimensions % [DimVarIndex,CellVarIndex]=find_field_indices(Data); % VarIndex=CellVarIndex{1}; % ONLY THE FIRST VAR GROUP IS AVERAGED % DimIndex=Data.VarDimIndex{VarIndex(1)};%indices of the dimensions of the first variable (common to all variables in the cell) % MeanData=Data;%transfer heading % MeanData.Time=[time(1) time(end)]; % MeanData.Action=Series.Action;%name of the processing programme % MeanData.ListDimName=Data.ListDimName(DimIndex);%name of dimension % MeanData.DimValue=Data.DimValue(DimIndex);%values of dimension (nbre of vectors) % MeanData.ListVarName=Data.ListVarName; % MeanData.VarDimIndex=Data.VarDimIndex; % MeanData.ListVarAttribute={'Role'};%list of variable attribute names A FAIRE: transferer les autres attributs % testsum=ones(size(VarIndex)); % indexfalse=0; % CoordName={}; % indexremove=[]; % if isfield(Data,'Role') % look for coordinate and flag variables % for ivar=1:length(VarIndex) % VarName=Data.ListVarName{VarIndex(ivar)}; % var_role=Data.Role{VarIndex(ivar)};%'role' of the variable % MeanData.Role{ivar}=var_role; % if isequal(var_role,'falseflag') % indexfalse=ivar; %test for false flag % indexremove=ivar; % FFName=VarName; % testsum(ivar)=0; % eval(['MeanData=rmfield(MeanData,''' VarName ''');']);%remove variable % end % if isequal(var_role,'warnflag') % testsum(ivar)=0; %do not sum warn flag % eval(['MeanData=rmfield(MeanData,''' VarName ''');']);%remove variable % indexremove=[indexremove ivar]; % end % if isequal(var_role,'coord_x')| isequal(var_role,'coord_y')|isequal(var_role,'coord_z') % eval(['MeanData.' VarName '=Data.' VarName ';']); % testsum(ivar)=0; % eval(['CoordName=[CoordName ''' VarName '''];']); % end % if testsum(ivar)~=0 % eval(['MeanData.' VarName '=zeros(size(Data.' VarName '));']);%initialise sum % end % end % end % findsum=find(testsum); % VarIndexSum=VarIndex(findsum);%indices of variables to sum (not coordinates nor flags) % if length(CoordName)==0 % if isempty(DimVarIndex)|isequal(DimVarIndex,0)% no coordinate variable for structured coordinates, prepare histograms % for ilist=1:length(VarIndexSum) % VarName=Data.ListVarName{VarIndexSum(ilist)}; % eval(['MeanData=rmfield(MeanData,''' VarName ''');']);%remove variable % indexremove=[indexremove ilist]; % eval(['[MeanData.' VarName 'hist,MeanData.' VarName 'val]=hist(Data.' VarName ',100);']);%make histo % eval(['sizhist=size(MeanData.' VarName 'hist);']) % if sizhist(1)==1 % eval(['MeanData.' VarName 'hist=MeanData.' VarName 'hist'';']) % end % eval(['maxval=max(MeanData.' VarName 'val);']); % eval(['minval=min(MeanData.' VarName 'val);']); % dC(ilist)=(maxval-minval)/100;%size of the histogram bin % end % else % % icoord=0; % % for ilist=1:length(DimVarIndex) % % VarDim=Data.ListVarName{DimVarIndex(ilist)}; % % icoord=icoord+1; % % % eval(['Coord{' num2str(icord) '}=[' CoordName ''' VarName ''']']); % % %eval(['Data.' CoordName{icoord} '=Data.' CoordName{icoord} '(indsel);']); % % end % end % end % if ~isempty(indexremove) % MeanData.ListVarName(VarIndex(indexremove))=[]; % MeanData.VarDimIndex(VarIndex(indexremove))=[]; % if isfield(MeanData,'Role')%generaliser aus autres attributs % MeanData.Role(VarIndex(indexremove))=[]; % end % end % % END OF INITIALISATION % % end % % % A FAIRE: regular grid if coord_x undefined % if indexfalse~=0 %suppress false data % eval(['testexist=isfield(Data,''' FFName ''');']) % if testexist % eval(['indsel=find(Data.' FFName '==0);']); % for icoord=1:length(CoordName) % eval(['Data.' CoordName{icoord} '=Data.' CoordName{icoord} '(indsel);']); % end % end % end % for ilist=1:length(VarIndexSum) % VarName=Data.ListVarName{VarIndexSum(ilist)}; % if indexfalse~=0 & testexist % eval(['Data.' VarName '=Data.' VarName '(indsel);']); % end % if length(CoordName)==0%no variable use dfor unstructured coordinates % if isempty(DimVarIndex)|isequal(DimVarIndex,0)% no coordinate variable for structured coordinates % % %update histogram with the current field #ifile % str_left=['[MeanData.' VarName 'val,MeanData.' VarName 'hist]=']; % str_right=['hist_update(MeanData.' VarName 'val,MeanData.' VarName 'hist,Data.' VarName ',dC(ilist));']; % eval([str_left str_right]);%update global histo % else % %INTERPOLER % % eval(['MeanData.' VarName '=MeanData.' VarName '+Data.' VarName ';']);%increment sum%CAS x,y change % end % else % if length(CoordName)==2 % eval(['test_interp= ~isequal(Data.' CoordName{1} ',MeanData.' CoordName{1} ... % ')|~isequal(Data.' CoordName{2} ',MeanData.' CoordName{2} ');']) % if test_interp % eval(['Data.' VarName '=griddata_uvmat(Data.' CoordName{1} ',Data.' CoordName{2}... % ',Data.' VarName ',MeanData.' CoordName{1} ',MeanData.' CoordName{2} ');']); % test_interpolate=1; % end % end % eval(['MeanData.' VarName '=MeanData.' VarName '+Data.' VarName ';']);%increment sum % end % end % end % end % if length(CoordName)~=0 | ~isequal(DimVarIndex,0)% no coordinate variable for structured coordinates % for ilist=1:length(VarIndexSum) % VarName=Data.ListVarName{VarIndexSum(ilist)}; % eval(['MeanData.' VarName '=MeanData.' VarName '/itime;']);%normalize sum by the number of fields % end % else % MeanData.NbDim=1; % MeanData.ListDimName={}; % MeanData.DimValue=[]; % for ilist=1:length(VarIndexSum) % VarName=Data.ListVarName{VarIndexSum(ilist)}; % MeanData.ListVarName=[MeanData.ListVarName {[VarName 'val']} {[VarName 'hist']}]; % MeanData.VarDimIndex=[MeanData.VarDimIndex {[ilist]} {[ilist]}]; % MeanData.ListDimName=[MeanData.ListDimName {[VarName 'val']}]; % eval(['MeanData.DimValue=[MeanData.DimValue length(MeanData.' VarName 'val)];']); % end % end % figure % haxes=axes; % plot_field(MeanData,haxes)%plot the resulting average % % change variable names for consitency with civ1 data (need to generalize these programs) % if length(MeanData.ListVarName) >= 4 & isequal(MeanData.ListVarName(1:4), {'X' 'Y' 'U' 'V'}) % MeanData.ListGlobalAttribute={'nb_coord','nb_dim','dt','absolut_time_T0','pixcmx','pixcmy','hart','civ','fix'}; % MeanData.nb_coord=2; % MeanData.nb_dim=2; % MeanData.dt=1; % MeanData.absolut_time_T0=0; % MeanData.pixcmx=1; %pix per cm (1 by default) % MeanData.pixcmy=1; %pix per cm (1 by default) % MeanData.hart=0; % if isequal(Data.CoordType,'px') % MeanData.civ=1; % else % MeanData.civ=0; % end % MeanData.fix=0; % MeanData.ListVarName(1:4)={'vec_X' 'vec_Y' 'vec_U' 'vec_V'}; % MeanData.vec_X=MeanData.X; % MeanData.vec_Y=MeanData.Y; % MeanData.vec_U=MeanData.U; % MeanData.vec_V=MeanData.V; % end % error=struct2nc(filemean,MeanData); %save result file % if isequal(error,0) % if test_interpolate % 'fields interpolated to the positions of the first one' % end % [filemean ' written'] % else % warndlg_uvmat(error,'ERROR') % end % end %---------------------------------------------------------------------- % --project fields on a projection object (e. g. a regular grid), possibly % merge several fields %---------------------------------------------------------------------- %INPUT: %num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) %num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) %num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ ) %num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ) %OTHER INPUTS given by the structure Series function GUI_input=merge_proj(num_i1,num_i2,num_j1,num_j2,Series); %requests for the visibility of input windows in the GUI series (activated directly by the selection in the menu ACTION) if ~exist('num_i1','var') GUI_input={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one') 'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default) 'RootFile';'on';... %root input file name ('on' by default) 'FileExt';'on';... %input file extension ('on' by default) 'NomType';'on';...%type of file indexing ('on' by default) 'NbSlice';'on'; ...%nbre of slices ('off' by default) 'VelTypeMenu';'one';...% menu for selecting the velocity type (civ1,..) options 'off'/'one'/'two', 'off' by default) 'FieldMenu';'one';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) 'CoordType';'on';...%can use a transform function 'off' by default 'GetObject';'on';...%can use projection object ,'off' by default %'GetMask';'on'...%can use mask option ,'off' by default %'PARAMETER'; options: name of the user defined parameter',repeat a line for each parameter ''}; return %exit the function end %------------------------------------------------- hseries=guidata(Series.hseries);%handles of the GUI series WaitbarPos=get(hseries.waitbar_frame,'Position'); %positiopn of waitbar frame %------------------------------------------------- %numbers of view fields (nbre of inputs in RootPath) testcell=iscell(Series.RootFile); if ~testcell Series.RootPath={Series.RootPath}; Series.RootFile={Series.RootFile}; Series.SubDir={Series.SubDir}; Series.FileExt={Series.FileExt}; Series.NomType={Series.NomType}; num_i1={num_i1}; num_i2={num_i2}; num_j1={num_j1}; num_j2={num_j2}; end nbview=length(Series.RootFile);%number of views (file series to merge) nbfield=size(num_i1{1},1)*size(num_i1{1},2);%number of fields in the time series transform=Series.CoordType; % field transform function hhh=which('mmreader'); for iview=1:nbview test_movie(iview)=0; if ~isequal(hhh,'')&& mmreader.isPlatformSupported() if isequal(lower(FileExt{iview}),'.avi') MovieObject{iview}=mmreader(fullfile(RootPath{iview},[RootFile{iview} FileExt{iview}])); test_movie(iview)=1; end end end %Calibration data and timing: read the ImaDoc files mode=''; %default timecell={}; itime=0; NbSlice_calib={}; %test for z index for iview=1:nbview%Loop on views XmlData{iview}=[];%default filebase{iview}=fullfile(Series.RootPath{iview},Series.RootFile{iview}); if exist([filebase{iview} '.xml'],'file') [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']); if isfield(XmlData{iview},'Time') itime=itime+1; timecell{itime}=XmlData{iview}.Time; end if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord') NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1); if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); end end elseif exist([filebase{iview} '.civ'],'file') [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']); itime=itime+1; timecell{itime}=time; XmlData{iview}.Time=time; GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0]; GeometryCalib.Tx=0; GeometryCalib.Ty=0; GeometryCalib.Tz=1; GeometryCalib.dpx=1; GeometryCalib.dpy=1; GeometryCalib.sx=1; GeometryCalib.Cx=0; GeometryCalib.Cy=0; GeometryCalib.f=1; GeometryCalib.kappa1=0; GeometryCalib.CoordUnit='cm'; XmlData{iview}.GeometryCalib=GeometryCalib; if error==1 msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file'); end end end %check coincidence in time multitime=0; if length(timecell)==0 time=[]; elseif length(timecell)==1 time=timecell{1}; elseif length(timecell)>1 multitime=1; for icell=1:length(timecell) if ~isequal(size(timecell{icell}),size(timecell{1})) msgbox_uvmat('WARNING','inconsistent time array dimensions in ImaDoc fields, the time for the first series is used') time=timecell{1}; multitime=0; break end end end if multitime for icell=1:length(timecell) time(icell,:,:)=timecell{icell}; end diff_time=max(max(diff(time))); if diff_time>0 msgbox_uvmat('WARNING',['times of series differ by more than ' num2str(diff_time)]) end end if size(time,2) < num_i2{1}(end) || size(time,3) < num_j2{1}(end)% ime array absent or too short in ImaDoc xml file' time=[]; end % Field and velocity type (the same for all views) Field_str=get(hseries.FieldMenu,'String'); val=get(hseries.FieldMenu,'Value'); FieldName=Field_str(val);%the same set of fields for all views VelType_str=get(hseries.VelTypeMenu,'String'); VelType_val=get(hseries.VelTypeMenu,'Value'); VelType=VelType_str{VelType_val}; %the same for all views if isequal(FieldName,'get_field...') hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI % hhget_field=guidata(hget_field);%handles of GUI elements in get_field SubField=get_field('read_get_field',hObject,eventdata,hget_field); %read the names of the variables to plot in the get_field GUI % if isequal(get(hhget_field.menu_coord,'Visible'),'on') % list_transform=get(hhget_field.menu_coord,'String'); % val_list=get(hhget_field.menu_coord,'Value'); % transform=list_transform{val_list}; % end end %detect whether all the files are 'images' or 'netcdf' testima=0; testvol=0; testcivx=0; testnc=0; FileExt=get(hseries.FileExt,'String'); for iview=1:nbview ext=FileExt{iview}; form=imformats(ext([2:end])); if isequal(lower(ext),'.vol') testvol=testvol+1; elseif ~isempty(form)||isequal(lower(ext),'.avi')% if the extension corresponds to an image format recognized by Matlab testima=testima+1; elseif isequal(ext,'.nc') testnc=testnc+1; end end if testvol msgbox_uvmat('ERROR','volume images not implemented yet') return end if testnc~=nbview && testima~=nbview && testvol~=nbview msgbox_uvmat('ERROR','need a set of images or a set of netcdf files with the same fields as input') return end if ~isequal(FieldName,'get_field...') testcivx=testnc; end %name of output files and directory: % res_subdir=fullfile(Series.RootPath{1},[Series.SubDir{1} '_STAT']); ProjectDir=fileparts(fileparts(Series.RootPath{1}));% preoject directory (GERK) prompt={['result directory (in' ProjectDir ')']}; RootPath=get(hseries.RootPath,'String'); SubDir=get(hseries.SubDir,'String'); if isequal(length(RootPath),1) fulldir=RootPath{1}; subdir='GRID'; res_subdir=fullfile(fulldir,subdir); else def={fullfile(ProjectDir,'0_RESULTS')}; dlgTitle='result directory'; lineNo=1; answer=msgbox_uvmat('INPUT_TXT',dlgTitle,def); fulldir=answer{1}; subdir=[]; dirlist=sort(Series.RootFile); for iview=1:nbview if ~isempty(subdir) subdir=[subdir '-']; end subdir=[subdir dirlist{iview}]; end res_subdir=fullfile(fulldir,subdir); end ext=FileExt{1}; if ~exist(fulldir,'dir') msgbox_uvmat('ERROR',['directory ' fulldir ' needs to be created']) return end if ~exist(res_subdir,'dir') dircur=pwd; cd(fulldir) error=mkdir(subdir); cd(dircur) end filebasesub=fullfile(res_subdir,Series.RootFile{1}); filebase_merge=fullfile(res_subdir,'merged');%root name for the merged files %projection object if isfield(Series,'sethandles') if ishandle(Series.sethandles.set_object) Series.ProjObject=read_set_object(Series.sethandles); if ~isfield(Series.ProjObject,'Style') msgbox_uvmat('ERROR','Undefined projection object style') return end if ~isequal(Series.ProjObject.Style,'plane') msgbox_uvmat('ERROR','The projection object must be a plane') return end end end %MAIN LOOP for ifile=1:nbfield stopstate=get(hseries.RUN,'BusyAction'); if isequal(stopstate,'queue')% enable STOP command from the 'series' interface update_waitbar(hseries.waitbar,WaitbarPos,ifile/nbfield) Amerge=0; %----------LOOP ON VIEWS---------------------- nbtime=0; for iview=1:nbview %name of the current file filename=name_generator(filebase{iview},num_i1{iview}(ifile),num_j1{iview}(ifile),Series.FileExt{iview},Series.NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile),SubDir{iview}); if ~exist(filename,'file') msgbox_uvmat('ERROR',['missing input file' filename]) break end %reading the current file if testima if test_movie(iview) Field{iview}.A=read(MovieObject{iview},num_i1{iview}(ifile)); else Field{iview}.A=read_image(filename,Series.NomType{iview},num_i1{iview}(ifile)); end % TODO: introduce ListVarName npxy=size(Field{iview}.A); Field{iview}.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers Field{iview}.AY=[npxy(1)-0.5 0.5]; Field{iview}.CoordType='px'; Field{iview}.AName='image'; else if testcivx [Field{iview},VelTypeOut]=read_civxdata(filename,FieldName,VelType); else [Field{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data Field{iview}.VarAttribute=SubField.VarAttribute; end if isfield(Field{iview},'Time') timeread(iview)=Field{iview}.Time; nbtime=nbtime+1; end end % coord transform % z index if ~isempty(NbSlice_calib) Field{iview}.ZIndex=mod(num_i1{iview}(ifile)-1,NbSlice_calib{1})+1; end if ~isequal(transform,'') Field{iview}=feval(Series.CoordType,Field{iview},XmlData{iview});%transform to phys if requested end if testcivx Field{iview}=calc_field(FieldName,Field{iview}); end %projection on object (gridded plane) if isfield(Series,'ProjObject') Field{iview}=proj_field(Field{iview},Series.ProjObject); end end %----------END LOOP ON VIEWS---------------------- %merge the nbview fields MergeData=merge_field(Field); if isfield(MergeData,'Txt') msgbox_uvmat('ERROR',MergeData.Txt) return end % generating the name of the merged field mergename=name_generator(filebase_merge,num_i1{iview}(ifile),num_j1{iview}(ifile),Series.FileExt{iview},Series.NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile)); % time: time_i=0;%default if isempty(time)% time from ImaDoc prevails time_i=sum(timeread)/nbtime; else time_i=(time(iview,num_i1{iview}(ifile),num_j1{iview}(ifile))+time(iview,num_i2{iview}(ifile),num_j2{iview}(ifile)))/2; end % recording the merged field if testima %in case of input images an image is produced if isa(MergeData.A,'uint8') bitdepth=8; elseif isa(MergeData.A,'uint16') bitdepth=16; end imwrite(MergeData.A,mergename,'BitDepth',bitdepth); %write xml calibration file siz=size(MergeData.A); npy=siz(1); npx=siz(2); if isfield(MergeData,'VarAttribute')&&isfield(MergeData.VarAttribute{1},'Coord_2')&&isfield(MergeData.VarAttribute{1},'Coord_1') Rangx=MergeData.VarAttribute{1}.Coord_2; Rangy=MergeData.VarAttribute{1}.Coord_1; elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY') Rangx=[MergeData.AX(1) MergeData.AX(end)]; Rangy=[MergeData.AY(1) MergeData.AY(end)]; else Rangx=[0.5 npx-0.5]; Rangy=[npy-0.5 0.5];%default end pxcmx=(npx-1)/(Rangx(2)-Rangx(1)); pxcmy=(npy-1)/(Rangy(1)-Rangy(2)); T_x=-pxcmx*Rangx(1)+0.5; T_y=-pxcmy*Rangy(2)+0.5; GeometryCal.focal=1; GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1]; GeometryCal.Tx_Ty_Tz=[T_x T_y 1]; ImaDoc.GeometryCalib=GeometryCal; t=struct2xml(ImaDoc); t=set(t,1,'name','ImaDoc'); save(t,[filebase_merge '.xml']) display([filebase_merge '.xml saved']) else MergeData.ListGlobalAttribute={'Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'}; MergeData.nb_coord=2; MergeData.nb_dim=2; MergeData.dt=1; MergeData.Time=time_i; error=struct2nc(mergename,MergeData); %save result file if isempty(error) display(['output file ' mergename ' written']) else display(error) end end end end %-------------------------------------------------------------------------- function MergeData=merge_field(Data) % initiate Matlab structure for physical field if isempty(Data)||~iscell(Data) MergeData=[]; return end MergeData=Data{1};%default error=0; nbview=length(Data); if nbview==1 return end for iview=1:nbview if ~isequal(MergeData.ListDimName,Data{iview}.ListDimName) error=1; end if ~isequal(MergeData.ListVarName,Data{iview}.ListVarName) error=1; end % if ~isequal(MergeData.VarDimIndex,Data{iview}.VarDimIndex) % error=1; % end end if error MergeData.Txt='ERROR: attempt at merging fields of incompatible type'; return end %group the variables (fields of 'FieldData') in cells of variables with the same dimensions %----------------------------------------------------------------- [CellVarIndex,NbDim,VarTypeCell]=find_field_indices(Data{1}); %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS % CellVarIndex=cells of variable index arrays ivar_new=0; % index of the current variable in the projected field icoord=0; for icell=1:length(CellVarIndex) if NbDim(icell)==1 continue end VarIndex=CellVarIndex{icell};% indices of the selected variables in the list FieldData.ListVarName VarType=VarTypeCell{icell}; ivar_X=VarType.coord_x; ivar_Y=VarType.coord_y; ivar_FF=VarType.errorflag; if isempty(ivar_X) test_grid=1;%test for input data on regular grid (e.g. image)coordinates else if length(ivar_Y)~=1 warndlg_uvmat('y coordinate missing in proj_field.m','ERROR') return end test_grid=0; end % DimIndices=Data{1}.VarDimIndex{VarIndex(1)};%indices of the dimensions of the first variable (common to all variables in the cell) %case of input fields with unstructured coordinates if ~test_grid for ivar=VarIndex VarName=MergeData.ListVarName{ivar}; for iview=1:nbview eval(['MergeData.' VarName '=[MergeData.' VarName '; Data{iview}.' VarName ';']) end end %case of fields defined on a structured grid else % DimValue=MergeData.DimValue(DimIndices);%set of dimension values testFF=0; for iview=2:nbview % if ~isequal(DimValue,Data{iview}.DimValue(DimIndices)) % MergeData.Txt='ERROR: attempt at merging structured fields with different sizes'; % return % end for ivar=VarIndex VarName=MergeData.ListVarName{ivar}; if isfield(MergeData,'VarAttribute') if length(MergeData.VarAttribute)>=ivar && isfield(MergeData.VarAttribute{ivar},'Role') && isequal(MergeData.VarAttribute{ivar}.Role,'errorflag') testFF=1; end end eval(['MergeData.' VarName '=MergeData.' VarName '+ Data{iview}.' VarName ';']) end end if testFF nbaver=nbview-MergeData.FF; indgood=find(nbaver>0); for ivar=VarIndex VarName=MergeData.ListVarName{ivar}; eval(['MergeData.' VarName '(indgood)=double(MergeData.' VarName '(indgood))./nbaver(indgood);']) end else for ivar=VarIndex VarName=MergeData.ListVarName{ivar}; eval(['MergeData.' VarName '=double(MergeData.' VarName ')./nbview;']) end end end end %----------------------------- function mouse_up_gui(ggg,eventdata,handles) if isequal(get(ggg,'SelectionType'),'alt') display('global CurData, UserData of GUI series') global CurData CurData=get(ggg,'UserData'); evalin('base','global CurData');%make CurData global in the workspace evalin('base','CurData'); %display CurData in the workspace commandwindow % plot_text(CurData) end % %---------------------------------------------------------------------- % % --- display image movie and display time average % %OBSOLETE: A SUPPRIMER % %---------------------------------------------------------------------- % function movie_ima(handles,filecell,filecell_1,num1,num_a,field) % % global hfig1 hfig2 hfig3 poscolbar % global A val HIST % % A=[];aviobj=[]; % % set(hfig1,'UserData','ima')% set the current field state to 'image' % set(handles.zoom,'Value',1); %put zoom on % nom_type=get(handles.file_input,'UserData'); % % field=get(handles.civ1,'UserData'); % % fields=field(1).fields; % set(handles.speed,'Visible','On')%show slider to set movie speed % set(handles.mo_speed_txt,'Visible','On') % % if ~isempty(filecell_1) % file1=get(handles.file1_input,'UserData'); % field1=file1.field; % scal_type1=field1.fields; % vel_type1=field1.vel_type; % filename_1=filecell_1(1);% first file name in the series % else % filename_1=[]; % end % scal_type{1}=field(1).fields; % vel_type{1}=field(1).vel_type; % % display the first field % [A,time,dt,rangx0,rangy0]=view_ima(handles,cell2mat(filecell(1)),filename_1,num1(1),num_a(1)); % % % calculate the histogram of the first image % nxy=size(A); % ndim=length(nxy); % if ndim==2 % case of B/W images % nxy(3)=1; % end % C=reshape(A,nxy(1)*nxy(2),nxy(3)); % Amaxmax=double(max(max(max(A)))); % Aminmin=double(min(min(min(A)))); % if isa(C,'uint8')|isa(C,'uint16') % C=double(C); % dC=1; % else % dC=(Amaxmax-Aminmin)/100; % end % val=[Aminmin:dC:Amaxmax];% define bins for histogram % HIST=hist(C,val);% initiate the global histogram % if ndim==2, HIST=HIST'; end; % % auto_scale=get(handles.auto_scale,'Value'); % min_input=str2num(get(handles.min_input,'String'));% select the minimum % max_input=str2num(get(handles.scale_input,'String'));% select the max % zoomstate=get(handles.zoom,'Value'); % % if isequal(get(handles.window_input,'String'),'avi'), % basename=get(handles.file_input,'String'); % prompt = {'file name';'frames per second';'frame resolution ([nbpixels x y])';'axis position relative to the frame'}; % dlg_title = 'select properties of the output avi movie'; % num_lines= 1; % def = {[basename '_out.avi'];'5';'[1024 768]';'[0.05 0.07 0.87 0.88]'}; % answer = inputdlg(prompt,dlg_title,num_lines,def); % aviname=answer{1}; % fps=str2num(answer{2}); % if exist(aviname,'file')==2 % delete(aviname); % end; % aviobj=avifile(aviname,'Compression','None','fps',fps); % % %display first view for tests % figure(2); % hh=get(gcf,'CurrentAxes'); % if isempty(hh), % hfig1=axes; % else % hfig1=hh; % end; % if isequal(filecell_1,{}) % filename_1=[]; % else % filename_1=cell2mat(filecell_1(1)); % end % poscolbar=[0.93 0.15 0.02 0.7]; % view_ima(handles,cell2mat(filecell(1)),filename_1,num1(1),num_a(1));% show the first field % nbpix=eval(answer{3}); % set(gcf,'Position',[1 1 nbpix])% resolution XVGA % set(hfig1,'Position',eval(answer{4})); % % msgbox({'adjust figure 2 with its matlab edit menu ' ;... % 'then type any keyboard key to get the avi movie as a copy of figure 2 display'}) % pause; % hh=colorbar; % poscolbar=get(hh,'Position'); % end % % %%%%%%%%%%%%%%%% % %mask and usrdfct % maskname=[]; %default % if isequal(get(handles.mask_test,'Value'),1) % maskbase=get(handles.mask_test,'UserData'); % end % % image or scalar processing programme set by user % % if (get(handles.usr_fct,'Value')==1) % % usrfct=get(handles.usr_fct,'UserData'); % % else % % usrfct=''; % % end % nburst=1; % nburst(1) =nbre of names in filename= nbre of bursts % set(handles.text_display_1,'String',['image movie']) % nbfield=length(filecell); % if nbfield >1 % for ifile=2:nbfield % stopstate=get(handles.run0,'BusyAction'); % if isequal(stopstate,'queue')% enable STOP command % pausetime=1.02-get(handles.speed,'Value'); % pause(pausetime) % if isequal(get(handles.mask_test,'Value'),1) % maskname=name_generator(maskbase,num1(ifile),1,'.png','png_series'); % end % if isequal(AName{1},'image') % A=read_image(cell2mat(filecell(ifile)),num1(ifile),maskname);% read the first image, num2 is the counter for avi files % else % read the first field from the netcdf file, imposing the pixel positions in the selected domain % [A,time(ifile),dtr,rgx,rgy,vt_out,erread]=read_scalar(filecell{ifile},vel_type,scal_type,rangx0,rangy0,nxy,maskname); % if erread==1; % errordlg({['no spatial derivative in ' filecell{ifile}]; 'run patch first'}); return % elseif erread==2; % errordlg(['no field ' vel_type{1} ' in ' filecell{ifile}]); return % elseif erread==3; % errordlg(['scalar ' scal_type{1} ' not found in' filecell{ifile}]); return % elseif erread==4; % errordlg(['all points aligned in' filecell{ifile}]); return % end % end % % % read the second image % if ~isempty(filecell_1) % if isequal(scal_type{1},'image') % A1=read_image(cell2mat(filecell_1(ifile)),num1(ifile),maskname);% read the second image, num2 is the counter for avi files % Avalue_1=double(A1(indy,indx,:)); % else % read the second field from the netcdf file, imposing the pixel positions in the selected domain % [Avalue_1,time1(ifile),dtr,rgx,rgy,vt_out,erread]=read_scalar(filecell_1{ifile},{vel_type1},{scal_type1},rangx0,rangy0,npxy,maskname,usrfct); % if erread==1; % errordlg({['no spatial derivative in ' filecell_1{ifile}]; 'run patch first'}); return % elseif erread==2; % errordlg(['no field ' vel_type1 ' in ' filecell_1{ifile}]); return % elseif erread==3; % errordlg(['scalar ' scal_type1 ' not found in' filecell_1{ifile}]); return % elseif erread==4; % errordlg(['all points aligned in' filecell_1{ifile}]); return % end % end % time(ifile)=(time(ifile)+time1(ifile))/2; % Avalue=Avalue-Avalue_1; % end % set(handles.abs_time,'String',time); % set(handles.field_counter,'String',num2str(num1(ifile))); % set(handles.a_input,'String',num2stra(num_a(ifile),nom_type)); % C=reshape(A,nxy(1)*nxy(2),nxy(3));% reshape in a vector % [val,HIST]=hist_update(val,HIST,C,dC); % [h,Amin,Amax]=plot_image(hfig1,rangx0,rangy0,1,scal_type{1},auto_scale,min_input,max_input,poscolbar,A); % set(handles.min_input,'String',num2str(Amin));% select the minimum % set(handles.scale_input,'String',num2str(Amax));% select the minimum % if ~isequal(aviobj,[]), % % mov=getframe(hfig1); % mov=getframe(gcf); % aviobj=addframe(aviobj,mov);end % if (get(handles.zoom,'Value') == get(handles.zoom,'Max')),zoom on,end % set(handles.field_counter,'String',num2str(num1(ifile))) % % end % end % end % end % aviobj=close(aviobj); % % %plot global image histogram % HIST=HIST/(nbfield*nxy(1)*nxy(2));% normalized by the number of points % axes(hfig2) %in main window % if ndim==2 % plot(val,HIST) % else % plot(val,HIST(:,1),'r',val,HIST(:,2),'g',val,HIST(:,3),'b') % end % residu=1-sum(HIST,1); % title(['histo, residu ' num2str(residu)]) % grid on % axes(hfig3) % cla %clear the second histogram window % %%%%%%%%%%%%% 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 %-------------------------------------------------------- %----------------------------------------------------------- % find the times corresponding to the first and last indices of a series % function displ_time(handles,times) hseries=get(handles.last_i,'parent'); SeriesData=get(hseries,'UserData');% first_i=str2num(get(handles.first_i,'String')); first_j=str2num(get(handles.first_j,'String')); last_i=str2num(get(handles.last_i,'String')); last_j=str2num(get(handles.last_j,'String')); % index_civ=get(handles.list_pair_civ,'Value'); % NomType=get(handles.NomType,'String'); NomType=SeriesData.NomType; mode_list=get(handles.mode,'String'); index_mode=get(handles.mode,'Value'); mode=mode_list{index_mode}; % ind_shift=0;%default time_first=[]; time_last=[]; if ~isfield(SeriesData,'Time') SeriesData.Time{1}=[]; end for iview=1:length(NomType) time_first_cell{iview}='?'; time_last_cell{iview}='?';%default time=SeriesData.Time{iview}; if isequal(NomType{iview},'_i1-i2_j')|isequal(NomType{iview},'_i_j1-j2')|isequal(NomType{iview},'#_ab')|isequal(NomType{iview},'_i1-i2') 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(times); if siz(1)>=last_i & siz(2)>=last_j 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 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 selection change in VelTypeMenu. function VelTypeMenu_Callback(hObject, eventdata, handles) % VelTypeList=get(handles.VelTypeMenu,'String'); % VelTypeIndex=get(handles.VelTypeMenu,'Value'); % VelTypeCell=get(handles.VelType,'String'); % VelTypeCell{1}=VelTypeList{VelTypeIndex}; % set(handles.VelType,'String',VelTypeCell) %-------------------------------------------------------------------- % --- Executes on button press in GetObject. function GetObject_Callback(hObject, eventdata, handles) hseries=get(handles.GetObject,'parent'); SeriesData=get(hseries,'UserData'); value=get(handles.GetObject,'Value'); if value set(handles.GetObject,'BackgroundColor',[1 1 0])%put unactivated buttons to yellow DataInit.ParentButton=handles.GetObject; hset_object=findobj(allchild(0),'Name','set_object');%find the set_object interface handle if ishandle(hset_object) [SeriesData.hset_object,SeriesData.sethandles]=set_object(DataInit); %open the set_object interface else DataInit.TITLE='POINTS';%default option [SeriesData.hset_object,SeriesData.sethandles]=set_object(DataInit); %open the set_object interface end else set(handles.GetObject,'BackgroundColor',[0 1 0])%put activated buttons to green if isfield(SeriesData,'hset_object')&& ishandle(SeriesData.hset_object) close(SeriesData.hset_object) end end set(hseries,'UserData',SeriesData) %-------------------------------------------------------------- function GetMask_Callback(hObject, eventdata, handles) value=get(handles.GetMask,'Value'); if value errordlg('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)), errordlg('Please put the help file uvmat_doc.html in the directory UVMAT/UVMAT_DOC') else web([helpfile '#series']) end