%'uvmat': function associated with the GUI 'uvmat.fig' for images and data field visualization %------------------------------------------------------------------------ % function huvmat=uvmat(input) % %OUTPUT % huvmat=current handles of the GUI uvmat.fig %% % %INPUT: % input: input file name (if character chain), or input image matrix to % visualize, or Matlab structure representing netcdf fieldname (with fieldname % ListVarName....) % %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA % Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr. %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA % This open 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 (open UVMAT/COPYING.txt) for more details. %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA % % Information stored on the interface:(use 'Export/field in workspace' in % the menu bar of uvmat to retrieve it) % .OpenParam: structure containing parameters defined when uvmat is opened % .PosColorbar: position (1x4 vector)of the colorbar (relative to the fig uvmat) % .PosSetObject: position of set_object % .PosGeometryCalib: size of set_object % .NbBuiltin: nbre of functions always displayed in transform_fct menu % .Object: cell array of structures representing the current projection objects, as produced by 'set_object.m'={[]} by default % .NewSeries: =0/1 flag telling whether a new field series has been opened % .FileName_1: name of the current second field (used to detect a constant field during file scanning) % .FileType: current file type, as defined by the fct get_file_type.m) % .i1_series,.i2_series,.j1_series,.j1_series: series of i1,i2,j1,j2 indices detected in the input dir,set by the fct find_file_series % .MovieObject: current movie object % .TimeUnit: unit for time % .XmlData: cell array of 1 or 2 structures representing the xml files associated with the input fieldname (containing timing and geometry calibration) % .Field: cell array of 1 or 2 structures representing the current input field(s) % .PlotAxes: field structure representing the current field plotted on the main axes (used for mouse operations) % .HistoAxes: idem for histogram axes % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% DATA FLOW (for run0_Callback) %%%%%%%%%%%%%%%%%%%%: % % % 1) Input filenames are determined by MenuBrowse (first field), MenuBrowse_1 % (second field), or by the stored file name .FileName_1, or as an input of uvmat. % 2) These functions call 'uvmat/display_file_name.m' which detects the file series, and fills the file index boxes % 3) Then 'uvmat/update_rootinfo.m' Updates information about a new field series (indices to scan, timing, calibration from an xml file) % 4) Then fieldname are opened and visualised by the main sub-function 'uvmat/refresh_field.m' % The function first reads the name of the input file(s) (one or two) from the edit boxes of the GUI % It then reads the input file(s) with the function read_field.m and perform the following list of operations: % % %%%%%%%% structure of uvmat/refresh_field.m %%%%%%%% % % Main input open second input open_1 % | | % read_field.m read_field.m % | | % Field{1} Field{2} % | | % --->transform fct<--- transform (e.g. phys.m) and combine input fieldname % | % (calc_tps.m) calculate tps coefficients (for filter projection or spatial derivatives). % | % UvData.Field-------------->histogram % _____________|____________ % | | % proj_field.m proj_field.m project the field on the projection objects (use calc_field.m) % | | % UvData.PlotAxes ViewData.PlotAxes (on view_field) % | | % plot_field.m (uvmat) plot_field.m (view_field) plot the projected fieldname % % %%%%%%%%%%%%%% SCALARS: %%%%%%%%%%%%??%%% % scalars are displayed either as an image or countour plot, either as a color of % velocity vectors. The scalar values in the first case is represented by % UvData.Field.A, and by UvData.Field.C in the second case. The corresponding set of X % and Y coordinates are represented by UvData.Field.AX and UvData.Field.AY, and .X and % .Y for C (the same as velocity vectors). If A is a nxxny matrix (scalar % on a regtular grid), then .AX andf.AY contains only two elements, represneting the % coordinates of the four image corners. The scalar name is represented by % the strings .AName and/or .CName. % If the scalar exists in an input open (image or scalar stored under its % name in a netcdf open), it is directly read at the level of Field{1}or Field{2}. % Else only its name AName is recorded in Field{i}, and its field is then calculated %by the fuction calc_scal after the coordinate transform or after projection on an edit_object % Properties attached to plotting figures (standard Matlab properties): % 'CurrentAxes'= gca or get(gcf,'CurrentAxes'); % 'CurrentPoint'=get(gcf,'CurrentPoint'): figure coordinates of the point over which the mouse is positioned % 'CurrentCharacter'=get(gcf,'CurrentCharacter'): last character typed over the figure where the mouse is positioned % 'WindowButtonMotionFcn': function permanently called by mouse motion over the figure % 'KeyPressFcn': function called by pressing a key on the key board % 'WindowButtonDownFcn': function called by pressing the mouse over the figure % 'WindowButtonUpFcn': function called by releasing the mouse pressure over the figure % Properties attached to plotting axes: % 'CurrentPoint'=get(gca,'CurrentPoint'); (standard Matlab) same as for the figure, but position in plot coordinates. % AxeData:=get(gca,'UserData'); % AxeData.Drawing = create: create a new object % = deform: modify an existing object by moving its defining create % = off: no current drawing action % = translate: translate an existing object % = calibration: move a calibration point % = CheckZoom: isolate a subregion for CheckZoom in=1 if an object is being currently drawn, 0 else (set to 0 by releasing mouse button) % .CurrentOrigin: Origin of a curently drawn edit_object % .CurrentLine: currently drawn menuline (A REVOIR) % .CurrentObject: handle of the currently drawn edit_object % .CurrentRectZoom: current rectangle used for CheckZoom % Properties attached to projection objects (create, menuline, menuplane...): % 'Tag'='proj_object': for all projection objects % ObjectData.Type=...: style of projection object: % .ProjMode % .Coord: defines the position of the object % .XMin,YMin.... % .XMax,YMax.... % .DX,DY,DZ % .Phi, .Theta, .Psi : Euler angles % .X,.Y,.U,.V.... : field data projected on the object % .IndexObj: index in the list of UvData.Object %during plotting % .plotaxes: handles of the current axes used to plot the result of field projection on the object % .plothandle: vector of handle(s) of the object graphic represnetation in all the opened plotting axes % To each projection object #iobj, corresponds an axis % Object{iobj}.plotaxes and nbobj representation graphs Object{iobj}.plothandles(:) (where nbobj is the % nbre of current objects opened in uvmat. Note that Object{iobj}.plothandles(iobj)=[] : an object is not represented in its own projection field; %------------------------------------------------------------------------ %------------------------------------------------------------------------ % I - MAIN FUNCTION uvmat %------------------------------------------------------------------------ %------------------------------------------------------------------------ function varargout = uvmat(varargin) % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name', mfilename, ... 'gui_Singleton', gui_Singleton, ... 'gui_OpeningFcn', @uvmat_OpeningFcn, ... 'gui_OutputFcn', @uvmat_OutputFcn, ... 'gui_LayoutFcn', [], ... 'gui_Callback', []); if nargin && ischar(varargin{1})&& ~isempty(regexp(varargin{1},'_Callback','once')) 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 the GUI uvmat is made visible. function uvmat_OpeningFcn(hObject, eventdata, handles, input ) %------------------------------------------------------------------------ %% Choose default command menuline output for uvmat (standard GUI) handles.output = hObject; %% Update handles structure (standard GUI) guidata(hObject, handles); %% add the path to uvmat (useful if uvmat has been opened in the working directory and a working directory change occured) path_uvmat=fileparts(which('uvmat')); %% set the position of colorbar and ancillary GUIs: set(hObject,'Units','Normalized') movegui(hObject,'center') UvData.OpenParam.PosColorbar=[0.805 0.022 0.019 0.445]; UvData.OpenParam.PosSetObject=[-0.05 -0.03 0.3 0.7]; %position for set_object UvData.OpenParam.PosGeometryCalib=[0.95 -0.03 0.28 1 ];%position for geometry_calib (TO IMPROVE) % UvData.OpenParam.CalSize=[0.28 1]; % UvData.PlotAxes=[];%initiate the record of plotted field % UvData.axes2=[]; % UvData.axes1=[]; AxeData.LimEditBox=1; %initialise AxeData set(handles.PlotAxes,'UserData',AxeData) %% set functions for the mouse and keyboard set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function set(hObject,'WindowButtonUpFcn',{'mouse_up',handles}) set(hObject,'DeleteFcn',{@closefcn})% %% initialisation % set(handles.ListObject,'Value',1)% default: empty projection objectproj_field % set(handles.ListObject,'String',{''}) % set(handles.ListObject_1,'Value',1)% default: empty projection objectproj_field % set(handles.ListObject_1,'String',{''}) set(handles.FieldName,'Value',1) set(handles.FieldName,'string',{''}) UvData.Object={[]}; %% TRANSFORM menu: builtin fcts transform_menu={'';'sub_field';'phys';'phys_polar'}; UvData.OpenParam.NbBuiltin=numel(transform_menu); %number of functions transform_path=fullfile(path_uvmat,'transform_field'); path_list=cell(UvData.OpenParam.NbBuiltin,1); path_list{1}=''; for ilist=2:UvData.OpenParam.NbBuiltin path_list{ilist}=transform_path; % set transform_path to the path_list end %% load the list of previously browsed files in menus Open, Open_1 and transform_fct dir_perso=prefdir; % path to the directory .matlab for personal data profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab if exist(profil_perso,'file') h=load (profil_perso); if isfield(h,'MenuFile')% load the menu of previously opened files for ifile=1:min(length(h.MenuFile),5) eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});']) eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',h.MenuFile{ifile});']) end end if isfield(h,'transform_fct') && iscell(h.transform_fct) % load the menu of transform fct set by user for ilist=1:length(h.transform_fct); if exist(h.transform_fct{ilist},'file') [path,file]=fileparts(h.transform_fct{ilist}); transform_menu=[transform_menu; {file}]; path_list=[path_list; {path}]; end end end end transform_menu=[transform_menu;{'more...'}];%append the option more.. to the menu set(handles.transform_fct,'String',transform_menu)% display the menu of transform fcts set(handles.transform_fct,'UserData',path_list)% store the corresponding list of path in UserData of uicontrol transform_fct set(handles.path_transform,'String','') set(handles.path_transform,'UserData',[]) %% case of an input argument for uvmat testinputfield=0; inputfile=[]; Field=[]; if exist('input','var') if ishandle(handles.UVMAT_title) delete(handles.UVMAT_title) end if isstruct(input) if isfield(input,'InputFile') inputfile=input.InputFile; end if isfield(input,'TimeIndex') set(handles.i1,num2str(input.TimeIndex)) end if isfield(input,'FieldsString') UvData.FieldsString=input.FieldsString; end elseif ischar(input)% file name introduced as input inputfile=input; elseif isnumeric(input)%simple matrix introduced as input sizinput=size(input); if sizinput(1)<=1 || sizinput(2)<=1 msgbox_uvmat('ERROR','bad input for uvmat: file name, structure or numerical matrix accepted') return end UvData.Field.ListVarName={'A','coord_y','coord_x'}; UvData.Field.VarDimName={{'coord_y','coord_x'},'cord_y','coord_x'}; UvData.Field.A=input; UvData.Field.coord_x=[0.5 size(input,2)-0.5]; UvData.Field.coord_y=[size(input,1)-0.5 0.5]; testinputfield=1; end else %% check the path and date of modification of all functions in uvmat path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat [infomsg,date_str,svn_info]=check_files;%check the path of the functions called by uvmat.m date_str=['last modification: ' date_str]; if ishandle(handles.UVMAT_title) set(handles.UVMAT_title,'String',... [{'Copyright LEGI UMR 5519 /CNRS-UJF-Grenoble INP, 2010'};... {'GNU General Public License'};... {path_to_uvmat};... {date_str};... infomsg]); end end set(handles.uvmat,'UserData',UvData) if ~isempty(inputfile) %%%%% display the input field %%%%%%% display_file_name(handles,inputfile) %%%%%%% testinputfield=1; end set_vec_col_bar(handles) %update the display of color code for vectors %------------------------------------------------------------------------ % --- Outputs from this function are returned to the command menuline. function varargout = uvmat_OutputFcn(hObject, eventdata, handles) varargout{1} = handles.output;% the only output argument is the handle to the GUI figure %------------------------------------------------------------------------ % --- executed when closing uvmat: delete or desactivate the associated figures if exist function closefcn(gcbo,eventdata) %------------------------------------------------------------------------ hh=findobj(allchild(0),'tag','view_field'); if ~isempty(hh) delete(hh) end hh=findobj(allchild(0),'tag','geometry_calib'); if ~isempty(hh) delete(hh) end hh=findobj(allchild(0),'tag','set_object'); if ~isempty(hh) hhh=findobj(hh,'tag','PLOT'); set(hhh,'enable','off') end %------------------------------------------------------------------------ %------------------------------------------------------------------------ % II - FUNCTIONS FOR INTRODUCING THE INPUT FILES % automatically sets the global properties when the rootfile name is introduced % then activate the view-field action if selected % it is activated either by clicking on the RootPath window or by the % browser %------------------------------------------------------------------------ %------------------------------------------------------------------------ % --- Executes on the menu Open/Browse... % search the files, recognize their type according to their name and fill the rootfile input windows function MenuBrowse_Callback(hObject, eventdata, handles) [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles); %oldfile=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]; oldfile=fullfile(RootPath,SubDir); if isempty(oldfile)||isequal(oldfile,'') %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,'MenuFile_1') oldfile=h.MenuFile_1; end end end [FileName, PathName] = uigetfile({'*.*','All Files(*.*)'},'Pick a file',oldfile); if ~ischar(FileName),return,end %abandon if the browser is cancelled fileinput=[PathName FileName];%complete file name %% display the selected field and related information display_file_name( handles,fileinput) % ----------------------------------------------------------------------- % --- Open again the file whose name has been recorded in MenuFile_1 function MenuFile_1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ fileinput=get(handles.MenuFile_1,'Label'); display_file_name( handles,fileinput) % ----------------------------------------------------------------------- % --- Open again the file whose name has been recorded in MenuFile_2 function MenuFile_2_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ fileinput=get(handles.MenuFile_2,'Label'); display_file_name(handles,fileinput) % ----------------------------------------------------------------------- % --- Open again the file whose name has been recorded in MenuFile_3 function MenuFile_3_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ fileinput=get(handles.MenuFile_3,'Label'); display_file_name(handles,fileinput) % ----------------------------------------------------------------------- % --- Open again the file whose name has been recorded in MenuFile_4 function MenuFile_4_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ fileinput=get(handles.MenuFile_4,'Label'); display_file_name(handles,fileinput) % ----------------------------------------------------------------------- % --- Open again the file whose name has been recorded in MenuFile_5 function MenuFile_5_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ fileinput=get(handles.MenuFile_5,'Label'); display_file_name(handles,fileinput) %------------------------------------------------------------------------ % --- Executes on the menu Open/Browse_1 for the second input field, % search the files, recognize their type according to their name and fill the rootfile input windows function MenuBrowse_1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ RootPath=get(handles.RootPath,'String'); [FileName, PathName] = uigetfile({'*.*','All Files(*.*)'},'Pick a file',RootPath); if ~ischar(FileName),return,end %abandon if the browser is cancelled fileinput_1=[PathName FileName];%complete file name % refresh the current displayed field set(handles.SubField,'Value',1) display_file_name(handles,fileinput_1,2) %update list of recent files in the menubar MenuFile_1=fileinput_1; 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_1_1,'Label',MenuFile_1) set(handles.MenuFile_2_1,'Label',MenuFile_2) set(handles.MenuFile_3_1,'Label',MenuFile_3) set(handles.MenuFile_4_1,'Label',MenuFile_4) set(handles.MenuFile_5_1,'Label',MenuFile_5) dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat else txt=ver('MATLAB'); Release=txt.Release; relnumb=str2double(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 % ----------------------------------------------------------------------- % --- Open again as second field the file whose name has been recorded in MenuFile_1 function MenuFile_1_1_Callback(hObject, eventdata, handles) % ----------------------------------------------------------------------- fileinput_1=get(handles.MenuFile_1_1,'Label'); set(handles.SubField,'Value',1) display_file_name(handles,fileinput_1,2) % ----------------------------------------------------------------------- % --- Open again as second field the file whose name has been recorded in MenuFile_2 function MenuFile_2_1_Callback(hObject, eventdata, handles) % ----------------------------------------------------------------------- fileinput_1=get(handles.MenuFile_2_1,'Label'); set(handles.SubField,'Value',1) display_file_name(handles,fileinput_1,2) % ----------------------------------------------------------------------- % --- Open again as second field the file whose name has been recorded in MenuFile_3 function MenuFile_3_1_Callback(hObject, eventdata, handles) % ----------------------------------------------------------------------- fileinput_1=get(handles.MenuFile_3_1,'Label'); set(handles.SubField,'Value',1) display_file_name(handles,fileinput_1,2) % ----------------------------------------------------------------------- % --- Open again as second field the file whose name has been recorded in MenuFile_4 function MenuFile_4_1_Callback(hObject, eventdata, handles) % ----------------------------------------------------------------------- fileinput_1=get(handles.MenuFile_4_1,'Label'); set(handles.SubField,'Value',1) display_file_name(handles,fileinput_1,2) % ----------------------------------------------------------------------- % --- Open again as second field the file whose name has been recorded in MenuFile_5 function MenuFile_5_1_Callback(hObject, eventdata, handles) % ----------------------------------------------------------------------- fileinput_1=get(handles.MenuFile_5_1,'Label'); set(handles.SubField,'Value',1) display_file_name(handles,fileinput_1,2) %------------------------------------------------------------------------ % --- Called by action in RootPath edit box function RootPath_Callback(hObject,eventdata,handles) %------------------------------------------------------------------------ % read the current input file name: [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles); if ~exist(fullfile(RootPath,SubDir),'dir') msgbox_uvmat('ERROR',['directory ' fullfile(RootPath,SubDir) ' does not exist']) return end % detect the file type, get the movie object if relevant, and look for the corresponding file series: [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]); % initiate the input file series and refresh the current field view: update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,1); %----------------------------------------------------------------------- % --- Called by action in RootPath_1 edit box function RootPath_1_Callback(hObject,eventdata,handles) % ----------------------------------------------------------------------- % update_rootinfo_1(hObject,eventdata,handles) [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles); if ~exist(fullfile(RootPath,SubDir),'dir') msgbox_uvmat('ERROR',['directory ' fullfile(RootPath,SubDir) ' does not exist']) return end % detect the file type, get the movie object if relevant, and look for the corresponding file series: [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]); % initiate the input file series and refresh the current field view: update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,2); %------------------------------------------------------------------------ % --- Called by action in RootFile edit box function SubDir_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ %refresh the menu of input fieldname Fields_Callback(hObject, eventdata, handles); % refresh the current field view run0_Callback(hObject, eventdata, handles); %------------------------------------------------------------------------ % --- Called by action in RootFile edit box function RootFile_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ RootPath_Callback(hObject,eventdata,handles) %----------------------------------------------------------------------- % --- Called by action in RootFile_1 edit box function RootFile_1_Callback(hObject, eventdata, handles) % ----------------------------------------------------------------------- RootPath_1_Callback(hObject,eventdata,handles) %------------------------------------------------------------------------ % --- Called by action in FileIndex edit box function FileIndex_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String')); set(handles.i1,'String',num2str(i1)); set(handles.i2,'String',num2str(i2)); set(handles.j1,'String',num2str(j1)); set(handles.j2,'String',num2str(j2)); % refresh the current field view run0_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ % --- Called by action in FileIndex_1 edit box function FileIndex_1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ run0_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ % --- Called by action in NomType edit box function NomType_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ i1=str2num(get(handles.i1,'String')); i2=str2num(get(handles.i2,'String')); j1=str2num(get(handles.j1,'String')); j2=str2num(get(handles.j2,'String')); FileIndex=fullfile_uvmat('','','','',get(handles.NomType,'String'),i1,i2,j1,j2); set(handles.FileIndex,'String',FileIndex) % refresh the current settings and refresh the field view RootPath_Callback(hObject,eventdata,handles) %------------------------------------------------------------------------ % --- Called by action in NomType edit box function NomType_1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ i1=str2num(get(handles.i1,'String')); i2=str2num(get(handles.i2,'String')); j1=str2num(get(handles.j1,'String')); j2=str2num(get(handles.j2,'String')); FileIndex=fullfile_uvmat('','','','',get(handles.NomType_1,'String'),i1,i2,j1,j2); set(handles.FileIndex_1,'String',FileIndex) % refresh the current settings and refresh the field view RootPath_1_Callback(hObject,eventdata,handles) %------------------------------------------------------------------------ % --- Fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput' function display_file_name(handles,fileinput,index) %------------------------------------------------------------------------ %% look for the input file existence if ~exist(fileinput,'file') msgbox_uvmat('ERROR',['input file ' fileinput ' does not exist']) return end %% set the mouse pointer to 'watch' set(handles.uvmat,'Pointer','watch') set(handles.RootPath,'BackgroundColor',[1 1 0]) drawnow %% define the relevant handles for the first field series (index=1) or the second file series (index=2) if ~exist('index','var') index=1; end if index==1 handles_RootPath=handles.RootPath; handles_SubDir=handles.SubDir; handles_RootFile=handles.RootFile; handles_FileIndex=handles.FileIndex; handles_NomType=handles.NomType; handles_FileExt=handles.FileExt; elseif index==2 handles_RootPath=handles.RootPath_1; handles_SubDir=handles.SubDir_1; handles_RootFile=handles.RootFile_1; handles_FileIndex=handles.FileIndex_1; handles_NomType=handles.NomType_1; handles_FileExt=handles.FileExt_1; set(handles.RootPath_1,'Visible','on') set(handles.RootFile_1,'Visible','on') set(handles.SubDir_1,'Visible','on'); set(handles.FileIndex_1,'Visible','on'); set(handles.FileExt_1,'Visible','on'); set(handles.NomType_1,'Visible','on'); end %% detect root name, nomenclature and indices in the input file name: [FilePath,FileName,FileExt]=fileparts(fileinput); % detect the file type, get the movie object if relevant, and look for the corresponding file series: % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]); %% open the file or fill the GUI uvmat according to the detected file type switch FileType case '' msgbox_uvmat('ERROR','invalid input file type') case 'txt' edit(fileinput) case 'figure' %display matlab figure hfig=open(fileinput); set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function case 'xml' % edit xml files t=xmltree(fileinput); % the xml file marks a project or project link, open datatree_browser if strcmp(get(t,1,'name'),'Project')&& exist(regexprep(fileinput,'.xml$',''),'dir') datatree_browser(fileinput) else % other xml file, open the xml editor editxml(fileinput); end case 'xls'% Excel file opended by editxml editxml(fileinput); otherwise set(handles_RootPath,'String',RootPath); rootname=fullfile(RootPath,SubDir,RootFile); set(handles_SubDir,'String',['/' SubDir]); set(handles_RootFile,'String',['/' RootFile]); %display the separator indices=fileinput(length(rootname)+1:end); indices(end-length(FileExt)+1:end)=[]; %remove extension set(handles_FileIndex,'String',indices); set(handles_NomType,'String',NomType); set(handles_FileExt,'String',FileExt); if index==1 % fill file index counters if the first file series is opened set(handles.i1,'String',num2str(i1)); set(handles.i2,'String',num2str(i2)); set(handles.j1,'String',num2stra(j1,NomType)); set(handles.j2,'String',num2stra(j2,NomType)); else %read the current field index to synchronise with the first series i1_s=str2num(get(handles.i1,'String')); i2_0=str2num(get(handles.i2,'String')); if ~isempty(i2_0) i2_s=i2_0; else i2_s=i2; end j1_0=stra2num(get(handles.j1,'String')); if ~isempty(j1_0) j1_s=j1_0; else j1_s=j1; end j2_0=stra2num(get(handles.j2,'String')); if ~isempty(j2_0) j2_s=j2_0; else j2_s=j2; end end % synchronise indices of the second input file if it exists if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers Input=read_GUI(handles.InputFile); if ~isfield(Input,'RootPath_1')||strcmp(Input.RootPath_1,'"') Input.RootPath_1=Input.RootPath; end if ~isfield(Input,'SubDir_1')||strcmp(Input.SubDir_1,'"') Input.SubDir_1=Input.SubDir; end if ~isfield(Input,'RootFile_1')||strcmp(Input.RootFile_1,'"') Input.RootFile_1=Input.RootFile; end if ~isfield(Input,'FileExt_1')||strcmp(Input.FileExt_1,'"') Input.FileExt_1=Input.FileExt; end if ~isfield(Input,'NomType_1')||strcmp(Input.NomType_1,'"') Input.NomType_1=Input.NomType; end %updtate the indices of the second field series to correspond to the newly opened one FileName_1=fullfile_uvmat(Input.RootPath_1,Input.SubDir_1,Input.RootFile_1,Input.FileExt_1,Input.NomType_1,i1_s,i2_s,j1_s,j2_s); if exist(FileName_1,'file') FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1_s,i2_s,j1_s,j2_s); else FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1,i2,j1,j2); msgbox_uvmat('WARNING','unable to synchronise the indices of the two series') end set(handles.FileIndex_1,'String',FileIndex_1) end %enable other menus set(handles.MenuOpen_1,'Enable','on') set(handles.MenuFile_1_1,'Enable','on') set(handles.MenuFile_2_1,'Enable','on') set(handles.MenuFile_3_1,'Enable','on') set(handles.MenuFile_4_1,'Enable','on') set(handles.MenuFile_5_1,'Enable','on') set(handles.MenuExport,'Enable','on') set(handles.MenuExportFigure,'Enable','on') set(handles.MenuExportMovie,'Enable','on') set(handles.MenuTools,'Enable','on') % initiate input file series and refresh the current field view: update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index); end %% update list of recent files in the menubar and save it for future opening MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};... {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}]; str_find=strcmp(fileinput,MenuFile); if isempty(find(str_find,1)) MenuFile=[{fileinput};MenuFile];%insert the current file if not already in the list end for ifile=1:min(length(MenuFile),5) eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});']) eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',MenuFile{ifile});']) end dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat else save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat end %% set back the mouse pointer to arrow set(handles.uvmat,'Pointer','arrow') %------------------------------------------------------------------------ % --- Update information about a new field series (indices to scan, timing, % calibration from an xml file, then refresh current plots function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,VideoObject,index) %------------------------------------------------------------------------ %% define the relevant handles depending on the index (1=first file series, 2= second file series) if ~exist('index','var') index=1; end if index==1 handles_RootPath=handles.RootPath; handles_Fields=handles.FieldName; elseif index==2 handles_RootPath=handles.RootPath_1; handles_Fields=handles.FieldName_1; end set(handles_RootPath,'BackgroundColor',[1 1 0]) drawnow set(handles.FieldName,'UserData',[])% reinialize data from uvmat opening UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface UvData.NewSeries=1; %flag for run0: begin a new series UvData.FileName_1='';% name of the current second field (used to detect a constant field during file scanning) UvData.FileType{index}=FileType; UvData.i1_series{index}=i1_series; UvData.i2_series{index}=i2_series; UvData.j1_series{index}=j1_series; UvData.j2_series{index}=j2_series; set(handles.FixVelType,'Value',0); %desactivate fixed veltype if index==1 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles); else [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles); end FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]; FileBase=fullfile(RootPath,RootFile); if ~exist(FileName,'file') msgbox_uvmat('ERROR',['input file ' FileName ' not found']); return end %% read timing and total frame number from the current file (movie files) !! may be overrid by xml file XmlData.Time=[];%default XmlData.GeometryCalib=[];%default TimeUnit='';%default Time=[]; testima=0; %test for image input imainfo=[]; ColorType='falsecolor'; %default hhh=[]; UvData.MovieObject{index}=VideoObject; if ~isempty(VideoObject) imainfo=get(VideoObject); testima=1; TimeUnit='s'; if isempty(j1_series); %frame index along i Time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)'; else Time=ones(size(i1_series,1),1)*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate); end %nbfield=imainfo.NumberOfFrames; set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec ColorType='truecolor'; elseif ~isempty(FileExt(2:end))&&(~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol'))%&& isequal(NomType,'*')% multi-frame image testima=1; if ~isequal(SubDir,'') RootFile=get(handles.RootFile,'String'); imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]); else imainfo=imfinfo([FileBase FileIndices FileExt]); end ColorType=imainfo.ColorType;%='truecolor' for color images if length(imainfo) >1 %case of image with multiple frames % nbfield=length(imainfo); % nbfield_j=1; end end if isfield(imainfo,'Width') && isfield(imainfo,'Height') if length(imainfo)>1 set(handles.num_Npx,'String',num2str(imainfo(1).Width));%fills nbre of pixels x box set(handles.num_Npy,'String',num2str(imainfo(1).Height));%fills nbre of pixels x box else set(handles.num_Npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box set(handles.num_Npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box end else set(handles.num_Npx,'String','');%fills nbre of pixels x box set(handles.num_Npy,'String','');%fills nbre of pixels x box end set(handles.CheckBW,'Value',strcmp(ColorType,'grayscale'))% select handles.CheckBW if grayscale image %% read parameters (time, geometric calibration..) from a documentation file (.xml advised) XmlFileName=find_imadoc(RootPath,SubDir,RootFile,FileExt); [tild,tild,DocExt]=fileparts(XmlFileName); warntext='';%default warning message NbSlice=1;%default set(handles.RootPath,'BackgroundColor',[1 1 1]) if ~isempty(XmlFileName) set(handles.view_xml,'Visible','on') set(handles.view_xml,'BackgroundColor',[1 1 0]) set(handles.view_xml,'String','view .xml') drawnow [XmlDataRead,warntext]=imadoc2struct(XmlFileName); if ~isempty(warntext) msgbox_uvmat('WARNING',warntext) end if isempty(XmlDataRead) set(handles.view_xml,'Visible','off') else set(handles.view_xml,'String',['view ' DocExt]) XmlData=XmlDataRead; if isfield(XmlData,'TimeUnit') if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit) TimeUnit=XmlData.TimeUnit; end end set(handles.view_xml,'BackgroundColor',[1 1 1]) drawnow if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib) if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y') set (handles.num_NbSlice,'String','volume') end hgeometry_calib=findobj('tag','geometry_calib'); if ~isempty(hgeometry_calib) GUserData=get(hgeometry_calib,'UserData'); if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,XmlFileName)) answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?'); if strcmp(answer,'Yes') geometry_calib(XmlFileName);%diplay the new calibration points and parameters in geometry_calib end end end end end end if ~(isfield(XmlData,'Time')&& ~isempty(XmlData.Time)) XmlData.Time=Time; %time set by video end %% store last index in handles.lat_i and .last_j nbfield=max(max(max(i2_series))); if isempty(nbfield) nbfield=max(max(max(i1_series))); end nbfield_j=max(max(max(j2_series))); if isempty(nbfield_j) nbfield_j=max(max(max(j2_series))); end if ~isempty(XmlData.Time) %transform .Time to a column vector if it is a line vector the nomenclature uses a single index if isequal(size(XmlData.Time,1),1) NomType=get(handles.NomType,'String'); XmlData.Time=(XmlData.Time)'; end end last_i_cell=get(handles.last_i,'String'); if isempty(nbfield) last_i_cell{1}=''; else last_i_cell{1}=num2str(nbfield); end set(handles.last_i,'String',last_i_cell) last_j_cell=get(handles.last_j,'String'); if isempty(nbfield_j) last_j_cell{1}=''; else last_j_cell{1}=num2str(nbfield_j); end set(handles.last_j,'String',last_j_cell); %% store geometric calibration in UvData if isfield(XmlData,'GeometryCalib') GeometryCalib=XmlData.GeometryCalib; if isempty(GeometryCalib) set(handles.pxcm,'String','') set(handles.pycm,'String','') set(handles.transform_fct,'Value',1); % no transform by default else if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||... (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0)) set(handles.pxcm,'String','var') set(handles.pycm,'String','var') elseif isfield(GeometryCalib,'fx_fy') pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx); pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy); set(handles.pxcm,'String',num2str(pixcmx)) set(handles.pycm,'String',num2str(pixcmy)) end if ~get(handles.CheckFixLimits,'Value') set(handles.transform_fct,'Value',3); % phys transform by default if fixedLimits is off end if isfield(GeometryCalib,'SliceCoord') siz=size(GeometryCalib.SliceCoord); if siz(1)>1 NbSlice=siz(1); set(handles.slices,'Visible','on') set(handles.slices,'Value',1) end if isfield(GeometryCalib,'VolumeScan') && isequal(GeometryCalib.VolumeScan,'y') set(handles.num_NbSlice,'String','volume') else set(handles.num_NbSlice,'String',num2str(NbSlice)) end slices_Callback([],[], handles) end end end %% update the data attached to the uvmat interface if ~isempty(TimeUnit) set(handles.time_txt,'String',['time (' TimeUnit ')']) end UvData.TimeUnit=TimeUnit; UvData.XmlData{index}=XmlData; UvData.NewSeries=1; % UvData.MovieObject=MovieObject; %display warning message if ~isequal(warntext,'') msgbox_uvmat('WARNING',warntext); end %% set default options in menu 'FieldName' switch FileType case {'civx','civdata'} [FieldList,ColorList]=calc_field; set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data set(handles_Fields,'Value',2) % set menu to 'velocity set(handles.ColorScalar,'Value',1) set(handles.ColorScalar,'String',ColorList) set(handles.Vectors,'Visible','on') set(handles.Coord_x,'Value',1); set(handles.Coord_x,'String',{'X'}); set(handles.Coord_y,'Value',1); set(handles.Coord_y,'String',{'Y'}); case 'netcdf' set(handles_Fields,'Value',1) set(handles_Fields,'String',{'get_field...'}) hget_field=get_field(FileName); hhget_field=guidata(hget_field); get_field('RUN_Callback',hhget_field.RUN,[],hhget_field); otherwise set(handles_Fields,'Value',1) % set menu to 'image' set(handles_Fields,'String',{'image'}) set(handles.Coord_x,'Value',1); set(handles.Coord_x,'String',{'AX'}); set(handles.Coord_y,'Value',1); set(handles.Coord_y,'String',{'AY'}); end set(handles.uvmat,'UserData',UvData) %% set index navigation options and refresh plots scan_option='i';%default state_j='off'; %default if index==2 if get(handles.scan_j,'Value') scan_option='j'; %keep the scan option for the second file series end if strcmp(get(handles.j1,'Visible'),'on') state_j='on'; end end [ref_j,ref_i]=find(squeeze(i1_series(1,:,:))); if ~isempty(j1_series) state_j='on'; if index==1 if isequal(ref_i,ref_i(1)*ones(size(ref_j)))% if ref_i is always equal to its first value scan_option='j'; %scan j indext end end end if isequal(scan_option,'i') diff_ref_i=diff(ref_i,1); if isempty(diff_ref_i) diff_ref_i=1; end if isequal (diff_ref_i,diff_ref_i(1)*ones(size(diff_ref_i))) set(handles.num_IndexIncrement,'String',num2str(diff_ref_i(1))) end set(handles.scan_i,'Value',1) scan_i_Callback([],[], handles); else diff_ref_j=diff(ref_j); if isempty(diff_ref_j) diff_ref_j=1; end if isequal (diff_ref_j,diff_ref_j(1)*ones(size(diff_ref_j))) set(handles.num_IndexIncrement,'String',num2str(diff_ref_j(1))) end set(handles.scan_j,'Value',1) scan_j_Callback([],[], handles); end set(handles.scan_j,'Visible',state_j) set(handles.j1,'Visible',state_j) set(handles.j2,'Visible',state_j) set(handles.last_j,'Visible',state_j); set(handles.frame_j,'Visible',state_j); set(handles.j_text,'Visible',state_j); if ~isempty(i2_series)||~isempty(j2_series) set(handles.CheckFixPair,'Visible','on') elseif index==1 set(handles.CheckFixPair,'Visible','off') end %% apply the effect of the transform fct and view the field transform=get(handles.path_transform,'UserData'); if index==2 && (~isa(transform,'function_handle')||nargin(transform)<3) set(handles.transform_fct,'value',2); % set transform to sub_field if the current fct doe not accept two input fields end transform_fct_Callback([],[],handles) mask_test=get(handles.CheckMask,'value'); if mask_test MaskData=get(handles.CheckMask,'UserData'); if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle) delete(MaskData.maskhandle) %delete old mask end CheckMask_Callback([],[],handles) end %------------------------------------------------------------------------ % --- switch file index scanning options scan_i and scan_j in an exclusive way function scan_i_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ if get(handles.scan_i,'Value')==1 set(handles.scan_i,'BackgroundColor',[1 1 0]) set(handles.scan_j,'Value',0) else set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784]) set(handles.scan_j,'Value',1) end scan_j_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ % --- switch file index scanning options scan_i and scan_j in an exclusive way function scan_j_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ if get(handles.scan_j,'Value')==1 set(handles.scan_j,'BackgroundColor',[1 1 0]) set(handles.scan_i,'Value',0) set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784]) % NomType=get(handles.NomType,'String'); % switch NomType % case {'_1_1-2','#_ab','%3dab'},% pair with j index % set(handles.CheckFixPair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off') % otherwise % set(handles.CheckFixPair,'Visible','off') % end else set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784]) set(handles.scan_i,'Value',1) set(handles.scan_i,'BackgroundColor',[1 1 0]) set(handles.CheckFixPair,'Visible','off') end %------------------------------------------------------------------------ function i1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ update_ij(handles,1) %------------------------------------------------------------------------ function i2_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ update_ij(handles,2) %------------------------------------------------------------------------ function j1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ update_ij(handles,3) %------------------------------------------------------------------------ function j2_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ update_ij(handles,4) %------------------------------------------------------------------------ %--- update the index display after action on edit boxes i1, i2, j1 or j2 function update_ij(handles,index_rank) NomType=get(handles.NomType,'String'); indices=get(handles.FileIndex,'String'); [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(indices);% the indices for the second series taken from FileIndex switch index_rank case 1 indices=fullfile_uvmat('','','','',NomType,stra2num(get(handles.i1,'String')),i2,j1,j2); set(handles.i1,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation case 2 indices=fullfile_uvmat('','','','',NomType,i1,stra2num(get(handles.i2,'String')),j1,j2); set(handles.i2,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation case 3 indices=fullfile_uvmat('','','','',NomType,i1,i2,stra2num(get(handles.j1,'String')),j2); set(handles.j1,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation case 4 indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,stra2num(get(handles.j2,'String'))); set(handles.j2,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation end set(handles.FileIndex,'String',indices) set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation % update the second index if relevant if strcmp(get(handles.FileIndex_1,'Visible'),'on') NomType_1=get(handles.NomType_1,'String'); indices_1=get(handles.FileIndex_1,'String'); [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(indices_1);% the indices for the second series taken from FileIndex_1 switch index_rank case 1 indices_1=fullfile_uvmat('','','','',NomType_1,stra2num(get(handles.i1,'String')),i2_1,j1_1,j2_1); case 2 indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,stra2num(get(handles.i2,'String')),j1_1,j2_1); case 3 indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,stra2num(get(handles.j1,'String')),j2_1); case 4 indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,j1_1,stra2num(get(handles.j2,'String'))); end set(handles.FileIndex_1,'String',indices_1) set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation end %------------------------------------------------------------------------ %------------------------------------------------------------------------ function slices_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ if get(handles.slices,'Value')==1 set(handles.slices,'BackgroundColor',[1 1 0]) set(handles.num_NbSlice,'Visible','on') set(handles.z_text,'Visible','on') set(handles.z_index,'Visible','on') num_NbSlice_Callback(hObject, eventdata, handles) else set(handles.num_NbSlice,'Visible','off') set(handles.slices,'BackgroundColor',[0.7 0.7 0.7]) set(handles.z_text,'Visible','off') set(handles.z_index,'Visible','off') set(handles.masklevel,'Value',1) set(handles.masklevel,'String',{'1'}) end %------------------------------------------------------------------------ function num_NbSlice_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ nb_slice_str=get(handles.num_NbSlice,'String'); if isequal(nb_slice_str,'volume') num=stra2num(get(handles.j1,'String')); last_j=get(handles.last_j,'String'); nbslice=str2double(last_j{1}); else num=str2double(get(handles.i1,'String')); nbslice=str2double(get(handles.num_NbSlice,'String')); end z=mod(num-1,nbslice)+1; set(handles.z_index,'String',num2str(z)) for ilist=1:nbslice list_index{ilist,1}=num2str(ilist); end set(handles.masklevel,'String',list_index) set(handles.masklevel,'Value',z) %------------------------------------------------------------------------ % --- Executes on button press in view_xml. function view_xml_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ %[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles); [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles); FileBase=fullfile(RootPath,RootFile); option=get(handles.view_xml,'String'); if isequal(option,'view .xml') FileXml=fullfile(RootPath,[SubDir '.xml']); if ~exist(FileXml,'file')% case of civ files , removes the extension for subdir FileXml=fullfile(RootPath,[regexprep(SubDir,'\..+$','') '.xml']); end heditxml=editxml(FileXml); end %------------------------------------------------------------------------ % --- Executes on button press in CheckMask. function CheckMask_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ %case of view mask selection if isequal(get(handles.CheckMask,'Value'),1) [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles); FileBase=fullfile(RootPath,RootFile); num_i1=stra2num(get(handles.i1,'String')); num_j1=stra2num(get(handles.j1,'String')); currentdir=pwd; cd(RootPath); maskfiles=dir('*_*mask_*.png');%look for a mask file cd(currentdir);%come back to the working directory mdetect=0; if ~isempty(maskfiles) for ilist=1:length(maskfiles) maskname=maskfiles(ilist).name;% take the first mask file in the list [tild,tild,tild,tild,tild,tild,tild,MaskExt,Mask_NomType{ilist}]=fileparts_uvmat(maskname); [tild,Name]=fileparts(maskname); Namedouble=double(Name); val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters ind_mask=findstr('mask',Name); i=ind_mask-1; while val(i)==0 && i>0 i=i-1; end nbmask_str=str2num(Name(i+1:ind_mask-1)); if ~isempty(nbmask_str) nbslice(ilist)=nbmask_str; % number of different masks (slices) end end if isequal(min(nbslice),max(nbslice)) nbslice=nbslice(1); else msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory') return end if ~isempty(nbslice) && Name(i)=='_' Mask.Base=[FileBase Name(i:ind_mask+3)]; Mask.NbSlice=nbslice; num_i1=mod(num_i1-1,nbslice)+1; Mask.NomType=regexprep(Mask_NomType{1},'0','');%remove '0' in nom type for masks [RootPath,RootFile]=fileparts(Mask.Base); maskname=fullfile_uvmat(RootPath,'',RootFile,'.png',Mask.NomType,num_i1,[],num_j1); %maskname=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);% mdetect=exist(maskname,'file'); if mdetect set(handles.num_NbSlice,'String',Name(i+1:ind_mask-1)); set(handles.num_NbSlice,'BackgroundColor',[1 1 0]) set(handles.CheckMask,'UserData',Mask); set(handles.CheckMask,'BackgroundColor',[1 1 0]) if nbslice > 1 set(handles.slices,'value',1) slices_Callback(hObject, eventdata, handles) end end end end errormsg=[];%default if mdetect==0 [FileName, PathName, filterindex] = uigetfile( ... {'*.png', ' (*.png)'; '*.png', '.png files '; ... '*.*', 'All Files (*.*)'}, ... 'Pick a mask file *.png',FileBase); if ~ischar(FileName),return,end %abandon if the browser is cancelled maskname=fullfile(PathName,FileName); [RootDir,SubDir,RootFile,tild,tild,tild,tild,tild,Mask.NomType]=fileparts_uvmat(maskname); Mask.Base=fullfile(RootDir,SubDir,RootFile); Mask.NbSlice=1; set(handles.CheckMask,'UserData',Mask); set(handles.CheckMask,'BackgroundColor',[1 1 0]) end if isempty(errormsg) errormsg=update_mask(handles,num_i1,num_j1); end if ~isempty(errormsg) set(handles.CheckMask,'Value',0) set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7]) end else % desactivate mask display MaskData=get(handles.CheckMask,'UserData'); if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle) delete(MaskData.maskhandle) end set(handles.CheckMask,'UserData',[]) UvData=get(handles.uvmat,'UserData'); if isfield(UvData,'MaskName') UvData=rmfield(UvData,'MaskName'); set(handles.uvmat,'UserData',UvData) end set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7]) end %------------------------------------------------------------------------ function errormsg=update_mask(handles,num_i1,num_j1) %------------------------------------------------------------------------ errormsg=[];%default MaskData=get(handles.CheckMask,'UserData'); if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle) uistack(MaskData.maskhandle,'top'); end num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1; [RootPath,RootFile]=fileparts(MaskData.Base); MaskName=fullfile_uvmat(RootPath,'',RootFile,'.png',MaskData.NomType,num_i1_mask,[],num_j1); UvData=get(handles.uvmat,'UserData'); %update mask image if the mask is new if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName)) UvData.MaskName=MaskName; %update the recorded name on UvData set(handles.uvmat,'UserData',UvData); if ~exist(MaskName,'file') if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle) delete(MaskData.maskhandle) end else %read mask image Mask.AName='image'; Mask.A=imread(MaskName); npxy=size(Mask.A); test_error=0; if length(npxy)>2 errormsg=[MaskName ' is not a grey scale image']; return elseif ~isa(Mask.A,'uint8') errormsg=[MaskName ' is not a 8 bit grey level image']; return end Mask.AX=[0.5 npxy(2)-0.5]; Mask.AY=[npxy(1)-0.5 0.5 ]; Mask.CoordUnit='pixel'; if isequal(get(handles.slices,'Value'),1) NbSlice=str2num(get(handles.num_NbSlice,'String')); num_i1=str2num(get(handles.i1,'String')); Mask.ZIndex=mod(num_i1-1,NbSlice)+1; end %px to phys or other transform on field menu_transform=get(handles.transform_fct,'String'); choice_value=get(handles.transform_fct,'Value'); transform_name=menu_transform{choice_value};%name of the transform fct given by the menu 'transform_fct' transform_list=get(handles.transform_fct,'UserData'); transform=transform_list{choice_value}; if ~isequal(transform_name,'') && ~isequal(transform_name,'px') if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority Calib=UvData.XmlData{1}.GeometryCalib; Mask=transform(Mask,UvData.XmlData{1}); end end flagmask=Mask.A < 200; %make brown color image imflag(:,:,1)=0.9*flagmask; imflag(:,:,2)=0.7*flagmask; imflag(:,:,3)=zeros(size(flagmask)); %update mask image hmask=[]; %default if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle) hmask=MaskData.maskhandle; end if ~isempty(hmask) set(hmask,'CData',imflag) set(hmask,'AlphaData',flagmask*0.6) set(hmask,'XData',Mask.AX); set(hmask,'YData',Mask.AY); % uistack(hmask,'top') else axes(handles.PlotAxes) hold on size(flagmask) % MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*flagmask); MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*ones(size(flagmask))); % set(MaskData.maskhandle,'AlphaData',0.6*flagmask) set(handles.CheckMask,'UserData',MaskData) end end end %------------------------------------------------------------------------ %------------------------------------------------------------------------ % III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT' %------------------------------------------------------------------------ %------------------------------------------------------------------------ % --- Executes on button press in runplus: make one step forward and call % --- run0. The step forward is along the fieldname series 1 or 2 depending on % --- the scan_i and scan_j check box (exclusive each other) function runplus_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow drawnow %TODO: introduce the option: increment ='*' to move to the next available view increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d % if isnan(increment) % set(handles.num_IndexIncrement,'String','1')%default value % increment=1; % end errormsg=runpm(hObject,eventdata,handles,increment); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg); end set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red %------------------------------------------------------------------------ % --- Executes on button press in runmin: make one step backward and call % --- run0. The step backward is along the fieldname series 1 or 2 depending on % --- the scan_i and scan_j check box (exclusive each other) function runmin_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow drawnow increment=-str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d % if isnan(increment) % set(handles.num_IndexIncrement,'String','1')%default value % increment=1; % end errormsg=runpm(hObject,eventdata,handles,increment); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg); end set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red %------------------------------------------------------------------------ % -- Executes on button press in Movie: make a series of +> steps function Movie_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow drawnow increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d % if isnan(increment) % set(handles.num_IndexIncrement,'String','1')%default value % increment=1; % end set(handles.STOP,'Visible','on') set(handles.speed,'Visible','on') set(handles.speed_txt,'Visible','on') set(handles.Movie,'BusyAction','queue') UvData=get(handles.uvmat,'UserData'); while get(handles.Movie,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command errormsg=runpm(hObject,eventdata,handles,increment); if ~isempty(errormsg) set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red return end pause(1.02-get(handles.speed,'Value'))% wait for next image end if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj), UvData.aviobj=close(UvData.aviobj); set(handles.uvmat,'UserData',UvData); end set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red %------------------------------------------------------------------------ % -- Executes on button press in Movie: make a series of <- steps function MovieBackward_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow drawnow increment=-str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d set(handles.STOP,'Visible','on') set(handles.speed,'Visible','on') set(handles.speed_txt,'Visible','on') set(handles.MovieBackward,'BusyAction','queue') UvData=get(handles.uvmat,'UserData'); while get(handles.MovieBackward,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command errormsg=runpm(hObject,eventdata,handles,increment); if ~isempty(errormsg) set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red return end pause(1.02-get(handles.speed,'Value'))% wait for next image end if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj), UvData.aviobj=close(UvData.aviobj); set(handles.uvmat,'UserData',UvData); end set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red %------------------------------------------------------------------------ function STOP_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.movie_pair,'BusyAction','Cancel') set(handles.movie_pair,'value',0) set(handles.Movie,'BusyAction','Cancel') set(handles.MovieBackward,'BusyAction','Cancel') set(handles.MenuExportMovie,'BusyAction','Cancel') set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red %------------------------------------------------------------------------ % --- function activated by runplus and run minus function errormsg=runpm(hObject,eventdata,handles,increment) %------------------------------------------------------------------------ errormsg='';%default %% check for movie pair status movie_status=get(handles.movie_pair,'Value'); if isequal(movie_status,1) STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active end %% read the current input file name(s) and field indices InputFile=read_GUI(handles.InputFile); InputFile.RootFile=regexprep(InputFile.RootFile,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string InputFile.SubDir=regexprep(InputFile.SubDir,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string FileExt=InputFile.FileExt; NomType=get(handles.NomType,'String'); i1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name) i2=[];%default if strcmp(get(handles.i2,'Visible'),'on') i2=str2num(get(handles.i2,'String')); end j1=[]; if strcmp(get(handles.j1,'Visible'),'on') j1=stra2num(get(handles.j1,'String')); end j2=j1; if strcmp(get(handles.j2,'Visible'),'on') j2=stra2num(get(handles.j2,'String')); end sub_value= get(handles.SubField,'Value'); if sub_value % a second input file has been entered [InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,InputFile.FileIndex_1,InputFile.FileExt_1,InputFile.NomType_1]=read_file_boxes_1(handles); [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(InputFile.FileIndex_1);% the indices for the second series taken from FileIndex_1 else filename_1=[]; end %% increment (or decrement) the field indices and update the input filename(s) if isempty(increment) set(handles.CheckFixPair,'Value',0) end CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(i2)&&isempty(j2)); % the pair i1-i2 or j1-j2 is imposed (check box CheckFixPair selected) if CheckFixPair if get(handles.scan_i,'Value')==1% case of scanning along index i i1=i1+increment; i2=i2+increment; if sub_value i1_1=i1_1+increment; i2_1=i2_1+increment; end else % case of scanning along index j (burst numbers) j1=j1+increment; j2=j2+increment; if sub_value j1_1=j1_1+increment; j2_1=j2_1+increment; end end % the pair i1-i2 or j1-j2 is free (check box CheckFixPair not selected): the list of existing indices recorded in UvData is used else UvData=get(handles.uvmat,'UserData'); ref_i=i1; if ~isempty(i2) ref_i=floor((i1+i2)/2);% current reference index i end ref_j=1; if ~isempty(j1) ref_j=j1; if ~isempty(j2) ref_j=floor((j1+j2)/2);% current reference index j end end if ~isempty(increment) if get(handles.scan_i,'Value')==1% case of scanning along index i ref_i=ref_i+increment;% increment the current reference index i else % case of scanning along index j (burst numbers) ref_j=ref_j+increment;% increment the current reference index j if scan_j option is used end else % free increment runaction=get(gcbo,'tag'); if strcmp(runaction,'runplus')||strcmp(runaction,'Movie')% if runplus or movie is activated step=1; else step=-1; end if get(handles.scan_i,'Value')==1% case of scanning along index i ref_i=ref_i+step; while ref_i>=0 && size(UvData.i1_series{1},3)>=ref_i+1 && UvData.i1_series{1}(1,ref_j+1,ref_i+1)==0 ref_i=ref_i+step; end else % case of scanning along index j (burst numbers) ref_j=ref_j+step; while ref_j>=0 && size(UvData.i1_series{1},2)>=ref_j+1 && UvData.i1_series{1}(1,ref_j+1,ref_i+1)==0 ref_j=ref_j+step; end end end if ref_i<0 errormsg='minimum i index reached'; elseif ref_j<0 errormsg='minimum j index reached'; elseif ref_i+1>size(UvData.i1_series{1},3) errormsg='maximum i index reached (reload the input file to update the index bound)'; elseif ref_j+1>size(UvData.i1_series{1},2) errormsg='maximum j index reached (reload the input file to update the index bound)'; end if ~isempty(errormsg),return,end siz=size(UvData.i1_series{1}); ref_indices=ref_i*siz(1)*siz(2)+ref_j*siz(1)+1:ref_i*siz(1)*siz(2)+(ref_j+1)*siz(1); i1_subseries=UvData.i1_series{1}(ref_indices); ref_indices=ref_indices(i1_subseries>0); if isempty(ref_indices)% case of pairs (free index i) ref_indices=ref_i*siz(1)*siz(2)+1:(ref_i+1)*siz(1)*siz(2); i1_subseries=UvData.i1_series{1}(ref_indices); ref_indices=ref_indices(i1_subseries>0); end if isempty(ref_indices),errormsg='no next frame: set num_IndexIncrement =''*'' to reach the next existing file';return end i1=UvData.i1_series{1}(ref_indices(end)); if ~isempty(UvData.i2_series{1}) i2=UvData.i2_series{1}(ref_indices(end)); end if ~isempty(UvData.j1_series{1}) j1=UvData.j1_series{1}(ref_indices(end)); end if ~isempty(UvData.j2_series{1}) j2=UvData.j2_series{1}(ref_indices(end)); end % case of a second file series if sub_value ref_i_1=i1_1; if ~isempty(i2_1) ref_i_1=floor((i1_1+i2_1)/2);% current reference index i end ref_j_1=1; if ~isempty(j1_1) ref_j_1=j1_1; if ~isempty(j2_1) ref_j_1=floor((j1_1+j2_1)/2);% current reference index j end end if ~isempty(increment) if get(handles.scan_i,'Value')==1% case of scanning along index i ref_i_1=ref_i_1+increment;% increment the current reference index i else % case of scanning along index j (burst numbers) ref_j_1=ref_j_1+increment;% increment the current reference index j if scan_j option is used end else % free increment, synchronise the ref indices with the first series ref_i_1=ref_i; ref_j_1=ref_j; end if numel(UvData.i1_series)==1 UvData.i1_series{2}=UvData.i1_series{1}; UvData.j1_series{2}=UvData.j1_series{1}; UvData.i2_series{2}=UvData.i2_series{1}; UvData.j2_series{2}=UvData.j2_series{1}; end if ref_i_1<0 errormsg='minimum i index reached'; elseif ref_j_1<0 errormsg='minimum j index reached'; elseif ref_i_1+1>size(UvData.i1_series{2},3) errormsg='maximum i index reached for the second series (reload the input file to update the index bound)'; elseif ref_j_1+1>size(UvData.i1_series{2},2) errormsg='maximum j index reached for the second series(reload the input file to update the index bound)'; end if ~isempty(errormsg),return,end siz=size(UvData.i1_series{2}); ref_indices=ref_i_1*siz(1)*siz(2)+ref_j_1*siz(1)+1:ref_i_1*siz(1)*siz(2)+(ref_j_1+1)*siz(1); i1_subseries=UvData.i1_series{2}(ref_indices); ref_indices=ref_indices(i1_subseries>0); if isempty(ref_indices)% case of pairs (free index i) ref_indices=ref_i_1*siz(1)*siz(2)+1:(ref_i_1+1)*siz(1)*siz(2); i1_subseries=UvData.i1_series{2}(ref_indices); ref_indices=ref_indices(i1_subseries>0); end i1_1=UvData.i1_series{2}(ref_indices(end)); if ~isempty(UvData.i2_series{2}) i2_1=UvData.i2_series{2}(ref_indices(end)); end if ~isempty(UvData.j1_series{2}) j1_1=UvData.j1_series{2}(ref_indices(end)); end if ~isempty(UvData.j2_series{2}) j2_1=UvData.j2_series{1}(ref_indices(end)); end else% the second series (if needed) is the same file as the first i1_1=i1; i2_1=i2; j1_1=j1; j2_1=j2; end end filename=fullfile_uvmat(InputFile.RootPath,InputFile.SubDir,InputFile.RootFile,FileExt,NomType,i1,i2,j1,j2); if sub_value filename_1=fullfile_uvmat(InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,InputFile.FileExt_1,InputFile.NomType_1,i1_1,i2_1,j1_1,j2_1); end %% refresh plots errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2,i1_1,i2_1,j1_1,j2_1); %% update the index counters if the index move is successfull if isempty(errormsg) set(handles.i1,'String',num2stra(i1,NomType,1)); if isequal(i2,i1) set(handles.i2,'String',''); else set(handles.i2,'String',num2stra(i2,NomType,1)); end set(handles.j1,'String',num2stra(j1,NomType,2)); if isequal(j2,j1) set(handles.j2,'String',''); else set(handles.j2,'String',num2stra(j2,NomType,2)); end indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2); set(handles.FileIndex,'String',indices); if ~isempty(filename_1) indices_1=fullfile_uvmat('','','','',InputFile.NomType_1,i1_1,i2_1,j1_1,j2_1); set(handles.FileIndex_1,'String',indices_1); end if isequal(movie_status,1) set(handles.movie_pair,'Value',1) movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated end end %------------------------------------------------------------------------ % --- Executes on button press in movie_pair: create an alternating movie with two view function movie_pair_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ %% stop movie action if the movie_pair button is off if ~get(handles.movie_pair,'value') set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off' set(handles.i2,'String','') set(handles.j2,'String','') return else set(handles.movie_pair,'BusyAction','queue') end %% initialisation set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow drawnow list_fields=get(handles.FieldName,'String');% list menu fields index_fields=get(handles.FieldName,'Value');% selected string index FieldName=list_fields{index_fields}; % selected field UvData=get(handles.uvmat,'UserData'); if isequal(FieldName,'image') index=1; [RootPath,SubDir,RootFile,FileIndices,Ext]=read_file_boxes(handles); NomType=get(handles.NomType,'String'); else list_fields=get(handles.FieldName_1,'String');% list menu fields index_fields=get(handles.FieldName_1,'Value');% selected string index FieldName=list_fields{index_fields}; % selected field if isequal(FieldName,'image') index=2; [RootPath,tild,RootFile,FileIndex_1,Ext,NomType]=read_file_boxes_1(handles); else msgbox_uvmat('ERROR','an image or movie must be first introduced as input') set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red set(handles.movie_pair,'Value',0) return end end num_i1=str2num(get(handles.i1,'String')); num_j1=stra2num(get(handles.j1,'String')); num_i2=str2num(get(handles.i2,'String')); num_j2=stra2num(get(handles.j2,'String')); if isempty(num_j2) if isempty(num_i2) msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie') set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red set(handles.movie_pair,'Value',0) return else num_j2=num_j1;%repeat the index i1 by default end end if isempty(num_i2) num_i2=num_i1;%repeat the index i1 by default end imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i2,[],num_j2); if strcmp(NomType,'*') num_frame=num_i2; else num_frame=num_j2; end if ~exist(imaname_1,'file') msgbox_uvmat('ERROR',['second input open (-) ' imaname_1 ' not found']); set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red set(handles.movie_pair,'Value',0) return end %% get the first image %Field.AName='image'; if index==1 Field_a=UvData.Field;% movie on the second field else Field_a=UvData.Field_1;% movie on the first field end %% read the second image MovieObject=[]; if numel(UvData.MovieObject)>=index MovieObject=UvData.MovieObject{index}; end [Field_b,ParamOut,errormsg] = read_field(imaname_1,UvData.FileType{index},MovieObject,num_frame) % Field_b.AX=Field_a.AX; % Field_b.AY=Field_a.AY; % % z index % nbslice=str2double(get(handles.num_NbSlice,'String')); % if ~isempty(nbslice) % Field_b.ZIndex=mod(num_i2-1,nbslice)+1; % end % Field_b.CoordUnit='pixel'; % % %% determine the input file type % if (test_1 && isfield(UvData,'MovieObject')&& numel(UvData.MovieObject>=2))||(~test_1 && ~isempty(UvData.MovieObject{1})) % FileType='movie'; % elseif isequal(lower(Ext),'.avi') % FileType='avi'; % elseif isequal(lower(Ext),'.vol') % FileType='vol'; % else % form=imformats(Ext(2:end)); % if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab % if isequal(NomType,'*'); % FileType='multimage'; % else % FileType='image'; % end % end % end % switch FileType % case 'movie' % if test_1 % Field_b.A=read(UvData.MovieObject{2},num_i2); % else % Field_b.A=read(UvData.MovieObject{1},num_i2); % end % case 'avi' % mov=aviread(imaname_1,num_i2); % Field_b.A=frame2im(mov(1)); % case 'vol' % Field_b.A=imread(imaname_1); % case 'multimage' % Field_b.A=imread(imaname_1,num_i2); % case 'image' % Field_b.A=imread(imaname_1); % end % if get(handles.slices,'Value') % Field.ZIndex=str2double(get(handles.z_index,'String')); % end %px to phys or other transform on field % menu_transform=get(handles.transform_fct,'String'); % choice_value=get(handles.transform_fct,'Value'); % transform_name=menu_transform{choice_value};%name of the transform fct given by the menu 'transform_fct' % transform_list=get(handles.transform_fct,'UserData'); transform=get(handles.path_transform,'UserData'); if ~isempty(transform) if isfield(UvData,'XmlData') && numel(UvData.XmlData)>=index %use geometry calib recorded from the ImaDoc xml file as first priority if index==2 Field_a=transform(Field_a,UvData.XmlData{index});%the first field has been stored without transform end Field_b=transform(Field_b,UvData.XmlData{index}); end end % make movie until movie speed is set to 0 or STOP is activated hima=findobj(handles.PlotAxes,'Tag','ima');% %handles.PlotAxes =main plotting window (A GENERALISER) set(handles.STOP,'Visible','on') set(handles.speed,'Visible','on') set(handles.speed_txt,'Visible','on') while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command % read and plot the series of images in non erase mode set(hima,'CData',Field_b.A); pause(1.02-get(handles.speed,'Value'));% wait for next image set(hima,'CData',Field_a.A); pause(1.02-get(handles.speed,'Value'));% wait for next image end set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red set(handles.movie_pair,'Value',0) %------------------------------------------------------------------------ % --- Executes on button press in run0. function run0_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow drawnow [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles); filename=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt]; filename_1='';%default FileIndex_1=''; if get(handles.SubField,'Value') [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles); filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1]; end num_i1=stra2num(get(handles.i1,'String')); num_i2=stra2num(get(handles.i2,'String')); num_j1=stra2num(get(handles.j1,'String')); num_j2=stra2num(get(handles.j2,'String')); [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(FileIndex_1); errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg); else set(handles.i1,'BackgroundColor',[1 1 1]) set(handles.i2,'BackgroundColor',[1 1 1]) set(handles.j1,'BackgroundColor',[1 1 1]) set(handles.j2,'BackgroundColor',[1 1 1]) set(handles.FileIndex,'BackgroundColor',[1 1 1]) set(handles.FileIndex_1,'BackgroundColor',[1 1 1]) end set(handles.run0,'BackgroundColor',[1 0 0]) %------------------------------------------------------------------------ % --- read the input files and refresh all the plots, including projection. % OUTPUT: % errormsg: error message char string =[] by default % INPUT: % filename: first input file (=[] in the absence of input file) % filename_1: second input file (=[] in the asbsenc of secodn input file) % num_i1,num_i2,num_j1,num_j2; frame indices % Field: structure describing an optional input field (then replace the input file) function errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1) %------------------------------------------------------------------------ %% initialisation abstime=[]; abstime_1=[]; dt=[]; if ~exist('Field','var') Field={}; end UvData=get(handles.uvmat,'UserData'); if ishandle(handles.UVMAT_title) %remove title panel on uvmat delete(handles.UVMAT_title) end %% determine the main input file information for action if ~exist(FileName,'file') errormsg=['input file ' FileName ' does not exist']; return end NomType=get(handles.NomType,'String'); NomType_1=''; if strcmp(get(handles.NomType_1,'Visible'),'on') NomType_1=get(handles.NomType_1,'String'); end %update the z position index nbslice_str=get(handles.num_NbSlice,'String'); if isequal(nbslice_str,'volume')%NOT USED z_index=num_j1; set(handles.z_index,'String',num2str(z_index)) else nbslice=str2num(nbslice_str); z_index=mod(num_i1-1,nbslice)+1; set(handles.z_index,'String',num2str(z_index)) end % refresh menu for save_mask if relevant masknumber=get(handles.masklevel,'String'); if length(masknumber)>=z_index set(handles.masklevel,'Value',z_index) end %% test for need of tps check_proj_tps=0; if (strcmp(UvData.FileType{1},'civdata')||strcmp(UvData.FileType{1},'civx')) for iobj=1:numel(UvData.Object) if isfield(UvData.Object{iobj},'ProjMode')&& strcmp(UvData.Object{iobj}.ProjMode,'filter') check_proj_tps=1; break end end end %% read the first input field ParamIn.ColorVar='';%default variable name for vector color frame_index=1;%default FieldName='';%default VelType='';%default switch UvData.FileType{1} case {'civx','civdata','netcdf'}; list_fields=get(handles.FieldName,'String');% list menu fields FieldName= list_fields{get(handles.FieldName,'Value')}; % selected field if ~strcmp(FieldName,'get_field...') if get(handles.FixVelType,'Value') VelTypeList=get(handles.VelType,'String'); VelType=VelTypeList{get(handles.VelType,'Value')}; end end if ~isempty(regexp(FieldName,'^vec(')) list_code=get(handles.ColorCode,'String');% list menu fields index_code=get(handles.ColorCode,'Value');% selected string index if ~strcmp(list_code{index_code},'black') && ~strcmp(list_code{index_code},'white') list_code=get(handles.ColorScalar,'String');% list menu fields index_code=get(handles.ColorScalar,'Value');% selected string index ParamIn.ColorVar= list_code{index_code}; % selected field end end case {'video','mmreader'} ParamIn=UvData.MovieObject{1}; if ~strcmp(NomType,'*') frame_index=num_j1;%frame index for movies or multimage else frame_index=num_i1; end case 'multimage' if ~strcmp(NomType,'*') frame_index=num_j1;%frame index for movies or multimage else frame_index=num_i1; end case 'vol' %TODO: update if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx') ParamIn.Npy=UvData.XmlData.Npy; ParamIn.Npx=UvData.XmlData.Npx; else errormsg='Npx and Npy need to be defined in the xml file for volume images .vol'; return end end if isstruct (ParamIn) ParamIn.FieldName=FieldName; ParamIn.VelType=VelType; XNameMenu=get(handles.Coord_x,'String'); ParamIn.Coord_x=XNameMenu(get(handles.Coord_x,'Value')); YNameMenu=get(handles.Coord_y,'String'); ParamIn.Coord_y=YNameMenu(get(handles.Coord_y,'Value')); end check_tps = 0; if strcmp(UvData.FileType{1},'civdata')&&~strcmp(ParamIn.FieldName,'velocity')&&~strcmp(ParamIn.FieldName,'get_field...') check_tps=1;%tps needed to get the requested field end [Field{1},ParamOut,errormsg] = read_field(FileName,UvData.FileType{1},ParamIn,frame_index); if ~isempty(errormsg) errormsg=['uvmat / refresh_field / read_field( ' FileName ') / ' errormsg]; return end if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy') set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface set(handles.num_Npy,'String',num2str(ParamOut.Npy)); end if isfield(ParamOut,'TimeIndex')% case of time obtained from get_field set(handles.i1,'String',num2str(ParamOut.TimeIndex)) end if isfield(ParamOut,'TimeValue') Field{1}.Time=ParamOut.TimeValue;% case of time obtained from get_field end Field{1}.ZIndex=z_index; %used for multiplane 3D calibration % end %% choose and read a second field FileName_1 if defined VelType_1=[];%default FieldName_1=[]; ParamIn_1=[]; ParamOut_1=[]; frame_index_1=1; if ~isempty(FileName_1) if ~exist(FileName_1,'file') errormsg=['second file ' FileName_1 ' does not exist']; return end Name=FileName_1; switch UvData.FileType{2} case {'civx','civdata','netcdf'}; list_fields=get(handles.FieldName_1,'String');% list menu fields if ischar(list_fields),list_fields={list_fields};end FieldName_1= list_fields{get(handles.FieldName_1,'Value')}; % selected field if ~strcmp(FieldName,'get_field...') if get(handles.FixVelType,'Value') VelTypeList=get(handles.VelType_1,'String'); VelType_1=VelTypeList{get(handles.VelType_1,'Value')};% read the velocity type. end end if strcmp(FieldName_1,'velocity')&& strcmp(get(handles.ColorCode,'Visible'),'on') list_code=get(handles.ColorCode,'String');% list menu fields index_code=get(handles.ColorCode,'Value');% selected string index if ~strcmp(list_code{index_code},'black') && ~strcmp(list_code{index_code},'white') list_code=get(handles.ColorScalar,'String');% list menu fields index_code=get(handles.ColorScalar,'Value');% selected string index ParamIn_1.ColorVar= list_code{index_code}; % selected field for vector color display end end case {'video','mmreader'} ParamIn_1=UvData.MovieObject{2}; if ~strcmp(NomType_1,'*') frame_index_1=j1_1;%frame index for movies or multimage else frame_index_1=i1_1; end case 'multimage' if ~strcmp(NomType_1,'*') frame_index_1=j1_1;%frame index for movies or multimage else frame_index_1=i1_1; end case 'vol' %TODO: update if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx') ParamIn_1.Npy=UvData.XmlData.Npy; ParamIn_1.Npx=UvData.XmlData.Npx; else errormsg='Npx and Npy need to be defined in the xml file for volume images .vol'; return end end if isequal(get(handles.NomType_1,'Visible'),'on') NomType_1=get(handles.NomType_1,'String'); else NomType_1=get(handles.NomType,'String'); end test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged if ~isequal(NomType_1,'*')&& isfield(UvData,'FileName_1') test_keepdata_1= strcmp(FileName_1,UvData.FileName_1) ;%&& strcmp(FieldName_1,UvData.FieldName_1); end if test_keepdata_1 Field{2}=UvData.Field_1;% keep the stored field ParamOut_1=UvData.ParamOut_1; else if isempty(ParamIn_1) || isstruct(ParamIn_1) ParamIn_1.FieldName=FieldName_1; ParamIn_1.VelType=VelType_1; ParamIn_1.GUIName='get_field_1'; end [Field{2},ParamOut_1,errormsg] = read_field(Name,UvData.FileType{2},ParamIn_1,frame_index_1); if ~isempty(errormsg) errormsg=['error in reading ' FieldName_1 ' in ' FileName_1 ': ' errormsg]; return end if isstruct(ParamOut_1)&&~strcmp(ParamOut_1.FieldName,'get_field...')&& (strcmp(UvData.FileType{2},'civdata')||strcmp(UvData.FileType{2},'civx'))... &&~strcmp(ParamOut_1.FieldName,'velocity') && ~strcmp(ParamOut_1.FieldName,'get_field...') if ~check_proj_tps % Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2}); end end end Field{2}.ZIndex=z_index;%used for multi-plane 3D calibration end %% update uvmat interface if isfield(ParamOut,'Npx') set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface set(handles.num_Npy,'String',num2str(ParamOut.Npy)); elseif isfield(ParamOut_1,'Npx') set(handles.num_Npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface set(handles.num_Npy,'String',num2str(ParamOut_1.Npy)); end %% update the display menu for the first velocity type (first menuline) test_veltype=0; % if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...') if (strcmp(UvData.FileType{1},'civx')||strcmp(UvData.FileType{1},'civdata'))&& ~strcmp(FieldName,'get_field...') test_veltype=1; set(handles.VelType,'Visible','on') set(handles.VelType_1,'Visible','on') set(handles.FixVelType,'Visible','on') menu=set_veltype_display(ParamOut.CivStage,UvData.FileType{1}); index_menu=strcmp(ParamOut.VelType,menu);%look for VelType in the menu index_val=find(index_menu,1); if isempty(index_val) index_val=1; end set(handles.VelType,'Value',index_val) if ~get(handles.SubField,'value') set(handles.VelType,'String',menu) set(handles.VelType_1,'Value',1) set(handles.VelType_1,'String',[{''};menu]) end else set(handles.VelType,'Visible','off') end % display the FieldName menu from the input file and pick the selected one: % if isstruct(ParamOut) % field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList); % set(handles.FieldName,'String',ParamOut.FieldList); %update the field menu % set(handles.FieldName,'Value',find(field_index,1)) % end %% update the display menu for the second velocity type (second menuline) test_veltype_1=0; if isempty(FileName_1) % set(handles.FieldName_1,'Value',1); %update the field menu % if isstruct(ParamOut) % set(handles.FieldName_1,'String',[{''};ParamOut.FieldList]); %update the field menu % end elseif ~test_keepdata_1 if (~strcmp(UvData.FileType{2},'netcdf')&&~strcmp(UvData.FileType{2},'civdata')&&~strcmp(UvData.FileType{2},'civx'))|| isequal(FieldName_1,'get_field...') set(handles.VelType_1,'Visible','off') else test_veltype_1=1; set(handles.VelType_1,'Visible','on') menu=set_veltype_display(ParamOut_1.CivStage,UvData.FileType{2}); index_menu=strcmp(ParamOut_1.VelType,menu); set(handles.VelType_1,'Value',1+find(index_menu,1)) set(handles.VelType_1,'String',[{''};menu]) end % update the second field menu: the same quantity if isstruct(ParamOut_1) set(handles.FieldName_1,'String',[{''};ParamOut_1.FieldList]); %update the field menu % display the FieldName menu from the input file and pick the selected one: field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList); set(handles.FieldName_1,'Value',find(field_index,1)+1) end end if test_veltype||test_veltype_1 set(handles.FixVelType,'Visible','on') else set(handles.FixVelType,'Visible','off') end % field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList); % set(handles.FieldName,'String',ParamOut.FieldList); %update the field menu % set(handles.FieldName,'Value',find(field_index,1)) %% introduce w as background image by default for a new series (only for nbdim=2) if ~isfield(UvData,'NewSeries') UvData.NewSeries=1; end %put W as background image by default if NbDim=2: if UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3); set(handles.SubField,'Value',1); set(handles.RootPath_1,'String','"') set(handles.RootFile_1,'String','"') set(handles.SubDir_1,'String','"'); indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2); set(handles.FileIndex_1,'String',indices) set(handles.FileExt_1,'String','"'); set(handles.FieldName_1,'Visible','on'); set(handles.FieldName_1,'Visible','on'); set(handles.RootPath_1,'Visible','on') set(handles.RootFile_1,'Visible','on') set(handles.SubDir_1,'Visible','on'); set(handles.FileIndex_1,'Visible','on'); set(handles.FileExt_1,'Visible','on'); set(handles.FieldName_1,'Visible','on'); Field{1}.AName='w'; end %% display time testimedoc=0; TimeUnit=''; if isfield(Field{1},'Time') abstime=Field{1}.Time;%time read from the netcdf input file end if numel(Field)==2 && isfield(Field{2},'Time') abstime_1=Field{2}.Time;%time read from the netcdf input file end if isfield(Field{1},'Dt') dt=Field{1}.Dt;%dt read from the netcdf input file if isfield(Field{1},'TimeUnit') TimeUnit=Field{1}.TimeUnit; end elseif numel(Field)==2 && isfield(Field{2},'Dt')%dt obtained from the second field if not defined in the first dt=Field{2}.Dt;%dt read from the netcdf input file if isfield(Field{2},'TimeUnit') TimeUnit=Field{2}.TimeUnit; end end % time from xml file overset previous result if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'Time') if isempty(num_i2)||isnan(num_i2) num_i2=num_i1; end if isempty(num_j1)||isnan(num_j1) num_j1=1; end if isempty(num_j2)||isnan(num_j2) num_j2=num_j1; end siz=size(UvData.XmlData{1}.Time); if ~isempty(num_i1)&& ~isempty(num_i2)&&siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2) abstime=(UvData.XmlData{1}.Time(num_i1,num_j1)+UvData.XmlData{1}.Time(num_i2,num_j2))/2;%overset the time read from files dt=(UvData.XmlData{1}.Time(num_i2,num_j2)-UvData.XmlData{1}.Time(num_i1,num_j1)); Field{1}.Dt=dt; if isfield(UvData.XmlData{1},'TimeUnit') TimeUnit=UvData.XmlData{1}.TimeUnit; end end if numel(UvData.XmlData)==2 if isempty(i2_1) i2_1=num_i1; end if isempty(j1_1) j1_1=1; end if isempty(j2_1) j2_1=j1_1; end siz=size(UvData.XmlData{2}.Time); if ~isempty(i1_1) && siz(1)>=max(i1_1,i2_1) && siz(2)>=max(j1_1,j2_1) abstime_1=(UvData.XmlData{2}.Time(i1_1,j1_1)+UvData.XmlData{2}.Time(i2_1,j2_1))/2;%overset the time read from files Field{2}.Dt=(UvData.XmlData{2}.Time(i2_1,j2_1)-UvData.XmlData{2}.Time(i1_1,j1_1)); end end end if ~isequal(numel(abstime),1) abstime=[]; end if ~isequal(numel(abstime_1),1) abstime_1=[]; end set(handles.abs_time,'String',num2str(abstime,5)) set(handles.abs_time_1,'String',num2str(abstime_1,5)) if isempty(dt)||isequal(dt,0) set(handles.Dt_txt,'String','') else if isempty(TimeUnit) set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) ' 10^(-3)'] ) else set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) ' m' TimeUnit] ) end end %% store the current open names, fieldname and vel types in uvmat interface UvData.FileName_1=FileName_1; UvData.ParamOut_1=ParamOut_1; if numel(Field)==2 UvData.Field_1=Field{2}; %store the second field for possible use at next RUN end %% apply coordinate transform or other user fct transform=get(handles.path_transform,'UserData'); if isempty(transform) UvData.Field=Field{1}; else XmlData=[];%default XmlData_1=[];%default if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority XmlData=UvData.XmlData{1}; if numel(UvData.XmlData)==2 XmlData_1=UvData.XmlData{2}; end end transform=get(handles.path_transform,'UserData'); switch nargin(transform) case 4 if length(Field)==2 UvData.Field=transform(Field{1},XmlData,Field{2},XmlData_1); else UvData.Field=transform(Field{1},XmlData); end case 3 if length(Field)==2 UvData.Field=transform(Field{1},XmlData,Field{2}); else UvData.Field=transform(Field{1},XmlData); end case 2 UvData.Field=transform(Field{1},XmlData); case 1 UvData.Field=transform(Field{1}); end end %% calculate tps coefficients if needed UvData.Field=calc_tps(UvData.Field,check_proj_tps); %% analyse input field %test_x=0; %test_z=0;% test for unstructured z coordinate %[errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(UvData.Field);% check the input field structure % if ~isempty(errormsg) % errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];% display error % return % end [CellInfo,NbDimArray,errormsg]=find_field_cells(UvData.Field);% analyse the input field structure if ~isempty(errormsg) errormsg=['uvmat /refresh_field / find_field_cells / ' errormsg];% display error return end NbDim=max(NbDimArray);% spatial dimension of the input field imax=find(NbDimArray==NbDim);% indices of field cells to consider if isfield(UvData.Field,'NbDim') NbDim=double(UvData.Field.NbDim);% deal with plane fields containing z coordinates end %% get bounds and mesh (needed to propose default options for projection objects) if NbDim>1 CoordMax=zeros(1,numel(imax)); CoordMin=zeros(1,numel(imax)); for ind=1:numel(imax) XName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(end)}; YName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(end-1)}; CoordMax(ind,1)=max(max(UvData.Field.(XName))); CoordMin(ind,1)=min(min(UvData.Field.(XName))); CoordMax(ind,2)=max(max(UvData.Field.(YName))); CoordMin(ind,2)=min(min(UvData.Field.(YName))); % test_x=1;%test for unstructured coordinates if NbDim==3 ZName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(1)}; CoordMax(imax(ind),3)=max(max(UvData.Field.(ZName))); CoordMin(ind,3)=min(min(UvData.Field.(ZName))); end switch CellInfo{imax(ind)}.CoordType case 'scattered' %unstructured coordinates NbPoints(ind)=CellInfo{imax(ind)}.CoordSize;% nbre of points Mesh(ind)=(prod(CoordMax(ind,:)-CoordMin(ind,:))/NbPoints)^(1/NbDim); %(volume or area per point)^(1/NbDim) case 'grid'%structured coordinate NbPoints=CellInfo{imax(ind)}.CoordSize;% nbre of points Mesh(ind)=min((CoordMax(ind,:)-CoordMin(ind,:))./NbPoints); end end UvData.Field.Mesh=min(Mesh); UvData.Field.XMax=max(CoordMax(ind,1)); UvData.Field.XMin=min(CoordMin(ind,1)); UvData.Field.YMax=max(CoordMax(ind,2)); UvData.Field.YMin=max(CoordMin(ind,2)); if NbDim==3 UvData.Field.ZMax=max(CoordMax(ind,3)); UvData.Field.ZMin=max(CoordMin(ind,3)); end % adjust the mesh to a value 1, 2 , 5 *10^n ord=10^(floor(log10(UvData.Field.Mesh)));%order of magnitude if UvData.Field.Mesh/ord>=5 UvData.Field.Mesh=5*ord; elseif UvData.Field.Mesh/ord>=2 UvData.Field.Mesh=2*ord; else UvData.Field.Mesh=ord; end % default projection plane if isempty(UvData.Object{1}) UvData.Object{1}.Type='plane';%main plotting plane UvData.Object{1}.ProjMode='projection';%main plotting plane UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat end %% 3D case (menuvolume) if NbDim==3% && UvData.NewSeries test_set_object=1; hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider if ~isempty(hset_object) %if set_object is detected delete(hset_object);% delete the GUI set_object if it does not fit end if test_set_object% reinitiate the GUI set_object delete_object(1);% delete the current projection object in the list UvData.Object, delete its graphic representations and update the list displayed in handles.ListObject and 2 UvData.Object{1}.NbDim=NbDim;%test for 3D objects UvData.Object{1}.RangeZ=UvData.Field.Mesh;%main plotting plane UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen UvData.Object{1}.Angle=[0 0 0]; UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR UvData.Object{1}.Name='1-PLANE'; UvData.Object{1}.enable_plot=1; set_object(UvData.Object{1},handles,ZBounds); set(handles.ListObject,'Value',1); set(handles.ListObject,'String',{'1-PLANE'}); set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor edit_object_Callback([],[], handles) end %multilevel case (single menuplane in a 3D space) elseif isfield(UvData,'Z') if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData') XmlData=UvData.XmlData{1}; if isfield(XmlData,'PlanePos') UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:); end if isfield(XmlData,'PlaneAngle') siz=size(XmlData.PlaneAngle); indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning) UvData.Object{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:); end elseif isfield(UvData,'ZIndex') UvData.Object{1}.ZObject=UvData.ZIndex; end end end testnewseries=UvData.NewSeries; UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback) set(handles.uvmat,'UserData',UvData) %% reset the min and max of scalar if only the mask is displayed(TODO: check the need) % if isfield(UvData,'Mask')&& ~isfield(UvData,'A') % set(handles.num_MinA,'String','0') % set(handles.num_MaxA,'String','255') % end %% usual 1D (x,y) plots if NbDim<=1 set(handles.Objects,'Visible','off') set(handles.ListObject_1_title,'Visible','off') set(handles.ListObject_1,'Visible','off') [PlotType,PlotParamOut]=plot_field(UvData.Field,handles.PlotAxes,read_GUI(handles.uvmat)); write_plot_param(handles,PlotParamOut) %update the auto plot parameters %% 2D or 3D fieldname are generally projected else set(handles.Objects,'Visible','on') set(handles.ListObject_1_title,'Visible','on') set(handles.ListObject_1,'Visible','on') %% Plot the projections on the selected projection objects % main projection object (uvmat display) list_object=get(handles.ListObject_1,'String'); if isequal(list_object,{''})%refresh list of objects if the menu is empty set(handles.ListObject,'Value',1) set(handles.ListObject,'String',{'plane'}) UvData.Object{1}.Type='plane';%main plotting plane UvData.Object{1}.ProjMode='projection';%main plotting plane UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat set(handles.ListObject_1,'Value',1) set(handles.ListObject_1,'String',{'plane'}) end IndexObj(1)=get(handles.ListObject_1,'Value');%selected projection object for main view if IndexObj(1)> numel(UvData.Object) IndexObj(1)=1;%select the first object if the selected one does not exist set(handles.ListObject_1,'Value',1) end IndexObj(2)=get(handles.ListObject,'Value');%selected projection object for main view if isequal(IndexObj(2),IndexObj(1)) IndexObj(2)=[]; end plot_handles{1}=handles; if isfield(UvData,'plotaxes')%case of movies haxes(1)=UvData.plotaxes; else haxes(1)=handles.PlotAxes; end PlotParam{1}=read_GUI(handles.uvmat); %default settings if vectors not visible if ~isfield(PlotParam{1},'Vectors') PlotParam{1}.Vectors.MaxVec=1; PlotParam{1}.Vectors.MinVec=0; PlotParam{1}.Vectors.CheckFixVecColor=1; PlotParam{1}.Vectors.ColCode1=0.33; PlotParam{1}.Vectors.ColCode2=0.66; PlotParam{1}.Vectors.ColorScalar={''}; PlotParam{1}.Vectors.ColorCode= {'rgb'}; end PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface %% second projection object (view_field display) if length( IndexObj)>=2 view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI if ~isempty(view_field_handle) plot_handles{2}=guidata(view_field_handle); haxes(2)=plot_handles{2}.PlotAxes; PlotParam{2}=read_GUI(handles.uvmat);%read plotting parameters on the uvmat interface PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field end end %% loop on the projection objects: one or two for imap=1:numel(IndexObj) iobj=IndexObj(imap); [ObjectData,errormsg]=proj_field(UvData.Field,UvData.Object{iobj});% project field on the object if ~isempty(errormsg) return end if testnewseries PlotParam{imap}.Scalar.CheckBW=[]; %B/W option depends on the input field (image or scalar) if isfield(ObjectData,'CoordUnit') PlotParam{imap}.Coordinates.CheckFixAspectRatio=1;% set x and y scaling equal if CoordUnit is defined (common unit for x and y) PlotParam{imap}.Coordinates.AspectRatio=1; %set aspect ratio to 1 end end %use of mask (TODO: check) if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A') flag_mask=double(ObjectData.Mask>200);%=0 for masked regions AX=ObjectData.AX;%x coordiantes for the scalar field AY=ObjectData.AY;%y coordinates for the scalar field MaskX=ObjectData.MaskX;%x coordiantes for the mask MaskY=ObjectData.MaskY;%y coordiantes for the mask if ~isequal(MaskX,AX)||~isequal(MaskY,AY) nxy=size(flag_mask); sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1); x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display %project on the positions of the scalar npxy=size(ObjectData.A); dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end); yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end); [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI); end AClass=class(ObjectData.A); ObjectData.A=flag_mask.*double(ObjectData.A); ObjectData.A=feval(AClass,ObjectData.A); % ind_off=[]; % if isfield(ObjectData,'ListVarName') % for ilist=1:length(ObjectData.ListVarName) % if isequal(ObjectData.ListVarName{ilist},'Mask')||isequal(ObjectData.ListVarName{ilist},'MaskX')||isequal(ObjectData.ListVarName{ilist},'MaskY') % ind_off=[ind_off ilist]; % end % end % ObjectData.ListVarName(ind_off)=[]; % VarDimIndex(ind_off)=[]; % ind_off=[]; % % end end if ~isempty(ObjectData) PlotType='none'; %default if imap==2 && isempty(view_field_handle) view_field(ObjectData) else [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap}); write_plot_param(plot_handles{imap},PlotParamOut) %update the auto plot parameters if isfield(Field,'Mesh')&&~isempty(Field.Mesh) ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot) end end end end %% update the mask if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on update_mask(handles,num_i1,num_i2); end %% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case) menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display ind_skip=[]; % nb_histo=1; Ustring=''; Vstring=''; % suppress coordinates from the histogram menu for ivar=1:numel(menu_histo)%l loop on field variables: if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role') Role=UvData.Field.VarAttribute{ivar}.Role; switch Role case {'coord_x','coord_y','coord_z','dimvar'} ind_skip=[ind_skip ivar]; case {'vector_x'} Ustring=UvData.Field.ListVarName{ivar}; ind_skip=[ind_skip ivar]; case {'vector_y'} Vstring=UvData.Field.ListVarName{ivar}; ind_skip=[ind_skip ivar]; end end DimCell=UvData.Field.VarDimName{ivar}; DimName=''; if ischar(DimCell) DimName=DimCell; elseif iscell(DimCell)&& numel(DimCell)==1 DimName=DimCell{1}; end if strcmp(DimName,menu_histo{ivar}) ind_skip=[ind_skip ivar]; end end menu_histo(ind_skip)=[];% remove skipped items if ~isempty(Ustring) menu_histo=[{[Ustring ',' Vstring]};menu_histo];% add U, V at the beginning if they exist end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % display menus and plot histograms test_v=0; if ~isempty(menu_histo) set(handles.histo1_menu,'Value',1) set(handles.histo1_menu,'String',menu_histo) histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram end end %------------------------------------------------------------------------ function histo1_menu_Callback(hObject, eventdata, handles) %-------------------------------------------- histo_menu=get(handles.histo1_menu,'String'); histo_value=get(handles.histo1_menu,'Value'); FieldName=histo_menu{histo_value}; UvData=get(handles.uvmat,'UserData'); Field=UvData.Field; r=regexp(FieldName,'(?.*)(?,)(?.*)','names'); FieldName_2=''; if ~isempty(r) FieldName=r.var1; FieldName_2=r.var2; end if ~isfield(UvData.Field,FieldName) msgbox_uvmat('ERROR',['no field ' FieldName ' for histogram']) return end FieldHisto=Field.(FieldName); if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto)) indsel=find(Field.FF==0);%find values marked as false if ~isempty(indsel) FieldHisto=FieldHisto(indsel); if ~isempty(FieldName_2) FieldHisto(:,:,2)=Field.(FieldName_2)(indsel); end end end if isempty(Field) msgbox_uvmat('ERROR',['empty field ' FieldName]) else nxy=size(FieldHisto); Amin=double(min(min(min(FieldHisto))));%min of field value Amax=double(max(max(max(FieldHisto))));%max of field value if isequal(Amin,Amax) cla(handles.HistoAxes) else Histo.ListVarName={FieldName,'histo'}; if isfield(Field,'NbDim') && isequal(Field.NbDim,3) Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram else if numel(nxy)==2 Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram else Histo.VarDimName={FieldName,{FieldName,'component'}}; %dimensions for the histogram end end %unit units=[]; %default for ivar=1:numel(Field.ListVarName) if strcmp(Field.ListVarName{ivar},FieldName) if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units') units=Field.VarAttribute{ivar}.units; break end end end if ~isempty(units) Histo.VarAttribute{1}.units=units; end eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo if isfield(Field,'NbDim') && isequal(Field.NbDim,3) C=reshape(double(FieldHisto),1,[]);% reshape in a vector Histo.histo(:,1)=hist(C, Histo.(FieldName)); %calculate histogram else for col=1:size(FieldHisto,3) B=FieldHisto(:,:,col); C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector Histo.histo(:,col)=hist(C, Histo.(FieldName)); %calculate histogram end end plot_field(Histo,handles.HistoAxes); hlegend=legend; if isempty(FieldName_2) set(hlegend,'String',FieldName) else set(hlegend,'String',{FieldName;FieldName_2}) end end end %------------------------------------------------------------------- % --- translate coordinate to matrix index %------------------------------------------------------------------- function [indx,indy]=pos2ind(x0,rangx0,nxy) indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel %------------------------------------------------------------------- % --- Executes on button press in 'CheckZoom'. %------------------------------------------------------------------- function CheckZoom_Callback(hObject, eventdata, handles) if (get(handles.CheckZoom,'Value') == 1); set(handles.CheckZoom,'BackgroundColor',[1 1 0]) set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes set(handles.CheckFixLimits,'BackgroundColor',[1 1 0]) else set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7]) end %------------------------------------------------------------------- % --- Executes on button press in 'CheckFixLimits'. %------------------------------------------------------------------- function CheckFixLimits_Callback(hObject, eventdata, handles) test=get(handles.CheckFixLimits,'Value'); if test set(handles.CheckFixLimits,'BackgroundColor',[1 1 0]) else set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7]) update_plot(handles); end %------------------------------------------------------------------- % --- Executes on button press in CheckFixAspectRatio. function CheckFixAspectRatio_Callback(hObject, eventdata, handles) %------------------------------------------------------------------- if get(handles.CheckFixAspectRatio,'Value') set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0]) update_plot(handles); else set(handles.CheckFixAspectRatio,'BackgroundColor',[0.7 0.7 0.7]) update_plot(handles); end %------------------------------------------------------------------- function num_AspectRatio_Callback(hObject, eventdata, handles) %------------------------------------------------------------------- set(handles.CheckFixAspectRatio,'Value',1)% select the fixed aspect ratio button set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])% mark in yellow update_plot(handles); %------------------------------------------------------------------- %------------------------------------------------------------------- %------------------------------------------------------------------- %----Executes on button press in 'record': records the current flags of manual correction. %------------------------------------------------------------------- function record_Callback(hObject, eventdata, handles) % [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles); [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles); FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]; %FileName=read_file_boxes(handles); [erread,message]=fileattrib(FileName); if ~isempty(message) && ~isequal(message.UserWrite,1) msgbox_uvmat('ERROR',['no writting access to ' FileName]) return end test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]); test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]); if ~test_civ2 && ~test_civ1 msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields') end if test_civ2 nbname='nb_vectors2'; flagname='vec2_FixFlag'; attrname='fix2'; end if test_civ1 nbname='nb_vectors'; flagname='vec_FixFlag'; attrname='fix'; end %write fix flags in the netcdf file UvData=get(handles.uvmat,'UserData'); hhh=which('netcdf.open');% look for built-in matlab netcdf library if ~isequal(hhh,'')% case of new builtin Matlab netcdf library nc=netcdf.open(FileName,'NC_WRITE'); netcdf.reDef(nc); netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1); dimid = netcdf.inqDimID(nc,nbname); try varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable catch varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist end netcdf.endDef(nc); netcdf.putVar(nc,varid,UvData.PlotAxes.FF); netcdf.close(nc); else %old netcdf library netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname) end %------------------------------------------------------------------- %----Correct the netcdf file, using toolbox (old versions of Matlab). %------------------------------------------------------------------- function netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname) nc=netcdf(FileName,'write'); %open netcdf file result=redef(nc); eval(['nc.' attrname '=1;']); theDim=nc(nbname) ;% get the number of velocity vectors nb_vectors=size(theDim); var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag var_FixFlag(1:nb_vectors)=AxeData.FF;% fin=close(nc); %------------------------------------------------------------------- % --- Executes on button press in SubField function SubField_Callback(hObject, eventdata, handles) %------------------------------------------------------------------- UvData=get(handles.uvmat,'UserData'); if get(handles.SubField,'Value')==0% if the subfield button is desactivated set(handles.RootPath_1,'String','') set(handles.RootFile_1,'String','') set(handles.SubDir_1,'String',''); set(handles.FileIndex_1,'String',''); set(handles.FileExt_1,'String',''); set(handles.RootPath_1,'Visible','off') set(handles.RootFile_1,'Visible','off') set(handles.SubDir_1,'Visible','off'); set(handles.NomType_1,'Visible','off'); set(handles.abs_time_1,'Visible','off') set(handles.FileIndex_1,'Visible','off'); set(handles.FileExt_1,'Visible','off'); set(handles.FieldName_1,'Value',1);%set to blank state set(handles.VelType_1,'Value',1);%set to blank state set(handles.num_Opacity,'String','')% desactivate opacity setting if ~strcmp(get(handles.VelType,'Visible'),'on') set(handles.VelType_1,'Visible','off') end if isfield(UvData,'XmlData_1') UvData=rmfield(UvData,'XmlData_1'); end set(handles.uvmat,'UserData',UvData); transform_fct_list=get(handles.transform_fct,'String'); transform_fct=transform_fct_list(get(handles.transform_fct,'Value')); if strcmp(transform_fct,'sub_field') set(handles.transform_fct,'Value',1)%suppress the sub_field transform transform_fct_Callback(hObject, eventdata, handles); else run0_Callback(hObject, eventdata, handles) end else MenuBrowse_1_Callback(hObject, eventdata, handles) end %------------------------------------------------------------------------ % --- read the data displayed for the input rootfile windows (new): TODO use read_GUI function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles) %------------------------------------------------------------------------ InputFile=read_GUI(handles.InputFile); RootPath=InputFile.RootPath; SubDir=regexprep(InputFile.SubDir,'/|\',''); RootFile=regexprep(InputFile.RootFile,'/|\',''); FileIndices=InputFile.FileIndex; FileExt=InputFile.FileExt; %------------------------------------------------------------------------ % ---- read the data displayed for the second input rootfile windows function [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomType_1]=read_file_boxes_1(handles) %------------------------------------------------------------------------ RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"') RootPath_1=get(handles.RootPath,'String'); end; SubDir_1=get(handles.SubDir_1,'String'); if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"') SubDir_1=get(handles.SubDir,'String'); end SubDir_1=regexprep(SubDir_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string RootFile_1=get(handles.RootFile_1,'String'); if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"') RootFile_1=get(handles.RootFile,'String'); end RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string FileIndex_1=get(handles.FileIndex_1,'String'); if isequal(get(handles.FileIndex_1,'Visible'),'off')|| isequal(FileIndex_1,'"') FileIndex_1=get(handles.FileIndex,'String'); end FileExt_1=get(handles.FileExt_1,'String'); if isequal(get(handles.FileExt_1,'Visible'),'off') || isequal(FileExt_1,'"') FileExt_1=get(handles.FileExt,'String');%read FileExt by default end NomType_1=get(handles.NomType_1,'String'); if isequal(get(handles.NomType_1,'Visible'),'off') || isequal(NomType_1,'"') NomType_1=get(handles.NomType,'String');%read FileExt by default end %------------------------------------------------------------------------ % --- Executes on menu selection FieldName function FieldName_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ list_fields=get(handles.FieldName,'String');% list menu fields index_fields=get(handles.FieldName,'Value');% selected string index field= list_fields{index_fields(1)}; % selected string if isequal(field,'get_field...') set(handles.FixVelType,'visible','off') set(handles.VelType,'visible','off') set(handles.VelType_1,'visible','off') [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles); FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]; hget_field=findobj(allchild(0),'name','get_field'); if ~isempty(hget_field) delete(hget_field) end get_field(FileName); return %no further action end UvData=get(handles.uvmat,'UserData'); %read the rootfile input display [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles); FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]; [tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]); if isequal(field,'image') if isfield(UvData.Field,'Civ2_ImageA')%get the corresponding input image in the netcdf file imagename=UvData.Field.Civ2_ImageA; elseif isfield(UvData.Field,'Civ1_ImageA')% imagename=UvData.Field.Civ1_ImageA; else SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.' imagename=fullfile_uvmat(RootPath,SubDirBase,RootFile,'.png',NomType,i1,[],j1,[]); end if ~exist(imagename,'file') [FileName,PathName] = uigetfile( ... {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)'; '*.jpg',' jpeg image files'; ... '*.png','.png image files'; ... '*.tif','.tif image files'; ... '*.avi;*.AVI','.avi movie files'; ... '*.vol','.volume images (png)'; ... '*.*', 'All Files (*.*)'}, ... 'Pick an image',imagename); if ~ischar(FileName),return,end %abandon if the browser is cancelled imagename=[PathName FileName]; end % display the selected field and related information display_file_name(handles,imagename)%display the image return else ext=get(handles.FileExt,'String'); if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file [FileName,PathName] = uigetfile( ... {'*.nc', ' (*.nc)'; '*.nc',' netcdf files'; ... '*.*', 'All Files (*.*)'}, ... 'Pick a netcdf file',FileBase); if ~ischar(FileName),return,end %abandon if the browser is cancelled FullFileName=[PathName FileName]; % display the selected field and related information display_file_name( handles,FullFileName) return end end indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2); set(handles.FileIndex,'String',indices) % set(handles.NomType,'String',NomType) %common to Fields_1_Callback list_fields_1=get(handles.FieldName_1,'String');% list menu fields field_1=''; if ~isempty(list_fields_1) field_1= list_fields_1{get(handles.FieldName_1,'Value')}; % selected string end if isequal(field,'image')||isequal(field_1,'image') set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons set(handles.TitleNpy,'Visible','on') set(handles.num_Npx,'Visible','on') set(handles.num_Npy,'Visible','on') else set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons set(handles.TitleNpy,'Visible','off') set(handles.num_Npx,'Visible','off') set(handles.num_Npy,'Visible','off') end if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1)) run0_Callback(hObject, eventdata, handles) end %--------------------------------------------------- % --- Executes on menu selection FieldName function FieldName_1_Callback(hObject, eventdata, handles) %------------------------------------------------- %% read input data check_new=~get(handles.SubField,'Value'); %check_new=1 if a second field was not previously entered UvData=get(handles.uvmat,'UserData'); if check_new && isfield(UvData,'XmlData') UvData.XmlData{2}=UvData.XmlData{1}; end if isfield(UvData,'Field_1') UvData=rmfield(UvData,'Field_1');% remove the stored second field (a new one needs to be read) end UvData.FileName_1='';% desactivate the use of a constant second file list_fields=get(handles.FieldName,'String');% list menu fields field= list_fields{get(handles.FieldName,'Value')}; % selected string list_fields=get(handles.FieldName_1,'String');% list menu fields field_1= list_fields{get(handles.FieldName_1,'Value')}; % selected string for the second field if isempty(field_1)%||(numel(UvData.FileType)>=2 && strcmp(UvData.FileType{2},'image')) set(handles.SubField,'Value',0) SubField_Callback(hObject, eventdata, handles) return else set(handles.SubField,'Value',1)%state that a second field is now entered end %% read the rootfile input display [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles); FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1]; [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String')); switch field_1 case 'get_field...' set_veltype_display(0) % no veltype display hget_field=findobj(allchild(0),'name','get_field_1'); if ~isempty(hget_field) delete(hget_field) end hget_field=get_field(FileName_1); set(hget_field,'name','get_field_1') hhget_field=guidata(hget_field); set(hhget_field.list_fig,'Value',1) set(hhget_field.list_fig,'String',{'uvmat'}) if check_new UvData.FileType{2}=UvData.FileType{1}; set(handles.FileIndex_1,'String',get(handles.FileIndex,'String')) set(handles.uvmat,'UserData',UvData) end case 'image' % get the image name corresponding to the current netcdf name (no unique correspondance) if isfield(UvData.Field,'Civ2_ImageA')%get the corresponding input image in the netcdf file imagename=UvData.Field.Civ2_ImageA; elseif isfield(UvData.Field,'Civ1_ImageA')% imagename=UvData.Field.Civ1_ImageA; else SubDirBase=regexprep(SubDir_1,'\..*','');%take the root part of SubDir, before the first dot '.' imagename=fullfile_uvmat(RootPath_1,SubDirBase,RootFile_1,'.png',get(handles.NomType,'String'),i1,[],j1); end if ~exist(imagename,'file') % browse for images if it is not found [FileName,PathName] = uigetfile( ... {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)'; '*.jpg',' jpeg image files'; ... '*.png','.png image files'; ... '*.tif','.tif image files'; ... '*.avi;*.AVI','.avi movie files'; ... '*.vol','.volume images (png)'; ... '*.*', 'All Files (*.*)'}, ... 'Pick an image',imagename); if ~ischar(FileName),return,end %abandon if the browser is cancelled imagename=[PathName FileName]; end if ~ischar(imagename)% quit if the browser has been closed set(handles.SubField,'Value',0) else %valid browser input: display the selected image set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons set(handles.TitleNpy,'Visible','on') set(handles.num_Npx,'Visible','on') set(handles.num_Npy,'Visible','on') display_file_name(handles,imagename,2)%display the imag end otherwise if check_new UvData.FileType{2}=UvData.FileType{1}; set(handles.FileIndex_1,'String',get(handles.FileIndex,'String')) set(handles.FileExt_1,'String',get(handles.FileExt,'String')) end if ~isequal(field,'image') set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons set(handles.TitleNpy,'Visible','off') set(handles.num_Npx,'Visible','off') set(handles.num_Npy,'Visible','off') end set(handles.uvmat,'UserData',UvData) if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1)) run0_Callback(hObject, eventdata, handles) end end %------------------------------------------------------------------------ % --- set the visibility of relevant velocity type menus: function menu=set_veltype_display(Civ,FileType) %------------------------------------------------------------------------ if ~exist('FileType','var') FileType='civx'; end switch FileType case 'civx' menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'}; if isequal(Civ,0) imax=0; elseif isequal(Civ,1) || isequal(Civ,2) imax=1; elseif isequal(Civ,3) imax=3; elseif isequal(Civ,4) || isequal(Civ,5) imax=4; elseif isequal(Civ,6) %patch2 imax=6; end case 'civdata' menu={'civ1';'filter1';'civ2';'filter2'}; if isequal(Civ,0) imax=0; elseif isequal(Civ,1) || isequal(Civ,2) imax=1; elseif isequal(Civ,3) imax=2; elseif isequal(Civ,4) || isequal(Civ,5) imax=3; elseif isequal(Civ,6) %patch2 imax=4; end end menu=menu(1:imax); %------------------------------------------------------------------------ % --- Executes on button press in FixVelType. function FixVelType_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ % refresh the current plot if the fixed veltype is unselected if ~get(handles.FixVelType,'Value') run0_Callback(hObject, eventdata, handles) end %------------------------------------------------------------------------ % --- Executes on button press in VelType. function VelType_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.FixVelType,'Value',1) run0_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ % --- Executes on choice selection in VelType_1. function VelType_1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.FixVelType,'Value',1)% the velocity type is now imposed by the GUI (not automatic) UvData=get(handles.uvmat,'UserData'); set(handles.run0,'BackgroundColor',[1 1 0])%paint run0 button in yellow to indicate its activation drawnow InputFile=read_GUI(handles.InputFile);% read the input file parameters [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles); [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles); FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];% name of the first input file check_refresh=0; if isempty(InputFile.VelType_1) FileName_1='';% we plot the first input field without the second field set(handles.SubField,'Value',0) SubField_Callback(hObject, eventdata, handles)% activate SubField_Callback and refresh current display, removing the second field elseif get(handles.SubField,'Value')% if subfield is already 'on' FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];% name of the second input file check_refresh=1;%will refresh the current display else% we introduce the same file (with a different field) for the second series FileName_1=FileName;% we compare two fields in the same file UvData.FileType{2}=UvData.FileType{1}; UvData.XmlData{2}= UvData.XmlData{1}; set(handles.SubField,'Value',1) transform=get(handles.path_transform,'UserData'); if (~isa(transform,'function_handle')||nargin(transform)<3) set(handles.transform_fct,'value',2); % set transform to sub_field if the current fct doe not accept two input fields transform_fct_Callback(hObject, eventdata, handles)% activate transform_fct_Callback and refresh current display else check_refresh=1; end end % refresh the current display if it has not been done previously if check_refresh UvData.FileName_1='';% desactivate the use of a constant second file set(handles.uvmat,'UserData',UvData) num_i1=stra2num(get(handles.i1,'String')); num_i2=stra2num(get(handles.i2,'String')); num_j1=stra2num(get(handles.j1,'String')); num_j2=stra2num(get(handles.j2,'String')); [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(['xx' FileIndex_1]); errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg); else set(handles.i1,'BackgroundColor',[1 1 1]) set(handles.i2,'BackgroundColor',[1 1 1]) set(handles.j1,'BackgroundColor',[1 1 1]) set(handles.j2,'BackgroundColor',[1 1 1]) set(handles.FileIndex,'BackgroundColor',[1 1 1]) set(handles.FileIndex_1,'BackgroundColor',[1 1 1]) end set(handles.run0,'BackgroundColor',[1 0 0]) end %----------------------------------------------- % --- reset civ buttons function reset_vel_type(handles_civ0,handle1) for ibutton=1:length(handles_civ0) set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784]) set(handles_civ0(ibutton),'Value',0) end if exist('handle1','var')%handles of selected button set(handle1,'BackgroundColor',[1 1 0]) end %------------------------------------------------------- % --- Executes on button press in MENUVOLUME. %------------------------------------------------------- function VOLUME_Callback(hObject, eventdata, handles) %errordlg('command VOL not implemented yet') if ishandle(handles.UVMAT_title) delete(handles.UVMAT_title) end UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface if isequal(get(handles.VOLUME,'Value'),1) set(handles.CheckZoom,'Value',0) set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7]) set(handles.edit_vect,'Value',0) edit_vect_Callback(hObject, eventdata, handles) set(handles.edit_object,'Value',0) set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7]) % set(handles.cal,'Value',0) % set(handles.cal,'BackgroundColor',[0 1 0]) set(handles.edit_vect,'Value',0) edit_vect_Callback(hObject, eventdata, handles) %initiate set_object GUI data.Name='VOLUME'; if isfield(UvData,'CoordType') data.CoordType=UvData.CoordType; end if isfield(UvData.Field,'Mesh')&~isempty(UvData.Field.Mesh) data.RangeX=[UvData.Field.XMin UvData.Field.XMax]; data.RangeY=[UvData.Field.YMin UvData.Field.YMax]; data.DX=UvData.Field.Mesh; data.DY=UvData.Field.Mesh; elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image np=size(UvData.Field.A); meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2); meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1); data.RangeY=max(meshx,meshy); data.RangeX=max(meshx,meshy); data.DX=max(meshx,meshy); end data.ParentButton=handles.VOLUME; PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes, % associate the set_object interface handle to the plotting axes set(hset_object,'Position',get(handles.uvmat,'Position')+UvData.OpenParam.PosSetObject) UvData.MouseAction='create_object'; else set(handles.VOLUME,'BackgroundColor',[0 1 0]) end set(handles.uvmat,'UserData',UvData) %------------------------------------------------------- function edit_vect_Callback(hObject, eventdata, handles) %------------------------------------------------------- % % UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface if isequal(get(handles.edit_vect,'Value'),1) test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]); test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]); if ~test_civ2 && ~test_civ1 msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields') end set(handles.record,'Visible','on') set(handles.edit_vect,'BackgroundColor',[1 1 0]) set(handles.edit_object,'Value',0) set(handles.CheckZoom,'Value',0) set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7]) % set(handles.create,'Value',0) % set(handles.create,'BackgroundColor',[0 1 0]) set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7]) set(gcf,'Pointer','arrow') % UvData.MouseAction='edit_vect'; else set(handles.record,'Visible','off') set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7]) end %---------------------------------------------- function save_mask_Callback(hObject, eventdata, handles) %----------------------------------------------------------------------- UvData=get(handles.uvmat,'UserData'); flag=1; npx=size(UvData.Field.A,2); npy=size(UvData.Field.A,1); xi=0.5:npx-0.5; yi=0.5:npy-0.5; [Xi,Yi]=meshgrid(xi,yi); if isfield(UvData,'Object') for iobj=1:length(UvData.Object) ObjectData=UvData.Object{iobj}; if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside')); flagobj=1; testphys=0; %coordinates in pixels by default if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys') if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib') Calib=UvData.XmlData{1}.GeometryCalib; testphys=1; end end if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style') if isequal(ObjectData.Type,'polygon') X=ObjectData.Coord(:,1); Y=ObjectData.Coord(:,2); if testphys [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases end flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside elseif isequal(ObjectData.Type,'ellipse') if testphys %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys end RangeX=max(ObjectData.RangeX); RangeY=max(ObjectData.RangeY); X2Max=RangeX*RangeX; Y2Max=RangeY*RangeY; distX=(Xi-ObjectData.Coord(1,1)); distY=(Yi-ObjectData.Coord(1,2)); flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1; elseif isequal(ObjectData.Type,'rectangle') if testphys %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys end distX=abs(Xi-ObjectData.Coord(1,1)); distY=abs(Yi-ObjectData.Coord(1,2)); flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY); end if isequal(ObjectData.ProjMode,'mask_outside') flagobj=~flagobj; end flag=flag & flagobj; end end end end % flag=~flag; %mask name RootPath=get(handles.RootPath,'String'); RootFile=get(handles.RootFile,'String'); RootFile=regexprep(RootFile,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string filebase=fullfile(RootPath,RootFile); list=get(handles.masklevel,'String'); masknumber=num2str(length(list)); maskindex=get(handles.masklevel,'Value'); mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex); %mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i'); imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 201 && isfield(UvData,'XmlData')&&~isempty(UvData.XmlData) XmlData=UvData.XmlData{1}; DataOut=feval(transform_handle,'*',XmlData); if isfield(DataOut,'CoordUnit') CoordUnit=DataOut.CoordUnit; end if isfield(DataOut,'InputFieldType') UvData.InputFieldType=DataOut.InputFieldType; end else DataOut=feval(transform_handle,'*'); end end set(handles.CheckFixLimits,'Value',0) set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7]) %% delete drawn objects if the output CooordUnit is different from the previous one if ~strcmp(CoordUnit,CoordUnitPrev) hother=findobj('Tag','proj_object');%find all the proj objects for iobj=1:length(hother) delete_object(hother(iobj)) end hother=findobj('Tag','DeformPoint');%find all the proj objects for iobj=1:length(hother) delete_object(hother(iobj)) end hh=findobj('Tag','calib_points'); if ~isempty(hh) delete(hh) end hhh=findobj('Tag','calib_marker'); if ~isempty(hhh) delete(hhh) end % if isfield(UvData,'Object') % UvData.Object=UvData.Object(1); % end set(handles.ListObject,'Value',1) set(handles.ListObject,'String',{''}) set(handles.ListObject_1,'Value',1) set(handles.ListObject_1,'String',{''}) set(handles.ViewObject,'value',0) ViewObject_Callback(hObject, eventdata, handles) set(handles.ViewField,'value',0) ViewField_Callback(hObject, eventdata, handles) set(handles.edit_object,'Value',0) edit_object_Callback(hObject, eventdata, handles) UvData.Object={[]}; end set(handles.uvmat,'UserData',UvData) %% refresh the current plot if isempty(list_path{ichoice}) || nargin(transform_handle)<3 set(handles.SubField,'Value',0) SubField_Callback(hObject, eventdata, handles) else run0_Callback(hObject, eventdata, handles) end %------------------------------------------------ %CALLBACKS FOR PLOTTING PARAMETERS %------------------------------------------------- %%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Plot coordinates %%%%%%%%%%%%%%%%%%%%%%%%%%%%% %------------------------------------------------------------------------ function num_MinX_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.CheckFixLimits,'Value',1) %suppress auto mode set(handles.CheckFixLimits,'BackgroundColor',[1 1 0]) update_plot(handles); %------------------------------------------------------------------------ function num_MaxX_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.CheckFixLimits,'Value',1) %suppress auto mode set(handles.CheckFixLimits,'BackgroundColor',[1 1 0]) update_plot(handles); %------------------------------------------------------------------------ function num_MinY_Callback(hObject, eventdata, handles) %------------------------------------------ set(handles.CheckFixLimits,'Value',1) %suppress auto mode set(handles.CheckFixLimits,'BackgroundColor',[1 1 0]) update_plot(handles); %------------------------------------------------------------------------ function num_MaxY_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.CheckFixLimits,'Value',1) %suppress auto mode set(handles.CheckFixLimits,'BackgroundColor',[1 1 0]) update_plot(handles); %%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Scalar or image representation %%%%%%%%%%%%%%%%%%%%%%%%%%%%% %------------------------------------------------------------------------ function num_MinA_Callback(hObject, eventdata, handles) %------------------------------------------ set(handles.CheckFixScalar,'Value',1) %suppress auto mode set(handles.CheckFixScalar,'BackgroundColor',[1 1 0]) MinA=str2double(get(handles.num_MinA,'String')); MaxA=str2double(get(handles.num_MaxA,'String')); if MinA>MaxA% switch minA and maxA in case of error MinA_old=MinA; MinA=MaxA; MaxA=MinA_old; set(handles.num_MinA,'String',num2str(MinA,5)); set(handles.num_MaxA,'String',num2str(MaxA,5)); end update_plot(handles); %------------------------------------------------------------------------ function num_MaxA_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.CheckFixScalar,'Value',1) %suppress auto mode set(handles.CheckFixScalar,'BackgroundColor',[1 1 0]) MinA=str2double(get(handles.num_MinA,'String')); MaxA=str2double(get(handles.num_MaxA,'String')); if MinA>MaxA% switch minA and maxA in case of error MinA_old=MinA; MinA=MaxA; MaxA=MinA_old; set(handles.num_MinA,'String',num2str(MinA,5)); set(handles.num_MaxA,'String',num2str(MaxA,5)); end update_plot(handles); %------------------------------------------------------------------------ function CheckFixScalar_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ test=get(handles.CheckFixScalar,'Value'); if test set(handles.CheckFixScalar,'BackgroundColor',[1 1 0]) else set(handles.CheckFixScalar,'BackgroundColor',[0.7 0.7 0.7]) update_plot(handles); end %------------------------------------------------------------------- function CheckBW_Callback(hObject, eventdata, handles) %------------------------------------------------------------------- update_plot(handles); %------------------------------------------------------------------- function num_Opacity_Callback(hObject, eventdata, handles) update_plot(handles); %------------------------------------------------------------------- %------------------------------------------------------------------- function ListContour_Callback(hObject, eventdata, handles) %------------------------------------------------------------------- val=get(handles.ListContour,'Value'); if val==2 set(handles.interval_txt,'Visible','on') set(handles.num_IncrA,'Visible','on') else set(handles.interval_txt,'Visible','off') set(handles.num_IncrA,'Visible','off') end update_plot(handles); %------------------------------------------------------------------- function num_IncrA_Callback(hObject, eventdata, handles) %------------------------------------------------------------------- update_plot(handles); %%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Vector representation %%%%%%%%%%%%%%%%%%%%%%%%%%%%% %------------------------------------------------------------------- function CheckHideWarning_Callback(hObject, eventdata, handles) %------------------------------------------------------------------- update_plot(handles); %------------------------------------------------------------------- function CheckHideFalse_Callback(hObject, eventdata, handles) %------------------------------------------------------------------- update_plot(handles); %------------------------------------------------------------------- function num_VecScale_Callback(hObject, eventdata, handles) %------------------------------------------------------------------- set(handles.CheckFixVectors,'Value',1); set(handles.CheckFixVectors,'BackgroundColor',[1 1 0]) update_plot(handles); %------------------------------------------------------------------- function CheckFixVectors_Callback(hObject, eventdata, handles) %------------------------------------------------------------------- test=get(handles.CheckFixVectors,'Value'); if test set(handles.CheckFixVectors,'BackgroundColor',[1 1 0]) else update_plot(handles); %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3)) set(handles.CheckFixVectors,'BackgroundColor',[0.7 0.7 0.7]) end %------------------------------------------------------------------------ % --- Executes on selection change in CheckDecimate4 (nb_vec/4). function CheckDecimate4_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ update_plot(handles); %------------------------------------------------------------------------ % --- Executes on selection change in ColorCode menu function ColorCode_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ % edit the choice for color code update_color_code_boxes(handles); update_plot(handles); %------------------------------------------------------------------------ function update_color_code_boxes(handles) %------------------------------------------------------------------------ list_code=get(handles.ColorCode,'String');% list menu fields colcode= list_code{get(handles.ColorCode,'Value')}; % selected field enable_slider='off';%default enable_bounds='off';%default enable_scalar='off';%default switch colcode case {'rgb','bgr'} enable_slider='on'; enable_bounds='on'; enable_scalar='on'; case '64 colors' enable_bounds='on'; enable_scalar='on'; end set(handles.Slider1,'Visible',enable_slider) set(handles.Slider2,'Visible', enable_slider) set(handles.num_ColCode1,'Visible',enable_slider) set(handles.num_ColCode2,'Visible',enable_slider) set(handles.TitleColCode1,'Visible',enable_slider) set(handles.TitleColCode2,'Visible',enable_slider) set(handles.CheckFixVecColor,'Visible',enable_bounds) set(handles.num_MinVec,'Visible',enable_bounds) set(handles.num_MaxVec,'Visible',enable_bounds) set(handles.ColorScalar,'Visible',enable_scalar) set_vec_col_bar(handles) %------------------------------------------------------------------ % --- Executes on selection change in ColorScalar: choice of the color code. function ColorScalar_Callback(hObject, eventdata, handles) %------------------------------------------------------------------ % edit the choice for color code list_scalar=get(handles.ColorScalar,'String');% list menu fields col_scalar= list_scalar{get(handles.ColorScalar,'Value')}; % selected field if isequal(col_scalar,'ima_cor') set(handles.CheckFixVecColor,'Value',1)%fixed scale by default ColorCode='rgb'; set(handles.num_MinVec,'String','0') set(handles.num_MaxVec,'String','1') set(handles.num_ColCode1,'String','0.333') set(handles.num_ColCode2,'String','0.666') else set(handles.CheckFixVecColor,'Value',0)%auto scale between min,max by default ColorCode='64 colors'; end ColorCodeList=get(handles.ColorCode,'String'); ichoice=find(strcmp(ColorCode,ColorCodeList),1); set(handles.ColorCode,'Value',ichoice)% set color code in the menu update_color_code_boxes(handles); %replot the current graph run0_Callback(hObject, eventdata, handles) %---------------------------------------------------------------- % -- Executes on slider movement to set the color code % function Slider1_Callback(hObject, eventdata, handles) %------------------------------------------------------------------ slider1=get(handles.Slider1,'Value'); min_val=str2num(get(handles.num_MinVec,'String')); max_val=str2num(get(handles.num_MaxVec,'String')); col=min_val+(max_val-min_val)*slider1; set(handles.num_ColCode1,'String',num2str(col)) if(get(handles.Slider2,'Value') < col)%move also the second slider at the same value if needed set(handles.Slider2,'Value',col) set(handles.num_ColCode2,'String',num2str(col)) end set_vec_col_bar(handles) update_plot(handles); %---------------------------------------------------------------- % Executes on slider movement to set the color code %---------------------------------------------------------------- function Slider2_Callback(hObject, eventdata, handles) slider2=get(handles.Slider2,'Value'); min_val=str2num(get(handles.num_MinVec,'String')); max_val=str2num(get(handles.num_MaxVec,'String')); col=min_val+(max_val-min_val)*slider2; set(handles.num_ColCode2,'String',num2str(col)) if(get(handles.Slider1,'Value') > col)%move also the first slider at the same value if needed set(handles.Slider1,'Value',col) set(handles.num_ColCode1,'String',num2str(col)) end set_vec_col_bar(handles) update_plot(handles); %---------------------------------------------------------------- % --- Execute on return carriage on the edit box corresponding to slider 1 %---------------------------------------------------------------- function num_ColCode1_Callback(hObject, eventdata, handles) set_vec_col_bar(handles) update_plot(handles); %---------------------------------------------------------------- % --- Execute on return carriage on the edit box corresponding to slider 2 %---------------------------------------------------------------- function num_ColCode2_Callback(hObject, eventdata, handles) set_vec_col_bar(handles) update_plot(handles); %------------------------------------------------------------------------ %------------------------------------------------------- % --- Executes on button press in CheckFixVecColor. %------------------------------------------------------- function VecColBar_Callback(hObject, eventdata, handles) set_vec_col_bar(handles) %------------------------------------------------------------------------ % --- Executes on button press in CheckFixVecColor. function CheckFixVecColor_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ if ~get(handles.CheckFixVecColor,'Value') update_plot(handles); end %------------------------------------------------------------------------ % --- Executes on selection change in num_MaxVec. function num_MinVec_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ max_vec_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ % --- Executes on selection change in num_MaxVec. function num_MaxVec_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.CheckFixVecColor,'Value',1) CheckFixVecColor_Callback(hObject, eventdata, handles) min_val=str2num(get(handles.num_MinVec,'String')); max_val=str2num(get(handles.num_MaxVec,'String')); slider1=get(handles.Slider1,'Value'); slider2=get(handles.Slider2,'Value'); colcode1=min_val+(max_val-min_val)*slider1; colcode2=min_val+(max_val-min_val)*slider2; set(handles.num_ColCode1,'String',num2str(colcode1)) set(handles.num_ColCode2,'String',num2str(colcode2)) update_plot(handles); %------------------------------------------------------------------------ % --- update the display of color code for vectors (on vecColBar) function set_vec_col_bar(handles) %------------------------------------------------------------------------ %get the image of the color display button 'VecColBar' in pixels set(handles.VecColBar,'Unit','pixel'); pos_vert=get(handles.VecColBar,'Position'); set(handles.VecColBar,'Unit','Normalized'); width=ceil(pos_vert(3)); height=ceil(pos_vert(4)); %get slider indications list=get(handles.ColorCode,'String'); ichoice=get(handles.ColorCode,'Value'); colcode.ColorCode=list{ichoice}; colcode.MinVec=str2num(get(handles.num_MinVec,'String')); colcode.MaxVec=str2num(get(handles.num_MaxVec,'String')); test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr'); if test3color colcode.ColCode1=str2num(get(handles.num_ColCode1,'String')); colcode.ColCode2=str2num(get(handles.num_ColCode2,'String')); end vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max [colorlist,col_vec]=set_col_vec(colcode,vec_C); oneheight=ones(1,height); A1=colorlist(col_vec,1)*oneheight; A2=colorlist(col_vec,2)*oneheight; A3=colorlist(col_vec,3)*oneheight; A(:,:,1)=A1'; A(:,:,2)=A2'; A(:,:,3)=A3'; set(handles.VecColBar,'Cdata',A) %------------------------------------------------------------------- function update_plot(handles) %------------------------------------------------------------------- UvData=get(handles.uvmat,'UserData'); AxeData=UvData.PlotAxes;% retrieve the current plotted data PlotParam=read_GUI(handles.uvmat); [tild,PlotParamOut]= plot_field(AxeData,handles.PlotAxes,PlotParam); write_plot_param(handles,PlotParamOut); %update the auto plot parameters %------------------------------------------------------------------------ %------------------------------------------------------------------------ % SELECTION AND EDITION OF PROJECTION OBJECTS %------------------------------------------------------------------------ %------------------------------------------------------------------------ % --- Executes on selection change in ListObject_1. function ListObject_1_Callback(hObject, eventdata, handles) list_str=get(handles.ListObject,'String'); UvData=get(handles.uvmat,'UserData'); ObjectData=UvData.Object{get(handles.ListObject_1,'Value')}; %% update the projection plot on uvmat ProjData= proj_field(UvData.Field,ObjectData);%project the current input field on object ObjectData plot_field(ProjData,handles.PlotAxes,read_GUI(handles.uvmat));% plot the projected field; %replot all the objects within the new projected field for IndexObj=1:numel(list_str) hobject=UvData.Object{IndexObj}.DisplayHandle.uvmat; if isempty(hobject) || ~ishandle(hobject) hobject=handles.PlotAxes; end if isequal(IndexObj,get(handles.ListObject,'Value')) objectcolor='m'; %paint in magenta the currently selected object in ListObject else objectcolor='b'; end UvData.Object{IndexObj}.DisplayHandle.uvmat=plot_object(UvData.Object{IndexObj},ObjectData,hobject,objectcolor);%draw the object in uvmat end set(handles.uvmat,'UserData',UvData) %% display the object parameters if the GUI set_object is already opened if ~get(handles.ViewObject,'Value') ZBounds=0; % default if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax') ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider end ObjectData.Name=list_str{get(handles.ListObject_1,'Value')}; set_object(ObjectData,[],ZBounds); set(handles.ViewObject,'Value',1)% show that the selected object in ListObject_1 is currently visualised end % desactivate the edit object mode set(handles.edit_object,'Value',0) set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) %------------------------------------------------------------------------ % --- Executes on selection change in ListObject. function ListObject_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ list_str=get(handles.ListObject,'String'); IndexObj=get(handles.ListObject,'Value');%present object selection %% The object is displayed in set_object if this GUI is already opened UvData=get(handles.uvmat,'UserData'); ObjectData=UvData.Object{IndexObj}; hset_object=findobj(allchild(0),'tag','set_object'); if ~isempty(hset_object) ZBounds=0; % default if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax') ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider end ObjectData.Name=list_str{IndexObj}; set_object(ObjectData,[],ZBounds); set(handles.ViewField,'Value',1)% show that the selected object in ListObject is currently visualised end %% desactivate the edit object mode set(handles.edit_object,'Value',0) set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) %% update the plot on view_field if view_field is already openened hview_field=findobj(allchild(0),'tag','view_field'); if isempty(hview_field) hhview_field.PlotAxes=[]; else Data=get(hview_field,'UserData'); hhview_field=guidata(hview_field); ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData [PlotType,PlotParam]=plot_field(ProjData,hhview_field.PlotAxes,read_GUI(hview_field));%read plotting parameters on the uvmat interfachhview_fiel write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object haxes=findobj(hview_field,'tag','axes3'); pos=get(hview_field,'Position'); if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table) h_TableDisplay=findobj(hview_field,'tag','TableDisplay'); pos_table=get(h_TableDisplay,'Position'); set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)]) drawnow% needed to change position before the next command set(hview_field,'UserData',Data);% restore the previously stored GUI position after GUI resizing else set(hview_field,'Position',Data.GUISize)% return to the previously stored GUI position and size end end %% update the color of the graphic object representation: the selected object in magenta, others in blue update_object_color(handles.PlotAxes,hhview_field.PlotAxes,UvData.Object{IndexObj}.DisplayHandle.uvmat) %------------------------------------------------------------------------ %--- update the color representation of objects (indicating the selected ones) function update_object_color(axes_uvmat,axes_view_field,DisplayHandle) %------------------------------------------------------------------------ if isempty(axes_view_field)% case with no view_field plot hother=[findobj(axes_uvmat,'Tag','proj_object');findobj(axes_uvmat,'Tag','DeformPoint')];%find all the proj object and deform point representations else hother=[findobj(axes_uvmat,'Tag','proj_object') ;findobj(axes_view_field,'Tag','proj_object');... %find all the proj object representations findobj(axes_uvmat,'Tag','DeformPoint'); findobj(axes_view_field,'Tag','DeformPoint')];%find all the deform point representations end for iobj=1:length(hother) if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch') set(hother(iobj),'EdgeColor','b') if isequal(get(hother(iobj),'FaceColor'),'m') set(hother(iobj),'FaceColor','b') end elseif isequal(get(hother(iobj),'Type'),'image') Acolor=get(hother(iobj),'CData'); Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2)); set(hother(iobj),'CData',Acolor); else set(hother(iobj),'Color','b') end set(hother(iobj),'Selected','off') end if ishandle(DisplayHandle) linetype=get(DisplayHandle,'Type'); if isequal(linetype,'line') set(DisplayHandle,'Color','m'); %set the selected object to magenta color elseif isequal(linetype,'rectangle') set(DisplayHandle,'EdgeColor','m'); %set the selected object to magenta color elseif isequal(linetype,'patch') set(DisplayHandle,'FaceColor','m'); %set the selected object to magenta color end SubObjectData=get(DisplayHandle,'UserData'); if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject) for iobj=1:length(SubObjectData.SubObject) hsub=SubObjectData.SubObject(iobj); if isequal(get(hsub,'Type'),'rectangle') set(hsub,'EdgeColor','m'); %set the selected object to magenta color elseif isequal(get(hsub,'Type'),'image') Acolor=get(hsub,'CData'); Acolor(:,:,1)=Acolor(:,:,3); set(hsub,'CData',Acolor); else set(hsub,'Color','m') end end end if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint) set(SubObjectData.DeformPoint,'Color','m') end end %------------------------------------------------------------------- % --- Executes on selection change in edit_object. function edit_object_Callback(hObject, eventdata, handles) %------------------------------------------------------------------- UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface hset_object=findobj(allchild(0),'Tag','set_object'); if get(handles.edit_object,'Value') set(handles.edit_object,'BackgroundColor',[1,1,0]) %suppress the other options set(handles.CheckZoom,'Value',0) CheckZoom_Callback(hObject, eventdata, handles) hgeometry_calib=findobj(allchild(0),'tag','geometry_calib'); if ishandle(hgeometry_calib) hhgeometry_calib=guidata(hgeometry_calib); set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7]) end set(handles.ViewObject,'value',1) ViewObject_Callback(hObject, eventdata, handles) else % desctivate object edit mode set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) if ~isempty(hset_object)% open the hhset_object=guidata(hset_object); set(hhset_object.PLOT,'enable','off'); set(get(hset_object,'children'),'enable','inactive') end end %------------------------------------------------------------------------ % --- Executes on button press in ViewObject. function ViewObject_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ check_view=get(handles.ViewObject,'Value'); if check_view %activate set_object IndexObj=get(handles.ListObject,'Value'); list_object=get(handles.ListObject,'String'); UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface UvData.Object{IndexObj}.Name=list_object{IndexObj}; if numel(UvData.Object)1 && ~isequal(IndexObj,IndexObj_1) % do not delete the object used for the uvmat plot delete_object(IndexObj) end %------------------------------------------------------------------------ %------------------------------------------------------------------------ % II - TOOLS FROM THE UPPER MENU BAR %------------------------------------------------------------------------ %------------------------------------------------------------------------ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Export Menu Callbacks %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %------------------------------------------------------------------------ % --- Executes on button press in Menu/Export/field in workspace. function MenuExportField_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ global Data_uvmat Data_uvmat=get(handles.uvmat,'UserData'); evalin('base','global Data_uvmat')%make CurData global in the workspace display('current field :') evalin('base','Data_uvmat') %display CurData in the workspace commandwindow; %brings the Matlab command window to the front %------------------------------------------------------------------------ % --- Executes on button press in Menu/Export/extract figure. function MenuExportFigure_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ % huvmat=get(handles.MenuExport,'parent'); hfig=figure; copyobj(handles.PlotAxes,hfig); map=colormap(handles.PlotAxes); colormap(map);%transmit the current colormap to the zoom fig colorbar % -------------------------------------------------------------------- function MenuExportAxis_Callback(hObject, eventdata, handles) answer=msgbox_uvmat('CONFIRMATION','select a figure/axis on which the current uvmat plot will be exported') if strcmp(answer,'Yes') hchild=get(handles.PlotAxes,'children'); copyobj(hchild,gca); end %------------------------------------------------------------------------ % -------------------------------------------------------------------- function MenuExportMovie_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- set(handles.MenuExportMovie,'BusyAction','queue')% activate the button huvmat=get(handles.run0,'parent'); UvData=get(huvmat,'UserData'); %[xx,xx,FileBase]=read_file_boxes(handles); [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles); FileBase=fullfile(RootPath,RootFile); %read the current input file name prompt = {'movie file name';'frames per second';'frame resolution (*[512x384] pixels)';'axis position relative to the frame';'total frame number (starting from the current uvmat display)'}; dlg_title = 'select properties of the output avi movie'; num_lines= 1; def = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'}; answer = inputdlg(prompt,dlg_title,num_lines,def,'on'); aviname=answer{1}; fps=str2double(answer{2}); % check for existing file with output name aviname if exist(aviname,'file') backup=aviname; testexist=2; while testexist==2 backup=[backup '~']; testexist=exist(backup,'file'); end [success,message]=copyfile(aviname,backup);%make backup of the existing file if isequal(success,1) delete(aviname)%delete existing file else msgbox_uvmat('ERROR',message) return end end %create avi open aviobj=avifile(aviname,'Compression','None','fps',fps); %display first view for tests newfig=figure; newaxes=copyobj(handles.PlotAxes,newfig);%new plotting axes in the new figure set(newaxes,'Tag','movieaxes') nbpix=[512 384]*str2double(answer{3}); set(gcf,'Position',[1 1 nbpix])% resolution XVGA set(newaxes,'Position',eval(answer{4})); map=colormap(handles.PlotAxes); colormap(map);%transmit the current colormap to the zoom fig msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;... ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']}); UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes set(huvmat,'UserData',UvData); increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d set(handles.STOP,'Visible','on') set(handles.speed,'Visible','on') set(handles.speed_txt,'Visible','on') set(handles.Movie,'BusyAction','queue') %imin=str2double(get(handles.i1,'String')); imax=str2double(answer{5}); % if isfield(UvData,'Time') htitle=get(newaxes,'Title'); xlim=get(newaxes,'XLim'); ylim=get(newaxes,'YLim'); set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0]) time_str=get(handles.abs_time,'String'); set(htitle,'String',['t=' time_str]) set(handles.speed,'Value',1) for i=1:imax if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command runpm(hObject,eventdata,handles,increment)% run plus drawnow time_str=get(handles.abs_time,'String'); if ishandle(htitle) set(htitle,'String',['t=' time_str]) end mov=getframe(newfig); aviobj=addframe(aviobj,mov); end end aviobj=close(aviobj); UvData=rmfield(UvData,'plotaxes'); %UvData.Object{1}.plotaxes=handles.PlotAxes; set(huvmat,'UserData',UvData); msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']}) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Projection Objects Menu Callbacks %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % ----------------------------------------------------------------------- function Menupoints_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ data.Type='points'; data.ProjMode='projection';%default data.ProjModeMenu={};% do not restrict ProjMode menus create_object(data,handles) % ----------------------------------------------------------------------- function Menuline_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ data.Type='line'; data.ProjMode='projection';%default data.ProjModeMenu={};% do not restrict ProjMode menus create_object(data,handles) %------------------------------------------------------------------------ function Menupolyline_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ data.Type='polyline'; data.ProjMode='projection';%default data.ProjModeMenu={};% do not restrict ProjMode menus create_object(data,handles) %------------------------------------------------------------------------ function Menupolygon_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ data.Type='polygon'; data.ProjMode='inside';%default data.ProjModeMenu={};% do not restrict ProjMode menus create_object(data,handles) %------------------------------------------------------------------------ function Menurectangle_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ data.Type='rectangle'; data.ProjMode='inside';%default data.ProjModeMenu={};% do not restrict ProjMode menus create_object(data,handles) %------------------------------------------------------------------------ function Menuellipse_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ data.Type='ellipse'; data.ProjMode='inside';%default data.ProjModeMenu={};% do not restrict ProjMode menus create_object(data,handles) %------------------------------------------------------------------------ function MenuMaskObject_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ data.Type='polygon'; data.TypeMenu={'polygon'}; data.ProjMode='mask_inside';%default data.ProjModeMenu={'mask_inside';'mask_outside'}; create_object(data,handles) %------------------------------------------------------------------------ function Menuplane_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ data.Type='plane'; data.ProjMode='projection';%default data.ProjModeMenu={};% do not restrict ProjMode menus create_object(data,handles) %------------------------------------------------------------------------ function Menuvolume_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ data.Type='volume'; data.ProjMode='interp';%default data.ProjModeMenu={}; % set(handles.create,'Visible','on') % set(handles.create,'Value',1) % VOLUME_Callback(hObject,eventdata,handles)data.ProjModeMenu={}; create_object(data,handles) %------------------------------------------------------------------------ % --- generic function used for the creation of a projection object function create_object(data,handles) %------------------------------------------------------------------------ % desactivate geometric calibration if opened hgeometry_calib=findobj(allchild(0),'tag','geometry_calib'); if ishandle(hgeometry_calib) hhgeometry_calib=guidata(hgeometry_calib); set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7]) end set(handles.edit_object,'Value',0); %suppress the object edit mode set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) ListObject=get(handles.ListObject,'String'); if ~strcmp(ListObject{end},'') ListObject=[ListObject;{''}]; %append a blank to the list (if nort already done) to indicate the creation of a new object set(handles.ListObject,'String',ListObject) end IndexObj=length(ListObject); set(handles.ListObject,'Value',IndexObj) UvData=get(handles.uvmat,'UserData'); UvData.Object{IndexObj}=[]; %create a new empty object UvData.Object{IndexObj}.DisplayHandle.uvmat=handles.PlotAxes; % axes for plot_object UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation data.Name=data.Type;% default name=type data.Coord=[0 0]; %default if isfield(UvData,'Field') Field=UvData.Field; if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh) data.RangeX=[UvData.Field.XMin UvData.Field.XMax]; if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')||strcmp(data.Type,'points') data.RangeY=UvData.Field.Mesh; else data.RangeY=[UvData.Field.YMin UvData.Field.YMax]; end data.DX=UvData.Field.Mesh; data.DY=UvData.Field.Mesh; end if isfield(Field,'NbDim')&& isequal(Field.NbDim,3) data.Coord=[0 0 0]; %default end if isfield(Field,'CoordUnit') data.CoordUnit=Field.CoordUnit; end end if ishandle(handles.UVMAT_title) delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered end hset_object=set_object(data,handles);% call the set_object interface hhset_object=guidata(hset_object); hchild=get(hset_object,'children'); set(hchild,'enable','on') set(handles.uvmat,'UserData',UvData) set(handles.CheckZoom,'Value',0) %desactivate the zoom for object creation by the mouse CheckZoom_Callback(handles.uvmat, [], handles) set(handles.delete_object,'Visible','on') %------------------------------------------------------------------------ function MenuBrowseObject_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ %get the object file [FileName, PathName, filterindex] = uigetfile( ... {'*.xml;*.mat', ' (*.xml,*.mat)'; '*.xml', '.xml files '; ... '*.mat', '.mat matlab files '}, ... 'Pick an xml Object file',get(handles.RootPath,'String')); fileinput=[PathName FileName];%complete file name sizf=size(fileinput); if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %read the file [data,heading]=xml2struct(fileinput); if ~strcmp(heading,'ProjObject') msgbox_uvmat('WARNING','The xml file does not have the heading ProjObject for projection objects') end [tild,data.Name]=fileparts(FileName);% object name set as file name ListObject=get(handles.ListObject,'String'); if ~strcmp(ListObject{end},'') ListObject=[ListObject;{''}]; %append a blank to the list (if not already done) to indicate the creation of a new object set(handles.ListObject,'String',ListObject) end IndexObj=length(ListObject); UvData=get(handles.uvmat,'UserData'); UvData.Object{IndexObj}=[]; %create a new empty object UvData.Object{IndexObj}.DisplayHandle.uvmat=[]; %no plot handle before plot_field operation UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation set(handles.uvmat,'UserData',UvData) set(handles.ListObject,'Value',IndexObj) hset_object=set_object(data);% call the set_object interface set(get(hset_object,'children'),'enable','on')% enable edit action on elements on GUI set_object set(handles.edit_object,'Value',0); %suppress the object edit mode set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) set(handles.delete_object,'Visible','on') %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % MenuEdit Callbacks %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %------------------------------------------------------------------------ function MenuEditObject_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.edit_object,'Value',1) edit_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ function MenuEditVectors_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.edit_vect,'Visible','on') set(handles.edit_vect,'Value',1) edit_vect_Callback(hObject, eventdata, handles) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % MenuTools Callbacks %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %------------------------------------------------------------------------ function MenuCalib_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface %suppress competing options set(handles.CheckZoom,'Value',0) set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7]) set(handles.ListObject,'Value',1) % initiate display of GUI geometry_calib data=[]; %default if isfield(UvData,'CoordType') data.CoordType=UvData.CoordType; end [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles); FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt]; set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib pos_uvmat=get(handles.uvmat,'Position'); pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.PosGeometryCalib(1)*pos_uvmat(3); pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.PosGeometryCalib(2)*pos_uvmat(4); pos_cal(3:4)=UvData.OpenParam.PosGeometryCalib(3:4).* pos_uvmat(3:4); geometry_calib(FileName,pos_cal);% call the geometry_calib interface set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action %------------------------------------------------------------------------ function MenuMask_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface ListObj=UvData.Object; select=zeros(1,numel(ListObj)); for iobj=1:numel(ListObj); if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside') select(iobj)=1; end end val=find(select); if isempty(val) msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar'); return else % set(handles.ListObject,'Max',2);%allow multiple selection set(handles.ListObject,'Value',val); flag=1; npx=size(UvData.Field.A,2); npy=size(UvData.Field.A,1); xi=0.5:npx-0.5; yi=0.5:npy-0.5; [Xi,Yi]=meshgrid(xi,yi); if isfield(UvData,'Object') for iobj=1:length(UvData.Object) ObjectData=UvData.Object{iobj}; if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside')); flagobj=1; testphys=0; %coordinates in pixels by default if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel') if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib') Calib=UvData.XmlData{1}.GeometryCalib; testphys=1; end end if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Type') if isequal(ObjectData.Type,'polygon') X=ObjectData.Coord(:,1); Y=ObjectData.Coord(:,2); if testphys [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases end flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside elseif isequal(ObjectData.Type,'ellipse') if testphys %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys end RangeX=max(ObjectData.RangeX); RangeY=max(ObjectData.RangeY); X2Max=RangeX*RangeX; Y2Max=RangeY*RangeY; distX=(Xi-ObjectData.Coord(1,1)); distY=(Yi-ObjectData.Coord(1,2)); flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1; elseif isequal(ObjectData.Type,'rectangle') if testphys %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys end distX=abs(Xi-ObjectData.Coord(1,1)); distY=abs(Yi-ObjectData.Coord(1,2)); flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY); end if isequal(ObjectData.ProjMode,'mask_outside') flagobj=~flagobj; end flag=flag & flagobj; end end end end %mask name RootPath=get(handles.RootPath,'String'); SubDir=get(handles.SubDir,'String'); RootFile=get(handles.RootFile,'String'); if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\')) RootFile(1)=[]; end % filebase=fullfile(RootPath,RootFile); list=get(handles.masklevel,'String'); masknumber=num2str(length(list)); maskindex=get(handles.masklevel,'Value'); % mask_name=fullfile_uvmat(RootPath,'',[RootFile '_' masknumber 'mask'],'.png','_1',maskindex); mask_name=fullfile_uvmat(RootPath,[SubDir '.mask'],'mask','.png','_1',maskindex); imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 201 Param.list_fields(ind_image)=[]; %suppress 'image' option end Param.index_fields=find(strcmp(FieldName,Param.list_fields));% selected string index Param.list_fields_1=get(handles.FieldName_1,'String');% list menu fields if ischar(Param.list_fields_1),Param.list_fields_1={Param.list_fields_1};end FieldName_1=Param.list_fields_1{get(handles.FieldName_1,'Value')}; ind_image=find(strcmp('image',Param.list_fields_1)); if ~isempty(ind_image) && numel(Param.list_fields_1)>1 Param.list_fields_1(ind_image)=[]; %suppress 'image' option end Param.index_fields_1=find(strcmp(FieldName_1,Param.list_fields_1));% selected string index Param.transform_str=get(handles.transform_fct,'String'); Param.transform_val=get(handles.transform_fct,'Value'); Param.Coord_x_str=get(handles.Coord_x,'String'); Param.Coord_x_val=get(handles.Coord_x,'Value'); Param.Coord_y_str=get(handles.Coord_y,'String'); Param.Coord_y_val=get(handles.Coord_y,'Value'); series(Param); %run the series interface %------------------------------------------------------------------------ % -- open the GUI civ.fig for PIV function MenuPIV_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles); FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt]; civ(FileName);% interface de civ(not in the uvmat file) % -------------------------------------------------------------------- function MenuHelp_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- path_to_uvmat=which ('uvmat');% check the path of uvmat pathelp=fileparts(path_to_uvmat); helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html'); if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package') else addpath (fullfile(pathelp,'uvmat_doc')) web(helpfile); end % -------------------------------------------------------------------- function MenuSetProject_Callback(hObject, eventdata, handles) RootPath=get(handles.RootPath,'String'); ProjectDir = uigetdir(fileparts(fileparts(RootPath)), 'select the project source directory'); datatree_browser(ProjectDir) % -------------------------------------------------------------------- function MenuBrowseProject_Callback(hObject, eventdata, handles) RootPath=get(handles.RootPath,'String'); ProjectDir = uigetdir(fileparts(fileparts(RootPath)), 'select the project directory'); datatree_browser(ProjectDir) % --- Executes on selection change in Coord_y. function Coord_y_Callback(hObject, eventdata, handles) % --- Executes on selection change in Coord_x. function Coord_x_Callback(hObject, eventdata, handles)