%'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....) %======================================================================= % Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France % http://www.legi.grenoble-inp.fr % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr % % This file is part of the toolbox UVMAT. % % UVMAT is free software; you can redistribute it and/or modify % it under the terms of the GNU General Public License as published % by the Free Software Foundation; either version 2 of the license, % or (at your option) any later version. % % UVMAT is distributed in the hope that it will be useful, % but WITHOUT ANY WARRANTY; without even the implied warranty of % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the % GNU General Public License (see LICENSE.txt) for more details. %======================================================================= % 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) % .PosGeometryCalib: size of set_object % .NbBuiltin: nbre of functions always displayed in TransformName menu % .ProjObject: 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 REFRESH_Callback) %%%%%%%%%%%%%%%%%%%%: % % % 1) Input filenames are determined by MenuBrowse (first field), MenuBrowseCampaign % (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 % | % (tps_coeff_field.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 set_field_list.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 axes are represented by UvData.Field.Coord_x and UvData.Field.Coord_y, and .X and % .Y for C (the same as velocity vectors). If A is a nxxny matrix (scalar % on a regtular grid), then .Coord_x andf.Coord_y contains only two elements, represneting the % axes 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 CheckEditObject % Properties attached to plotting figures (standard Matlab properties): % 'CurrentAxes'= gca or get(gcf,'CurrentAxes'); % 'CurrentPoint'=get(gcf,'CurrentPoint'): figure axes 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 axes. % 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 CheckEditObject % .CurrentLine: currently drawn menuline (A REVOIR) % .CurrentObject: handle of the currently drawn CheckEditObject % .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 % .Coordinates: 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.ProjObject %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 the GUI, colorbar and ancillary GUIs: set(hObject,'Units','pixels')% set(0,'Units','pixels'); ScreenSize=get(0,'ScreenSize');%size of the current screen Width=1050; Height=700; %adjust to screen size (reduced by a min margin) RescaleFactor=min((ScreenSize(3)-80)/Width,(ScreenSize(4)-80)/Height); if RescaleFactor>1 RescaleFactor=RescaleFactor/2+1/2; %reduce the rescale factor to provide an increased margin for a big screen end Width=Width*RescaleFactor; Height=Height*RescaleFactor; LeftX=80*RescaleFactor;%position of the left fig side, in pixels (put to the left side, with some margin) LowY=round(ScreenSize(4)/2-Height/2); % put at the middle height on the screen set(hObject,'Position',[LeftX LowY Width Height]) UvData.PosColorbar=[0.80 0.02 0.018 0.445]; AxeData.LimEditBox=1; %initialise AxeData set(handles.PlotAxes,'UserData',AxeData) %% set functions for the mouse and keyboard set(hObject,'WindowKeyPressFcn',{'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})% set(hObject,'ResizeFcn',{@ResizeFcn,handles})% %% initialisation set(handles.FieldName,'Value',1) set(handles.FieldName,'string',{''}) UvData.ProjObject={[]}; %% 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 TransformName dir_perso=prefdir; % path to the directory .matlab containing the personal data of the current user profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmat_perso.mat' in .matlab if exist(profil_perso,'file')% if the file exists h=load (profil_perso); % open the personal file if isfield(h,'MenuFile')% load the saved menu of previously opened files for ifile=1:min(length(h.MenuFile),5) set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile}); end end if isfield(h,'MenuCampaign')% load the saved menu of previously opened campaigns for ifile=1:min(length(h.MenuCampaign),5) set(handles.(['MenuCampaign_' num2str(ifile)]),'Label',h.MenuCampaign{ifile}); end end if isfield(h,'RootPath') set(handles.RootPath,'UserData',h.RootPath); %store the previous campaign in the UserData of RootPath 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.TransformName,'String',transform_menu)% display the menu of transform fcts set(handles.TransformName,'UserData',path_list)% store the corresponding list of path in UserData of uicontrol transform_fct set(handles.TransformPath,'String','') set(handles.TransformPath,'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) %%%%%%% 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) %------------------------------------------------------------------------ % delete GUI 'view_field' if detected hh=findobj(allchild(0),'tag','view_field'); if ~isempty(hh) delete(hh) end % delete GUI 'geometry_calib' if detected hh=findobj(allchild(0),'tag','geometry_calib'); if ~isempty(hh) delete(hh) end % desable set_object editing action if detected hh=findobj(allchild(0),'name','set_object'); if ~isempty(hh) hhh=findobj(hh,'tag','PLOT'); set(hhh,'enable','off') end %delete the bowser if detected hh=findobj(allchild(0),'tag','browser'); if ~isempty(hh) delete(hh) end %------------------------------------------------------------------------ %--- activated when resizing the GUI view_field function ResizeFcn(gcbo,eventdata,handles) %------------------------------------------------------------------------ set(handles.uvmat,'Units','pixels') size_fig=get(handles.uvmat,'Position'); ColumnWidth=max(150,0.18*size_fig(3)); ColumnWidth=min(ColumnWidth,250); % width of the right side display column, between 150 and 250, depending on the fig width %% position of panel InputFile set(handles.InputFile,'Units','pixels') pos_InputFile=get(handles.InputFile,'Position');% [lower x lower y width height] for text_display pos_InputFile(1)=0; pos_InputFile(2)=size_fig(4)-pos_InputFile(4); % set frame InputFile to the top of the fig pos_InputFile(3)=size_fig(3); set(handles.InputFile,'Position',pos_InputFile);% [lower x lower y width height] for text_display %% reset position of text_display and TableDisplay set(handles.text_display,'Units','pixels') set(handles.TableDisplay,'Units','pixels') pos_1=get(handles.text_display,'Position');% [lower x lower y width height] for text_display pos_1(3)=1.2*ColumnWidth; pos_1(1)=size_fig(3)-pos_1(3); % set text display to the right of the fig pos_1(2)=size_fig(4)-pos_InputFile(4)-pos_1(4); % set text display to the top of the fig set(handles.text_display,'Position',pos_1) set(handles.TableDisplay,'Position',[pos_1(1) 10 pos_1(3) 5*pos_1(4)]) % reset position of CheckTable set(handles.CheckTable,'Units','pixels') pos_CheckTable=get(handles.CheckTable,'Position');% [lower x lower y width height] for CheckHold pos_CheckTable(1)=pos_1(1)-pos_CheckTable(3); % set 'CheckHold' to the right of the fig pos_CheckTable(2)=pos_InputFile(2)-pos_CheckTable(4); % set 'CheckHold' to the lower edge of text display set(handles.CheckTable,'Position',pos_CheckTable) %% reset position of CheckHold % pos_CheckHold=get(handles.CheckHold,'Position');% [lower x lower y width height] for CheckHold % pos_CheckHold(1)=size_fig(3)-pos_CheckHold(3); % set 'CheckHold' to the right of the fig % pos_CheckHold(2)=pos_1(2)-pos_CheckHold(4); % set 'CheckHold' to the lower edge of text display % set(handles.CheckHold,'Position',pos_CheckHold) %% reset position of Coordinates panel set(handles.Coordinates,'Units','pixels') pos_2=get(handles.Coordinates,'Position');% [lower x lower y width height] for frame 'Coordinates' pos_2(3)=ColumnWidth; pos_2(1)=size_fig(3)-pos_2(3); % set 'Coordinates' to the right of the fig pos_2(2)=pos_1(2)-pos_2(4); % set 'Coordinates' to the lower edge of text display, allowing a margin for CheckHold set(handles.Coordinates,'Position',pos_2) %% reset position of Axes panel set(handles.Axes,'Units','pixels') pos_3=get(handles.Axes,'Position');% [lower x lower y width height] for frame 'Coordinates' pos_3(3)=ColumnWidth; pos_3(1)=size_fig(3)-pos_3(3); % set 'Coordinates' to the right of the fig pos_3(2)=pos_2(2)-pos_3(4); % set 'Coordinates' to the lower edge of text display, allowing a margin for CheckHold set(handles.Axes,'Position',pos_3) %% reset position of Scalar set(handles.Scalar,'Units','pixels') pos_4=get(handles.Scalar,'Position'); % [lower x lower y width height] for frame 'Scalar' pos_4(3)=ColumnWidth; pos_4(1)=size_fig(3)-pos_4(3); % set 'Scalar' to the right of the fig if strcmp(get(handles.Scalar,'Visible'),'on') pos_4(2)=pos_3(2)-pos_4(4); % set 'Scalar' to the lower edge of frame 'Coordinates' if visible else pos_4(2)=pos_3(2);% set 'Scalar' to the lower edge of frame 'text display' if unvisible end set(handles.Scalar,'Position',pos_4) %% reset position of Vectors set(handles.Vectors,'Units','pixels') pos_5=get(handles.Vectors,'Position'); pos_5(3)=ColumnWidth; pos_5(1)=size_fig(3)-pos_5(3); if strcmp(get(handles.Vectors,'visible'),'on') pos_5(2)=pos_4(2)-pos_5(4); else pos_5(2)=pos_4(2); end set(handles.Vectors,'Position',pos_5) %% reset position and scale of axis pos(1)=0.2*size_fig(3)+35; pos(2)=35; pos(3)=0.77*size_fig(3)-1.2*ColumnWidth; pos(4)=size_fig(4)-60; set(handles.PlotAxes,'Units','pixels') set(handles.PlotAxes,'Position',pos) set(handles.PlotAxes,'Units','normalized') %------------------------------------------------------------------------ %------------------------------------------------------------------------ % II - TOOLS FROM THE UPPER MENU BAR %------------------------------------------------------------------------ %------------------------------------------------------------------------ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Open Menu Callbacks %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %------------------------------------------------------------------------ % --- Executes on the menu Open/Browse...fill_GUI % 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]; if isempty(oldfile) %loads the previously stored file name and set it as default in the file_input box oldfile=get(handles.RootPath,'UserData'); end fileinput=uigetfile_uvmat('pick an input file',oldfile); hh=dir(fileinput); if numel(hh)>1fill_GUI msgbox_uvmat('ERROR','invalid input, probably a broken link'); else %% display the selected field and related information if ~isempty(fileinput) set(handles.SubField,'Value',0) desable_subfield(handles) display_file_name(handles,fileinput) end end % ----------------------------------------------------------------------- % --- Open again the file whose name has been recorded in MenuFile function MenuFile_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ fileinput=get(hObject,'Label'); set(handles.SubField,'Value',0) desable_subfield(handles) errormsg=display_file_name( handles,fileinput); if ~isempty(errormsg) set(hObject,'Label','') 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(get(hObject,'Label'),MenuFile); MenuFile(str_find)=[];% suppress the input file to the list for ifile=1:numel(MenuFile) set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile}); end end % ----------------------------------------------------------------------- % --- Executes on the menu Open/Browse campaign... % --- search the file inside a campaign, using the GUI browse_data % ----------------------------------------------------------------------- function MenuBrowseCampaign_Callback(hObject, eventdata, handles) % set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0]) % drawnow [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles); DataSeries=fullfile(RootPath,SubDir); if isempty(DataSeries) %loads the previously stored file name and set it as default in the file_input box DataSeries=get(handles.RootPath,'UserData'); end OutPut=browse_data(DataSeries,'on');% open the GUI browse_data to get select a campaign dir, experiment and device if ~isfield(OutPut,'Campaign') return end DataSeries=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1}); fileinput=uigetfile_uvmat('pick an input file',DataSeries); hh=dir(fileinput); if numel(hh)>1 msgbox_uvmat('ERROR','invalid input, probably a broken link'); return end %% update the list of campaigns in the menubar MenuCampaign=[{get(handles.MenuCampaign_1,'Label')};{get(handles.MenuCampaign_2,'Label')};... {get(handles.MenuCampaign_3,'Label')};{get(handles.MenuCampaign_4,'Label')};{get(handles.MenuCampaign_5,'Label')}]; check_dir=isempty(find(strcmp(DataSeries,MenuCampaign))); if check_dir %insert the new campaign in the list if it is not found MenuCampaign(end)=[]; %suppress the last item MenuCampaign=[{DataSeries};MenuCampaign];%insert the new campaign for ilist=1:numel(MenuCampaign) set(handles.(['MenuCampaign_' num2str(ilist)]),'Label',MenuCampaign{ilist}) end % save the list for future opening: dir_perso=prefdir; profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); if exist(profil_perso,'file') save (profil_perso,'MenuCampaign','RootPath','-append'); %store the file names for future opening of uvmat else save (profil_perso,'MenuCampaign','RootPath','-V6'); %store the file names for future opening of uvmat end end %% display the selected field and related information %display_file_name( handles,fullfile(DirName,FileName)) display_file_name( handles,fileinput) set(handles.MenuOpenCampaign,'ForegroundColor',[0 0 0]) % ----------------------------------------------------------------------- % --- Open again as second field the file whose name has been recorded in MenuFile_1 % ----------------------------------------------------------------------- function MenuCampaign_Callback(hObject, eventdata, handles) set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0]) OutPut=browse_data(get(hObject,'Label'),'on');% open the GUI browse_data to get select a campaign dir, experiment and device if isfield(OutPut,'Campaign') fileinput=uigetfile_uvmat('pick an input file',fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1})); hh=dir(fileinput); if numel(hh)>1 msgbox_uvmat('ERROR','invalid input, probably a broken link'); else display_file_name(handles,fileinput) end end set(handles.MenuOpenCampaign,'ForegroundColor',[0 0 0]) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % 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 disp('Data_uvmat.Field=') evalin('base','Data_uvmat.Field') %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) %------------------------------------------------------------------------ hfig=figure; hc=copyobj(handles.PlotAxes,hfig); set(hc,'Position',[0.1 0.1 0.8 0.8]) h=findobj(handles.PlotAxes,'tag','ima'); %look for image in the plot if ~isempty(h) map=colormap(handles.PlotAxes); colormap(map);%transmit the current colormap to the new fig colorbar end % -------------------------------------------------------------------- function MenuExportAxis_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- ListFig=findobj(allchild(0),'Type','figure'); nb_option=0; menu={}; for ilist=1:numel(ListFig) FigName=get(ListFig(ilist),'name'); if isempty(FigName) FigName=['figure ' num2str(ListFig(ilist))]; end if ~strcmp(FigName,'uvmat') ListAxes=findobj(ListFig(ilist),'Type','axes'); ListTags=get(ListAxes,'Tag'); if ~isempty(ListTags) && ~isempty(find(~strcmp('Colorbar',ListTags), 1)) ListAxes=ListAxes(~strcmp('Colorbar',ListTags)); if numel(ListAxes)==1 nb_option=nb_option+1; menu{nb_option}=FigName ; AxesHandle(nb_option)=ListAxes; else nb_axis=0; for iaxes=1:numel(ListAxes) nb_axis=nb_axis+1; nb_option=nb_option+1; menu{nb_option}=[FigName '_' num2str(nb_axis)]; AxesHandle(nb_option)=ListAxes(nb_axis); end end end end end if isempty(menu) answer=msgbox_uvmat('INPUT_Y-N','no existing plotting axes available, create new figure?'); if strcmp(answer,'Yes') hfig=figure; copyobj(handles.PlotAxes,hfig); else return end map=colormap(handles.PlotAxes); colormap(map);%transmit the current colormap to the zoom fig colorbar else answer=msgbox_uvmat('INPUT_MENU','select a figure/axis on which the current uvmat plot will be exported',menu); if isempty(answer) return else axes(AxesHandle(answer)) hold on hchild=get(handles.PlotAxes,'children'); copyobj(hchild,gca); end end %------------------------------------------------------------------------ % -------------------------------------------------------------------- function MenuExportMovie_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- set(handles.MenuExportMovie,'BusyAction','queue')% activate the button [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles); FileBase=fullfile(RootPath,RootFile); %% create a fig and axis for movies figure_movie=findobj(allchild(0),'name','figure_movie'); if ~isempty(figure_movie) delete(figure_movie)%delete existing figure_movie end figure_movie=figure; nbpix=[640 480];% resolution VGA set(figure_movie,'name','figure_movie','Position',[1 1 nbpix]) newaxes=copyobj(handles.PlotAxes,figure_movie);%new plotting axes in the new figure set(newaxes,'Tag','movieaxes') %% display time if defined in uvmat time_str=get(handles.TimeValue,'String'); if ~isempty(time_str) htitle=get(newaxes,'Title'); set(htitle,'String',['t=' time_str]) end map=colormap(handles.PlotAxes); colormap(map);%transmit the current colormap to the zoom fig colorbar %% create the GUI set_movie %set(0,'Units','points') %ScreenSize=get(0,'ScreenSize');% get the size of the screen, to put the fig on the upper right Position=get(figure_movie,'Position'); Position(2)=Position(2)+1.2*Position(4); Position(3)=1.5*Position(3); Position(4)=Position(4)/2; hfig=findobj(allchild(0),'Tag','set_movie'); if ~isempty(hfig),delete(hfig), end; %delete existing version of the GUI hfig=figure('name','set_movie','tag','set_movie','MenuBar','none','NumberTitle','off','Units','pixels',... 'Position',Position); BackgroundColor=get(hfig,'Color'); hh=0.14; % box height (relative) % first raw of the GUI uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.95-hh/2 0.9 hh/2],'BackgroundColor',BackgroundColor,... 'String','movie name:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center');%title uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.95-1.5*hh 0.9 hh],'tag','MovieName','BackgroundColor',[1 1 1],... 'String',fullfile(RootPath,[SubDir '.movie'], [RootFile '.avi']),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''MovieName'': name (with path) of the movie to create');%edit box uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.95-2.5*hh 0.33 hh/2],'BackgroundColor',BackgroundColor,... 'String','frames per second:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center');%title uicontrol('Style','text','Units','normalized', 'Position', [0.3 0.95-2.5*hh 0.33 hh/2],'BackgroundColor',BackgroundColor,... 'String','resolution:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center');%title uicontrol('Style','text','Units','normalized', 'Position', [0.55 0.95-2.5*hh 0.33 hh/2],'BackgroundColor',BackgroundColor,... 'String','total nbre of frames:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center');%title uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.95-3.5*hh 0.3 hh],'tag','num_FramePerSecond','BackgroundColor',[1 1 1],... 'String','10','FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_FramePerSecond'': nbre of frames per second');%edit box uicontrol('Style','listbox','Units','normalized', 'Position', [0.35 0.15 0.3 3*hh],'tag','MovieSize','BackgroundColor',[1 1 1],... 'Callback',@(hObject,eventdata)set_movie_size_Callback(hObject,eventdata),'String',{'640x480(VGA)';'720x480(mpeg2 16/9)';'1280x720(HD)'},... 'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''MovieSize'': resolution of the movie');%menu uicontrol('Style','edit','Units','normalized', 'Position', [0.65 0.95-3.5*hh 0.3 hh],'tag','num_FrameNumber','BackgroundColor',[1 1 1],... 'String','10','FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_FrameNumber'': total nbre of frames');%edit box uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.05 0.15 0.25 hh],'BackgroundColor',[1 0 0],'String','START','Callback',@(hObject,eventdata)set_movie_START_Callback(hObject,eventdata),... 'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''APPLY'': apply the output to the current field series in uvmat'); uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.7 0.15 0.25 hh],'Callback',@(hObject,eventdata)set_movie_Cancel_Callback(hObject,eventdata),... 'String','Cancel','FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''Cancel'': quit GUI without action'); uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.05 0.9 hh/2],'BackgroundColor',BackgroundColor,... 'String','will extract the result of ++> on uvmat: adjust figure_movie with its Matlab edit menu, then press ''START ''','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center');%title drawnow %------------------------------------------------------------------------ % function called by selecting movie size in the GUI set_movie function set_movie_size_Callback(hObject,eventdata) hset_movie=get(hObject,'parent'); hMovieSize=findobj(hset_movie,'Tag','MovieSize'); nbpix=[640 480; 720 480; 1280 720]; SizeOption=get(hMovieSize,'Value'); nbpix=nbpix(SizeOption,:); %% look for movie fig figure_movie=findobj(allchild(0),'name','figure_movie'); if isempty(figure_movie) figure_movie=figure; set(figure_movie,'name','figure_movie','Position',[1 1 nbpix]) huvmat=findobj(allchild(0),'tag','uvmat'); hhuvmat=guidata(huvmat); newaxes=copyobj(hhuvmat.PlotAxes,figure_movie);%new plotting axes in the new figure set(newaxes,'Tag','movieaxes') %% display time if defined in uvmat time_str=get(hhuvmat.TimeValue,'String'); if ~isempty(time_str) htitle=get(newaxes,'Title'); set(htitle,'String',['t=' time_str]) end map=colormap(handles.PlotAxes); colormap(map);%transmit the current colormap to the zoom fig colorbar else Pos=get(figure_movie,'Position'); set(figure_movie,'Position',[Pos(1) Pos(2) nbpix]) end %------------------------------------------------------------------------ % function called by pressing APPLY in the GUI set_movie function set_movie_START_Callback(hObject,eventdata) %------------------------------------------------------------------------ %% read info from the GUI set_movie hset_movie=get(hObject,'parent'); hMovieName=findobj(hset_movie,'Tag','MovieName'); MovieName=get(hMovieName,'String'); hFramePerSecond=findobj(hset_movie,'Tag','num_FramePerSecond'); fps=str2double(get(hFramePerSecond,'String')); hFrameNumber=findobj(hset_movie,'Tag','num_FrameNumber'); FrameNumber=str2double(get(hFrameNumber,'String'));% total nbre of frames %% create the movie file MovieDir=fileparts(MovieName); if ~exist(MovieDir,'dir') [success,message]=mkdir(MovieDir); if ~isequal(success,1) msgbox_uvmat('ERROR',message) return end [success,message] = fileattrib(MovieDir,'+w','g','s');% allow writing access for the group of users, recursively in the folder if success==0 msgbox_uvmat('WARNING',{['unable to set group write access to ' MovieDir ':']; message});%error message for directory creation end end if exist(MovieName,'file') backup=MovieName; testexist=2; while testexist==2 backup=[backup '~']; testexist=exist(backup,'file'); end [success,message]=copyfile(MovieName,backup);%make backup of the existing file if isequal(success,1) delete(MovieName)%delete existing file else msgbox_uvmat('ERROR',message) return end end %create avi open %aviobj=avifile(MovieName,'Compression','None','fps',fps); aviobj = VideoWriter(MovieName,'Uncompressed AVI'); open(aviobj) %% get info from uvmat and adjust it huvmat=findobj(allchild(0),'Tag','uvmat'); hhuvmat=guidata(huvmat); increment=str2num(get(hhuvmat.num_IndexIncrement,'String')); %get the field increment from uvmat set(hhuvmat.STOP,'Visible','on') set(hhuvmat.speed,'Visible','on') set(hhuvmat.speed_txt,'Visible','on') set(hhuvmat.Movie,'BusyAction','queue') set(hhuvmat.speed,'Value',1) figure_movie=findobj(allchild(0),'name','figure_movie'); hhuvmat.PlotAxes=findobj(figure_movie,'Tag','movieaxes');% the axis in the new figure becomes the current main plotting axes for i=1:FrameNumber if get(hhuvmat.speed,'Value')~=0 && isequal(get(hhuvmat.MenuExportMovie,'BusyAction'),'queue') % enable STOP command runpm(hObject,eventdata,hhuvmat,increment)% run plus drawnow time_str=get(hhuvmat.TimeValue,'String'); htitle=get(hhuvmat.PlotAxes,'Title'); Title=get(htitle,'String'); set(htitle,'String',regexprep(Title,'t=\d+.\d*',['t=' time_str])) mov=getframe(figure_movie); % aviobj=addframe(aviobj,mov); writeVideo(aviobj,mov); end end close(aviobj); msgbox_uvmat('CONFIRMATION',{['movie ' MovieName ' created '];['with ' num2str(FrameNumber) ' frames']}) %------------------------------------------------------------------------ % function called by pressing APPLY in the GUI set_slices function set_movie_Cancel_Callback(hObject,eventdata) %------------------------------------------------------------------------ delete(hObject) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % 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) % ----------------------------------------------------------------------- % --- Callback of the Menu command line %------------------------------------------------------------------------ function Menuline_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ data.Type='line'; data.ProjMode='projection';%default data.ProjModeMenu={};% do not restrict ProjMode menus create_object(data,handles) % ----------------------------------------------------------------------- % --- Callback of the Menu command line_x %------------------------------------------------------------------------ function Menuline_x_Callback(hObject, eventdata, handles) data.Type='line_x'; data.ProjMode='projection';%default data.ProjModeMenu={};% do not restrict ProjMode menus create_object(data,handles) % ----------------------------------------------------------------------- % --- Callback of the Menu command line_y % ----------------------------------------------------------------------- function Menuline_y_Callback(hObject, eventdata, handles) data.Type='line_y'; 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 Menuplane_z_Callback(hObject, eventdata, handles) data.Type='plane_z'; 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_lin';%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 concurrent tools set(handles.MenuRuler,'checked','off')%desactivate ruler hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');% search the GUI geometric calibration if ishandle(hgeometry_calib) hhgeometry_calib=guidata(hgeometry_calib); set(hhgeometry_calib.CheckEnableMouse,'Value',0)% desactivate mouse action in geometry_calib set(hhgeometry_calib.CheckEnableMouse,'BackgroundColor',[0.7 0.7 0.7]) end set(handles.CheckEditObject,'Value',0) %desactivate the object edit mode CheckEditObject_Callback([],[],handles) set(handles.CheckViewObject,'Value',0) % desactivate view_object (new object created) set(handles.CheckZoomFig,'Value',0) %desactivate zoom sub fig set(handles.CheckZoom,'Value',0) %desactivate the zoom action set(handles.MenuObject,'checked','on')% indicate object creation for mouse pointer display if ishandle(handles.UVMAT_title) delete(handles.UVMAT_title) %delete the initial display of uvmat if no field has been entered yet end %% initiate the new projection object UvData=get(handles.uvmat,'UserData'); data.Name=data.Type;% default name=type data.Coord=[0 0]; %default check_plot=0; if isfield(UvData,'Field') if isfield(UvData.Field,'NbDim')&& isequal(UvData.Field.NbDim,3) data.Coord=[0 0 0]; %default end if isfield(UvData.Field,'CoordUnit') data.CoordUnit=UvData.Field.CoordUnit; end if isfield(UvData.Field,'CoordMesh')&&~isempty(UvData.Field.CoordMesh) %data.RangeX=[UvData.Field.XMin UvData.Field.XMax]; data.DX=UvData.Field.CoordMesh; data.DY=UvData.Field.CoordMesh; switch data.Type case {'line','polyline','points'} data.RangeY=UvData.Field.CoordMesh; case 'line_x' check_plot=1; %plot the line directly when set_object is opened data.Type='line'; data.RangeX=UvData.Field.XMin ; data.RangeY=UvData.Field.CoordMesh; data.Coord=[UvData.Field.XMin (UvData.Field.YMin +UvData.Field.YMax)/2;... UvData.Field.XMax (UvData.Field.YMin +UvData.Field.YMax)/2];% put line at the middle of the y axis case 'line_y' check_plot=1; %plot the line directly when set_object is opened data.Type='line'; data.RangeX=UvData.Field.YMin ; data.RangeY=UvData.Field.CoordMesh; data.Coord=[(UvData.Field.XMin+UvData.Field.XMax)/2 UvData.Field.YMin;... (UvData.Field.XMin +UvData.Field.XMax)/2 UvData.Field.YMax];% put line at the middle of the y axis case {'rectangle','ellipse'} data.RangeY=[UvData.Field.YMin UvData.Field.YMax]; data.RangeX=UvData.Field.CoordMesh; data.RangeY=UvData.Field.CoordMesh; case 'plane_z' data.Angle=[0 90]; data.DX=UvData.Field.CoordMesh; data.DY=UvData.Field.CoordMesh; data.RangeZ=UvData.Field.CoordMesh; data.Coord=[]; otherwise data.RangeY=[UvData.Field.YMin UvData.Field.YMax]; end end if isfield(UvData.Field,'ProjModeRequest') data.ProjMode=UvData.Field.ProjModeRequest;%set the request proj mode option by default end end hset_object=set_object(data,handles);% call the GUI set_object hchild=get(hset_object,'children'); set(hchild,'enable','on') set(handles.DeleteObject,'Visible','on')% make the object delete button visible if check_plot hhset_object=guidata(hset_object); set_object('REFRESH_Callback',1,[],hhset_object);% call the GUI set_object end set(handles.CheckViewField,'Visible','on') set(handles.DeleteObject,'Visible','on') set(handles.ListObject_1,'Visible','on') set(handles.ListObject_1_title,'Visible','on') %------------------------------------------------------------------------ function MenuBrowseObject_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ %get the object file fileinput=uigetfile_uvmat('pick an xml object file:',get(handles.RootPath,'String'),'.xml'); if ~isempty(fileinput) %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 ListObject=get(handles.ListObject,'String'); ListObject=[ListObject;{data.Name}]; IndexObj=length(ListObject); UvData=get(handles.uvmat,'UserData'); UvData.ProjObject{IndexObj}=[]; %create a new empty object UvData.ProjObject{IndexObj}.DisplayHandle.uvmat=[]; %no plot handle before plot_field operation UvData.ProjObject{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation set(handles.uvmat,'UserData',UvData) set(handles.CheckViewObject,'Value',1) set(handles.CheckViewField,'Value',1) hset_object=set_object(data);% call the set_object interface hhset_object=guidata(hset_object); set_object('REFRESH_Callback',hObject,eventdata,hhset_object);% plot projection set(handles.CheckEditObject,'Value',0); %suppress the object edit mode CheckEditObject_Callback([],[],handles) set(handles.DeleteObject,'Visible','on') end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % MenuTools Callbacks %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %------------------------------------------------------------------------ function MenuCalib_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ %% suppress the second field if exists if get(handles.SubField,'Value') set(handles.SubField,'Value',0) SubField_Callback(hObject, eventdata, handles) end UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface %% suppress competing tools set(handles.MenuRuler,'checked','off')%desactivate ruler set(handles.CheckZoom,'Value',0) set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7]) set(handles.ListObject,'Value',1) %% initiate display of the 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 geometry_calib(FileName);% 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 % -------------------------------------------------------------------- % --- set the slice plane ro the set of slice planes when volume scan is used function MenuSetSlice_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- %% suppress the second input field if exists if get(handles.SubField,'Value') set(handles.SubField,'Value',0) SubField_Callback(hObject, eventdata, handles) end UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface % check=0; if isfield(UvData,'XmlData')&&isfield(UvData.XmlData{1},'GeometryCalib')&& isfield(UvData.XmlData{1}.GeometryCalib,'SliceCoord') GeometryCalib=UvData.XmlData{1}.GeometryCalib; else msgbox_uvmat('ERROR','3D geometric calibration needed before defining slices') return end SliceCoord=GeometryCalib.SliceCoord; InterfaceCoord=min(SliceCoord(:,3)); if isfield(GeometryCalib,'InterfaceCoord') InterfaceCoord=GeometryCalib.InterfaceCoord(1,3); end NbSlice=size(SliceCoord,1); CheckVolumeScan=0; if isfield(GeometryCalib,'CheckVolumeScan') CheckVolumeScan=GeometryCalib.CheckVolumeScan; end RefractionIndex=1.33; CheckRefraction=0;% default value of the check box refraction if isfield(GeometryCalib,'RefractionIndex') RefractionIndex=GeometryCalib.RefractionIndex; CheckRefraction=1; end SliceAngle=[0 0 0]; if isfield(GeometryCalib,'SliceAngle') SliceAngle=GeometryCalib.SliceAngle; end %% create the GUI set_slice set(0,'Units','points') ScreenSize=get(0,'ScreenSize');% get the size of the screen, to put the fig on the upper right Width=350;% fig width in points (1/72 inch) Height=min(0.8*ScreenSize(4),300); Left=ScreenSize(3)- Width-40; %right edge close to the right, with margin=40 Bottom=ScreenSize(4)-Height-40; %put fig at top right hfig=findobj(allchild(0),'Tag','set_slice'); if ~isempty(hfig),delete(hfig), end; %delete existing version of the GUI hfig=figure('name','set_slices','tag','set_slice','MenuBar','none','NumberTitle','off','Units','pixels','Position',[Left,Bottom,Width,Height],'UserData',GeometryCalib); BackgroundColor=get(hfig,'Color'); hh=0.14; % box height (relative) ii=0.01; % gap between uicontrols ww=(1-5*ii)/4; % box width (relative) % first raw of the GUI uicontrol('Style','text','Units','normalized', 'Position', [2*ii+ww 0.95-ii-0.25*hh ww hh/2],'BackgroundColor',BackgroundColor,... 'String','first','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center');%title uicontrol('Style','text','Units','normalized', 'Position', [3*ii+2*ww 0.95-ii-0.25*hh ww hh/2],'BackgroundColor',BackgroundColor,... 'String','last','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center');%title uicontrol('Style','text','Units','normalized', 'Position', [4*ii+3*ww 0.95-ii-0.25*hh ww hh/2],'BackgroundColor',BackgroundColor,... 'String','surface','Visible','off','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center');%title % raw 2 of the GUI uicontrol('Style','text','Units','normalized', 'Position', [ii 0.95-2*ii-0.75*hh ww hh/2],'BackgroundColor',BackgroundColor,... 'String','Z','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right');%title uicontrol('Style','edit','Units','normalized', 'Position', [2*ii+ww 0.95-2*ii-hh ww hh],'tag','num_Z_1','BackgroundColor',[1 1 1],... 'String',num2str(SliceCoord(1,3)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_Z_1'': z position of first slice');%edit box uicontrol('Style','edit','Units','normalized', 'Position', [3*ii+2*ww 0.95-2*ii-hh ww hh],'tag','num_Z_2','BackgroundColor',[1 1 1],... 'String',num2str(SliceCoord(end,3)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_Z_2'': z position of last slice');%edit box uicontrol('Style','edit','Units','normalized', 'Position', [4*ii+3*ww 0.95-2*ii-hh ww hh],'tag','num_H','BackgroundColor',[1 1 1],... 'String',num2str(InterfaceCoord),'Visible','off','FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_H'': z position of the water surface (=Z_1 in air)');%edit box % raw 3 of the GUI hcheckrefraction=uicontrol('Style','checkbox','Units','normalized', 'Position', [2*ii+ww 0.95-3*ii-2*hh 2*ww hh],'tag','CheckRefraction','BackgroundColor',BackgroundColor,... 'Callback',@(hObject,eventdata)set_slice_CheckRefraction_Callback(hObject,eventdata),... 'String','refraction','Value',CheckRefraction,'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''CheckRefraction'':=1 to provide refraction correction'); uicontrol('Style','text','Units','normalized', 'Position', [2*ii+2*ww 0.95-3*ii-1.75*hh ww hh/2],'BackgroundColor',BackgroundColor,'Tag','Refraction_title',... 'String','index','Visible','off','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right');%title uicontrol('Style','edit','Units','normalized', 'Position', [4*ii+3*ww 0.95-3*ii-2*hh ww hh],'tag','num_RefractionIndex','BackgroundColor',[1 1 1],... 'String',num2str(RefractionIndex),'Visible','off','FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_RefractionIndex'': refraction index of water'); % raw 4 of the GUI uicontrol('Style','text','Units','normalized', 'Position', [ii 0.95-4*ii-3.25*hh ww hh],'BackgroundColor',BackgroundColor,'Tag','NbSlice_title',... 'String','NbSlice','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right');%title uicontrol('Style','edit','Units','normalized', 'Position', [2*ii+ww 0.95-4*ii-3*hh ww hh],'tag','num_NbSlice','BackgroundColor',[1 1 1],... 'String',num2str(NbSlice),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_NbSlice'':number of slices');%edit box uicontrol('Style','checkbox','Units','normalized', 'Position', [3*ii+2*ww 0.95-4*ii-3*hh 2*ww hh],'tag','CheckVolumeScan','BackgroundColor',BackgroundColor,... 'String','volume scan','Value',CheckVolumeScan,'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''CheckVolumeScan'':=1 for volume scan (z varies with j index)'); % raw 5 of the GUI uicontrol('Style','text','Units','normalized', 'Position', [2*ii+2*ww 0.95-3*ii-3.5*hh ww hh/2],'BackgroundColor',BackgroundColor,... 'String','first','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center');%title uicontrol('Style','text','Units','normalized', 'Position', [3*ii+3*ww 0.95-3*ii-3.5*hh ww hh/2],'BackgroundColor',BackgroundColor,... 'String','last','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center');%title uicontrol('Style','text','Units','normalized', 'Position', [ii 0.95-5*ii-4*hh 2*ww hh/2],'BackgroundColor',BackgroundColor,'Tag','Angle_title_1',... 'String','tild angle x axis','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center');%title uicontrol('Style','text','Units','normalized', 'Position', [ii 0.95-6*ii-5*hh 2*ww hh/2],'BackgroundColor',BackgroundColor,'Tag','Angle_title_2',... 'String','tild angle y axis','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center');%title % raw 6 of the GUI uicontrol('Style','edit','Units','normalized', 'Position', [3*ii+2*ww 0.95-5*ii-4.2*hh ww hh],'tag','num_SliceAngle_1_1','BackgroundColor',[1 1 1],... 'String',num2str(SliceAngle(1)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_1_1'':first slice angle of inclination around the x axis');%edit box uicontrol('Style','edit','Units','normalized', 'Position', [4*ii+3*ww 0.95-5*ii-4.2*hh ww hh],'tag','num_SliceAngle_1_2','BackgroundColor',[1 1 1],... 'String',num2str(SliceAngle(1)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_1_2'':last slice angle of inclination around the x axis');%edit box uicontrol('Style','edit','Units','normalized', 'Position', [3*ii+2*ww 0.95-6*ii-5.2*hh ww hh],'tag','num_SliceAngle_2_1','BackgroundColor',[1 1 1],... 'String',num2str(SliceAngle(2)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_2_1'':first slice angle of inclination around the y axis');%edit box uicontrol('Style','edit','Units','normalized', 'Position', [4*ii+3*ww 0.95-6*ii-5.2*hh ww hh],'tag','num_SliceAngle_2_2','BackgroundColor',[1 1 1],... 'String',num2str(SliceAngle(2)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_2_2'':last slice angle of inclination around the y axis');%edit box % raw 7 of the GUI: pushbuttons wwp=(1-4*ii)/3; %width of the push buttons uicontrol('Style','pushbutton','Units','normalized', 'Position', [ii ii wwp hh],'BackgroundColor',[1 0 0],'String','APPLY','Callback',@(hObject,eventdata)set_slice_APPLY_Callback(hObject,eventdata),... 'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''APPLY'': apply the output to the current field series in uvmat'); uicontrol('Style','pushbutton','Units','normalized', 'Position', [2*ii+wwp ii wwp hh],'BackgroundColor',[1 0 0],'String','REPLICATE','Callback',@(hObject,eventdata)set_slice_REPLICATE_Callback(hObject,eventdata),... 'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''REPLICATE'': replicate the output for a series of experiments'); uicontrol('Style','pushbutton','Units','normalized', 'Position', [3*ii+2*wwp ii wwp hh],'Callback',@(hObject,eventdata)set_slice_Cancel_Callback(hObject,eventdata),... 'String','Cancel','FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''Cancel'': quit GUI without action'); drawnow set_slice_CheckRefraction_Callback(hcheckrefraction,[]) %------------------------------------------------------------------------ % function called by selecting CheckRefraction in the GUI set_slices function set_slice_CheckRefraction_Callback(hObject,eventdata) %------------------------------------------------------------------------ hset_slice=get(hObject,'parent'); h_refraction(1)=findobj(hset_slice,'String','surface'); h_refraction(2)=findobj(hset_slice,'Tag','num_H'); h_refraction(3)=findobj(hset_slice,'String','index'); h_refraction(4)=findobj(hset_slice,'Tag','num_RefractionIndex'); if isequal(get(hObject,'Value'),1) set(h_refraction,'Visible','on') else set(h_refraction,'Visible','off') end %------------------------------------------------------------------------ % function called by pressing APPLY in the GUI set_slices function set_slice_APPLY_Callback(hObject,eventdata) %------------------------------------------------------------------------ set(hObject,'BackgroundColor',[1 1 0]);% paint button in yellow to indicate action drawnow %% get the uvmat GUI data and read the current xml file huvmat=findobj(allchild(0),'Tag','uvmat'); hhuvmat=guidata(huvmat); [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(hhuvmat); FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];%name of the current input file [RootPath,SubDir,RootFile,tild,tild,tild,tild,FileExt]=fileparts_uvmat(FileName); XmlFile=find_imadoc(RootPath,SubDir,RootFile,FileExt);%find name of the relevant xml file [s,errormsg]=imadoc2struct(XmlFile,'GeometryCalib');%read the xml file if~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) return end GeometryCalib=s.GeometryCalib;% get thegeometric calibration data %% read the content of the GUI set_slice hset_slice=get(hObject, 'parent'); hZ=findobj(hset_slice,'Tag','num_Z_1'); Z_plane=str2num(get(hZ,'String'));% set of Z positions explicitly entered as a Matlab vector SliceData=read_GUI(hset_slice); GeometryCalib.NbSlice=SliceData.NbSlice; GeometryCalib.CheckVolumeScan=SliceData.CheckVolumeScan; if numel(Z_plane)<=2 Z_plane=linspace(SliceData.Z(1),SliceData.Z(2),SliceData.NbSlice); else set(hZ,'String',num2str(Z_plane))% restitute the display qfter reqding by read_GUI end GeometryCalib.SliceCoord=Z_plane'*[0 0 1]; GeometryCalib.SliceAngle=zeros(GeometryCalib.NbSlice,3); Angle_1=linspace(SliceData.SliceAngle_1(1),SliceData.SliceAngle_1(2),SliceData.NbSlice); Angle_2=linspace(SliceData.SliceAngle_2(1),SliceData.SliceAngle_2(2),SliceData.NbSlice); GeometryCalib.SliceAngle(:,1)=Angle_1';%rotation around x axis (to generalise) GeometryCalib.SliceAngle(:,2)=Angle_2';%rotation around y axis (to generalise) GeometryCalib.SliceAngle(:,3)=0; if SliceData.CheckRefraction GeometryCalib.InterfaceCoord=[0 0 SliceData.H]; GeometryCalib.RefractionIndex=SliceData.RefractionIndex; elseif isfield(GeometryCalib,'RefractionIndex') GeometryCalib=rmfield(GeometryCalib,'RefractionIndex'); GeometryCalib=rmfield(GeometryCalib,'InterfaceCoord'); end %% store the result in the xml file used for calibration errormsg=update_imadoc(GeometryCalib,XmlFile,'GeometryCalib');% introduce the calibration data in the xml file if strcmp(errormsg,'') msgbox_uvmat('CONFIRMATION',['slice positions saved in ' XmlFile]); else msgbox_uvmat('ERROR',errormsg); end %% display image with new calibration in the currently opened uvmat interface %set(hhuvmat.CheckFixLimits,'Value',0)% put FixedLimits option to 'off' to plot the whole image uvmat('InputFileREFRESH_Callback',huvmat,[],hhuvmat); %file input with xml reading in uvmat, show the image in phys coordinates set(hObject,'BackgroundColor',[1 0 0]);% paint button back to red delete(hset_slice) %------------------------------------------------------------------------ % function called by pressing REPLICATE in the GUI set_slices function set_slice_REPLICATE_Callback(hObject,eventdata) %------------------------------------------------------------------------ set(hObject,'BackgroundColor',[1 1 0]) drawnow %% read the GUI set_slice SliceData=read_GUI(get(hObject,'parent')); %% get info on the GUI uvmat huvmat=findobj(allchild(0),'Tag','uvmat'); hhuvmat=guidata(huvmat); RootPath=read_file_boxes(hhuvmat); OutPutDir=uigetfile_uvmat('choose an image folder to document with slice position?',fileparts(RootPath),'uigetdir'); OutPut=browse_data(OutPutDir,'off','on'); nbcalib=0; for ilist=1:numel(OutPut.Experiment) for idevice=1:numel(OutPut.DataSeries) SubDirBase=regexprep(OutPut.DataSeries{idevice},'\..+$',''); XmlFile=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},[SubDirBase '.xml']); % read the current xml file if exist(XmlFile,'file') [s,errormsg]=imadoc2struct(XmlFile,'GeometryCalib'); if ~isempty(errormsg) msgbox_uvmat('ERROR',['error in reading ' XmlFile ': ' errormsg]) return end GeometryCalib=s.GeometryCalib; GeometryCalib.NbSlice=SliceData.NbSlice; GeometryCalib.CheckVolumeScan=SliceData.CheckVolumeScan; Z_plane=linspace(SliceData.Z(1),SliceData.Z(2),SliceData.NbSlice); GeometryCalib.SliceCoord=Z_plane'*[0 0 1]; GeometryCalib.SliceAngle=zeros(GeometryCalib.NbSlice,3); Angle_1=linspace(SliceData.SliceAngle_1(1),SliceData.SliceAngle_1(2),SliceData.NbSlice); Angle_2=linspace(SliceData.SliceAngle_2(1),SliceData.SliceAngle_2(2),SliceData.NbSlice); GeometryCalib.SliceAngle(:,1)=Angle_1';%rotation around x axis (to generalise) GeometryCalib.SliceAngle(:,2)=Angle_2';%rotation around y axis (to generalise) GeometryCalib.SliceAngle(:,3)=0; if SliceData.CheckRefraction GeometryCalib.InterfaceCoord=[0 0 SliceData.H]; GeometryCalib.RefractionIndex=SliceData.RefractionIndex; elseif isfield(GeometryCalib,'RefractionIndex') GeometryCalib=rmfield(GeometryCalib,'RefractionIndex'); GeometryCalib=rmfield(GeometryCalib,'InterfaceCoord'); end % update the current xml file errormsg=update_imadoc(GeometryCalib,XmlFile,'GeometryCalib');% introduce the calibration data in the xml file if ~strcmp(errormsg,'') msgbox_uvmat('ERROR',errormsg); else display([XmlFile ' updated with slice positions']) nbcalib=nbcalib+1; end end end end set(hObject,'BackgroundColor',[1 0 0]) msgbox_uvmat('CONFIMATION',[SubDirBase ' calibrated with slice positions for ' num2str(nbcalib) ' experiments']); %------------------------------------------------------------------------ % function called by pressing Cancel in the GUI set_slices function set_slice_Cancel_Callback(hObject,eventdata) %------------------------------------------------------------------------ hset_slice=get(hObject,'parent'); delete(hset_slice) %----------------------------------------------------------------------- function MenuLIFCalib_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ %% read UvData properties stored on the uvmat interface UvData=get(handles.uvmat,'UserData'); if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib') XmlData=UvData.XmlData{1}; else msgbox_uvmat('ERROR','geometric calibration needed: use Tools/geometric calibration in the menu bar'); return end %% read lines currently drawn ListObj=UvData.ProjObject; select=zeros(1,numel(ListObj)); for iobj=1:numel(ListObj); if isfield(ListObj{iobj},'Type') && strcmp(ListObj{iobj}.Type,'line') select(iobj)=1; end end val=find(select); if numel(val)<2 msgbox_uvmat('ERROR','light rays must be defined by at least two lines created by Projection object/line in the menu bar'); return else set(handles.ListObject,'Value',val);% show the selected lines on the list ObjectData=UvData.ProjObject(val); for iobj=1:length(ObjectData) xA(iobj)=ObjectData{iobj}.Coord(1,1); yA(iobj)=ObjectData{iobj}.Coord(1,2); xB(iobj)=ObjectData{iobj}.Coord(2,1); yB(iobj)=ObjectData{iobj}.Coord(2,2); end end %% find the origin as intersection of the two first lines (see http://www.ahristov.com/tutorial/geometry-games/intersection-lines.html ) x1=xA(1);x2=xB(1); x3=xA(2);x4=xB(2); y1=yA(1);y2=yB(1); y3=yA(2);y4=yB(2); D = (x1-x2)*(y3-y4) -(y1-y2)*(x3-x4); if D==0 msgbox_uvmat('ERROR','the two lines are parallel'); return end x0=((x3-x4)*(x1*y2-y1*x2)-(x1-x2)*(x3*y4-y3*x4))/D; y0=((y3-y4)*(x1*y2-y1*x2)-(y1-y2)*(x3*y4-y3*x4))/D; XmlData.Illumination.Origin=[x0 y0]; XmlData.PolarCentre=[x0 y0]; %% display the current image in polar axes with origin at the illumination source currentdir=pwd; uvmatpath=fileparts(which('uvmat')); cd(fullfile(uvmatpath,'transform_field')); phys_polar=str2func('phys_polar'); cd(currentdir) DataOut=phys_polar(UvData.Field,XmlData); view_field(DataOut); %% use the third line for reference luminosity if numel(val)==3 x_ref=linspace(ObjectData{3}.Coord(1,1),ObjectData{3}.Coord(2,1),10); y_ref=linspace(ObjectData{3}.Coord(1,2),ObjectData{3}.Coord(2,2),10); x_ref=x_ref-x0; y_ref=y_ref-y0; [theta_ref,r_ref] = cart2pol(x_ref,y_ref);%theta_ref and r_ref are the polar coordinates of the points on the line theta_ref=theta_ref*180/pi; figure plot(theta_ref,r_ref) azimuth_ima=linspace(DataOut.Coord_y(1),DataOut.Coord_y(2),size(DataOut.A,1));%profile of x index on the transformed image dist_source = interp1(theta_ref,r_ref,azimuth_ima); dist_source_pixel=round(size(DataOut.A,2)*(dist_source-DataOut.Coord_x(1))/(DataOut.Coord_x(2)-DataOut.Coord_x(1))); line_nan= isnan(dist_source_pixel); dist_source_pixel(line_nan)=1; width=20; %number of pixels used for reference DataOut.A=double(DataOut.A); Anorm=zeros(size(DataOut.A)); Aval=mean(mean(DataOut.A)); for iline=1:size(DataOut.A,1) lum(iline)=mean(DataOut.A(iline,dist_source_pixel(iline):dist_source_pixel(iline)+width)); Anorm(iline,:)=uint16(Aval*DataOut.A(iline,:)/lum(iline)); end lum(line_nan)=NaN; figure plot(1:size(DataOut.A,1),lum) end ImaName=regexprep([get(handles.RootFile,'String') get(handles.FileIndex,'String')],'//',''); NewImageName=fullfile(get(handles.RootPath,'String'),'polar',[ImaName get(handles.FileExt,'String')]); imwrite(Anorm,NewImageName,'BitDepth',16) %% record the origin in the xml file XmlFileName=find_imadoc(get(handles.RootPath,'String'),get(handles.SubDir,'String'),get(handles.RootFile,'String'),get(handles.FileExt,'String')); answer=msgbox_uvmat('INPUT_Y-N','save the illumination origin in the current xml file?'); if strcmp(answer,'Yes') t=xmltree(XmlFileName); %read the file title=get(t,1,'name'); if ~strcmp(title,'ImaDoc') msgbox_uvmat('ERROR','wrong xml file'); return end % backup the output file if it already exist, and read it backupfile=XmlFileName; testexist=2; while testexist==2 backupfile=[backupfile '~']; testexist=exist(backupfile,'file'); end [success,message]=copyfile(XmlFileName,backupfile);%make backup if success~=1 errormsg=['errror in xml file backup: ' message]; return end uid_illumination=find(t,'ImaDoc/Illumination'); if isempty(uid_illumination) %if GeometryCalib does not already exists, create it [t,uid_illumination]=add(t,1,'element','Illumination'); end uid_origin=find(t,'ImaDoc/Illumination/Origin'); if ~isempty(uid_origin) %if GeometryCalib does not already exists, create it t=delete(t,uid_origin); end % save the illumination origin t=struct2xml(XmlData.Illumination,t,uid_illumination); save(t,XmlFileName); end %------------------------------------------------------------------------ function MenuMask_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface ListObj=UvData.ProjObject; 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,'Value',val); flag=1; if ~isfield(UvData.Field,'A') msgbox_uvmat('ERROR','an image needs to be opened to set the mask size'); return end 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); for iobj=1:length(UvData.ProjObject) ObjectData=UvData.ProjObject{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 pos=[X Y zeros(size(X))]; if isfield(Calib,'SliceCoord') && length(Calib.SliceCoord)>=3 if isfield(Calib,'SliceAngle')&&~isequal(Calib.SliceAngle,[0 0 0]) om=norm(Calib.SliceAngle);%norm of rotation angle in radians OmAxis=Calib.SliceAngle/om; %unit vector marking the rotation axis cos_om=cos(pi*om/180); sin_om=sin(pi*om/180); pos=cos_om*pos+sin_om*cross(OmAxis,pos)+(1-cos_om)*(OmAxis*pos')*OmAxis; end pos(:,1)=pos(:,1)+Calib.SliceCoord(1); pos(:,2)=pos(:,2)+Calib.SliceCoord(2); pos(:,3)=pos(:,3)+Calib.SliceCoord(3); end [X,Y]=px_XYZ(Calib,pos(:,1),pos(:,2),pos(:,3)); 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 %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 list=get(handles.masklevel,'String'); masknumber=num2str(length(list)); maskindex=get(handles.masklevel,'Value'); 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 msgbox_uvmat('ERROR','invalid input, probably a broken link'); else %% display the selected field and related information if isempty(fileinput) errormsg='aborted'; else display_file_name(handles,fileinput,1) end end else % initiate the input file series and refresh the current field view: errormsg=update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,1); end %% refresh the second series if relevant if ~isempty(errormsg) && get(handles.SubField,'Value') [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles); % 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,FileInfo,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]); if isempty(i1_series) fileinput=uigetfile_uvmat('pick an input file for the second line',fullfile(RootPath,SubDir)); hh=dir(fileinput); if numel(hh)>1 msgbox_uvmat('ERROR','invalid input, probably a broken link'); else %% display the selected field and related information if isempty(fileinput) errormsg='aborted'; else display_file_name(handles,fileinput,2) end end else % initiate the input file series and inputfilerefresh the current field view: errormsg=update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,2); end end if ~isempty(errormsg) set(handles.InputFileREFRESH,'BackgroundColor',[1 0 1])% put back button color to magenta, input not succesfull end set(handles.uvmat,'Pointer','arrow')% set back the mouse pointer to arrow %------------------------------------------------------------------------ % --- Fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput' function errormsg=display_file_name(handles,fileinput,index) %------------------------------------------------------------------------ %% look for the input file existence errormsg='';%default if ~exist(fileinput,'file') errormsg=['input file ' fileinput ' does not exist']; msgbox_uvmat('ERROR',errormsg) return end %% 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'); set(handles.TimeName_1,'Visible','on') set(handles.TimeValue_1,'Visible','on') end set(handles.InputFileREFRESH,'BackgroundColor',[1 1 0])% paint REFRESH button to yellow to visualise root file input set(handles.uvmat,'Pointer','watch') % set the mouse pointer to 'watch' drawnow %% detect root name, nomenclature and indices in the input file name: [FilePath,FileName,FileExt]=fileparts(fileinput); % detect the file type, get the movie object if relevant, and look for the corresponding file series: % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]); FileType=FileInfo.FileType; if strcmp(FileType,'txt') try edit(fileinput) catch ME msgbox_uvmat('ERROR','invalid intput file') end return elseif strcmp(FileType,'xml') editxml(fileinput) return elseif strcmp(FileType,'figure') open(fileinput) return end %% 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); set(handles_SubDir,'String',['/' SubDir]); set(handles_RootFile,'String',['/' RootFile]); %display the separator if strcmp(NomType,'level') rootname=fullfile(RootPath,SubDir,'level'); rr=regexp(fileinput,['^' rootname '(?\d+)/' RootFile '(?\d+)' FileExt '$'],'names'); if ~isempty(rr) set(handles_FileIndex,'String',rr.i); end else rootname=fullfile(RootPath,SubDir,RootFile); indices=fileinput(length(rootname)+1:end); indices(end-length(FileExt)+1:end)=[]; %remove extension set(handles_FileIndex,'String',indices); end 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.MenuOpenCampaign,'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 inputfilerefresh the current field view: update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,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) set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile}); %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','RootPath','-append'); %store the file names for future opening of uvmat else save (profil_perso,'MenuFile','RootPath','-V6'); %store the file names for future opening of uvmat end set(handles.InputFileREFRESH,'BackgroundColor',[1 0 0])% paint back button to red to indicate update is finished set(handles.uvmat,'Pointer','arrow')% set back the mouse pointer to arrow %------------------------------------------------------------------------ % --- Update information about a new field series (indices to scan, timing, % calibration from an xml file, then inputfilerefresh current plots function errormsg=update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,VideoObject,index) %------------------------------------------------------------------------ errormsg=''; %default error msg %% 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_Fields=handles.FieldName; elseif index==2 handles_Fields=handles.FieldName_1; end set(handles.FixVelType,'Value',0); %desactivate fixed veltype by default %% record info in UserData of the figure uvmat UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface UvData.NewSeries=1; %flag for REFRESH: 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}=FileInfo.FileType; UvData.FileInfo{index}=FileInfo; UvData.MovieObject{index}=VideoObject; UvData.i1_series{index}=i1_series; UvData.i2_series{index}=i2_series; UvData.j1_series{index}=j1_series; UvData.j2_series{index}=j2_series; nbfield=max(max(max(i2_series)));% total number of fields (i index) if isempty(nbfield) nbfield=max(max(max(i1_series))); end nbfield_j=max(max(max(j2_series)));% number of fields along j index if isempty(nbfield_j) nbfield_j=max(max(max(j1_series))); end %% read timing and total frame number from the current file (e.g. movie files) TimeUnit='';%default TimeName='';%default XmlData.Time=[];%default ColorType='falsecolor'; %default if isfield(FileInfo,'FrameRate')% frame rate given in the file (case of video data) TimeUnit='s'; if isempty(j1_series); %frame index along i XmlData.Time=zeros(FileInfo.NumberOfFrames+1,2); XmlData.Time(:,2)=(0:1/FileInfo.FrameRate:(FileInfo.NumberOfFrames)/FileInfo.FrameRate)'; else XmlData.Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/FileInfo.FrameRate:(FileInfo.NumberOfFrames)/FileInfo.FrameRate); end if strcmp(FileInfo.FileType,'rdvision') TimeName='timestamp'; else TimeName='video'; end end if isfield(FileInfo,'ColorType') ColorType=FileInfo.ColorType;%='truecolor' for color images 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) XmlData.GeometryCalib=[];%default if index==1 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles); else [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles); end XmlFileName=find_imadoc(RootPath,SubDir,RootFile,FileExt); [tild,tild,DocExt]=fileparts(XmlFileName); warntext='';%default warning message NbSlice=1;%default ImaDoc_str=''; if ~isempty(XmlFileName) set(handles.view_xml,'Visible','on') set(handles.view_xml,'BackgroundColor',[1 1 0])% paint to yellow color to indicate reading of the xml file set(handles.view_xml,'String','view .xml') drawnow [XmlDataRead,warntext]=imadoc2struct(XmlFileName); if ~isempty(warntext) msgbox_uvmat('WARNING',warntext) end if ~isempty(XmlDataRead) ImaDoc_str=['view ' DocExt]; % DocExt= '.xml' or .civ (obsolete case) if isfield(XmlDataRead,'TimeUnit')&& ~isempty(XmlDataRead.TimeUnit) TimeUnit=XmlDataRead.TimeUnit; end if isfield(XmlDataRead,'Time')&& ~isempty(XmlDataRead.Time) XmlData.Time=XmlDataRead.Time; if XmlDataRead.Time(1,:)==XmlDataRead.Time(2,:)% case starting with index 1 sizDti=size(XmlDataRead.Time,1)-1;%size of the time vector explicitly defined in the xml file ind_start=1; else sizDti=size(XmlDataRead.Time,1);% case starting with index 0 ind_start=0; end % complement the input if the whole time series is not defined % if size(i1_series,3)>size(XmlDataRead.Time,1)-ind_start %only the first time interval is defined, extrapolate to the whole series % Dti_total=XmlDataRead.Time(end)-XmlDataRead.Time(1);%total time interval covered by the time vector % missing_indices=sizDti+1+ind_start:size(i1_series,3)+1;% remaining set of frame indices for which time needs to be found % repeat_nbre=1+floor((missing_indices-sizDti-ind_start)/(sizDti-1));% number of repetitions of Dti % time_indices=1+mod(missing_indices-sizDti-1,sizDti-1); % for j=1:size(XmlDataRead.Time,2) % XmlData.Time(missing_indices,j)=XmlDataRead.Time(time_indices,j)+repeat_nbre'*Dti_total; % end % % update the xml file with NbDti % t=xmltree(XmlFileName); % uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti') % if isempty(uid_NbDti) % uid_BurstTiming=find(t,'ImaDoc/Camera/BurstTiming') % [t,uid_NbDti]=add(t,uid_BurstTiming,'element','NbDti'); % end % [t,uid_NbDti]=add(t,uid_NbDti,'chardata',num2str(repeat_nbre(end)-1)); % save(t,XmlFileName) % end end set(handles.view_xml,'BackgroundColor',[1 1 1])% paint back to white drawnow if isfield(XmlDataRead, 'GeometryCalib') && ~isempty(XmlDataRead.GeometryCalib) XmlData.GeometryCalib=XmlDataRead.GeometryCalib; if isfield(XmlData.GeometryCalib,'CheckVolumeScan') && isequal(XmlData.GeometryCalib.CheckVolumeScan,1) set (handles.slices,'String','volume') end % check whether the GUI geometry_calib is opened hgeometry_calib=findobj('tag','geometry_calib'); if ~isempty(hgeometry_calib) % check whether the display of the GUI geometry_calib is consistent with the current calib param GUserData=get(hgeometry_calib,'UserData'); if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,XmlFileName)) answer=msgbox_uvmat('INPUT_Y-N','refresh the display of the GUI 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 isempty(ImaDoc_str) set(handles.view_xml,'Visible','off') % no .xml (or .civ) file detected else set(handles.view_xml,'String',ImaDoc_str)% indicate that a xml file has been detected end %% Define timing % time not set by the input file: images or civ data: indicate that time is read from the xml file FileType=FileInfo.FileType; if isfield(XmlData,'Time')&& ~isempty(XmlData.Time) && ... (strcmp(FileType,'image')|| strcmp(FileType,'multimage'))%||strcmp(FileType,'civdata')||strcmp(FileType,'civx')) TimeName='xml'; elseif strcmp(FileType,'civdata')% ajouter pivdata_fluidimage TimeName='civdata'; elseif strcmp(FileType,'civx') TimeName='civx'; end if index==1 set(handles.TimeName,'String',TimeName) else set(handles.TimeName_1,'String',TimeName) set(handles.TimeName_1,'Visible','on') end %% store last index in handles.MaxIndex_i and .MaxIndex_j if isfield(XmlData,'Time')&& ~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) XmlData.Time=(XmlData.Time)'; end end last_i_cell=get(handles.MaxIndex_i,'String'); if isempty(nbfield) last_i_cell{index}=''; else last_i_cell{index}=num2str(nbfield); end set(handles.MaxIndex_i,'String',last_i_cell) last_j_cell=get(handles.MaxIndex_j,'String'); if isempty(nbfield_j) last_j_cell{index}=''; else last_j_cell{index}=num2str(nbfield_j); end set(handles.MaxIndex_j,'String',last_j_cell); %% store geometric calibration in UvData if isfield(XmlData,'GeometryCalib') GeometryCalib=XmlData.GeometryCalib; if isempty(GeometryCalib) set(handles.pxcmx,'String','') set(handles.pxcmy,'String','') set(handles.pxcmx,'Visible','off') set(handles.pxcmy,'Visible','off') if index==1 set(handles.TransformName,'Value',1); % no transform by default end else set(handles.pxcmx,'Visible','on') set(handles.pxcmy,'Visible','on') 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.pxcmx,'String','var') set(handles.pxcmy,'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.pxcmx,'String',num2str(pixcmx)) set(handles.pxcmy,'String',num2str(pixcmy)) end if ~get(handles.CheckFixLimits,'Value')&& index==1 set(handles.TransformName,'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,'CheckVolumeScan') && isequal(GeometryCalib.CheckVolumeScan,1) set(handles.num_NbSlice,'Visible','off') else set(handles.num_NbSlice,'Visible','on') 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) if index==2 && isfield(UvData,'TimeUnit') && ~strcmp(UvData.TimeUnit,TimeUnit) msgbox_uvmat('WARNING',['time unit for second file series ' TimeUnit ' inconsistent with first series']) else UvData.TimeUnit=TimeUnit; end end UvData.XmlData{index}=XmlData; UvData.NewSeries=1; %display warning message if ~isequal(warntext,'') msgbox_uvmat('WARNING',warntext); end %% set default options in menu 'FieldName' switch FileType case {'civx','civdata','pivdata_fluidimage'} [FieldList,ColorList]=set_field_list('U','V','C'); set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data set(handles_Fields,'Value',2) % set menu to 'velocity if index==1 set(handles.FieldName_1,'Value',1); set(handles.FieldName_1,'String',[{''};{'image'};FieldList;{'get_field...'}]);%standard menu for civx data reproduced for the second field end 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,'String','Y'); case 'netcdf' set(handles_Fields,'Value',1) set(handles_Fields,'String',{'get_field...'}) if index==1 FieldName_Callback([],[], handles) else FieldName_1_Callback([],[], handles) end 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','Coord_x'); set(handles.Coord_y,'String','Coord_y'); end set(handles.uvmat,'UserData',UvData) %% set index navigation options 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.MaxIndex_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.TransformPath,'UserData'); if index==2 && (~isa(transform,'function_handle')||nargin(transform)<3) set(handles.TransformName,'value',2); % set transform to sub_field if the current fct doe not accept two input fields end set(handles.InputFileREFRESH,'BackgroundColor',[1 0 0])% set button color to red to indicate that refresh has been updated TransformName_Callback([],[],handles)% callback for the selection of transform function, then refresh the current plot 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_j,'Value',0) else 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_i,'Value',0) else set(handles.scan_i,'Value',1) 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'); if strcmp(NomType,'level') indices=get(handles.i1,'String'); else 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); case 2 indices=fullfile_uvmat('','','','',NomType,i1,stra2num(get(handles.i2,'String')),j1,j2); case 3 indices=fullfile_uvmat('','','','',NomType,i1,i2,stra2num(get(handles.j1,'String')),j2); case 4 indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,stra2num(get(handles.j2,'String'))); end end set(handles.FileIndex,'String',indices) % 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 strcmp(get(handles.slices,'String'),'slices') if get(handles.slices,'Value')==1 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.z_text,'Visible','off') set(handles.z_index,'Visible','off') set(handles.masklevel,'Value',1) set(handles.masklevel,'String',{'1'}) end end %------------------------------------------------------------------------ function num_NbSlice_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ mode=get(handles.slices,'String'); nb_slice_str=get(handles.num_NbSlice,'String'); if strcmp(mode,'volume') z=stra2num(get(handles.j1,'String')); else num=str2double(get(handles.i1,'String')); nbslice=str2double(get(handles.num_NbSlice,'String')); z=mod(num-1,nbslice)+1; end 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) % if TimeName defined, open the xml file corresponding to the first file % series, else open the xml file corresponding to the second series if isempty(get(handles.TimeName,'String'))% open the xml file corresponding to the secodn file series [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles); else [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles); end 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]=read_file_boxes(handles); MaskSubDir=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.' MaskPath=fullfile(RootPath,[MaskSubDir '.mask']); mdetect=0; if exist(MaskPath,'dir') ListStruct=dir(MaskPath);%look for a mask file ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files ListFiles=ListCells(1,:);%list of file and dri names ListFiles=ListFiles(~check_dir);%list of file names (excluding dir) if ~isempty(ListFiles) for ifile=1:numel(ListFiles) [tild,tild,MaskExt]=fileparts(ListFiles{1}); [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileInfo]=find_file_series(MaskPath,ListFiles{ifile},0); MaskFileType=MaskFileInfo.FileType; if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series) mdetect=1; end if ~strcmp(MaskFile{ifile},MaskFile{1}) mdetect=0;% cancel detection test in case of multiple masks, use the brower for selection break end end end RootPath=MaskPath; end if mdetect==0 MaskFullName=uigetfile_uvmat('pick a mask image file:',RootPath,'image'); if isempty(MaskFullName) set(handles.CheckMask,'Value',0) end [MaskPath,MaskName,MaskExt]=fileparts(MaskFullName); [tild,tild,MaskFile,i1_series,i2_series,j1_series,j2_series,MaskNomType]=find_file_series(MaskPath,[MaskName MaskExt],0); if ~(isempty(i2_series) && isempty(j2_series)) MaskNomType='*'; end end Mask.Path=MaskPath; if isempty(MaskFile) Mask.File=''; elseif ischar(MaskFile) Mask.File=MaskFile; else Mask.File=MaskFile{1}; end Mask.Ext=MaskExt; Mask.NomType=MaskNomType; set(handles.CheckMask,'UserData',Mask); errormsg=update_mask(handles); 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) %------------------------------------------------------------------------ errormsg=[];%default Mask=get(handles.CheckMask,'UserData'); MaskIndex=1; if strcmp(get(handles.z_index,'Visible'),'on') MaskIndex=str2num(get(handles.z_index,'String')); end if isfield(Mask,'maskhandle')&& ishandle(Mask.maskhandle) uistack(Mask.maskhandle,'top'); end MaskName=fullfile_uvmat(Mask.Path,'',Mask.File,Mask.Ext,Mask.NomType,MaskIndex); 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(Mask,'maskhandle')&& ishandle(Mask.maskhandle) delete(Mask.maskhandle) end else %read mask image [MaskField,tild,errormsg] = read_field(MaskName,'image'); if ~isempty(errormsg) return end npxy=size(MaskField.A); if length(npxy)>2 errormsg=[MaskName ' is not a grey scale image']; return elseif ~isa(MaskField.A,'uint8') errormsg=[MaskName ' is not a 8 bit grey level image']; return end MaskField.ZIndex=MaskIndex; %px to phys or other transform on field menu_transform=get(handles.TransformName,'String'); choice_value=get(handles.TransformName,'Value'); transform_name=menu_transform{choice_value};%name of the transform fct given by the menu 'transform_fct' transform=get(handles.TransformPath,'UserData'); 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; MaskField=transform(MaskField,UvData.XmlData{1}); end end flagmask=MaskField.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(Mask,'maskhandle')&& ishandle(Mask.maskhandle) hmask=Mask.maskhandle; end if ~isempty(hmask) set(hmask,'CData',imflag) set(hmask,'AlphaData',flagmask*0.6) set(hmask,'XData',MaskField.Coord_x); set(hmask,'YData',MaskField.Coord_y); % uistack(hmask,'top') else axes(handles.PlotAxes) hold on Mask.maskhandle=image(MaskField.Coord_x,MaskField.Coord_y,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*ones(size(flagmask))); set(handles.CheckMask,'UserData',Mask) end end end %------------------------------------------------------------------------ %------------------------------------------------------------------------ % III - MAIN InputFileREFRESH FUNCTIONS : 'FRAME PLOT' %------------------------------------------------------------------------ %------------------------------------------------------------------------ % --- Executes on button press in runplus: make one step forward and call % --- InputFileREFRESH. 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 increment=str2double(get(handles.num_IndexIncrement,'String')); %get the field increment d if isnan(increment)% case of free increment: move to next available field index increment='+'; 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 in red %------------------------------------------------------------------------ % --- Executes on button press in runmin: make one step backward and call % --- InputFileREFRESH. 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=-str2double(get(handles.num_IndexIncrement,'String')); %get the field increment d if isnan(increment)% case of free increment: move to previous available field index increment='-'; 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 in 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=str2double(get(handles.num_IndexIncrement,'String')); %get the field increment d if isnan(increment)% case of free increment: move to next available field index increment='+'; 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=-str2double(get(handles.num_IndexIncrement,'String')); %get the field increment d if isnan(increment)% case of free increment: move to next available field index increment='-'; end 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 movie_status 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=InputFile.NomType; [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(InputFile.FileIndex);% check back the indices used if isempty(i1) i1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name) elseif isempty(j1) && strcmp(get(handles.j1,'Visible'),'on') j1=str2num(get(handles.j1,'String'));%case of indexed movie end if movie_status% we read the second index from the edit box i2=str2num(get(handles.i2,'String'));%read the field indices (for movie, it is not given by the file name) if strcmp(get(handles.j2,'Visible'),'on') j2=str2num(get(handles.j2,'String'));% end 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 if isempty(i1_1) i1_1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name) elseif isempty(j1_1) && strcmp(get(handles.j1,'Visible'),'on') j1_1=str2num(get(handles.j1,'String'));%case of indexed movie end else filename_1=[]; end %% increment (or decrement) the field indices and update the input filename(s) if ~isnumeric(increment)% undefined increment value 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 && isnumeric(increment) 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 isnumeric(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(increment,'+')% 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 isnumeric(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)&&~isempty(InputFile.NomType_1) 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)&&~isempty(InputFile.NomType_1) 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); if ~isempty(InputFile.NomType_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 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); %% refresh plots 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); errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2,i1_1,i2_1,j1_1,j2_1); else errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2); end set(handles.InputFileREFRESH,'BackgroundColor',[1 0 0]) set(handles.runplus,'BackgroundColor',[1 0 0]) set(handles.runmin,'BackgroundColor',[1 0 0]) %% 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 if strcmp(NomType,'level') indices=num2str(i1); else indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2); end 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 else if isempty(i2), set(handles.i2,'String',''); end % suppress the second index display if not used if isempty(j2), set(handles.j2,'String',''); end 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','')% the second i index display is suppressed set(handles.j2,'String','')% the second j index display is suppressed set(handles.Dt_txt,'String','')% the time interval indication is suppressed return end %% check the input file indexing: [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles); NomType=get(handles.NomType,'String'); if ~isempty(find(regexp(NomType,'-'))) msgbox_uvmat('ERROR','The movie pair requires file series with a single index on the first input line') return end filename=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];% build the input file name (first line) set(handles.movie_pair,'BusyAction','queue')% set(handles.CheckFixPair,'Value',1)% impose fixed pair (needed for function runpm) set(handles.REFRESH,'BackgroundColor',[1 1 0])%paint the command button in yellow to indicate its activity set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow to indicate its activity 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 % if isequal(FieldName,'image') % index=1; % 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,SubDir,RootFile,FileIndex_1,Ext,NomType]=read_file_boxes_1(handles);% get info from the second input line % 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')); %% determine the name 'imaname_1' of the second file in the pair imaname_1=''; if isempty(num_j2)% no second j index indicated if isempty(num_i2) if strcmp(get(handles.j2,'Visible'),'on') %if the j box is visible imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,num_i1,[],num_j1+1); end if exist(imaname_1,'file') num_j2=num_j1+1;% look by default for the next j index as the second file set(handles.j2,'String',num2stra(num_j2,NomType)); else imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,num_i1+1,[],num_j1); if exist(imaname_1,'file') num_i2=num_i1+1; set(handles.i2,'String',num2str(num_i2)); else 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 end end 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 if isempty(num_j1) num_j1=1; end if isempty(num_j2) num_j2=num_j1;%repeat the index i1 by default end imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,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 %% display the first field in the pair (including possibly a background field from second line input filename_1) 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);% get the indices of the second series from the string FileIndex_1 if isempty(j1_1)% case of movies, the index is not given by file index j1_1=num_j1; end 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) set(handles.REFRESH,'BackgroundColor',[1 0 0])% set button color to red, update successfull else msgbox_uvmat('ERROR',errormsg); set(handles.REFRESH,'BackgroundColor',[1 0 1])% keep button color magenta, input not succesfull end UvData=get(handles.uvmat,'UserData'); Field_a=UvData.Field;% movie on the field defined by the second input line %% display time interval for the image pair if isfield(UvData,'XmlData')&&isfield(UvData.XmlData{1},'Time')... && size(UvData.XmlData{1}.Time,1)>=num_i2+1 && size(UvData.XmlData{1}.Time,2)>=num_j2+1 dt=(UvData.XmlData{1}.Time(num_i2+1,num_j2+1)-UvData.XmlData{1}.Time(num_i1+1,num_j1+1)); if isfield(UvData,'TimeUnit') set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) ' m' UvData.TimeUnit] ) else set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) ' 10^(-3)'] ) end else set(handles.Dt_txt,'String','') end %% read the second field if isempty(UvData.MovieObject) [Field_b,ParamOut,errormsg] = read_field(imaname_1,UvData.FileType{index},[],num_frame); else [Field_b,ParamOut,errormsg] = read_field(imaname_1,UvData.FileType{1},UvData.MovieObject{1},num_frame); end if ~isempty(errormsg) msgbox_uvmat('ERROR',['Error in reading second image: ' errormsg]) return end %% apply phys or other transform on the two input fields transform=get(handles.TransformPath,'UserData'); if ~isempty(transform) if isfield(UvData,'XmlData') && ~isempty(UvData.XmlData) %use geometry calib recorded from the ImaDoc xml file as first priority if nargin(transform)>=2 Field_b=transform(Field_b,UvData.XmlData{1}); else Field_b=transform(Field_b); end 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') % enable STOP command % read and plot the series of images in non erase mode set(hima,'CData',Field_b.A); %TODO: generalise to other kinds of fields 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) set(handles.Dt_txt,'String','') %------------------------------------------------------------------------ % --- Executes on button press in InputFileREFRESH. function REFRESH_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.REFRESH,'BackgroundColor',[1 1 0])%paint the REFRESH button in yellow to indicate its activity drawnow [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);%read the features of the input file name (first line) [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(FileIndex);% check back the indices used if isempty(i2), set(handles.i2,'String',''); end % suppress the second i index display if not used if isempty(j2), set(handles.j2,'String',''); end % suppress the second j index display if not used if strcmp(get(handles.NomType,'String'),'level') jindex=str2num(get(handles.j1,'String')); filename=[fullfile(RootPath,SubDir,['level' num2str(jindex)],RootFile) FileIndex FileExt];% build the input file name (first line) else filename=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];% build the input file name (first line) end filename_1='';%default second file name FileIndex_1=''; if get(handles.SubField,'Value')% if a second file is introduced [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);%read the features of the input file name (second line) filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1]; %build the input file name (second line) 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);% get the indices of the second series from the string FileIndex_1 if isempty(j1_1)% case of movies, the index is not given by file index j1_1=num_j1; end % in case of movies the index is set by edit boxes i1 or j1 (case of movies indexed by index i) errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1); ResizeFcn(handles.uvmat,[],handles) if isempty(errormsg) set(handles.REFRESH,'BackgroundColor',[1 0 0])% set button color to red, update successfull else msgbox_uvmat('ERROR',errormsg); set(handles.REFRESH,'BackgroundColor',[1 0 1])% keep button color magenta, input not succesfull end %------------------------------------------------------------------------ % --- read the input files and inputfilerefresh 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 asbsence of second input file) % num_i1,num_i2,num_j1,num_j2; frame indices % i1_1,i2_1,j1_1,j2_1: frame indices for the second input file (needed if FileName_1 is not empty) %------------------------------------------------------------------------ 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 pointer=get(handles.uvmat,'Pointer'); if strcmp(pointer,'watch')% reinitialise the mouse if stuck to 'watch' set(handles.CheckZoom,'Value',0) pointer='arrow'; end set(handles.uvmat,'Pointer','watch') drawnow 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 mode_slice=get(handles.slices,'String'); if strcmp(mode_slice,'volume') z_index=num_j1; set(handles.z_index,'String',num2str(z_index)) else nbslice=str2num(get(handles.num_NbSlice,'String')); z_index=mod(num_i1-1,nbslice)+1; set(handles.z_index,'String',num2str(z_index)) end % inputfilerefresh 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.ProjObject) if isfield(UvData.ProjObject{iobj},'ProjMode')&& strcmp(UvData.ProjObject{iobj}.ProjMode,'interp_tps') 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','pivdata_fluidimage'}; 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 % case of input vector field, get the scalar used for vector color 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','rdvision'} ParamIn=UvData.MovieObject{1}; % movie object if strcmp(NomType,'*') frame_index=num_i1;%frame index from a single movies or multimage else frame_index=num_j1;% frame index from a set of indexed movies end case 'multimage' if ~strcmp(NomType,'*') MaxIndex_j_cell=get(handles.MaxIndex_j,'String'); if num_j1>str2num(MaxIndex_j_cell{1}) errormsg='specified frame index exceeds file content'; return else frame_index=num_j1;%frame index for movies or multimage end else MaxIndex_i_cell=get(handles.MaxIndex_i,'String'); if num_i1>str2num(MaxIndex_i_cell{1}) errormsg='specified frame index exceeds file content'; return else frame_index=num_i1; end 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; ParamIn.Coord_x=get(handles.Coord_x,'String'); ParamIn.Coord_y=get(handles.Coord_y,'String'); ParamIn.Coord_z=get(handles.Coord_z,'String'); ParamIn.CheckCoordIndex=strcmp(get(handles.SwitchCoordIndex,'String'),'dim'); TimeName=get(handles.TimeName,'String'); r=regexp(TimeName,'^(?(dim:)|(var:))','names');%look for 'var:' or 'dim:' at the beginning of time name if ~isempty(r) frame_index=num_i1;%time index chosen by i1 if strcmp(r.type,'dim:') ParamIn.TimeDimName=TimeName(5:end); elseif strcmp(r.type,'var:') ParamIn.TimeVarName=TimeName(5:end); end end 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 Field{1}.ZIndex=z_index; %used for multiplane 3D calibration %% 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 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_1,'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 isempty(FieldName_1) FieldName_1=FieldName;% if blank reproduce the field name of the first field end if ~isempty(regexp(FieldName_1,'^vel'))&& 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 for movies or multimage frame_index_1=i1_1; else frame_index_1=j1_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) ; 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.Coord_x=get(handles.Coord_x,'String'); ParamIn_1.Coord_y=get(handles.Coord_y,'String'); end [Field{2},ParamOut_1,errormsg] = read_field(FileName_1,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 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 (strcmp(UvData.FileType{1},'civx')||strcmp(UvData.FileType{1},'civdata')||strcmp(UvData.FileType{1},'pivdata_fluidimage'))... && ~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 %% update the display menu for the second velocity type (second menuline) test_veltype_1=0; if isempty(FileName_1) elseif ~test_keepdata_1 if (strcmp(UvData.FileType{2},'civx')||strcmp(UvData.FileType{2},'civdata')||strcmp(UvData.FileType{1},'pivdata_fluidimage'))... && ~strcmp(FieldName_1,'get_field...') 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]) else set(handles.VelType_1,'Visible','off') end % update the second field menu: the same quantity if isstruct(ParamOut_1) % display the FieldName menu from the input file and pick the selected one: FieldList=get(handles.FieldName_1,'String'); field_index=strcmp(ParamOut_1.FieldName,FieldList); if ~isempty(field_index) set(handles.FieldName_1,'Value',find(field_index,1)) end end end if test_veltype||test_veltype_1 set(handles.FixVelType,'Visible','on') else set(handles.FixVelType,'Visible','off') end %% 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 value of the current file abstime=[];%default inputs dt=[]; TimeUnit=''; if isfield(UvData,'TimeUnit') TimeUnit=UvData.TimeUnit;%retrieve info from update_rootinfo end TimeName=get(handles.TimeName,'String'); % time from xml file or video movie if strcmp(TimeName,'xml')||strcmp(TimeName,'video') 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) && num_i1>=0 &&siz(1)>=max(num_i1+1,num_i2+1) && siz(2)>=max(num_j1+1,num_j2+1) abstime=(UvData.XmlData{1}.Time(num_i1+1,num_j1+1)+UvData.XmlData{1}.Time(num_i2+1,num_j2+1))/2;%overset the time read from files dt=(UvData.XmlData{1}.Time(num_i2+1,num_j2+1)-UvData.XmlData{1}.Time(num_i1+1,num_j1+1)); Field{1}.Dt=dt; if isfield(UvData.XmlData{1},'TimeUnit') TimeUnit=UvData.XmlData{1}.TimeUnit; end end end % time in the input file, not defined in a xml file or movie if isempty(abstime) if (strcmp(TimeName,'civdata')||strcmp(TimeName,'civx')||strcmp(TimeName,'timestamp'))&&isfield(Field{1},'Time') abstime=Field{1}.Time; elseif ~isempty(regexp(TimeName,'^att:', 'once')) abstime=Field{1}.(TimeName(5:end));%the time is an attribute selected by get_file if isfield(Field{1},[TimeName(5:end) 'Unit']) TimeUnit=Field{1}.([TimeName(5:end) 'Unit']); else TimeUnit=''; end elseif ~isempty(regexp(TimeName,'^var:')) abstime=Field{1}.(TimeName(5:end));%the time is a variale selected by get_file % TODO: look for time unit attribute elseif ~isempty(regexp(TimeName,'^dim:')) abstime=str2num(get(handles.i1,'String')); TimeUnit='index'; end if isfield(Field{1},'Dt') dt=Field{1}.Dt;%dt read from the netcdf input file 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 end end set(handles.TimeValue,'String',num2str(abstime)) %% display time value of the second current file if relevant abstime_1=[]; if ~isempty(FileName_1) TimeName_1=get(handles.TimeName_1,'String');% indicate whether time is from xml or video % time from xml file or video movie as a second file series if strcmp(TimeName_1,'xml')||strcmp(TimeName_1,'video') 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+1,i2_1+1) && siz(2)>=max(j1_1+1,j2_1+1) abstime_1=(UvData.XmlData{2}.Time(i1_1+1,j1_1+1)+UvData.XmlData{2}.Time(i2_1+1,j2_1+1))/2;%overset the time read from files Field{2}.Dt=(UvData.XmlData{2}.Time(i2_1+1,j2_1+1)-UvData.XmlData{2}.Time(i1_1+1,j1_1+1)); end end end % get time in the input file of the second series, not defined in a xml file or movie if isempty(abstime_1) && numel(Field)==2 if strcmp(TimeName_1,'civdata')||strcmp(TimeName_1,'civx') abstime_1=Field{2}.Time; elseif ~isempty(regexp(TimeName_1,'^att:')) ||~isempty(regexp(TimeName_1,'^dim:'))||~isempty(regexp(TimeName_1,'^var:')) abstime_1=Field{2}.(TimeName_1(5:end));%the time is an attribute or variale selected by get_file end end set(handles.TimeValue_1,'String',num2str(abstime_1,5)) end 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 %% Time title with unit if isempty(abstime)&&isempty(abstime_1) Time_title=''; else Time_title='Time'; if ~isempty(TimeUnit) Time_title=['Time (' TimeUnit ')']; end end set(handles.Time_title,'String',Time_title) %% 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.TransformPath,'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 isfield(UvData,'TransformInput') XmlData.TransformInput=UvData.TransformInput; end if numel(UvData.XmlData)==2 XmlData_1=UvData.XmlData{2}; end end 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 %% get bounds and dimensions of the input field UvData.Field=find_field_bounds(UvData.Field); testnewseries=UvData.NewSeries; UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback) %% calculate tps coefficients if needed UvData.Field=tps_coeff_field(UvData.Field,check_proj_tps); %% 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 UvData.Field.NbDim<=1 set(handles.Objects,'Visible','off') set(handles.CheckFixAspectRatio,'Value',0) [PlotType,PlotParamOut,haxes]=plot_field(UvData.Field,handles.PlotAxes,read_GUI(handles.uvmat)); UvData.PlotAxes=UvData.Field; %store data for further plot modifications errormsg=fill_GUI(PlotParamOut,handles.uvmat); for list={'Scalar','Vectors'} if ~isfield(PlotParamOut,list{1}) set(handles.(list{1}),'Visible','off') end end set(handles.Histogram,'Visible','off') set(handles.HistoMenu,'Visible','off') set(handles.HistoAxes,'Visible','off') hlegend=findobj(handles.uvmat,'Tag','HistoLegend'); if ~isempty(hlegend) delete(hlegend) end cla(handles.HistoAxes)% clear the curves and legend in histogram axes set(handles.uvmat,'UserData',UvData) %% 2D or 3D fieldname are generally projected else set(handles.Objects,'Visible','on') %% Plot the projections on the selected projection objects %if no projection object exists, create a default one if isempty(UvData.ProjObject{1}) set(handles.ListObject,'Value',1) set(handles.ListObject,'String',{'plane'}) UvData.ProjObject{1}.Type='plane';%main plotting plane UvData.ProjObject{1}.ProjMode='projection';%main plotting plane UvData.ProjObject{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat UvData.ProjObject{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat set(handles.ListObject_1,'Value',1) set(handles.ListObject_1,'String',{'plane'}) if UvData.Field.NbDim==3 %3D case % ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider % ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider UvData.ProjObject{1}.NbDim=3;%test for 3D objects UvData.ProjObject{1}.RangeZ=UvData.Field.CoordMesh;%main plotting plane UvData.ProjObject{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen UvData.ProjObject{1}.Angle=[0 0]; elseif isfield(UvData,'Z') %multilevel case (single menuplane in a 3D space) if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData') XmlData=UvData.XmlData{1}; if isfield(XmlData,'PlanePos') UvData.ProjObject{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.ProjObject{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:); end elseif isfield(UvData,'ZIndex') UvData.ProjObject{1}.ZObject=UvData.ZIndex; end end end IndexObj=get(handles.ListObject_1,'Value');%selected projection object for main view if IndexObj> numel(UvData.ProjObject) IndexObj=1;%select the first object if the selected one does not exist set(handles.ListObject_1,'Value',1) end if get(handles.CheckViewField,'Value') IndexObj_2=get(handles.ListObject,'Value');%selected projection object for view_field if ~isequal(IndexObj_2,IndexObj(1)) IndexObj(2)=IndexObj_2; end 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 %% 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(view_field_handle); end end %% loop on the projection objects: one or two for imap=1:numel(IndexObj) iobj=IndexObj(imap); if numel(UvData.ProjObject)=3 && UvData.ProjObject{iobj}.Coord(1,3)UvData.Field.ZMin) UvData.ProjObject{iobj}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen end end [ObjectData,errormsg]=proj_field(UvData.Field,UvData.ProjObject{iobj});% project field on the object if ~isempty(errormsg) errormsg=['projection on ' UvData.ProjObject{iobj}.Type ': ' 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}.Axes.CheckFixAspectRatio=1;% set x and y scaling equal if CoordUnit is defined (common unit for x and y) PlotParam{imap}.Axes.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 Coord_x=ObjectData.Coord_x;%x coordiantes for the scalar field Coord_y=ObjectData.Coord_y;%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,Coord_x)||~isequal(MaskY,Coord_y) 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.Coord_y(end)-ObjectData.Coord_y(1))/(npxy(1)-1);%grid mesh in y dxy(2)=(ObjectData.Coord_x(end)-ObjectData.Coord_x(1))/(npxy(2)-1);%grid mesh in x xi=ObjectData.Coord_x(1):dxy(2):ObjectData.Coord_x(end); yi=ObjectData.Coord_y(1):dxy(1):ObjectData.Coord_y(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); end set(handles.uvmat,'UserData',UvData) if ~isempty(ObjectData) if imap==2 && isempty(view_field_handle) view_field(ObjectData) else [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap}); if ~isempty(regexp(PlotType,'^error'))%exit in case of plotting error if ~isempty(regexp(PlotType,'attempt to plot two vector fields')) set(handles.CheckEditObject,'Value',1) CheckEditObject_Callback([], [], handles)% propose to edit the main projection plane hset_object=findobj(allchild(0),'Tag','set_object');%find the GUI set_object hhset_object=guidata(hset_object);% set(hhset_object.ProjMode,'Value',2); set_object('ProjMode_Callback',hset_object,[],hhset_object); end return end if imap==1 errormsg=fill_GUI(PlotParamOut,handles.uvmat); else errormsg=fill_GUI(PlotParamOut,view_field_handle);%TODO: check effect on text display end for list={'Scalar','Vectors'} if ~isfield(PlotParamOut,list{1}) set(plot_handles{imap}.(list{1}),'Visible','off') end end if isfield(Field,'CoordMesh')&&~isempty(Field.CoordMesh) ObjectData.CoordMesh=Field.CoordMesh; % 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); 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 axes 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.HistoMenu,'Value',1) set(handles.HistoMenu,'String',menu_histo) set(handles.Histogram,'Visible','on') set(handles.HistoMenu,'Visible','on') set(handles.HistoAxes,'Visible','on') HistoMenu_Callback(handles.HistoMenu, [], handles)% plot first histogram end end if UvData.Field.NbDim==3 set(handles.CheckEditObject,'Value',1) CheckEditObject_Callback(handles.uvmat, [], handles) end %ResizeFcn(handles.uvmat,[],handles) set(handles.uvmat,'Pointer',pointer) %------------------------------------------------------------------------ function HistoMenu_Callback(hObject, eventdata, handles) %-------------------------------------------- %% get the current field stored in uvmat user data UvData=get(handles.uvmat,'UserData'); Field=UvData.Field; %% get from the menu 'HistoMenu' the name(s) of the fields to use histo_menu=get(handles.HistoMenu,'String'); histo_value=get(handles.HistoMenu,'Value'); FieldName=histo_menu{histo_value}; r=regexp(FieldName,'(?.*)(?,)(?.*)','names'); FieldName_2=''; if ~isempty(r) FieldName=r.var1;% name of first variable FieldName_2=r.var2;% name of second variable end if ~isfield(UvData.Field,FieldName) msgbox_uvmat('ERROR',['no field ' FieldName ' for histogram']) return end %% extract the fields to use % eliminate false data if relevant (false flag FF exists) check_false=0; if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(Field.(FieldName))) indsel=find(Field.FF==0);%find values marked as false if ~isempty(indsel) FieldHisto=Field.(FieldName)(indsel);%field of the first variable (U) if ~isempty(FieldName_2) if isfield(Field,'NbDim') && Field.NbDim==3 FieldHisto(:,:,:,2)=Field.(FieldName_2)(indsel);%field of the second variable (U) else FieldHisto(:,:,2)=Field.(FieldName_2)(indsel);%field of the second variable (U) end end check_false=1; end end % no false data if ~check_false FieldHisto=Field.(FieldName);%field of the first variable (U) if ~isempty(FieldName_2) if isfield(Field,'NbDim') && Field.NbDim==3 FieldHisto(:,:,:,2)=Field.(FieldName_2);%field of the second variable (V) else FieldHisto(:,:,2)=Field.(FieldName_2);%field of the second variable (V) end end end %% calculate and plot Histogram if isempty(Field) msgbox_uvmat('ERROR',['empty field ' FieldName]) else nxy=size(FieldHisto); Amin=double(min(min(min(min(FieldHisto)))));%min of field value Amax=double(max(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 VarMesh=(Amax-Amin)/100; ord=10^(floor(log10(VarMesh)));%order of magnitude if VarMesh/ord >=5 VarMesh=5*ord; elseif VarMesh/ord >=2 VarMesh=2*ord; else VarMesh=ord; end Amin=VarMesh*(ceil(Amin/VarMesh)); Amax=VarMesh*(floor(Amax/VarMesh)); Histo.(FieldName)=Amin:VarMesh:Amax; %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=findobj(handles.uvmat,'Tag','HistoLegend'); if isempty(hlegend) hlegend=legend; set(hlegend,'Tag','HistoLegend') end 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') set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes set(handles.CheckZoomFig,'Value',0)%desactivate zoom fig end %------------------------------------------------------------------------ % --- Executes on button press in CheckZoomFig. %------------------------------------------------------------------------ function CheckZoomFig_Callback(hObject, eventdata, handles) if get(handles.CheckZoomFig,'Value') set(handles.CheckZoom,'value',0) end %------------------------------------------------------------------------ % --- Executes on button press in 'CheckFixLimits'. %------------------------------------------------------------------------ function CheckFixLimits_Callback(hObject, eventdata, handles) if ~get(handles.CheckFixLimits,'Value') update_plot(handles) set(handles.CheckZoom,'Value',0) end %------------------------------------------------------------------------ % --- Executes on button press in CheckFixAspectRatio. function CheckFixAspectRatio_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ update_plot(handles); %------------------------------------------------------------------------ function num_AspectRatio_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.CheckFixAspectRatio,'Value',1)% select the fixed aspect ratio button update_plot(handles); %------------------------------------------------------------------------ %----Executes on button press in 'record': records the current flags of manual correction. %------------------------------------------------------------------------ function record_Callback(hObject, eventdata, handles) [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles); FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]; [erread,message]=fileattrib(FileName); if ~isempty(message) && ~isequal(message.UserWrite,1) msgbox_uvmat('ERROR',['no writting access to ' FileName]) return end MenuVelType=get(handles.VelType,'String'); test_civ2=strcmp(MenuVelType{get(handles.VelType,'Value')},'civ2'); test_civ1=strcmp(MenuVelType{get(handles.VelType,'Value')},'civ1'); if ~test_civ2 && ~test_civ1 msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields') end if test_civ2 nbname='nb_vec_2'; flagname='Civ2_FF'; CivStage=5; end if test_civ1 nbname='nb_vec_1'; flagname='Civ1_FF'; CivStage=2; 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 builtin Matlab netcdf library nc=netcdf.open(FileName,'NC_WRITE'); netcdf.reDef(nc); netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),'CivStage',CivStage); 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) if get(handles.SubField,'Value')==0% if the subfield button is desactivated desable_subfield(handles) transform_fct_list=get(handles.TransformName,'String'); transform_fct=transform_fct_list(get(handles.TransformName,'Value')); if strcmp(transform_fct,'sub_field') set(handles.TransformName,'Value',1)%suppress the sub_field transform TransformName_Callback(hObject, eventdata, handles); else REFRESH_Callback(hObject, eventdata, handles) end else fileinput_1=uigetfile_uvmat('select a second input file:',get(handles.RootPath,'String')); if isempty(fileinput_1) set(handles.SubField,'Value',0) else % refresh the current displayed field 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) end end %----------------------------------------------------------------------- % --- desactivate display used for a second file series %----------------------------------------------------------------------- function desable_subfield(handles) 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.FileIndex_1,'Visible','off'); set(handles.FileExt_1,'Visible','off'); set(handles.TimeName_1,'String',''); set(handles.TimeName_1,'Visible','off'); set(handles.TimeValue_1,'String',''); set(handles.TimeValue_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 FieldList=get(handles.FieldName,'String'); if numel(FieldList)>1 % if a choice of fields exists set(handles.FieldName_1,'Value',1)% set second field choice to blank set(handles.FieldName_1,'String',[{''};FieldList])% reproduce the menu FieldName plus a blank option else set(handles.FieldName_1,'String',{''})% set second field choice to blank end if ~strcmp(get(handles.VelType,'Visible'),'on') set(handles.VelType_1,'Visible','off') end UvData=get(handles.uvmat,'UserData'); if isfield(UvData,'XmlData_1') UvData=rmfield(UvData,'XmlData_1'); end set(handles.uvmat,'UserData',UvData); %------------------------------------------------------------------------ % --- read the data displayed for the input rootfile windows (new): TODO use read_GUI %------------------------------------------------------------------------ function [RootPath,SubDir,RootFile,FileIndices,FileExt,NomType]=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; NomType=InputFile.NomType; %------------------------------------------------------------------------ % ---- 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) %------------------------------------------------------------------------ %% read data from uvmat UvData=get(handles.uvmat,'UserData'); 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 [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]); switch field case 'get_field...' %% fill the axes and variables from selections in get_field ParamIn.Title='get_field: choose input field for display in uvmat' ; % in case of civ data, we use the civ choice as default input for the GUI get_field if strcmp(get(handles.VelType,'Visible'),'on') ParamIn.SwitchVarIndexTime='attribute'; ListVelType=get(handles.VelType,'String'); VelType=ListVelType{get(handles.VelType,'Value')}; switch VelType case 'civ1' ParamIn.TimeAttrName='Civ1_Time'; ParamIn.vector_x='Civ1_U'; ParamIn.vector_y='Civ1_V'; ParamIn.vec_color='Civ1_C'; case 'filter1' ParamIn.TimeAttrName='Civ1_Time'; ParamIn.vector_x='Civ1_U_smooth'; ParamIn.vector_y='Civ1_V_smooth'; case 'civ2' ParamIn.TimeAttrName='Civ2_Time'; ParamIn.vector_x='Civ2_U'; ParamIn.vector_y='Civ2_V'; case 'filter2' ParamIn.TimeAttrName='Civ2_Time'; ParamIn.vector_x='Civ2_U_smooth'; ParamIn.vector_y='Civ2_V_smooth'; ParamIn.vec_color='Civ2_C'; end end % VelType menu desactivated set(handles.FixVelType,'visible','off') set(handles.VelType,'Visible','off') %read selection from get_field [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles); FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]; GetFieldData=get_field(FileName,ParamIn);% inport field names from the GUI get_field FieldList={}; VecColorList={''}; XName=''; YName=''; ZName=''; switch GetFieldData.FieldOption case 'vectors' UName=GetFieldData.PanelVectors.vector_x; VName=GetFieldData.PanelVectors.vector_y; if isfield(GetFieldData,'Coordinates') YName=GetFieldData.Coordinates.Coord_y; if isfield(GetFieldData.Coordinates,'Coord_z') ZName=GetFieldData.Coordinates.Coord_z; end end CName=GetFieldData.PanelVectors.vec_color; FieldList={['vec(' UName ',' VName ')'];... ['norm(' UName ',' VName ')'];... UName;VName}; VecColorList={['norm(' UName ',' VName ')'];... UName;VName}; if ~isempty(CName) VecColorList=[{CName};VecColorList]; end case 'scalar' AName=GetFieldData.PanelScalar.scalar; if isfield(GetFieldData,'Coordinates') YName=GetFieldData.Coordinates.Coord_y; if isfield(GetFieldData.Coordinates,'Coord_z') ZName=GetFieldData.Coordinates.Coord_z; end end FieldList={AName}; case '1D plot' YName=GetFieldData.PanelOrdinate.ordinate; case 'civdata...'%reinitiate input, return to automatic civ data reading display_file_name(handles,FileName,1) end % get time as file index, attribute, variable or matrix index if ~strcmp(GetFieldData.FieldOption,'civdata...') if isfield(GetFieldData,'Coordinates') XName=GetFieldData.Coordinates.Coord_x; set(handles.SwitchCoordIndex,'String','var'); % variable used as coordinate else set(handles.SwitchCoordIndex,'String','dim'); % matrix index used a coordinate end TimeNameStr=GetFieldData.Time.SwitchVarIndexTime; switch TimeNameStr case 'file index' set(handles.TimeName,'String',''); case 'attribute' set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]); case 'variable' set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName]) set(handles.NomType,'String','*') set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')]) set(handles.i1,'String','1')% set counter to 1 (now the time index in the input matrix) MaxIndex_i=get(handles.MaxIndex_i,'String'); MaxIndex_i{1}=num2str(GetFieldData.Time.TimeDimension); set(handles.MaxIndex_i,'String',MaxIndex_i)%TODO: record time unit UvData=get(handles.uvmat,'UserData'); UvData.TimeUnit=GetFieldData.Time.TimeUnit; set(handles.uvmat,'UserData',UvData); set(handles.FileIndex,'String','') ParamIn.TimeVarName=GetFieldData.Time.TimeName; case 'matrix index' set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]); set(handles.NomType,'String','*') set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')]) set(handles.i1,'String','1')% set counter to 1 (now the time index in the input matrix) MaxIndex_i=get(handles.MaxIndex_i,'String'); MaxIndex_i{1}=num2str(GetFieldData.Time.TimeDimension); set(handles.MaxIndex_i,'String',MaxIndex_i)%TODO: record time unit UvData=get(handles.uvmat,'UserData'); UvData.TimeUnit=GetFieldData.Time.TimeUnit; set(handles.uvmat,'UserData',UvData); set(handles.FileIndex,'String','') ParamIn.TimeDimName=GetFieldData.Time.TimeName; end set(handles.Coord_x,'String',XName) % if ischar(YName) % YName={YName}; % end set(handles.Coord_y,'String',YName) set(handles.Coord_z,'String',ZName) set(handles.FieldName,'Value',1) set(handles.FieldName,'String',[FieldList; {'get_field...'}]); set(handles.ColorScalar,'Value',1) set(handles.ColorScalar,'String',VecColorList); UvData.FileType{1}='netcdf'; set(handles.uvmat,'UserData',UvData) REFRESH_Callback(hObject, eventdata, handles) end case 'image' %% look for image corresponding to civ data 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') imagename=uigetfile_uvmat('Pick an image file',imagename,'image'); if isempty(imagename) return end end % display the selected field and related information display_file_name(handles,imagename)%display the image otherwise REFRESH_Callback(hObject, eventdata, handles) end %---------------------------------------------------------------- % --- Executes on menu selection FieldName_1 function FieldName_1_Callback(hObject, eventdata, handles) %------------------------------------------------- %%%%%% TODO: modify like FieldName_Callback %% 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...' %% fill the axes and variables from selections in get_field ParamIn=[]; % in case of civ data, we use the civ choice as default input for the GUI get_field if strcmp(get(handles.VelType_1,'Visible'),'on') ParamIn.SwitchVarIndexTime='attribute'; ListVelType=get(handles.VelType_1,'String'); VelType=ListVelType{get(handles.VelType_1,'Value')}; switch VelType case 'civ1' ParamIn.TimeAttrName='Civ1_Time'; ParamIn.vector_x='Civ1_U'; ParamIn.vector_y='Civ1_V'; ParamIn.vec_color='Civ1_C'; case 'filter1' ParamIn.TimeAttrName='Civ1_Time'; ParamIn.vector_x='Civ1_U_smooth'; ParamIn.vector_y='Civ1_V_smooth'; case 'civ2' ParamIn.TimeAttrName='Civ2_Time'; ParamIn.vector_x='Civ2_U'; ParamIn.vector_y='Civ2_V'; case 'filter2' ParamIn.TimeAttrName='Civ2_Time'; ParamIn.vector_x='Civ2_U_smooth'; ParamIn.vector_y='Civ2_V_smooth'; ParamIn.vec_color='Civ2_C'; end end % VelType menu desactivated set(handles.FixVelType,'visible','off') set(handles.VelType,'Visible','off') %read selection from get_field [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles); FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]; GetFieldData=get_field(FileName,ParamIn);% inport field names from the GUI get_field FieldList={}; VecColorList={}; switch GetFieldData.FieldOption case 'vectors' UName=GetFieldData.PanelVectors.vector_x; VName=GetFieldData.PanelVectors.vector_y; YName=GetFieldData.Coordinates.Coord_y; CName=GetFieldData.PanelVectors.vec_color; FieldList={['vec(' UName ',' VName ')'];... ['norm(' UName ',' VName ')'];... UName;VName}; VecColorList={['norm(' UName ',' VName ')'];... UName;VName}; if ~isempty(CName) VecColorList=[{CName};VecColorList]; end case 'scalar' AName=GetFieldData.PanelScalar.scalar; YName=GetFieldData.Coordinates.Coord_y; FieldList={AName}; case '1D plot' YName=GetFieldData.PanelOrdinate.ordinate; case 'civdata...'%reinitiate input, return to automatic civ data reading display_file_name(handles,FileName,1) end if ~strcmp(GetFieldData.FieldOption,'civdata...') XName=GetFieldData.Coordinates.Coord_x; TimeNameStr=GetFieldData.Time.SwitchVarIndexTime; switch TimeNameStr case 'file index' set(handles.TimeName_1,'String',''); case 'attribute' set(handles.TimeName_1,'String',['att:' GetFieldData.Time.TimeName]); case 'variable' set(handles.TimeName_1,'String',['var:' GetFieldData.Time.TimeName]) set(handles.NomType_1,'String','*') set(handles.RootFile_1,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')]) set(handles.FileIndex_1,'String','') ParamIn.TimeVarName=GetFieldData.Time.TimeName; case 'matrix_index' set(handles.TimeName_1,'String',['dim:' GetFieldData.Time.TimeName]); set(handles.NomType_1,'String','*') set(handles.RootFile_1,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')]) set(handles.FileIndex_1,'String','') ParamIn.TimeDimName_1=GetFieldData.Time.TimeName; end set(handles.Coord_x,'String',XName) % if ischar(YName) % YName={YName}; % end set(handles.Coord_y,'String',YName) set(handles.FieldName_1,'Value',1) set(handles.FieldName_1,'String',[FieldList; {'get_field...'}]); set(handles.ColorScalar,'Value',1) set(handles.ColorScalar,'String',VecColorList); UvData.FileType{2}='netcdf'; set(handles.uvmat,'UserData',UvData) REFRESH_Callback(hObject, eventdata, handles) end case 'image' %% look for image corresponding to civ data 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 [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles); SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.' imagename=fullfile_uvmat(RootPath,SubDirBase,RootFile,'.png','_1',i1,[],j1,[]); end if ~exist(imagename,'file') imagename=uigetfile_uvmat('Pick an image file',imagename,'image'); end if isempty(imagename) set(handles.SubField,'Value',0) return else display_file_name(handles,imagename,2)%display the image as second field end otherwise check_refresh=1; if check_new% if a second field was not previously entered, we just read another field in the first input file set(handles.FileIndex_1,'String',get(handles.FileIndex,'String')) set(handles.FileExt_1,'String',get(handles.FileExt,'String')) UvData.FileType{2}=UvData.FileType{1}; UvData.XmlData{2}= UvData.XmlData{1}; transform=get(handles.TransformPath,'UserData'); if (~isa(transform,'function_handle')||nargin(transform)<3) set(handles.uvmat,'UserData',UvData) set(handles.TransformName,'value',2); % set transform fct to 'sub_field' if the current fct does not accept two input fields TransformName_Callback(hObject, eventdata, handles)% activate transform_fct_Callback and refresh current plot check_refresh=0; end end if ~isequal(field,'image') set(handles.TitleNpxy,'Visible','off')% visible npx,pxcm... buttons set(handles.num_Npx,'Visible','off') set(handles.num_Npy,'Visible','off') end set(handles.uvmat,'UserData',UvData) if check_refresh && ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1)) REFRESH_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 imin=1; 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','pivdata_fluidimage'} 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 Civ==6 %patch2 imax=4; else imax=4;imin=3; end end menu=menu(imin:imax); %------------------------------------------------------------------------ % --- Executes on button press in FixVelType. function FixVelType_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ % inputfilerefresh the current plot if the fixed veltype is unselected if ~get(handles.FixVelType,'Value') REFRESH_Callback(hObject, eventdata, handles) end %------------------------------------------------------------------------ % --- Executes on button press in VelType. function VelType_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ set(handles.FixVelType,'Value',1) REFRESH_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.InputFileREFRESH,'BackgroundColor',[1 1 0])%paint REFRESH 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 plot, 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 plot 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.TransformPath,'UserData'); if (~isa(transform,'function_handle')||nargin(transform)<3) set(handles.uvmat,'UserData',UvData) set(handles.TransformName,'value',2); % set transform fct to 'sub_field' if the current fct does not accept two input fields TransformName_Callback(hObject, eventdata, handles)% activate transform_fct_Callback and refresh current plot else check_refresh=1; end end % inputfilerefresh the current plot 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.InputFileREFRESH,'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.CheckEditObject,'Value',0) % set(handles.CheckEditObject,'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,'CoordMesh')&& ~isempty(UvData.Field.CoordMesh) data.RangeX=[UvData.Field.XMin UvData.Field.XMax]; data.RangeY=[UvData.Field.YMin UvData.Field.YMax]; data.DX=UvData.Field.CoordMesh; data.DY=UvData.Field.CoordMesh; elseif isfield(UvData.Field,'Coord_x')&& isfield(UvData.Field,'Coord_y') && isfield(UvData.Field,'A')%only image np=size(UvData.Field.A); meshx=(UvData.Field.Coord_x(end)-UvData.Field.Coord_x(1))/np(2); meshy=abs(UvData.Field.Coord_y(end)-UvData.Field.Coord_y(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,'name','set_object') 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) %------------------------------------------------------- % if isequal(get(handles.edit_vect,'Value'),1) VelTypeMenu=get(handles.VelType,'String'); VelType=VelTypeMenu{get(handles.VelType,'Value')}; if ~strcmp(VelType,'civ2') && ~strcmp(VelType,'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.CheckEditObject,'Value',0) set(handles.CheckZoom,'Value',0) set(gcf,'Pointer','arrow') 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,'ProjObject') for iobj=1:length(UvData.ProjObject) ObjectData=UvData.ProjObject{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=[]; if isfield(UvData,'XmlData')&&~isempty(UvData.XmlData) XmlData=UvData.XmlData{1}; end if isfield(UvData,'TransformInput') XmlData.TransformInput=UvData.TransformInput; end UvData.Field.Action.RUN=0;% indicate that the transform fct is called only to get input param DataOut=feval(transform_handle,UvData.Field,XmlData);% execute the transform fct to get the required conditions if isfield(DataOut,'CoordUnit')% set the requested coord unit (info used to possibly delete the current projection objects) CoordUnit=DataOut.CoordUnit; end if isfield(DataOut,'InputFieldType')% to be used to impose a type of input file (eg. for image transform) UvData.InputFieldType=DataOut.InputFieldType; end if isfield(DataOut,'TransformInput')% used to add transform parameters at selection of the transform fct UvData.TransformInput=DataOut.TransformInput; end end end %% delete drawn objects if the output CooordUnit is different from the previous one if ~strcmp(CoordUnit,CoordUnitPrev) % for iobj=1:numel(UvData.ProjObject) % delete_object(iobj) % end set(handles.CheckFixLimits,'Value',0) hother=findobj('Tag','proj_object');%find all the proj objects for iobj=1:length(hother) delete(hother(iobj)) end hother=findobj('Tag','DeformPoint');%find all the proj objects for iobj=1:length(hother) delete(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 set(handles.ListObject,'Value',1) set(handles.ListObject,'String',{''}) set(handles.ListObject_1,'Value',1) set(handles.ListObject_1,'String',{''}) set(handles.CheckViewObject,'value',0) CheckViewObject_Callback(hObject, eventdata, handles) set(handles.CheckViewField,'value',0) CheckViewField_Callback(hObject, eventdata, handles) set(handles.CheckEditObject,'Value',0) CheckEditObject_Callback(hObject, eventdata, handles) UvData.ProjObject={[]}; end set(handles.uvmat,'UserData',UvData) set(handles.TransformName,'backgroundColor',[1 1 1])% indicate desactivation of the menu drawnow %% inputfilerefresh the current plot if isempty(list_path{ichoice}) || nargin(transform_handle)<3 set(handles.SubField,'Value',0) SubField_Callback(hObject, eventdata, handles) else REFRESH_Callback(hObject, eventdata, handles) end %------------------------------------------------ %CALLBACKS FOR PLOTTING PARAMETERS %------------------------------------------------- %%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Plot axes %%%%%%%%%%%%%%%%%%%%%%%%%%%%% %------------------------------------------------------------------------ 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% option 'contours' set(handles.interval_txt,'Visible','on') set(handles.num_IncrA,'Visible','on') set(handles.num_IncrA,'String','')% refresh contour interval % set(handles.opacity_txt,'Visible','off') % set(handles.num_Opacity,'Visible','off') else % option 'image' set(handles.interval_txt,'Visible','off') set(handles.num_IncrA,'Visible','off') % set(handles.opacity_txt,'Visible','on') % set(handles.num_Opacity,'Visible','on') 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) %------------------------------------------------------------------- if ~get(handles.CheckFixVectors,'Value') update_plot(handles); end %------------------------------------------------------------------------ % --- Executes on selection change in CheckDecimate4 (nb_vec/4). %------------------------------------------------------------------------ function CheckDecimate4_Callback(hObject, eventdata, handles) if isequal(get(handles.CheckDecimate4,'Value'),1) set(handles.CheckDecimate16,'Value',0) end update_plot(handles); %------------------------------------------------------------------------ % --- Executes on selection change in CheckDecimate16 (nb_vec/16). %------------------------------------------------------------------------ function CheckDecimate16_Callback(hObject, eventdata, handles) if isequal(get(handles.CheckDecimate16,'Value'),1) set(handles.CheckDecimate4,'Value',0) end 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 REFRESH_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) %------------------------------------------------------------------------ num_MaxVec_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,'Units','pixel'); pos_vert=get(handles.VecColBar,'Position'); set(handles.VecColBar,'Units','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) %------------------------------------------------------------------- set(handles.REFRESH,'BackgroundColor',[1 1 0]);% display plot activity by yellow color drawnow UvData=get(handles.uvmat,'UserData'); AxeData=[]; if isfield(UvData,'PlotAxes') AxeData=UvData.PlotAxes;% retrieve the current plotted data end PlotParam=read_GUI(handles.uvmat); [tild,PlotParamOut]= plot_field(AxeData,handles.PlotAxes,PlotParam); errormsg=fill_GUI(PlotParamOut,handles.uvmat); if isempty(errormsg) set(handles.REFRESH,'BackgroundColor',[1 0 0]);% operation finished, back to red color else msgbox_uvmat('ERROR',errormsg) set(handles.REFRESH,'BackgroundColor',[1 0 1]);% magenta color: graph still needs to be updated end %------------------------------------------------------------------------ %------------------------------------------------------------------------ % 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.ProjObject{get(handles.ListObject_1,'Value')}; %% update the projection plot on uvmat [ProjData,errormsg]= proj_field(UvData.Field,ObjectData);%project the current input field on object ObjectData if ~isempty(errormsg) msgbox_uvmat('ERROR',['projection on ' UvData.ProjObject{iobj}.Type ': ' errormsg ]) return end plot_field(ProjData,handles.PlotAxes,read_GUI(handles.uvmat));% plot the projected field; UvData.PlotAxes=ProjData;% store the plotted field for further update %replot all the objects within the new projected field for IndexObj=1:numel(list_str) hobject=UvData.ProjObject{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.ProjObject{IndexObj}.DisplayHandle.uvmat=plot_object(UvData.ProjObject{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.CheckViewObject,'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')}; hset_object=set_object(ObjectData,[],ZBounds); set(hset_object,'name','set_object') set(handles.CheckViewObject,'Value',1)% show that the selected object in ListObject_1 is currently visualised end % desactivate the edit object mode set(handles.CheckEditObject,'Value',0) % set(handles.CheckEditObject,'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 UvData=get(handles.uvmat,'UserData'); if numel(UvData.ProjObject)1 && ~isequal(IndexObj,IndexObj_1) % do not delete the object used for the uvmat plot delete_object(IndexObj) end %'DeleteObject': delete a projection object, defined by its index in the Uvmat list or by its graphic handle %------------------------------------------------------------------------ % function DeleteObject(hObject) % % INPUT: % hObject: object index (if integer) or handle of the graphic object. If % hObject is a subobject, the parent object is detected and deleted. function delete_object(IndexObj) huvmat=findobj('tag','uvmat');%handles of the uvmat interface UvData=get(huvmat,'UserData'); hlist_object=findobj(huvmat,'Tag','ListObject');%handles of the object list in the uvmat interface list_str=get(hlist_object,'String');%objet list if ~isempty(UvData) && isfield(UvData, 'ProjObject') && length(UvData.ProjObject)>=IndexObj if isfield(UvData.ProjObject{IndexObj},'DisplayHandle') && isfield(UvData.ProjObject{IndexObj}.DisplayHandle,'uvmat') hdisplay=UvData.ProjObject{IndexObj}.DisplayHandle.uvmat;%handle of the object graphic representation in uvmat for iview=1:length(hdisplay) if ishandle(hdisplay(iview)) && ~isequal(hdisplay(iview),0) ObjectData=get(hdisplay(iview),'UserData'); if isfield(ObjectData,'SubObject') && ~isempty(ObjectData.SubObject) delete(ObjectData.SubObject(ishandle(ObjectData.SubObject)));% delete the graphic 'sub-objects (e.g. projection bounds) end if isfield(ObjectData,'DeformPoint')&& ~isempty(ObjectData.DeformPoint) delete(ObjectData.DeformPoint(ishandle(ObjectData.DeformPoint)));% delete the graphic deformation points delete(hdisplay(iview))% delete the main graphic representation of the object end end ishandle(hdisplay(iview)) end for iobj=IndexObj+1:length(UvData.ProjObject) hdisplay=UvData.ProjObject{iobj}.DisplayHandle.uvmat; for iview=1:length(hdisplay) if ishandle(hdisplay(iview)) && ~isequal(hdisplay(iview),0) PlotData=get(hdisplay(iview),'UserData'); PlotData.IndexObj=iobj-1; set(hdisplay(iview),'UserData',PlotData); end end end end UvData.ProjObject(IndexObj)=[]; end if numel(list_str)>=IndexObj list_str(IndexObj)=[]; end set(huvmat,'UserData',UvData); set(hlist_object,'String',list_str) set(hlist_object,'Value',length(list_str)) hlist_object_1=findobj(huvmat,'Tag','ListObject_1');%handles of the first object list in the uvmat interface old_index=get(hlist_object_1,'Value'); set(hlist_object_1,'String',list_str) if IndexObj<=old_index set(hlist_object_1,'Value',old_index-1) end %TODO: use to modify fill_GUI %'write_plot_param': update the plotting parameters on the uvmat or view_field interface after a plotting operation function write_plot_param(handles,PlotParam) %% axes if isempty(PlotParam.Axes) set(handles.Axes,'Visible','off') set(handles.PlotAxes,'Visible','off') set(handles.text_display,'Visible','off') set(handles.TableDisplay,'Visible','on') else set(handles.Axes,'Visible','on') set(handles.PlotAxes,'Visible','on') set(handles.text_display,'Visible','on') % if isfield(handles,'TableDisplay') % set(handles.TableDisplay,'Visible','off') % end Coordinates=PlotParam.Axes; if isfield(Coordinates,'CheckFixAspectRatio') if Coordinates.CheckFixAspectRatio set(handles.CheckFixAspectRatio,'Value',1) else set(handles.CheckFixAspectRatio,'Value',0) end end if isfield(Coordinates,'AspectRatio') set(handles.num_AspectRatio,'String',num2str(Coordinates.AspectRatio)) end if isfield(Coordinates,'MinX') set(handles.num_MinX,'String',num2str(Coordinates.MinX,4)); set(handles.num_MaxX,'String',num2str(Coordinates.MaxX,4)); set(handles.num_MinY,'String',num2str(Coordinates.MinY,4)); set(handles.num_MaxY,'String',num2str(Coordinates.MaxY,4)); else set(handles.num_MinX,'String',''); set(handles.num_MaxX,'String',''); set(handles.num_MinY,'String',''); set(handles.num_MaxY,'String',''); end end %% scalar or image parameters if isfield(PlotParam,'Scalar') set(handles.Scalar,'Visible','on') if isfield(PlotParam.Scalar,'MaxA') set(handles.num_MaxA,'String',num2str(PlotParam.Scalar.MaxA,3)); end if isfield(PlotParam.Scalar,'MinA') set(handles.num_MinA,'String',num2str(PlotParam.Scalar.MinA,3)); end if isfield(PlotParam.Scalar,'IncrA') set(handles.num_IncrA,'String',num2str(PlotParam.Scalar.IncrA,3)) end set(handles.CheckBW,'Value',PlotParam.Scalar.CheckBW) if isfield(PlotParam.Scalar,'Opacity')&&isfield(handles,'num_Opacity') set(handles.num_Opacity,'String',num2str(PlotParam.Scalar.Opacity)) end else set(handles.Scalar,'Visible','off') end %% parameter for vector field if isfield(PlotParam,'Vectors') set(handles.Vectors,'Visible','on') if isfield(PlotParam.Vectors,'VecScale') set(handles.num_VecScale,'String',num2str(PlotParam.Vectors.VecScale,3)) end if isfield(PlotParam.Vectors,'MinC')&& isfield(PlotParam.Vectors,'MaxC') MinC=PlotParam.Vectors.MinC; MaxC=PlotParam.Vectors.MaxC; set(handles.num_MinVec,'String', num2str(MinC,3)); set(handles.num_MaxVec,'String',num2str(MaxC,3)); list=get(handles.ColorCode,'String'); ichoice=get(handles.ColorCode,'Value'); color_option=list{ichoice}; test3color=strcmp(color_option,'rgb')||strcmp(color_option,'bgr'); if test3color% need to update color thresholds set(handles.num_ColCode1,'Visible','on') set(handles.num_ColCode2,'Visible','on') set(handles.Slider1,'Visible','on') set(handles.Slider2,'Visible','on') set(handles.num_ColCode1,'String',num2str(PlotParam.Vectors.ColCode1,3)) set(handles.num_ColCode2,'String',num2str(PlotParam.Vectors.ColCode2,3)) set(handles.Slider1,'Value',(PlotParam.Vectors.ColCode1-MinC)/(MaxC-MinC)) set(handles.Slider2,'Value',(PlotParam.Vectors.ColCode2-MinC)/(MaxC-MinC)) else set(handles.num_ColCode1,'Visible','off') set(handles.num_ColCode2,'Visible','off') set(handles.Slider1,'Visible','off') set(handles.Slider2,'Visible','off') end end else set(handles.Vectors,'Visible','off') if isfield(handles,'edit_vect') set(handles.edit_vect,'Visible','off') set(handles.record,'Visible','off') end end % -------------------------------------------------------------------- % --- Executes on button press in CheckTable. % -------------------------------------------------------------------- function CheckTable_Callback(hObject, eventdata, handles) if get(handles.CheckTable,'Value') set(handles.TableDisplay,'Visible','on') else set(handles.TableDisplay,'Visible','off') end