Added source files

src/dic/Beginner4.m

@@ -0,0 +1,810 @@
+function varargout = Beginner4(varargin)
+% BEGINNER4 MATLAB code for Beginner4.fig
+%      BEGINNER4, by itself, creates a new BEGINNER4 or raises the existing
+%      singleton*.
+%
+%      H = BEGINNER4 returns the handle to a new BEGINNER4 or the handle to
+%      the existing singleton*.
+%
+%      BEGINNER4('CALLBACK',hObject,eventData,handles,...) calls the local
+%      function named CALLBACK in BEGINNER4.M with the given input arguments.
+%
+%      BEGINNER4('Property','Value',...) creates a new BEGINNER4 or raises
+%      the existing singleton*.  Starting from the left, property value pairs are
+%      applied to the GUI before Beginner4_OpeningFcn gets called.  An
+%      unrecognized property name or invalid value makes property application
+%      stop.  All inputs are passed to Beginner4_OpeningFcn via varargin.
+%
+%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
+%      instance to run (singleton)".
+%
+% See also: GUIDE, GUIDATA, GUIHANDLES
+
+% Edit the above text to modify the response to help Beginner4
+
+% Last Modified by GUIDE v2.5 23-May-2018 01:44:50
+
+% Begin initialization code - DO NOT EDIT
+gui_Singleton = 1;
+gui_State = struct('gui_Name',       mfilename, ...
+                   'gui_Singleton',  gui_Singleton, ...
+                   'gui_OpeningFcn', @Beginner4_OpeningFcn, ...
+                   'gui_OutputFcn',  @Beginner4_OutputFcn, ...
+                   'gui_LayoutFcn',  [] , ...
+                   'gui_Callback',   []);
+if nargin && ischar(varargin{1})
+    gui_State.gui_Callback = str2func(varargin{1});
+end
+
+if nargout
+    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
+else
+    gui_mainfcn(gui_State, varargin{:});
+end
+% End initialization code - DO NOT EDIT
+
+% --- Executes just before Beginner4 is made visible.
+function Beginner4_OpeningFcn(hObject, eventdata, handles, varargin)
+% This function has no output args, see OutputFcn.
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+% varargin   command line arguments to Beginner4 (see VARARGIN)
+
+% Choose default command line output for Beginner4
+handles.output = hObject;
+handles.Load_RADIO ='Images';  
+axes(handles.axes7);cla;imshow((imread('lines.png')),[]);
+axes(handles.axes8);cla;imshow(imread('Shan_Logo1.jpg'),[]);
+axes(handles.axes6);cla;imshow(imread('iisc_logo.png'),[]);
+
+seting_buttons_state(hObject, eventdata, handles,0)
+set(handles.push_start_DIC, 'Enable','off');
+set(handles.Status_check,'String','In pixels');
+% set(handles.txt_ref, 'String','Hi');
+
+handles.image_crop =0;
+
+% show_the_image1()
+% handles.aarea  = 'Default';
+% handles.filename_RADIO ='DEFORMED';
+
+handles.val_overlap= 0.5;
+handles.val_windowsize_x = 64;
+handles.val_windowsize_y = 64;
+handles.val_dicmethod = 'method_2';
+% handles.flg1= 0;
+handles.displayData = 'U';
+handles.scal =1;
+handles.val_scal=1;
+handles.Logfile =1;
+handles.select_resolution=0;
+
+axes(handles.axes3);cla;imshow(imread('p1.png') ,[]);
+set(handles.checkbox1_LogFile,'Value',1);
+seting_buttons_state(hObject, eventdata, handles,0)
+        
+% set(handles.TEXT2,'String','In pixels');
+% set(handles.Status_check,'String','In pixels');
+
+
+
+
+% Update handles structurelogfile
+guidata(hObject, handles);
+
+
+% UIWAIT makes Beginner4 wait for user response (see UIRESUME)
+% uiwait(handles.figure1);
+
+
+% --- Outputs from this function are returned to the command line.
+function varargout = Beginner4_OutputFcn(hObject, eventdata, handles)
+% varargout  cell array for returning output args (see VARARGOUT);
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Get default command line output from handles structure
+varargout{1} = handles.output;
+
+
+% --- Executes on button press in LogFile_check.
+function LogFile_check_Callback(hObject, eventdata, handles)
+% hObject    handle to LogFile_check (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hint: get(hObject,'Value') returns toggle state of LogFile_check
+
+
+% --- Executes on button press in push_load_reference.
+function push_load_reference_Callback(hObject, eventdata, handles)
+% hObject    handle to push_load_reference (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+
+% --- Executes on button press in push_load_deformed.
+function push_load_deformed_Callback(hObject, eventdata, handles)
+% hObject    handle to push_load_deformed (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+
+% --- Executes on button press in push_startDIC.
+function push_startDIC_Callback(hObject, eventdata, handles)
+% hObject    handle to push_startDIC (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+
+% --- Executes on button press in pushbutton5.
+function pushbutton5_Callback(hObject, eventdata, handles)
+% hObject    handle to pushbutton5 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+
+% --- Executes on button press in checkbox1_LogFile.
+function checkbox1_LogFile_Callback(hObject, eventdata, handles)
+% hObject    handle to checkbox1_LogFile (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hint: get(hObject,'Value') returns toggle state of checkbox1_LogFile
+handles.Logfile= get(hObject,'Value');
+guidata(hObject, handles)
+
+
+
+% --- Executes on button press in push_start_DIC.
+function push_start_DIC_Callback(hObject, eventdata, handles)
+% hObject    handle to push_start_DIC (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+Files = dir(handles.path);
+% tmp=length(Files)
+[~,Ref_name,EXT] = fileparts(handles.val_filename_1);
+tmpp=0;
+
+
+   if iscell(handles.def_name)==1 
+        tmpp = numel(handles.def_name);
+        FFiles=handles.def_name;
+    else
+        tmpp = 1;
+        FFiles={handles.def_name};
+    end
+    frame_no=tmpp;
+
+    
+  
+    
+    try
+    [user_response, destination ] = gui_confirm_DICstart2(tmpp,handles.path);
+    catch
+        user_response='NO';
+    end
+
+        
+switch lower(user_response)
+case 'no'
+	% take no action
+case 'yes'
+seting_buttons_state11(hObject, eventdata, handles,0)
+pause(0.1)
+%   s1= handles.val_filename_1;
+%   s=strfind(s1,'.');s1(s(end)+1:length(s1)-1);
+%   
+    imr11 = imread(handles.val_filename_1); 
+    IM1 = imr11;
+    imr1=preset_image(imr11);
+    flies = {};
+    M=[];
+
+    
+hhhh = waitbar(0,'Please wait...');
+
+    
+  DATA=[];  
+    kkk=0;
+   for k =1:tmpp
+    
+      waitbar(k/length(Files),hhhh);
+    
+        FileNames = FFiles{k};
+        file = strcat(handles.path, FFiles{k});
+        DefaultORcrop='Full Frame';
+        if strcmp(file, handles.val_filename_1)==0
+        
+             
+             imr22 = imread(file);            
+             imr2=preset_image(imr22);
+             DefaultORcrop='Full Frame';
+
+             if handles.image_crop ==1
+                 DefaultORcrop='Crop';
+                 yD= handles.Cordinates;
+                 im1 = imr1( yD(2):yD(2)+yD(4),yD(1):yD(1)+yD(3),:);
+                 im2 = imr2( yD(2):yD(2)+yD(4),yD(1):yD(1)+yD(3),:);
+                 IM = IM1( yD(2):yD(2)+yD(4),yD(1):yD(1)+yD(3),:);
+                 
+             else handles.image_crop ==0;
+                 im1 = imr1;
+                 im2 = imr2;
+                 IM = IM1;
+             end
+
+        windowsize_x = handles.val_windowsize_x; 
+        windowsize_y= handles.val_windowsize_y;
+        overlap= handles.val_overlap;  
+        iu_max =32;
+        iv_max =32;
+        dt = 1;
+        dic_type = handles.val_dicmethod;
+        i_recur = 1;
+        i_plot=0;
+
+        
+        
+       [MM, AA]=DIC_Data_check_Beginner3(im1, im2, windowsize_x, windowsize_y, overlap, iu_max, iv_max,...
+           handles.scal,FileNames, IM,destination, handles.val_dicmethod,handles.select_resolution, handles.Cordinates, IM1);
+       
+       
+%     figure,imshow(im2,[]), title(strcat('Vector Field:-:', FileNames))
+        else
+            
+            MM = [0 0 0 0 0 0 0 0];
+            dic_type = 'Not-Procssed, Same Image';
+            windowsize_x = 0;
+            overlap=0;
+        end
+        
+       flies{k} = FileNames;
+    
+       M=[M;MM];
+       AA.name=FileNames;
+       DATA{k}=AA;
+      
+   end
+   
+% %    save strcat(destination, 'DATA') DATA;
+   
+   
+    des=strcat(destination,'\DATA');
+    save(des,'DATA')
+
+   
+   if (handles.Logfile==1), myLogfile(destination, 'Image',frame_no,DefaultORcrop, Ref_name, dic_type, ...
+        windowsize_x,overlap); end
+
+        M = round(M*1000)/1000;
+seting_buttons_state11(hObject, eventdata, handles,1)
+try   
+close(hhhh)
+catch
+end
+
+Mean_U = M(:,1);
+Mean_V = M(:,2);
+MIN_U = M(:,3);
+MAX_U = M(:,4);
+MIN_V = M(:,5);
+MAX_V = M(:,6);
+StdDev_U = M(:,7);
+StdDev_V = M(:,8);
+
+
+% Tabb11 = table(flies', Mean_U, Mean_V, StdDev_U, StdDev_V );
+Tabb11 = table(flies', Mean_U, Mean_V, MIN_U, MAX_U,  MIN_V, MAX_V,StdDev_U, StdDev_V );
+writetable(Tabb11,strcat(destination, '\result11_summary' ))
+
+end
+guidata(hObject, handles)
+
+
+
+
+
+
+% --- Executes on button press in pushbutton9.
+function pushbutton9_Callback(hObject, eventdata, handles)
+% hObject    handle to pushbutton9 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+open('Help_DIC_BJ2.pdf');
+
+
+% --- Executes on button press in push_reference.
+function push_reference_Callback(hObject, eventdata, handles)
+% hObject    handle to push_reference (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+Sw= handles.Load_RADIO;
+
+
+
+switch Sw
+    
+  case {'Images'}
+      
+        files= uigetfile_with_preview2();
+        
+        if ~strcmp(files,'') 
+            
+         seting_buttons(hObject, eventdata, handles);
+         seting_buttons_state(hObject, eventdata, handles,0)            
+         set(handles.push_deformed, 'Enable','on');
+            
+            
+            
+        
+% % %         seting_buttons_state(hObject, eventdata, handles,1)            
+        s=files; s=s(1:max(find(s=='\'))); pathname=s;
+        s=files; s=s(max(find(s=='\'))+1:end); filename=s;
+        handles.val_filename_1 = strcat(pathname, filename);
+        
+        
+        set(handles.txt_ref, 'String','filename');
+        guidata(hObject, handles);
+%        set(handles.push_reference,'String',filename);
+         set(handles.txt_ref, 'String', filename );
+
+        tmp = imread(handles.val_filename_1);
+       
+        handles.val_file_1 = (tmp);
+        [~,~,EXT] = fileparts(handles.val_filename_1);
+        handles.EXT=EXT;
+        handles.path= pathname;
+        handles.Cordinates = [1 1 size(handles.val_file_1,2) size(handles.val_file_1,1)];
+        
+        handles.Scal=1;  
+        set(handles.Status_check ,'String',' ');
+        handles.image_crop =0;
+        guidata(hObject, handles);
+        
+        
+        files= dir(pathname);
+        
+        
+        axes(handles.axes3);cla;imshow(handles.val_file_1 ,[]);
+        
+        set(handles.number_image,'String','');
+        end
+        
+%     end
+    
+
+    
+  case {'Video'}
+      
+        
+
+  otherwise
+    disp('Unknown method')
+    
+end
+ set(handles.push_start_DIC, 'Enable','off');
+
+
+
+
+
+
+
+
+
+% --- Executes on button press in push_deformed.
+function push_deformed_Callback(hObject, eventdata, handles)
+% hObject    handle to push_deformed (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% % % Files = dir(handles.path);
+% tmp=length(Files)
+try 
+[~,Ref_name,EXT] = fileparts(handles.val_filename_1);
+catch
+    EXT = 0;
+end
+% % % % % % % % % % % % % tmp=0;
+    
+    
+      [filename_def, pathname_def, filterindex_def] = uigetfile( ...
+       {strcat('*', EXT), strcat(EXT,'-files') },  ...
+         'MultiSelect', 'on', 'Selet the DEFORMED images', handles.path);
+     
+handles.def_name= filename_def;
+handles.def_path= pathname_def;
+handles.correctSelect= filterindex_def;
+% % set(handles.push_deformed,'String',filename_def(end));
+im1=imread(handles.val_filename_1);
+
+if filterindex_def==1
+    seting_buttons_state(hObject, eventdata, handles,1)
+    if iscell(filename_def)==1 
+        tmp = strcat(num2str(numel(filename_def)), 'files selected');
+%         set(handles.push_deformed,'String',filename_def{end});
+        im2 = imread(strcat(pathname_def, filename_def{end}));            
+        axes(handles.axes3);cla;imshow(imread(strcat(pathname_def,filename_def{end})) ,[]);
+        set(handles.push_start_DIC, 'Enable','on');
+    else
+        tmp = strcat('1', 'files selected');
+%         set(handles.push_deformed,'String',filename_def);
+        im2 = imread(strcat(pathname_def, filename_def));            
+        axes(handles.axes3);cla;imshow(imread(strcat(pathname_def,filename_def)) ,[]);
+        set(handles.push_start_DIC, 'Enable','on');
+    end
+  set(handles.number_image,'String',tmp);
+  
+    if ~(isequal(size(im1),size(im2)))
+        gui_DIC_sizeCheck1('Title','ERROR');
+        tmp = strcat('0', 'files selected');
+        set(handles.number_image,'String',tmp);
+        set(handles.push_start_DIC, 'Enable','off');
+        seting_buttons_state(hObject, eventdata, handles,0);
+        set(handles.push_deformed, 'Enable','on');
+    end
+  
+  
+  
+  
+else
+    tmp = strcat('0', 'files selected');
+    set(handles.number_image,'String',tmp);
+    set(handles.push_start_DIC, 'Enable','off');
+
+end
+
+
+seting_buttons(hObject, eventdata, handles);
+
+
+guidata(hObject, handles);
+
+
+% --- Executes when selected object is changed in uibuttongroup5.
+function uibuttongroup5_SelectionChangedFcn(hObject, eventdata, handles)
+% hObject    handle to the selected object in uibuttongroup5 
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+c= get(hObject,'String');
+%%%%%%%%%%%seting_buttons_state(hObject, eventdata, handles,0);
+% set(handles.push_reference,'String','Reference');
+% set(handles.push_deformed,'String','Deformed');
+
+seting_buttons_state(hObject, eventdata, handles,0);
+
+ switch c
+  
+  case {'Images'}
+    handles.Load_RADIO ='Images';  
+%     guidata(hObject, handles);
+   
+  case 'Video'
+    handles.Load_RADIO ='Video';
+    
+    EXT='avi';
+    [filename_def, pathname_def, filterindex_def] = uigetfile( ...
+           {strcat('*', EXT), strcat(EXT,'-files') });
+
+       
+    if filterindex_def==1
+    %   seting_buttons_state(hObject, eventdata, handles,1)
+    %   set(handles.number_image,'String',tmp);
+    
+     mkdir(pathname_def,'images101');
+
+    vdo= VideoReader(strcat(pathname_def, '\' ,filename_def));
+    ii = 1;
+
+    while hasFrame(vdo)
+       img = readFrame(vdo);
+       filename = [sprintf('%03d',ii) '.jpg'];
+       fullname = fullfile(pathname_def, 'images101',filename);
+       imwrite(img,fullname)    % Write out to a JPEG file (img1.jpg, img2.jpg, etc.)
+       ii = ii+1;
+    end
+        
+        handles.path= pathname_def;
+        
+        handles.Load_RADIO ='Images';  
+        guidata(hObject, handles)
+    
+    else
+        handles.Load_RADIO ='Images';
+        seting_buttons_state(hObject, eventdata, handles,0)
+        set(handles.radiobutton14, 'Value',0);
+        set(handles.radiobutton13, 'Value',1);
+        
+        guidata(hObject, handles)
+%         tmp = strcat('0', 'files selected');
+%         set(handles.number_image,'String',tmp);
+%         set(handles.push_start_DIC, 'Enable','off');
+
+    end   
+      
+    
+%     guidata(hObject, handles);
+otherwise
+    disp('Unknown method')
+
+  
+ end
+ 
+ seting_buttons(hObject, eventdata, handles);
+ 
+ guidata(hObject, handles);
+  
+ 
+ 
+   function seting_buttons(hObject, eventdata, handles)
+ 
+        button_list1 =[ handles.radio_scal_full   handles.radio_Scal_inpixel ];
+        button_list2 =[ handles.radio_scal_crop  handles.radio_Scal_inmicron];
+        set(button_list1, 'Value',1);
+        set(button_list2, 'Value',0);
+        guidata(hObject, handles);
+ 
+        
+     function seting_buttons_state11(hObject, eventdata, handles,flg)
+ 
+        button_list1 =[ handles.radio_scal_full   handles.radio_Scal_inpixel handles.push_start_DIC];
+        button_list2 =[ handles.radio_scal_crop  handles.radio_Scal_inmicron handles.push_deformed];
+        button_list3 =[handles.push_reference];
+       
+        if flg==0
+        set(button_list1, 'Enable','off');
+        set(button_list2, 'Enable','off');
+        set(button_list3, 'Enable','off');end
+        if flg==1
+        set(button_list1, 'Enable','on');
+        set(button_list2, 'Enable','on'); 
+        set(button_list3, 'Enable','on'); end
+    
+    
+        guidata(hObject, handles);
+ 
+
+
+        
+
+     function seting_buttons_state(hObject, eventdata, handles,flg)
+ 
+        button_list1 =[ handles.radio_scal_full   handles.radio_Scal_inpixel handles.push_start_DIC];
+        button_list2 =[ handles.radio_scal_crop  handles.radio_Scal_inmicron handles.push_deformed];
+        
+       
+        if flg==0
+        set(button_list1, 'Enable','off');
+        set(button_list2, 'Enable','off'); end
+        if flg==1
+        set(button_list1, 'Enable','on');
+        set(button_list2, 'Enable','on'); end
+    
+    
+        guidata(hObject, handles);
+ 
+        
+        
+
+% --- Executes on button press in radio_scal_full.
+function radio_scal_full_Callback(hObject, eventdata, handles)
+% hObject    handle to radio_scal_full (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hint: get(hObject,'Value') returns toggle state of radio_scal_full
+
+
+% --- Executes on button press in radio_Scal_inmicron.
+function radio_Scal_inmicron_Callback(hObject, eventdata, handles)
+% hObject    handle to radio_Scal_inmicron (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hint: get(hObject,'Value') returns toggle state of radio_Scal_inmicron
+
+
+% --- Executes during object creation, after setting all properties.
+function number_image_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to number_image (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+
+% --- Executes when selected object is changed in uibuttongroup6.
+function uibuttongroup6_SelectionChangedFcn(hObject, eventdata, handles)
+% hObject    handle to the selected object in uibuttongroup6 
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+handles.aarea= get(hObject,'String');
+% ea= get(hObject,'value')
+
+
+  switch handles.aarea
+  
+   case {'Crop'}
+%        handles.val_filename_Crop = imread(handles.val_filename_2);
+%        imtool(handles.val_filename_Crop )
+        handles.image_crop =1;   
+%         handles.val_filename_Crop = handles.val_file_1 ; handles.val_filename_1
+        handles.val_filename_Crop = imread(handles.val_filename_1);
+        
+      
+        [~, yD1 ]= gui_Image_Crop_1(handles.val_filename_Crop);
+        
+        if ~isempty(yD1)
+            
+            if numel(size(handles.val_filename_Crop))==2
+                s = size(handles.val_filename_Crop); s(3)=1;
+            elseif numel(size(handles.val_filename_Crop))==3
+                s = size(handles.val_filename_Crop); 
+            end
+        
+            yD = cordinate_filter_mex(yD1, s);
+            
+        else yD=[];
+        end
+        
+      
+        if ~isempty(yD)
+            yD= round(yD);
+            handles.Cordinates=yD;
+            handles.val_filename_Crop = ...
+            handles.val_filename_Crop( yD(2):yD(2)+yD(4),yD(1):yD(1)+yD(3),:);
+
+            axes(handles.axes3);cla;imshow(handles.val_filename_Crop)
+            handles.file_1 = handles.val_file_1;
+            guidata(hObject, handles);
+        else
+            seting_buttons(hObject, eventdata, handles);
+            handles.image_crop =0;
+            guidata(hObject, handles);
+        end
+        
+        
+   case {'Full Frame'}
+       handles.image_crop =0;
+       handles.val_file_1 = imread(handles.val_filename_1);
+       axes(handles.axes3);cla;imshow(handles.val_file_1 )
+       handles.file_1 = handles.val_file_1;
+       handles.Cordinates = [1 1 size(handles.val_file_1,2) size(handles.val_file_1,1)];
+       
+       guidata(hObject, handles);
+  end
+
+
+% --- Executes when selected object is changed in uibuttongroup7.
+function uibuttongroup7_SelectionChangedFcn(hObject, eventdata, handles)
+% hObject    handle to the selected object in uibuttongroup7 
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+cc= get(hObject,'String');
+
+ switch cc
+  
+  case {'In pixels'}
+    handles.Scal=1;  
+%     guidata(hObject, handles);
+    tmp3= 'In Pixels';
+    handles.select_resolution=0;
+    guidata(hObject, handles);
+%     set(handles.TEXT2,'String',tmp3);
+    set(handles.Status_check,'String',tmp3);
+   
+  case 'In micron'
+      
+      try 
+          
+%           BIKI=gui_set_resolution_3(handles.path,handles.EXT);
+          BIKI=gui_set_resolution_3(1,handles.path,handles.EXT);
+      catch 
+          BIKI='aadata';
+      end
+    if ~ strcmp(BIKI,'aadata')
+      BJ = BIKI;
+      if isstr(BIKI), BIKI=str2num(BIKI); end
+      if ~isstr(BJ), BJ=num2str(BJ); end
+      
+      
+    
+    
+    tmp3= strcat('1 pixel= ',BJ,' micron');
+%     set(handles.TEXT2,'String',tmp3);
+    set(handles.Status_check ,'String',tmp3);
+    handles.scal=BIKI;
+    handles.select_resolution=1;
+    else
+%         set(handles.Status_check ,'String','NOT Selected', 'DefaultTextColor','green');
+      set(handles.radio_Scal_inmicron, 'Value',0);
+      set(handles.radio_Scal_inpixel, 'Value',1);
+      set(handles.Status_check ,'String','In Pixel', 'DefaultTextColor','green');
+      handles.scal=1;
+      handles.select_resolution=0;
+      
+    end
+
+%     handles.scal=str2num(BIKI)
+    
+    
+    guidata(hObject, handles);
+
+
+ 
+
+otherwise
+    disp('Unknown method.')
+
+  
+ end
+  
+guidata(hObject, handles)
+
+
+% --- Executes during object creation, after setting all properties.
+function Status_check_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to Status_check (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+
+% --- Executes on button press in radiobutton14.
+function radiobutton14_Callback(hObject, eventdata, handles)
+% hObject    handle to radiobutton14 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hint: get(hObject,'Value') returns toggle state of radiobutton14
+
+
+% --- Executes on button press in radiobutton13.
+function radiobutton13_Callback(hObject, eventdata, handles)
+% hObject    handle to radiobutton13 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hint: get(hObject,'Value') returns toggle state of radiobutton13
+
+
+% --- Executes during object creation, after setting all properties.
+function txt_ref_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to txt_ref (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+
+% --- Executes during object creation, after setting all properties.
+function text21_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to text21 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+
+% --- Executes during object creation, after setting all properties.
+function axes6_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to axes6 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: place code in OpeningFcn to populate axes6
+
+
+% --- Executes during object creation, after setting all properties.
+function axes7_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to axes7 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: place code in OpeningFcn to populate axes7
+
+
+% --- Executes during object creation, after setting all properties.
+function axes8_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to axes8 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: place code in OpeningFcn to populate axes8

src/dic/DIC_Data_check_Beginner3.m

@@ -0,0 +1,150 @@
+function [M, A]=DIC_Data_check_Beginner3(im1, im2, windowsize_x, windowsize_y, overlap, iu_max, iv_max, inum1, FileNames,IM,Hpath, method, pix_mic, cordinates,IM1)
+
+flg1= 0;
+i_recur = 0;
+
+if pix_mic==0 
+    inum =inum1;
+else
+    inum =inum1*1e-6;
+end
+
+
+if (any( size(im1)~=size(im2)) )
+    gui_DIC_sizeCheck1('Title','ERROR');
+    flg1=1;
+end
+
+
+if overlap > 0.9 
+    gui_DIC_overlapCheck('Title','ERROR');
+    flg1=1;
+end
+ 
+if (flg1==0)
+   
+    switch  method
+        
+        case 'method_1'
+    
+           [xi,yi,iu,iv,da]=DIC_mqd5s( im1', im2', windowsize_x, windowsize_y, ...
+			       overlap, overlap, iu_max, iv_max, i_recur);                                
+                        
+           [iu_ft, iv_ft, iu_ip, iv_ip] = DIC_filter2(iu, iv, 2, 1.5, 2, 0 );
+           [iu_s, iv_s] = DIC_smooth(iu_ip, iv_ip, 2);
+           
+           iu_s(isnan(iu_s))=0; iv_s(isnan(iv_s))=0;
+           iu_s = iu_s*inum; iv_s = iv_s*inum; % xi = xi*inum; yi = yi*inum;
+           [x11 y11]= meshgrid(min(xi):max(xi),min(yi):max(yi));
+           [a, b]=meshgrid(yi,xi);
+           F = TriScatteredInterp(b(:),a(:),iu_s(:),'natural');
+           U_inp = F(x11,y11);
+           F = TriScatteredInterp(b(:),a(:),iv_s(:),'natural');
+           V_inp = F(x11,y11);
+           
+           M =[mean(iu_s(:)) mean(iv_s(:)) ...
+               min(iu_s(:)) max(iu_s(:))  min(iv_s(:)) max(iv_s(:))...
+               std2(iu_s)  std2(iv_s)];
+           
+           A.iu_s =iu_s;
+           A.iv_s =iv_s;
+           A.U_inp =U_inp;
+           A.V_inp =V_inp;
+           A.xi = xi;
+           A.yi = yi;
+           
+           
+           
+           
+       case 'method_2'
+  
+  
+           iu_max=windowsize_x; iv_max=windowsize_y;
+           [xi,yi,iu,iv]=DIC_cor5( im1', im2', windowsize_x, windowsize_y, ...
+			       overlap, overlap, iu_max, iv_max, i_recur);   
+            iu(1,:)=nan; iu(end,:)=nan;iu(:,1)=nan; iu(:,end)=nan;
+            iv(1,:)=nan; iv(end,:)=nan;iv(:,1)=nan; iv(:,end)=nan;
+                        
+           [iu_ft, iv_ft, iu_ip, iv_ip] = DIC_filter2(iu, iv, 2, 2.0, 2, 0 );
+           [iu_s, iv_s] = DIC_smooth(iu_ip, iv_ip, 2);
+           iv_s=-iv_s;
+           iu_s(isnan(iu_s))=0; iv_s(isnan(iv_s))=0;
+           iu_s = iu_s*inum; iv_s = iv_s*inum; % xi = xi*inum; yi = yi*inum;
+           [x11 y11]= meshgrid(min(xi):max(xi),min(yi):max(yi));
+           [a, b]=meshgrid(yi,xi);
+
+           F = TriScatteredInterp(b(:),a(:),iu_s(:),'natural');
+           U_inp = F(x11,y11);
+           F = TriScatteredInterp(b(:),a(:),iv_s(:),'natural');
+           V_inp = F(x11,y11);
+           
+%             M =[mean(iu_s(:)) mean(iv_s(:)) std2(iu_s)  std2(iv_s)];
+
+            M =[mean(iu_s(:)) mean(iv_s(:)) ...
+               min(iu_s(:)) max(iu_s(:))  min(iv_s(:)) max(iv_s(:))...
+               std2(iu_s)  std2(iv_s)];
+
+           A.iu_s =iu_s;
+           A.iv_s =iv_s;
+           A.U_inp =U_inp;
+           A.V_inp =V_inp;
+           A.xi = xi;
+           A.yi = yi;
+           
+
+      
+    end    
+           
+           [xx, yy]= meshgrid(xi,yi);
+           fig122=figure; set(fig122, 'Visible', 'off');
+           imshow(IM*0.5),colormap(gray),hold on, 
+           quiver (xx,yy, iu_s',-iv_s','g'), axis equal;
+           T=strcat('Vector Field--', FileNames);
+           title(T);
+           TT= strcat(Hpath,'\',T);
+           saveas(gcf, TT);
+           close(fig122)
+
+           if pix_mic==0, titl='[Pixel]';
+           else titl='[m]';
+           end
+     
+%%%           if ~max((U_inp(:)))==0; ttm=max(abs(U_inp(:)));else ttm=1e-4; end
+           ttm= max(U_inp(:));
+           fig126=figure; set(fig126, 'Visible', 'off');
+           imagesc(U_inp,[min(U_inp(:)), ttm]), 
+           colormap(jet), hcb=colorbar;title(hcb,titl),
+           axis image %Tt=strcat('U--', FileNames); title(Tt);
+           Tt=strcat('Displacement along X, File-', FileNames); title(Tt); xlabel('X-direction (pixels)'), ylabel('Y-direction (pixels)')
+           saveas(gcf, strcat(Hpath,'\',Tt))
+           close(fig126)
+
+
+           image_background2(IM1 , xi,yi,U_inp,cordinates,titl, Tt,Hpath);    
+
+
+%%%           if ~max(V_inp(:))==0; ttm=max(abs(V_inp(:)));else ttm=1e-4; end
+           ttm=max(V_inp(:));
+           fig125=figure; set(fig125, 'Visible', 'off');
+           imagesc(V_inp,[min(V_inp(:)), ttm]);
+           colormap(jet), hcb=colorbar;title(hcb,titl);
+           axis image %Tt=strcat('U--', FileNames); title(Tt);
+           Tt=strcat('Displacement along Y, File-', FileNames); title(Tt); xlabel('X-direction (pixels)'), ylabel('Y-direction (pixels)')
+           saveas(gcf, strcat(Hpath,'\',Tt))
+           close(fig125)
+
+
+
+           image_background2(IM1 , xi,yi,V_inp,cordinates,titl, Tt, Hpath);    
+           
+           Tt=strcat('Displacement Magnitude, File-', FileNames);
+           image_background2(IM1 , xi,yi,sqrt(U_inp.^2+V_inp.^2),cordinates,titl, Tt, Hpath);    
+
+           
+
+          
+    
+end
+
+
+

src/dic/DIC_Linear_Interp_vector3.m

@@ -0,0 +1,81 @@
+
+function[ u_inp1 ] = DIC_Linear_Interp_vector3( ui )
+%========================================================================
+
+tmp=ui;
+[row,col]=find(isnan(ui(2:end-1,2:end-1))); row=row+1; col=col+1;
+try
+for ii=1:numel(col)
+    ro=row(ii);cl=col(ii);
+%     tmp(ro,cl)= (ui(ro-1,cl)+ui(ro+1,cl)+ui(ro,cl-1)+ui(ro,cl+1))/4;
+    tmp11=[ui(ro-1,cl) ui(ro+1,cl) ui(ro,cl-1) ui(ro,cl+1)];
+    chk_nan= ~isnan(tmp11);
+    tmp11(isnan(tmp11))=0;
+    tmp(ro,cl)= sum(tmp11.*chk_nan)/ sum(chk_nan(:));
+    
+end
+catch
+end
+
+
+
+
+[row,col]=find(isnan(ui(2:end-1,1))); row=row+1;
+try
+for ii=1:numel(col)
+    ro=row(ii);cl=col(ii);
+    if ~isnan(ui(ro,2))
+        tmp(ro,1)= ui(ro,2);
+    else tmp(ro,1)= tmp(ro,2);
+    end
+end
+catch
+end
+
+
+[row,col]=find(isnan(ui(2:end-1,end))); row=row+1;
+try
+for ii=1:numel(col)
+    ro=row(ii);cl=col(ii);
+    if ~isnan(ui(ro,end-1))
+    tmp(ro,end)= ui(ro,end-1);
+    else
+        tmp(ro,end)= tmp(ro,end-1);
+    end
+end
+catch
+end
+
+[row,col]=find(isnan(ui(end,2:end-1))); col=col+1;
+try
+for ii=1:numel(row)
+    cl=col(ii);
+    if ~isnan(ui(end-1,cl))
+        tmp(end,cl)= ui(end-1,cl);
+    else
+        tmp(end,cl)= tmp(end-1,cl);
+    end
+end
+catch
+end
+
+[row,col]=find(isnan(ui(1,2:end-1))); col=col+1;
+try
+for ii=1:numel(row)
+    ro=row(ii);cl=col(ii);
+    if ~isnan(ui(2,cl))
+        tmp(1,cl)= ui(2,cl);
+    else
+        tmp(1,cl)= tmp(2,cl);
+    end
+        
+end
+catch
+end
+
+if isnan(ui(1,1)), tmp(1,1)=tmp(2,2);end
+if isnan(ui(end,end)), tmp(end,end)=tmp(end-1,end-1);end
+if isnan(ui(1,end)), tmp(1,end)=tmp(2,end-1);end
+if isnan(ui(end,1)), tmp(end,1)=tmp(end-1,2);end
+
+u_inp1=tmp;

src/dic/DIC_check_vector.m

@@ -0,0 +1,25 @@
+function[ iu_f, iv_f, i_cond ] = DIC_check_vector( iu, iv, vec_std, i_filter )
+%========================================================================
+%%========================================================================
+
+mx = size(iu,1);
+my = size(iu,2);
+
+
+if i_filter == 2
+
+[ iu_f, i_cond ] = DIC_vector_filter_median2( iu, vec_std );
+[ iv_f, i_cond ] = DIC_vector_filter_median2( iv, vec_std );
+
+
+iu_f = iu_f - iv_f*0;
+iv_f = iv_f - iu_f*0;
+
+else
+    iu_f=iu;
+    iv_f=iv;
+    
+end
+
+
+

src/dic/DIC_cor5.m

@@ -0,0 +1,90 @@
+function [xi, yi, iu, iv] = DIC_cor5( im1, im2, ...
+			     nx_pixel, ny_pixel, ...
+			     overlap_x, overlap_y, ...
+			     iu_max, iv_max, ...
+			     i_mode )
+%========================================================================
+%======================================================================
+
+
+% set area of search
+p_search = 1/3; 			% percentage of subwindow
+
+nx = size(im1,1);
+ny = size(im1,2);
+
+pixel_twx = ceil(p_search*nx_pixel);
+pixel_twy = ceil(p_search*ny_pixel);
+
+%   (dx_center and dy_center)
+[ xi, yi, nx_start, ny_start, nx_overlap, ny_overlap, dx_center, dy_center ] ...
+    = diccwindowsize32( 'mqd', ...
+			  nx, ny, nx_pixel, ny_pixel, overlap_x, overlap_y );
+
+% total number of vectors
+mx = max(size(xi));
+my = max(size(yi));
+
+if rem(ny_pixel,2)==0, tem=ny_pixel;
+else tem=ceil((ny_pixel+ny_pixel-1)/2); end
+
+for iy = 1: my
+
+  c_proc = strcat( 'process accomplished :  ', ...
+		   num2str( 100*(iy-1)/(my-1),' %03.0f' ), '/100' );
+  disp( c_proc )
+
+  for ix = 1: mx
+
+    ix1 = xi(ix) - dx_center;
+    ix2 = ix1 + nx_pixel - 1;
+    iy1 = yi(iy) - dy_center;
+    iy2 = iy1 + ny_pixel - 1;
+
+    wn=nx_pixel/4;
+    ix11 = xi(ix) - dx_center -wn; if(ix11<1), ix11=1; end
+    ix22 = ix1 + nx_pixel - 1+ wn; if(ix22>size(im2,1)), ix22=size(im2,1); end
+    
+    iy11 = yi(iy) - dy_center -wn; if(iy11<1), iy11=1; end
+    iy22 = iy1 + ny_pixel - 1 + wn; if(iy22>size(im2,2)), iy22=size(im2,2);end
+    
+    f1 = im1( ix1:ix2, iy1:iy2 );
+    f2 = im2( ix11:ix22, iy11:iy22 );
+    
+    C3=dic_xcor_m_mex(f1, f2);
+    [ ip_x3, ip_y3, MMR] = findpeak32_mex( C3, 1);
+    
+    SNR  = 3.00;
+    PPR = 1.10;
+       
+    tx = round(size(C3,1)/2);
+    ix_peak =  -( ip_y3-tx);
+    iy_peak = ( ip_x3-tx);
+
+%
+% --- eliminate odd displacement
+%
+
+   if (iu_max == 0) & (iv_max == 0)
+      u_max_dipl = p_search*nx_pixel;
+      v_max_dipl = p_search*ny_pixel;
+   else
+      u_max_dipl = iu_max;
+      v_max_dipl = iv_max;
+   end
+
+   if ( abs(ix_peak) > u_max_dipl ) | ( abs(iy_peak) > v_max_dipl )
+     ix_peak = NaN;
+     iy_peak = NaN;
+   end
+
+    is_x(ix,iy) = ix_peak;
+    is_y(ix,iy) = iy_peak;
+
+   end
+end 
+  iu = -is_x;
+  iv = is_y;
+
+
+

src/dic/DIC_filter2.m

@@ -0,0 +1,28 @@
+function [iu_ft,iv_ft,iu_ip,iv_ip]=DIC_filter2( iu,iv, ...
+						i_filter, vec_std,...
+						i_interp, i_plot)
+%========================================================================
+%%========================================================================
+%
+% Local fitering to smooth 
+%
+
+if i_filter ~= 0
+
+  [ iu_ft, iv_ft, i_cond ] = DIC_check_vector( iu, iv, vec_std, i_filter );
+
+end
+
+
+if i_interp ~= 0 
+
+  [ iu_ip ] = DIC_interp_vector( iu_ft, i_interp );
+  [ iv_ip ] = DIC_interp_vector( iv_ft, i_interp );
+
+else
+    
+  iu_ip = iu_ft;
+  iv_ip = iv_ft;
+
+end
+

src/dic/DIC_interp_vector.m

@@ -0,0 +1,11 @@
+function[ uo ] = DIC_interp_vector( ui, ii )
+%========================================================================
+
+uo = ui;
+
+% interpolation
+
+[ uo ] = DIC_spline_Interp_vector2( ui );
+
+
+

src/dic/DIC_mqd5s.m

@@ -0,0 +1,96 @@
+function [xi, yi, iu, iv, D] = DIC_mqd5s( im1, im2, ...
+			     windo_x, windo_y, ...
+			     X_overlap, Y_overlap, ...
+			     u_max, v_max, ...
+			     i_mode )
+%========================================================================
+%%
+
+
+% set filter to eliminate stray vectors: 1-std, 2-median
+i_filter = 2;
+
+% Set threshold value (times of standard deviation) 
+% Vectors will be eliminated if exceeded
+vec_std = 1.5;
+
+% set interpolation of missing vector	: 1-linear, 2-spline, 3-kriging
+i_interp = 2;
+
+% SNR: signal to noise ratio to find peak
+r_SNR = 3.0;
+
+% r_peak: ratio of maximum and mean
+r_MMR = 1.10;
+
+% r_peak: ratio of 1st peak and 2nd peak
+r_PPR = 1.1;
+
+% set area of search
+p_search = 1/2; 			% percentage of subwindow
+
+% min and max values for MQD
+d_min      = 10^(-5);
+d_max      = Inf;
+
+%========================================================================
+
+
+% --- initialization
+%
+
+im1 = double(im1);
+im2 = double(im2);
+
+nx = size(im1,1);
+ny = size(im1,2);
+
+% Get the seacrh area
+if ( u_max <= 0 ) | ( v_max <= 0 ) 
+  x_maxDis = ceil( p_search*windo_x );
+  y_maxDis = ceil( p_search*windo_y );
+else
+    
+  x_maxDis = floor( u_max );
+  y_maxDis = floor( v_max );
+  if x_maxDis >= windo_x
+     x_maxDis = windo_x;
+  end
+  if y_maxDis >= windo_y
+     y_maxDis = windo_y;
+  end
+end
+
+X_search  = 2*x_maxDis + 1;
+Y_search  = 2*y_maxDis + 1;
+
+% to obtain the center locations of all the subwindows
+%   (dx_center and dy_center)
+[ xi, yi, nx_start, ny_start, nx_overlap, ny_overlap, dx_center, dy_center ] ...
+    = diccwindowsize2( 'mqd', nx, ny, windo_x, windo_y, X_overlap, Y_overlap );
+
+dx_center
+
+dy_center
+
+
+bx=xi-dx_center+windo_x/2;
+by=yi-dy_center+windo_y/2;
+
+
+% number of vectors in x and y
+mx = max(size(xi));
+my = max(size(yi));
+
+
+  [xi,yi,iu,iv]=DIC_cor5( im1, im2, ...
+			     windo_x, windo_y, ...
+			     X_overlap, Y_overlap, ...
+			     u_max, v_max, ...
+			     i_mode )
+D=[];
+
+  
+  
+  
+  

src/dic/DIC_smooth.m

@@ -0,0 +1,9 @@
+function [iu_s,iv_s] = DIC_smooth( iu, iv, i_plot)
+%========================================================================
+%
+%========================================================================
+
+iu_s = DIC_smooth_data(iu);
+iv_s = DIC_smooth_data(iv);
+
+i_plot =i_plot *1;

src/dic/DIC_smooth_data.m

@@ -0,0 +1,8 @@
+function [y] = DIC_smooth_data(f)
+%========================================================================
+%%========================================================================
+
+H= [1 2 1; 2 4 2; 1 2 1];     
+H= H / sum(H(:));
+
+y=imfilter(f,H,'replicate');

src/dic/DIC_spline_Interp_vector2.m

@@ -0,0 +1,19 @@
+function[ tmp1] = DIC_spline_Interp_vector2( ui )
+%========================================================================
+%========================================================================
+
+[ u_inp1 ] = DIC_Linear_Interp_vector3( ui );
+tmp=u_inp1;
+
+[row,col]=find(isnan(ui)); %row=row1+2; col=col1+2;
+[X, Y]= meshgrid(1:size(tmp,2),1:size(tmp,1));
+Vq = interp2(X,Y,tmp,row,col);
+
+tmp1=tmp;
+
+for ii=1:numel(row)
+    tmp1(row(ii),col(ii))=Vq(ii);
+end
+
+if any(isnan(tmp1)), tmp1=u_inp1; end
+

src/dic/DIC_vector_filter_median2.m

@@ -0,0 +1,38 @@
+function[ uo, ii ] = DIC_vector_filter_median2( ui, vec_std )
+%========================================================================
+dia=4;
+err_int = 0.25;
+u_new=zeros(size(ui,1)+dia, size(ui,2)+dia)+nan;
+u_new(3:end-2, 3:end-2)=ui;
+uo= zeros(size(ui));
+[row, col]=size(ui);
+ii=0;
+for ri=1:row
+    for ci=1:col
+        tmp1 = u_new(ri:ri+4, ci:ci+4);
+        
+        
+        tmp = find(~isnan(tmp1));
+        f = tmp1(tmp);
+
+        [f_mean  f_std  f_med] = dic_filterHist3(f);
+        
+        if abs( ui(ri,ci) - f_med ) > (max(err_int, vec_std*f_std))
+            uo(ri,ci)=nan; ii=1;
+        else
+            uo(ri,ci)=ui(ri,ci); 
+        end
+        
+    end
+end
+
+
+
+
+
+
+
+
+
+
+

src/dic/cordinate_filter.m

@@ -0,0 +1,14 @@
+function yD = cordinate_filter(yD1, s)
+%#codegen
+
+if ~isempty(yD1)
+
+    yD= round(yD1);
+
+else
+    yD=[];
+end
+
+
+
+

src/dic/dic_filterHist3.m

@@ -0,0 +1,11 @@
+function[ u_mean, u_std, u_med] = dic_filterHist3( u )
+
+limt = 2.0;
+
+f = u(~isnan(u));
+tm=   f.*(abs(f-mean(f))<(limt*std(f)));
+tm=tm(find(tm));
+
+u_mean=mean(tm);
+u_std= std(tm);
+u_med= median(tm);

src/dic/dic_xcor_m.m

@@ -0,0 +1,217 @@
+function C = dic_xcor_m(varargin)
+
+%#codegen
+
+[T, A] = ParseInputs(varargin{:});
+
+%   Haralick and Shapiro, Volume II (p. 317),    
+%      "Fast Normalized Cross-Correlation", by J. P. Lewis, Industrial Light & Magic.
+%
+
+xcorr_TA = xcorr2_fast(T,A);
+
+[m, n] = size(T);
+mn = m*n;
+
+local_sum_A = local_sum(A,m,n);
+local_sum_A2 = local_sum(A.*A,m,n);
+
+% Note: diff_local_sums should be nonnegative, but may have negative
+% values due to round off errors. Below, we use max to ensure the
+% radicand is nonnegative.
+diff_local_sums = ( local_sum_A2 - (local_sum_A.^2)/mn );
+denom_A = sqrt( max(diff_local_sums,0) ); 
+
+denom_T = sqrt(mn-1)*std(T(:));
+denom = denom_T*denom_A;
+numerator = (xcorr_TA - local_sum_A*sum(T(:))/mn );
+
+% We know denom_T~=0 from input parsing;
+% so denom is only zero where denom_A is zero, and in 
+% these locations, C is also zero.
+C = zeros(size(numerator));
+tol = sqrt( eps( max(abs(denom(:)))) );
+i_nonzero = find(denom > tol);
+C(i_nonzero) = numerator(i_nonzero) ./ denom(i_nonzero);
+
+% Another numerics backstop. If any of the coefficients are outside the
+% range [-1 1], the numerics are unstable to small variance in A or T. In
+% these cases, set C to zero to reflect undefined 0/0 condition.
+C( ( abs(C) - 1 ) > sqrt(eps(1)) ) = 0;
+
+%-------------------------------
+% Function  local_sum
+%
+function local_sum_A = local_sum(A,m,n)
+
+% We thank Eli Horn for providing this code, used with his permission,
+% to speed up the calculation of local sums. The algorithm depends on
+% precomputing running sums as described in "Fast Normalized
+% Cross-Correlation", by J. P. Lewis, Industrial Light & Magic.
+
+B = padarray(A,[m n]);
+s = cumsum(B,1);
+c = s(1+m:end-1,:)-s(1:end-m-1,:);
+s = cumsum(c,2);
+local_sum_A = s(:,1+n:end-1)-s(:,1:end-n-1);
+
+%-------------------------------
+% Function  xcorr2_fast
+%
+function cross_corr = xcorr2_fast(T,A)
+
+T_size = size(T);
+A_size = size(A);
+outsize = A_size + T_size - 1;
+
+% figure out when to use spatial domain vs. freq domain
+conv_time = time_conv2(T_size,A_size); % 1 conv2
+fft_time = 1*time_fft2(outsize); % 2 fft2 + 1 ifft2
+
+cross_corr = conv2(rot90(T,2),A);
+
+
+%-------------------------------
+% Function  freqxcorr
+%
+function xcorr_ab = freqxcorr(a,b,outsize)
+  
+% calculate correlation in frequency domain
+Fa = fft2(rot90(a,2),outsize(1),outsize(2));
+Fb = fft2(b,outsize(1),outsize(2));
+% xcorr_ab = ifft2(Fa .* Fb,'symmetric');
+xcorr_ab = real(ifft2(Fa .* Fb));
+
+%-------------------------------
+% Function  time_conv2
+%
+function time = time_conv2(obssize,refsize)
+
+% time a spatial domain convolution for 10-by-10 x 20-by-20 matrices
+
+% a = ones(10);
+% b = ones(20);
+% mintime = 0.1;
+
+% t1 = cputime;
+% t2 = t1;
+% k = 0;
+% while (t2-t1)<mintime
+%     c = conv2(a,b);
+%     k = k + 1;
+%     t2 = cputime;
+% end
+% t_total = (t2-t1)/k;
+
+% % convolution time = K*prod(size(a))*prod(size(b))
+% % t_total = K*10*10*20*20 = 40000*K
+% K = t_total/40000;
+
+% K was empirically calculated by the commented-out code above.
+K = 2.7e-8; 
+            
+% convolution time = K*prod(obssize)*prod(refsize)
+time =  K*prod(obssize)*prod(refsize);
+
+
+%-------------------------------
+% Function  time_fft2
+%
+function time = time_fft2(outsize)
+
+% time a frequency domain convolution by timing two one-dimensional ffts
+
+R = outsize(1);
+S = outsize(2);
+
+% Tr = time_fft(R);
+% K_fft = Tr/(R*log(R)); 
+
+% K_fft was empirically calculated by the 2 commented-out lines above.
+K_fft = 3.3e-7; 
+Tr = K_fft*R*log(R);
+
+if S==R
+    Ts = Tr;
+else
+%    Ts = time_fft(S);  % uncomment to estimate explicitly
+   Ts = K_fft*S*log(S); 
+end
+
+time = S*Tr + R*Ts;
+
+% %-------------------------------
+% % Function time_fft
+% %
+% function T = time_fft(M)
+
+% % time a complex fft that is M elements long
+
+% vec = complex(ones(M,1),ones(M,1));
+% mintime = 0.1; 
+
+% t1 = cputime;
+% t2 = t1;
+% k = 0;
+% while (t2-t1) < mintime
+%     dummy = fft(vec);
+%     k = k + 1;
+%     t2 = cputime;
+% end
+% T = (t2-t1)/k;
+
+
+%-----------------------------------------------------------------------------
+function [T, A] = ParseInputs(varargin)
+
+narginchk(2,2)
+
+T = varargin{1};
+A = varargin{2};
+
+validateattributes(T,{'logical','numeric'},{'real','nonsparse','2d','finite'},mfilename,'T',1)
+validateattributes(A,{'logical','numeric'},{'real','nonsparse','2d','finite'},mfilename,'A',2)
+
+checkSizesTandA(T,A)
+
+% See geck 342320. If either A or T has a minimum value which is negative, we
+% need to shift the array so all values are positive to ensure numerically
+% robust results for the normalized cross-correlation.
+A = shiftData(A);
+T = shiftData(T);
+
+checkIfFlat(T);
+
+%-----------------------------------------------------------------------------
+function B = shiftData(A)
+
+B = double(A);
+
+is_unsigned = isa(A,'uint8') || isa(A,'uint16') || isa(A,'uint32');
+if ~is_unsigned
+    
+    min_B = min(B(:)); 
+    
+    if min_B < 0
+        B = B - min_B;
+    end
+    
+end
+
+%-----------------------------------------------------------------------------
+function checkSizesTandA(T,A)
+
+if numel(T) < 2
+ %   error(message('images:xcorr2_norm:invalidTemplate'))
+end
+
+if size(A,1)<size(T,1) || size(A,2)<size(T,2) 
+%    error(message('images:xcorr2_norm:invalidSizeForA'))
+end
+
+%-----------------------------------------------------------------------------
+function checkIfFlat(T)
+
+if std(T(:)) == 0
+ %   error(message('images:xcorr2_norm:sameElementsInTemplate'))
+end

src/dic/diccwindowsize32.m

@@ -0,0 +1,46 @@
+function [ xi, yi, nx_start, ny_start, nx_overlap, ny_overlap, dxcenter, dycenter ] ...
+    = diccwindowsize32( type, ...
+			  nx, ny, nx_pixel, ny_pixel, ...
+			  overlap_x, overlap_y )
+          
+%========================================================================
+% BJM
+%Created 4-02-2013
+%Modified: 6-02-2013, 10-04-2014     1-11-2017    
+%========================================================================
+
+bordr = 1/4;
+
+if type == 'mqd'
+  nx_start = nx_pixel*bordr;
+  ny_start = ny_pixel*bordr;
+else
+  nx_start = 1;
+  ny_start = 1;
+end
+
+if mod(nx_pixel, 2) == 0
+  dxc = nx_pixel/2 + 0.5;
+else
+  dxc = nx_pixel/2;
+end
+
+if mod(ny_pixel, 2) == 0
+  dyc = ny_pixel/2 + 0.5;
+else
+  dyc = ny_pixel/2;
+end
+
+
+% number of vectors
+
+dycenter=ny_pixel/2+0.5;
+dxcenter=nx_pixel/2+0.5;
+
+xi=(floor(nx_pixel/2+nx_pixel*bordr)+0.5: ceil((1-overlap_x)*nx_pixel):(nx-ceil(nx_pixel/2+nx_pixel*bordr)+1));
+yi=(floor(ny_pixel/2+ny_pixel*bordr)+0.5: ceil((1-overlap_y)*ny_pixel):(ny-ceil(ny_pixel/2+ny_pixel*bordr)+1));
+
+
+nx_overlap = floor( nx_pixel*overlap_x );
+ny_overlap = floor( ny_pixel*overlap_y );
+

src/dic/findpeak32.m

@@ -0,0 +1,6 @@
+function [xpeak, ypeak, max_f] = findpeak32(f,subpixel)
+[max_f, imax] = max(abs(f(:)));
+[ypeak, xpeak] = ind2sub(size(f),imax(1));
+   
+    
+end

src/dic/freezeColors.m

@@ -0,0 +1,275 @@
+function freezeColors(varargin)
+% freezeColors  Lock colors of plot, enabling multiple colormaps per figure. (v2.3)
+%
+%   Problem: There is only one colormap per figure. This function provides
+%       an easy solution when plots using different colomaps are desired 
+%       in the same figure.
+%
+%   freezeColors freezes the colors of graphics objects in the current axis so 
+%       that subsequent changes to the colormap (or caxis) will not change the
+%       colors of these objects. freezeColors works on any graphics object 
+%       with CData in indexed-color mode: surfaces, images, scattergroups, 
+%       bargroups, patches, etc. It works by converting CData to true-color rgb
+%       based on the colormap active at the time freezeColors is called.
+%
+%   The original indexed color data is saved, and can be restored using
+%       unfreezeColors, making the plot once again subject to the colormap and
+%       caxis.
+%
+%
+%   Usage:
+%       freezeColors        applies to all objects in current axis (gca),
+%       freezeColors(axh)   same, but works on axis axh.
+%
+%   Example:
+%       subplot(2,1,1); imagesc(X); colormap hot; freezeColors
+%       subplot(2,1,2); imagesc(Y); colormap hsv; freezeColors etc...
+%
+%       Note: colorbars must also be frozen. Due to Matlab 'improvements' this can
+%				no longer be done with freezeColors. Instead, please
+%				use the function CBFREEZE by Carlos Adrian Vargas Aguilera
+%				that can be downloaded from the MATLAB File Exchange
+%				(http://www.mathworks.com/matlabcentral/fileexchange/24371)
+%
+%       h=colorbar; cbfreeze(h), or simply cbfreeze(colorbar)
+%
+%       For additional examples, see test/test_main.m
+%
+%   Side effect on render mode: freezeColors does not work with the painters
+%       renderer, because Matlab doesn't support rgb color data in
+%       painters mode. If the current renderer is painters, freezeColors
+%       changes it to zbuffer. This may have unexpected effects on other aspects
+%	      of your plots.
+%
+%       See also unfreezeColors, freezeColors_pub.html, cbfreeze.
+%
+%
+%   John Iversen (iversen@nsi.edu) 3/23/05
+%
+
+%   Changes:
+%   JRI (iversen@nsi.edu) 4/19/06   Correctly handles scaled integer cdata
+%   JRI 9/1/06   should now handle all objects with cdata: images, surfaces, 
+%                scatterplots. (v 2.1)
+%   JRI 11/11/06 Preserves NaN colors. Hidden option (v 2.2, not uploaded)
+%   JRI 3/17/07  Preserve caxis after freezing--maintains colorbar scale (v 2.3)
+%   JRI 4/12/07  Check for painters mode as Matlab doesn't support rgb in it.
+%   JRI 4/9/08   Fix preserving caxis for objects within hggroups (e.g. contourf)
+%   JRI 4/7/10   Change documentation for colorbars
+
+% Hidden option for NaN colors:
+%   Missing data are often represented by NaN in the indexed color
+%   data, which renders transparently. This transparency will be preserved
+%   when freezing colors. If instead you wish such gaps to be filled with 
+%   a real color, add 'nancolor',[r g b] to the end of the arguments. E.g. 
+%   freezeColors('nancolor',[r g b]) or freezeColors(axh,'nancolor',[r g b]),
+%   where [r g b] is a color vector. This works on images & pcolor, but not on
+%   surfaces.
+%   Thanks to Fabiano Busdraghi and Jody Klymak for the suggestions. Bugfixes 
+%   attributed in the code.
+
+% Free for all uses, but please retain the following:
+%   Original Author:
+%   John Iversen, 2005-10
+%   john_iversen@post.harvard.edu
+
+appdatacode = 'JRI__freezeColorsData';
+
+[h, nancolor] = checkArgs(varargin);
+
+%gather all children with scaled or indexed CData
+cdatah = getCDataHandles(h);
+
+%current colormap
+cmap = colormap;
+nColors = size(cmap,1);
+cax = caxis;
+
+% convert object color indexes into colormap to true-color data using 
+%  current colormap
+for hh = cdatah',
+    g = get(hh);
+    
+    %preserve parent axis clim
+    parentAx = getParentAxes(hh);
+    originalClim = get(parentAx, 'clim');    
+   
+    %   Note: Special handling of patches: For some reason, setting
+    %   cdata on patches created by bar() yields an error,
+    %   so instead we'll set facevertexcdata instead for patches.
+    if ~strcmp(g.Type,'patch'),
+        cdata = g.CData;
+    else
+        cdata = g.FaceVertexCData; 
+    end
+    
+    %get cdata mapping (most objects (except scattergroup) have it)
+    if isfield(g,'CDataMapping'),
+        scalemode = g.CDataMapping;
+    else
+        scalemode = 'scaled';
+    end
+    
+    %save original indexed data for use with unfreezeColors
+    siz = size(cdata);
+    setappdata(hh, appdatacode, {cdata scalemode});
+
+    %convert cdata to indexes into colormap
+    if strcmp(scalemode,'scaled'),
+        %4/19/06 JRI, Accommodate scaled display of integer cdata:
+        %       in MATLAB, uint * double = uint, so must coerce cdata to double
+        %       Thanks to O Yamashita for pointing this need out
+        idx = ceil( (double(cdata) - cax(1)) / (cax(2)-cax(1)) * nColors);
+    else %direct mapping
+        idx = cdata;
+        %10/8/09 in case direct data is non-int (e.g. image;freezeColors)
+        % (Floor mimics how matlab converts data into colormap index.)
+        % Thanks to D Armyr for the catch
+        idx = floor(idx);
+    end
+    
+    %clamp to [1, nColors]
+    idx(idx<1) = 1;
+    idx(idx>nColors) = nColors;
+
+    %handle nans in idx
+    nanmask = isnan(idx);
+    idx(nanmask)=1; %temporarily replace w/ a valid colormap index
+
+    %make true-color data--using current colormap
+    realcolor = zeros(siz);
+    for i = 1:3,
+        c = cmap(idx,i);
+        c = reshape(c,siz);
+        c(nanmask) = nancolor(i); %restore Nan (or nancolor if specified)
+        realcolor(:,:,i) = c;
+    end
+    
+    %apply new true-color color data
+    
+    %true-color is not supported in painters renderer, so switch out of that
+    if strcmp(get(gcf,'renderer'), 'painters'),
+        set(gcf,'renderer','opengl');
+    end
+    
+    %replace original CData with true-color data
+    if ~strcmp(g.Type,'patch'),
+        set(hh,'CData',realcolor);
+    else
+        set(hh,'faceVertexCData',permute(realcolor,[1 3 2]))
+    end
+    
+    %restore clim (so colorbar will show correct limits)
+    if ~isempty(parentAx),
+        set(parentAx,'clim',originalClim)
+    end
+    
+end %loop on indexed-color objects
+
+
+% ============================================================================ %
+% Local functions
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% getCDataHandles -- get handles of all descendents with indexed CData
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function hout = getCDataHandles(h)
+% getCDataHandles  Find all objects with indexed CData
+
+%recursively descend object tree, finding objects with indexed CData
+% An exception: don't include children of objects that themselves have CData:
+%   for example, scattergroups are non-standard hggroups, with CData. Changing
+%   such a group's CData automatically changes the CData of its children, 
+%   (as well as the children's handles), so there's no need to act on them.
+
+error(nargchk(1,1,nargin,'struct'))
+
+hout = [];
+if isempty(h),return;end
+
+ch = get(h,'children');
+for hh = ch'
+    g = get(hh);
+    if isfield(g,'CData'),     %does object have CData?
+        %is it indexed/scaled?
+        if ~isempty(g.CData) && isnumeric(g.CData) && size(g.CData,3)==1, 
+            hout = [hout; hh]; %#ok<AGROW> %yes, add to list
+        end
+    else %no CData, see if object has any interesting children
+            hout = [hout; getCDataHandles(hh)]; %#ok<AGROW>
+    end
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% getParentAxes -- return handle of axes object to which a given object belongs
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function hAx = getParentAxes(h)
+% getParentAxes  Return enclosing axes of a given object (could be self)
+
+error(nargchk(1,1,nargin,'struct'))
+%object itself may be an axis
+if strcmp(get(h,'type'),'axes'),
+    hAx = h;
+    return
+end
+
+parent = get(h,'parent');
+if (strcmp(get(parent,'type'), 'axes')),
+    hAx = parent;
+else
+    hAx = getParentAxes(parent);
+end
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% checkArgs -- Validate input arguments
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function [h, nancolor] = checkArgs(args)
+% checkArgs  Validate input arguments to freezeColors
+
+nargs = length(args);
+error(nargchk(0,3,nargs,'struct'))
+
+%grab handle from first argument if we have an odd number of arguments
+if mod(nargs,2),
+    h = args{1};
+    if ~ishandle(h),
+        error('JRI:freezeColors:checkArgs:invalidHandle',...
+            'The first argument must be a valid graphics handle (to an axis)')
+    end
+    % 4/2010 check if object to be frozen is a colorbar
+    if strcmp(get(h,'Tag'),'Colorbar'),
+      if ~exist('cbfreeze.m'),
+        warning('JRI:freezeColors:checkArgs:cannotFreezeColorbar',...
+            ['You seem to be attempting to freeze a colorbar. This no longer'...
+            'works. Please read the help for freezeColors for the solution.'])
+      else
+        cbfreeze(h);
+        return
+      end
+    end
+    args{1} = [];
+    nargs = nargs-1;
+else
+    h = gca;
+end
+
+%set nancolor if that option was specified
+nancolor = [nan nan nan];
+if nargs == 2,
+    if strcmpi(args{end-1},'nancolor'),
+        nancolor = args{end};
+        if ~all(size(nancolor)==[1 3]),
+            error('JRI:freezeColors:checkArgs:badColorArgument',...
+                'nancolor must be [r g b] vector');
+        end
+        nancolor(nancolor>1) = 1; nancolor(nancolor<0) = 0;
+    else
+        error('JRI:freezeColors:checkArgs:unrecognizedOption',...
+            'Unrecognized option (%s). Only ''nancolor'' is valid.',args{end-1})
+    end
+end
+
+

src/dic/gui_DIC_overlapCheck.m

@@ -0,0 +1,81 @@
+function varargout = gui_DIC_overlapCheck(varargin)
+% GUI_DIC_OVERLAPCHECK MATLAB code for gui_DIC_overlapCheck.fig
+%      GUI_DIC_OVERLAPCHECK, by itself, creates a new GUI_DIC_OVERLAPCHECK or raises the existing
+%      singleton*.
+%
+%      H = GUI_DIC_OVERLAPCHECK returns the handle to a new GUI_DIC_OVERLAPCHECK or the handle to
+%      the existing singleton*.
+%
+%      GUI_DIC_OVERLAPCHECK('CALLBACK',hObject,eventData,handles,...) calls the local
+%      function named CALLBACK in GUI_DIC_OVERLAPCHECK.M with the given input arguments.
+%
+%      GUI_DIC_OVERLAPCHECK('Property','Value',...) creates a new GUI_DIC_OVERLAPCHECK or raises the
+%      existing singleton*.  Starting from the left, property value pairs are
+%      applied to the GUI before gui_DIC_overlapCheck_OpeningFcn gets called.  An
+%      unrecognized property name or invalid value makes property application
+%      stop.  All inputs are passed to gui_DIC_overlapCheck_OpeningFcn via varargin.
+%
+%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
+%      instance to run (singleton)".
+%
+% See also: GUIDE, GUIDATA, GUIHANDLES
+
+% Edit the above text to modify the response to help gui_DIC_overlapCheck
+
+% Last Modified by GUIDE v2.5 27-Dec-2017 13:10:48
+
+% Begin initialization code - DO NOT EDIT
+gui_Singleton = 1;
+gui_State = struct('gui_Name',       mfilename, ...
+                   'gui_Singleton',  gui_Singleton, ...
+                   'gui_OpeningFcn', @gui_DIC_overlapCheck_OpeningFcn, ...
+                   'gui_OutputFcn',  @gui_DIC_overlapCheck_OutputFcn, ...
+                   'gui_LayoutFcn',  [] , ...
+                   'gui_Callback',   []);
+if nargin && ischar(varargin{1})
+    gui_State.gui_Callback = str2func(varargin{1});
+end
+
+if nargout
+    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
+else
+    gui_mainfcn(gui_State, varargin{:});
+end
+% End initialization code - DO NOT EDIT
+
+
+% --- Executes just before gui_DIC_overlapCheck is made visible.
+function gui_DIC_overlapCheck_OpeningFcn(hObject, eventdata, handles, varargin)
+% This function has no output args, see OutputFcn.
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+% varargin   command line arguments to gui_DIC_overlapCheck (see VARARGIN)
+
+% Choose default command line output for gui_DIC_overlapCheck
+handles.output = hObject;
+
+% Update handles structure
+guidata(hObject, handles);
+
+% UIWAIT makes gui_DIC_overlapCheck wait for user response (see UIRESUME)
+% uiwait(handles.figure1);
+
+
+% --- Outputs from this function are returned to the command line.
+function varargout = gui_DIC_overlapCheck_OutputFcn(hObject, eventdata, handles) 
+% varargout  cell array for returning output args (see VARARGOUT);
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Get default command line output from handles structure
+varargout{1} = handles.output;
+
+
+% --- Executes on button press in pushbutton1.
+function pushbutton1_Callback(hObject, eventdata, handles)
+% hObject    handle to pushbutton1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+delete(handles.figure1);

src/dic/gui_DIC_sizeCheck.m

@@ -0,0 +1,206 @@
+function varargout = gui_DIC_sizeCheck(varargin)
+% GUI_DIC_SIZECHECK MATLAB code for gui_DIC_sizeCheck.fig
+%      GUI_DIC_SIZECHECK by itself, creates a new GUI_DIC_SIZECHECK or raises the
+%      existing singleton*.
+%
+%      H = GUI_DIC_SIZECHECK returns the handle to a new GUI_DIC_SIZECHECK or the handle to
+%      the existing singleton*.
+%
+%      GUI_DIC_SIZECHECK('CALLBACK',hObject,eventData,handles,...) calls the local
+%      function named CALLBACK in GUI_DIC_SIZECHECK.M with the given input arguments.
+%
+%      GUI_DIC_SIZECHECK('Property','Value',...) creates a new GUI_DIC_SIZECHECK or raises the
+%      existing singleton*.  Starting from the left, property value pairs are
+%      applied to the GUI before gui_DIC_sizeCheck_OpeningFcn gets called.  An
+%      unrecognized property name or invalid value makes property application
+%      stop.  All inputs are passed to gui_DIC_sizeCheck_OpeningFcn via varargin.
+%
+%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
+%      instance to run (singleton)".
+%
+% See also: GUIDE, GUIDATA, GUIHANDLES
+
+% Edit the above text to modify the response to help gui_DIC_sizeCheck
+
+% Last Modified by GUIDE v2.5 27-Dec-2017 11:33:02
+
+% Begin initialization code - DO NOT EDIT
+gui_Singleton = 1;
+gui_State = struct('gui_Name',       mfilename, ...
+                   'gui_Singleton',  gui_Singleton, ...
+                   'gui_OpeningFcn', @gui_DIC_sizeCheck_OpeningFcn, ...
+                   'gui_OutputFcn',  @gui_DIC_sizeCheck_OutputFcn, ...
+                   'gui_LayoutFcn',  [] , ...
+                   'gui_Callback',   []);
+if nargin && ischar(varargin{1})
+    gui_State.gui_Callback = str2func(varargin{1});
+end
+
+if nargout
+    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
+else
+    gui_mainfcn(gui_State, varargin{:});
+end
+% End initialization code - DO NOT EDIT
+
+% --- Executes just before gui_DIC_sizeCheck is made visible.
+function gui_DIC_sizeCheck_OpeningFcn(hObject, eventdata, handles, varargin)
+% This function has no output args, see OutputFcn.
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+% varargin   command line arguments to gui_DIC_sizeCheck (see VARARGIN)
+
+% Choose default command line output for gui_DIC_sizeCheck
+handles.output = 'Yes';
+
+% Update handles structure
+guidata(hObject, handles);
+
+% Insert custom Title and Text if specified by the user
+% Hint: when choosing keywords, be sure they are not easily confused 
+% with existing figure properties.  See the output of set(figure) for
+% a list of figure properties.
+if(nargin > 3)
+    for index = 1:2:(nargin-3),
+        if nargin-3==index, break, end
+        switch lower(varargin{index})
+         case 'title'
+          set(hObject, 'Name', varargin{index+1});
+         case 'string'
+          set(handles.text1, 'String', varargin{index+1});
+        end
+    end
+end
+
+% Determine the position of the dialog - centered on the callback figure
+% if available, else, centered on the screen
+FigPos=get(0,'DefaultFigurePosition');
+OldUnits = get(hObject, 'Units');
+set(hObject, 'Units', 'pixels');
+OldPos = get(hObject,'Position');
+FigWidth = OldPos(3);
+FigHeight = OldPos(4);
+if isempty(gcbf)
+    ScreenUnits=get(0,'Units');
+    set(0,'Units','pixels');
+    ScreenSize=get(0,'ScreenSize');
+    set(0,'Units',ScreenUnits);
+
+    FigPos(1)=1/2*(ScreenSize(3)-FigWidth);
+    FigPos(2)=2/3*(ScreenSize(4)-FigHeight);
+else
+    GCBFOldUnits = get(gcbf,'Units');
+    set(gcbf,'Units','pixels');
+    GCBFPos = get(gcbf,'Position');
+    set(gcbf,'Units',GCBFOldUnits);
+    FigPos(1:2) = [(GCBFPos(1) + GCBFPos(3) / 2) - FigWidth / 2, ...
+                   (GCBFPos(2) + GCBFPos(4) / 2) - FigHeight / 2];
+end
+FigPos(3:4)=[FigWidth FigHeight];
+set(hObject, 'Position', FigPos);
+set(hObject, 'Units', OldUnits);
+
+% Show a question icon from dialogicons.mat - variables questIconData
+% and questIconMap
+load dialogicons.mat
+
+IconData=questIconData;
+questIconMap(256,:) = get(handles.figure1, 'Color');
+IconCMap=questIconMap;
+
+Img=image(IconData, 'Parent', handles.axes1);
+set(handles.figure1, 'Colormap', IconCMap);
+
+set(handles.axes1, ...
+    'Visible', 'off', ...
+    'YDir'   , 'reverse'       , ...
+    'XLim'   , get(Img,'XData'), ...
+    'YLim'   , get(Img,'YData')  ...
+    );
+
+% Make the GUI modal
+set(handles.figure1,'WindowStyle','modal')
+
+% UIWAIT makes gui_DIC_sizeCheck wait for user response (see UIRESUME)
+uiwait(handles.figure1);
+
+% --- Outputs from this function are returned to the command line.
+function varargout = gui_DIC_sizeCheck_OutputFcn(hObject, eventdata, handles)
+% varargout  cell array for returning output args (see VARARGOUT);
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Get default command line output from handles structure
+varargout{1} = handles.output;
+
+% The figure can be deleted now
+delete(handles.figure1);
+
+% --- Executes on button press in pushbutton1.
+function pushbutton1_Callback(hObject, eventdata, handles)
+% hObject    handle to pushbutton1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+handles.output = get(hObject,'String');
+
+% Update handles structure
+guidata(hObject, handles);
+
+% Use UIRESUME instead of delete because the OutputFcn needs
+% to get the updated handles structure.
+uiresume(handles.figure1);
+
+% --- Executes on button press in pushbutton2.
+function pushbutton2_Callback(hObject, eventdata, handles)
+% hObject    handle to pushbutton2 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+handles.output = get(hObject,'String');
+
+% Update handles structure
+guidata(hObject, handles);
+
+% Use UIRESUME instead of delete because the OutputFcn needs
+% to get the updated handles structure.
+uiresume(handles.figure1);
+
+
+% --- Executes when user attempts to close figure1.
+function figure1_CloseRequestFcn(hObject, eventdata, handles)
+% hObject    handle to figure1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+if isequal(get(hObject, 'waitstatus'), 'waiting')
+    % The GUI is still in UIWAIT, us UIRESUME
+    uiresume(hObject);
+else
+    % The GUI is no longer waiting, just close it
+    delete(hObject);
+end
+
+
+% --- Executes on key press over figure1 with no controls selected.
+function figure1_KeyPressFcn(hObject, eventdata, handles)
+% hObject    handle to figure1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Check for "enter" or "escape"
+if isequal(get(hObject,'CurrentKey'),'escape')
+    % User said no by hitting escape
+    handles.output = 'No';
+    
+    % Update handles structure
+    guidata(hObject, handles);
+    
+    uiresume(handles.figure1);
+end    
+    
+if isequal(get(hObject,'CurrentKey'),'return')
+    uiresume(handles.figure1);
+end    

src/dic/gui_DIC_sizeCheck1.m

@@ -0,0 +1,81 @@
+function varargout = gui_DIC_sizeCheck1(varargin)
+% GUI_DIC_SIZECHECK1 MATLAB code for gui_DIC_sizeCheck1.fig
+%      GUI_DIC_SIZECHECK1, by itself, creates a new GUI_DIC_SIZECHECK1 or raises the existing
+%      singleton*.
+%
+%      H = GUI_DIC_SIZECHECK1 returns the handle to a new GUI_DIC_SIZECHECK1 or the handle to
+%      the existing singleton*.
+%
+%      GUI_DIC_SIZECHECK1('CALLBACK',hObject,eventData,handles,...) calls the local
+%      function named CALLBACK in GUI_DIC_SIZECHECK1.M with the given input arguments.
+%
+%      GUI_DIC_SIZECHECK1('Property','Value',...) creates a new GUI_DIC_SIZECHECK1 or raises the
+%      existing singleton*.  Starting from the left, property value pairs are
+%      applied to the GUI before gui_DIC_sizeCheck1_OpeningFcn gets called.  An
+%      unrecognized property name or invalid value makes property application
+%      stop.  All inputs are passed to gui_DIC_sizeCheck1_OpeningFcn via varargin.
+%
+%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
+%      instance to run (singleton)".
+%
+% See also: GUIDE, GUIDATA, GUIHANDLES
+
+% Edit the above text to modify the response to help gui_DIC_sizeCheck1
+
+% Last Modified by GUIDE v2.5 27-Dec-2017 12:07:24
+
+% Begin initialization code - DO NOT EDIT
+gui_Singleton = 1;
+gui_State = struct('gui_Name',       mfilename, ...
+                   'gui_Singleton',  gui_Singleton, ...
+                   'gui_OpeningFcn', @gui_DIC_sizeCheck1_OpeningFcn, ...
+                   'gui_OutputFcn',  @gui_DIC_sizeCheck1_OutputFcn, ...
+                   'gui_LayoutFcn',  [] , ...
+                   'gui_Callback',   []);
+if nargin && ischar(varargin{1})
+    gui_State.gui_Callback = str2func(varargin{1});
+end
+
+if nargout
+    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
+else
+    gui_mainfcn(gui_State, varargin{:});
+end
+% End initialization code - DO NOT EDIT
+
+
+% --- Executes just before gui_DIC_sizeCheck1 is made visible.
+function gui_DIC_sizeCheck1_OpeningFcn(hObject, eventdata, handles, varargin)
+% This function has no output args, see OutputFcn.
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+% varargin   command line arguments to gui_DIC_sizeCheck1 (see VARARGIN)
+
+% Choose default command line output for gui_DIC_sizeCheck1
+handles.output = hObject;
+
+% Update handles structure
+guidata(hObject, handles);
+
+% UIWAIT makes gui_DIC_sizeCheck1 wait for user response (see UIRESUME)
+% uiwait(handles.figure1);
+
+
+% --- Outputs from this function are returned to the command line.
+function varargout = gui_DIC_sizeCheck1_OutputFcn(hObject, eventdata, handles) 
+% varargout  cell array for returning output args (see VARARGOUT);
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Get default command line output from handles structure
+varargout{1} = handles.output;
+
+
+% --- Executes on button press in pushbutton1.
+function pushbutton1_Callback(hObject, eventdata, handles)
+% hObject    handle to pushbutton1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+delete(handles.figure1);

src/dic/gui_Image_Crop_1.m

@@ -0,0 +1,271 @@
+function varargout = gui_Image_Crop_1(varargin)
+% GUI_IMAGE_CROP_1 MATLAB code for gui_Image_Crop_1.fig
+%      GUI_IMAGE_CROP_1 by itself, creates a new GUI_IMAGE_CROP_1 or raises the
+%      existing singleton*.
+%
+%      H = GUI_IMAGE_CROP_1 returns the handle to a new GUI_IMAGE_CROP_1 or the handle to
+%      the existing singleton*.
+%
+%      GUI_IMAGE_CROP_1('CALLBACK',hObject,eventData,handles,...) calls the local
+%      function named CALLBACK in GUI_IMAGE_CROP_1.M with the given input arguments.
+%
+%      GUI_IMAGE_CROP_1('Property','Value',...) creates a new GUI_IMAGE_CROP_1 or raises the
+%      existing singleton*.  Starting from the left, property value pairs are
+%      applied to the GUI before gui_Image_Crop_1_OpeningFcn gets called.  An
+%      unrecognized property name or invalid value makes property application
+%      stop.  All inputs are passed to gui_Image_Crop_1_OpeningFcn via varargin.
+%
+%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
+%      instance to run (singleton)".
+%
+% See also: GUIDE, GUIDATA, GUIHANDLES
+
+% Edit the above text to modify the response to help gui_Image_Crop_1
+
+% Last Modified by GUIDE v2.5 02-Aug-2018 19:55:47
+
+% Begin initialization code - DO NOT EDIT
+gui_Singleton = 1;
+gui_State = struct('gui_Name',       mfilename, ...
+                   'gui_Singleton',  gui_Singleton, ...
+                   'gui_OpeningFcn', @gui_Image_Crop_1_OpeningFcn, ...
+                   'gui_OutputFcn',  @gui_Image_Crop_1_OutputFcn, ...
+                   'gui_LayoutFcn',  [] , ...
+                   'gui_Callback',   []);
+if nargin && ischar(varargin{1})
+    gui_State.gui_Callback = str2func(varargin{1});
+end
+
+if nargout
+    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
+else
+    gui_mainfcn(gui_State, varargin{:});
+end
+% End initialization code - DO NOT EDIT
+
+% --- Executes just before gui_Image_Crop_1 is made visible.
+function gui_Image_Crop_1_OpeningFcn(hObject, eventdata, handles, varargin)
+% This function has no output args, see OutputFcn.
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+% varargin   command line arguments to gui_Image_Crop_1 (see VARARGIN)
+
+% Choose default command line output for gui_Image_Crop_1
+handles.output = 'Cancel';
+
+% Update handles structure
+guidata(hObject, handles);
+
+% Insert custom Title and Text if specified by the user
+% Hint: when choosing keywords, be sure they are not easily confused 
+% with existing figure properties.  See the output of set(figure) for
+% a list of figure properties.
+if(nargin > 3)
+    for index = 1:2:(nargin-3),
+        if nargin-3==index, break, end
+        switch lower(varargin{index})
+         case 'title'
+          set(hObject, 'Name', varargin{index+1});
+         case 'string'
+          set(handles.text1, 'String', varargin{index+1});
+        end
+    end
+end
+
+% Determine the position of the dialog - centered on the callback figure
+% if available, else, centered on the screen
+FigPos=get(0,'DefaultFigurePosition');
+OldUnits = get(hObject, 'Units');
+set(hObject, 'Units', 'pixels');
+OldPos = get(hObject,'Position');
+FigWidth = OldPos(3);
+FigHeight = OldPos(4);
+if isempty(gcbf)
+    ScreenUnits=get(0,'Units');
+    set(0,'Units','pixels');
+    ScreenSize=get(0,'ScreenSize');
+    set(0,'Units',ScreenUnits);
+
+    FigPos(1)=1/2*(ScreenSize(3)-FigWidth);
+    FigPos(2)=2/3*(ScreenSize(4)-FigHeight);
+else
+    GCBFOldUnits = get(gcbf,'Units');
+    set(gcbf,'Units','pixels');
+    GCBFPos = get(gcbf,'Position');
+    set(gcbf,'Units',GCBFOldUnits);
+    FigPos(1:2) = [(GCBFPos(1) + GCBFPos(3) / 2) - FigWidth / 2, ...
+                   (GCBFPos(2) + GCBFPos(4) / 2) - FigHeight / 2];
+end
+FigPos(3:4)=[FigWidth FigHeight];
+set(hObject, 'Position', FigPos);
+set(hObject, 'Units', OldUnits);
+
+% Show a question icon from dialogicons.mat - variables questIconData
+% and questIconMap
+load dialogicons.mat
+
+IconData=questIconData;
+questIconMap(256,:) = get(handles.figure1, 'Color');
+IconCMap=questIconMap;
+
+% Img=image(IconData, 'Parent', handles.axes1);
+% set(handles.figure1, 'Colormap', IconCMap);
+
+% set(handles.axes1, ...
+%     'Visible', 'off', ...
+%     'YDir'   , 'reverse'       , ...
+%     'XLim'   , get(Img,'XData'), ...
+%     'YLim'   , get(Img,'YData')  ...
+%     );
+
+% Make the GUI modal
+set(handles.figure1,'WindowStyle','modal')
+
+
+handles.image=varargin{1};
+axes(handles.axes3);cla;imshow(handles.image,[]);
+
+
+set(handles.push_CANCEL, 'Enable','off');
+set(handles.push_CROP, 'Enable','off');
+
+
+message = sprintf('Draw a box over the image to select the ROI');
+h1=msgbox(message);
+handles.h1=h1; 
+uiwait(h1);
+
+% set(handles.push_CANCEL, 'Enable','on');
+
+handles.LOC =[];
+handles.output = 'CANCEL';
+
+
+guidata(hObject, handles);
+
+
+
+axes(handles.axes3);cla;imshow(handles.image,[]);
+h = imrect;
+% h=0;
+
+if sum(size(h))>1
+    set(handles.push_CANCEL, 'Enable','on');
+    set(handles.push_CROP, 'Enable','on');
+    handles.h=h;
+%     getPosition(h)
+    guidata(hObject, handles);
+    uiwait(handles.figure1);
+    
+end
+
+
+
+if sum(size(h))==0
+    try, close(handles.h1), catch, end
+    uiresume(handles.figure1);
+%     delete(handles.figure1);
+%         delete(handles.figure1);
+%  figure1_CloseRequestFcn(handles.figure1,eventdata, handles);
+end
+
+
+% --- Outputs from this function are returned to the command line.
+function varargout = gui_Image_Crop_1_OutputFcn(hObject, eventdata, handles)
+% varargout  cell array for returning output args (see VARARGOUT);
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Get default command line output from handles structure
+varargout{1} = handles.output;
+varargout{2} = handles.LOC;
+% guidata(hObject, handles);
+% The figure can be deleted now
+delete(handles.figure1);
+
+% --- Executes on button press in push_CROP.
+function push_CROP_Callback(hObject, eventdata, handles)
+% hObject    handle to push_CROP (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+handles.output = get(hObject,'String');
+
+
+handles.LOC=getPosition(handles.h);
+
+
+
+
+
+% Update handles structure
+guidata(hObject, handles);
+
+% Use UIRESUME instead of delete because the OutputFcn needs
+% to get the updated handles structure.
+uiresume(handles.figure1);
+
+% --- Executes on button press in push_CANCEL.
+function push_CANCEL_Callback(hObject, eventdata, handles)
+% hObject    handle to push_CANCEL (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+handles.output = get(hObject,'String');
+
+handles.LOC= [];
+% Update handles structure
+guidata(hObject, handles);
+
+% Use UIRESUME instead of delete because the OutputFcn needs
+% to get the updated handles structure.
+uiresume(handles.figure1);
+
+
+% --- Executes when user attempts to close figure1.
+function figure1_CloseRequestFcn(hObject, eventdata, handles)
+% % % % % hObject    handle to figure1 (see GCBO)
+% % % % % eventdata  reserved - to be defined in a future version of MATLAB
+% % % % % handles    structure with handles and user data (see GUIDATA)
+% % % % 
+% % % % if isequal(get(hObject, 'waitstatus'), 'waiting')
+% % % %     % The GUI is still in UIWAIT, us UIRESUME
+% % % %     try close(handles.h1), catch, end 
+% % % %     uiresume(hObject);
+% % % % else
+% % % %     % The GUI is no longer waiting, just close it
+% % % %     try close(handles.h1), catch, end 
+% % % %     delete(hObject);
+% % % % end
+    try close(handles.h1), catch, end 
+
+
+% --- Executes on key press over figure1 with no controls selected.
+function figure1_KeyPressFcn(hObject, eventdata, handles)
+% hObject    handle to figure1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Check for "enter" or "escape"
+if isequal(get(hObject,'CurrentKey'),'escape')
+    % User said no by hitting escape
+    handles.output = 'CANCEL';
+    
+    % Update handles structure
+    guidata(hObject, handles);
+    
+    uiresume(handles.figure1);
+end    
+    
+if isequal(get(hObject,'CurrentKey'),'return')
+    uiresume(handles.figure1);
+end    
+
+
+% --- Executes on button press in push_RESET.
+function push_RESET_Callback(hObject, eventdata, handles)
+% hObject    handle to push_RESET (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)

src/dic/gui_ask_cal_KNOWN_Point.m

@@ -0,0 +1,338 @@
+function varargout = gui_ask_cal_KNOWN_Point(varargin)
+% GUI_ASK_CAL_KNOWN_POINT MATLAB code for gui_ask_cal_KNOWN_Point.fig
+%      GUI_ASK_CAL_KNOWN_POINT by itself, creates a new GUI_ASK_CAL_KNOWN_POINT or raises the
+%      existing singleton*.
+%
+%      H = GUI_ASK_CAL_KNOWN_POINT returns the handle to a new GUI_ASK_CAL_KNOWN_POINT or the handle to
+%      the existing singleton*.
+%
+%      GUI_ASK_CAL_KNOWN_POINT('CALLBACK',hObject,eventData,handles,...) calls the local
+%      function named CALLBACK in GUI_ASK_CAL_KNOWN_POINT.M with the given input arguments.
+%
+%      GUI_ASK_CAL_KNOWN_POINT('Property','Value',...) creates a new GUI_ASK_CAL_KNOWN_POINT or raises the
+%      existing singleton*.  Starting from the left, property value pairs are
+%      applied to the GUI before gui_ask_cal_KNOWN_Point_OpeningFcn gets called.  An
+%      unrecognized property name or invalid value makes property application
+%      stop.  All inputs are passed to gui_ask_cal_KNOWN_Point_OpeningFcn via varargin.
+%
+%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
+%      instance to run (singleton)".
+%
+% See also: GUIDE, GUIDATA, GUIHANDLES
+
+% Edit the above text to modify the response to help gui_ask_cal_KNOWN_Point
+
+% Last Modified by GUIDE v2.5 03-Aug-2018 03:25:03
+
+% Begin initialization code - DO NOT EDIT
+gui_Singleton = 1;
+gui_State = struct('gui_Name',       mfilename, ...
+                   'gui_Singleton',  gui_Singleton, ...
+                   'gui_OpeningFcn', @gui_ask_cal_KNOWN_Point_OpeningFcn, ...
+                   'gui_OutputFcn',  @gui_ask_cal_KNOWN_Point_OutputFcn, ...
+                   'gui_LayoutFcn',  [] , ...
+                   'gui_Callback',   []);
+if nargin && ischar(varargin{1})
+    gui_State.gui_Callback = str2func(varargin{1});
+end
+
+if nargout
+    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
+else
+    gui_mainfcn(gui_State, varargin{:});
+end
+% End initialization code - DO NOT EDIT
+
+% --- Executes just before gui_ask_cal_KNOWN_Point is made visible.
+function gui_ask_cal_KNOWN_Point_OpeningFcn(hObject, eventdata, handles, varargin)
+% This function has no output args, see OutputFcn.
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+% varargin   command line arguments to gui_ask_cal_KNOWN_Point (see VARARGIN)
+
+% Choose default command line output for gui_ask_cal_KNOWN_Point
+handles.output = 'Cancel';
+
+% Update handles structure
+guidata(hObject, handles);
+
+% Insert custom Title and Text if specified by the user
+% Hint: when choosing keywords, be sure they are not easily confused 
+% with existing figure properties.  See the output of set(figure) for
+% a list of figure properties.
+if(nargin > 3)
+    for index = 1:2:(nargin-3),
+        if nargin-3==index, break, end
+        switch lower(varargin{index})
+         case 'title'
+          set(hObject, 'Name', varargin{index+1});
+         case 'string'
+          set(handles.text1, 'String', varargin{index+1});
+        end
+    end
+end
+
+% Determine the position of the dialog - centered on the callback figure
+% if available, else, centered on the screen
+FigPos=get(0,'DefaultFigurePosition');
+OldUnits = get(hObject, 'Units');
+set(hObject, 'Units', 'pixels');
+OldPos = get(hObject,'Position');
+FigWidth = OldPos(3);
+FigHeight = OldPos(4);
+if isempty(gcbf)
+    ScreenUnits=get(0,'Units');
+    set(0,'Units','pixels');
+    ScreenSize=get(0,'ScreenSize');
+    set(0,'Units',ScreenUnits);
+
+    FigPos(1)=1/2*(ScreenSize(3)-FigWidth);
+    FigPos(2)=2/3*(ScreenSize(4)-FigHeight);
+else
+    GCBFOldUnits = get(gcbf,'Units');
+    set(gcbf,'Units','pixels');
+    GCBFPos = get(gcbf,'Position');
+    set(gcbf,'Units',GCBFOldUnits);
+    FigPos(1:2) = [(GCBFPos(1) + GCBFPos(3) / 2) - FigWidth / 2, ...
+                   (GCBFPos(2) + GCBFPos(4) / 2) - FigHeight / 2];
+end
+FigPos(3:4)=[FigWidth FigHeight];
+set(hObject, 'Position', FigPos);
+set(hObject, 'Units', OldUnits);
+
+% Show a question icon from dialogicons.mat - variables questIconData
+% and questIconMap
+% load dialogicons.mat
+% 
+% IconData=questIconData;
+% questIconMap(256,:) = get(handles.figure1, 'Color');
+% IconCMap=questIconMap;
+% 
+% % Img=image(IconData, 'Parent', handles.axes1);
+% set(handles.figure1, 'Colormap', IconCMap);
+% 
+% set(handles.axes1, ...
+%     'Visible', 'off', ...
+%     'YDir'   , 'reverse'       , ...
+%     'XLim'   , get(Img,'XData'), ...
+%     'YLim'   , get(Img,'YData')  ...
+%     );
+
+% Make the GUI modal
+set(handles.figure1,'WindowStyle','modal')
+
+set(handles.push_SET, 'Enable','off');
+set(handles.edit1, 'Enable','off');
+set(handles.push_CANCEL, 'Enable','off');
+
+handles.value=0;
+handles.image=varargin{1};
+guidata(hObject, handles);
+
+axes(handles.axes3); imshow(handles.image,[]); 
+get_coordinates1(hObject, eventdata, handles);
+
+
+
+
+
+% UIWAIT makes gui_ask_cal_KNOWN_Point wait for user response (see UIRESUME)
+uiwait(handles.figure1);
+
+
+function get_coordinates1(hObject, eventdata, handles)
+
+xx=[];
+yy=[];
+iter=0;
+
+%  clf
+%  axes(handles.axes1); imshow(handles.image,[]); 
+  
+ 
+ while 1
+
+        
+        
+        [x y button]=ginput(1);
+        
+%         if button==27
+%             xx=[];
+%             yy=[];
+%             iter=0;
+%         end
+%         
+        
+        if button==3
+            
+            
+            
+            if iter==2, 
+                xx=xx(end); yy=yy(end);
+                iter=1;
+            end
+            
+            
+            xx=[xx;x];
+            yy=[yy;y];
+            iter=iter+1;
+            
+            
+            imshow(handles.image,[]),     
+            h=line(xx,yy);
+            h.LineWidth=2;
+            h.Color=[1 0 0];
+            pause(0.2)
+
+    if iter==2,     break; end
+            
+        end
+        
+ end
+ 
+ set(handles.push_SET, 'Enable','on');
+ set(handles.edit1, 'Enable','on');
+ set(handles.push_CANCEL, 'Enable','on');
+ set(handles.text_DISPLAY, 'String',num2str(handles.value));
+
+ 
+ handles.xx=xx(end-1:end);
+ handles.yy=yy(end-1:end);
+ varargout{2}=handles.xx;
+ varargout{3}=handles.yy;
+ 
+guidata(hObject, handles);
+
+
+% --- Outputs from this function are returned to the command line.
+function varargout = gui_ask_cal_KNOWN_Point_OutputFcn(hObject, eventdata, handles)
+% varargout  cell array for returning output args (see VARARGOUT);
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Get default command line output from handles structure
+varargout{1} = handles.output;
+varargout{2}=handles.xx;
+varargout{3}=handles.yy;
+varargout{4}=handles.value;
+% The figure can be deleted now
+delete(handles.figure1);
+
+% --- Executes on button press in push_SET.
+function push_SET_Callback(hObject, eventdata, handles)
+% hObject    handle to push_SET (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+handles.output = get(hObject,'String');
+
+% Update handles structure
+guidata(hObject, handles);
+
+% Use UIRESUME instead of delete because the OutputFcn needs
+% to get the updated handles structure.
+uiresume(handles.figure1);
+
+% --- Executes on button press in push_CANCEL.
+function push_CANCEL_Callback(hObject, eventdata, handles)
+% hObject    handle to push_CANCEL (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+handles.output = get(hObject,'String');
+
+% Update handles structure
+guidata(hObject, handles);
+
+% Use UIRESUME instead of delete because the OutputFcn needs
+% to get the updated handles structure.
+uiresume(handles.figure1);
+
+
+% --- Executes when user attempts to close figure1.
+function figure1_CloseRequestFcn(hObject, eventdata, handles)
+% hObject    handle to figure1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+if isequal(get(hObject, 'waitstatus'), 'waiting')
+    % The GUI is still in UIWAIT, us UIRESUME
+    uiresume(hObject);
+else
+    % The GUI is no longer waiting, just close it
+    delete(hObject);
+end
+
+
+% --- Executes on key press over figure1 with no controls selected.
+function figure1_KeyPressFcn(hObject, eventdata, handles)
+% hObject    handle to figure1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Check for "enter" or "escape"
+if isequal(get(hObject,'CurrentKey'),'escape')
+    % User said no by hitting escape
+    handles.output = 'No';
+    
+    % Update handles structure
+    guidata(hObject, handles);
+    
+    uiresume(handles.figure1);
+end    
+    
+if isequal(get(hObject,'CurrentKey'),'return')
+    uiresume(handles.figure1);
+end    
+
+
+
+function edit1_Callback(hObject, eventdata, handles)
+% hObject    handle to edit1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of edit1 as text
+%        str2double(get(hObject,'String')) returns contents of edit1 as a double
+value = str2double(get(hObject,'String')) ;
+
+if(isnan(value)), handles.value=0; end
+if(~isnan(value)), handles.value=value; end
+set(handles.text_DISPLAY, 'String',num2str(handles.value));
+
+guidata(hObject, handles);
+
+
+% --- Executes during object creation, after setting all properties.
+function edit1_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to edit1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+% --- Executes on button press in push_RESET.
+function push_RESET_Callback(hObject, eventdata, handles)
+% hObject    handle to push_RESET (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+set(handles.push_SET, 'Enable','off');
+set(handles.edit1, 'Enable','off');
+
+imshow(handles.image,[]),     
+get_coordinates1(hObject, eventdata, handles)
+
+
+% --- Executes during object creation, after setting all properties.
+function text_DISPLAY_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to text_DISPLAY (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called

src/dic/gui_ask_calibration1.m

@@ -0,0 +1,289 @@
+function varargout = gui_ask_calibration1(varargin)
+% GUI_ASK_CALIBRATION1 MATLAB code for gui_ask_calibration1.fig
+%      GUI_ASK_CALIBRATION1 by itself, creates a new GUI_ASK_CALIBRATION1 or raises the
+%      existing singleton*.
+%
+%      H = GUI_ASK_CALIBRATION1 returns the handle to a new GUI_ASK_CALIBRATION1 or the handle to
+%      the existing singleton*.
+%
+%      GUI_ASK_CALIBRATION1('CALLBACK',hObject,eventData,handles,...) calls the local
+%      function named CALLBACK in GUI_ASK_CALIBRATION1.M with the given input arguments.
+%
+%      GUI_ASK_CALIBRATION1('Property','Value',...) creates a new GUI_ASK_CALIBRATION1 or raises the
+%      existing singleton*.  Starting from the left, property value pairs are
+%      applied to the GUI before gui_ask_calibration1_OpeningFcn gets called.  An
+%      unrecognized property name or invalid value makes property application
+%      stop.  All inputs are passed to gui_ask_calibration1_OpeningFcn via varargin.
+%
+%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
+%      instance to run (singleton)".
+%
+% See also: GUIDE, GUIDATA, GUIHANDLES
+
+% Edit the above text to modify the response to help gui_ask_calibration1
+
+% Last Modified by GUIDE v2.5 10-May-2018 13:04:12
+
+% Begin initialization code - DO NOT EDIT
+gui_Singleton = 1;
+gui_State = struct('gui_Name',       mfilename, ...
+                   'gui_Singleton',  gui_Singleton, ...
+                   'gui_OpeningFcn', @gui_ask_calibration1_OpeningFcn, ...
+                   'gui_OutputFcn',  @gui_ask_calibration1_OutputFcn, ...
+                   'gui_LayoutFcn',  [] , ...
+                   'gui_Callback',   []);
+if nargin && ischar(varargin{1})
+    gui_State.gui_Callback = str2func(varargin{1});
+end
+
+if nargout
+    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
+else
+    gui_mainfcn(gui_State, varargin{:});
+end
+% End initialization code - DO NOT EDIT
+
+% --- Executes just before gui_ask_calibration1 is made visible.
+function gui_ask_calibration1_OpeningFcn(hObject, eventdata, handles, varargin)
+% This function has no output args, see OutputFcn.
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+% varargin   command line arguments to gui_ask_calibration1 (see VARARGIN)
+
+% Choose default command line output for gui_ask_calibration1
+handles.output = 'Yes';
+
+% Update handles structure
+guidata(hObject, handles);
+
+% Insert custom Title and Text if specified by the user
+% Hint: when choosing keywords, be sure they are not easily confused 
+% with existing figure properties.  See the output of set(figure) for
+% a list of figure properties.
+if(nargin > 3)
+    for index = 1:2:(nargin-3),
+        if nargin-3==index, break, end
+        switch lower(varargin{index})
+         case 'title'
+          set(hObject, 'Name', varargin{index+1});
+         case 'string'
+          set(handles.text1, 'String', varargin{index+1});
+        end
+    end
+end
+
+% Determine the position of the dialog - centered on the callback figure
+% if available, else, centered on the screen
+FigPos=get(0,'DefaultFigurePosition');
+OldUnits = get(hObject, 'Units');
+set(hObject, 'Units', 'pixels');
+OldPos = get(hObject,'Position');
+FigWidth = OldPos(3);
+FigHeight = OldPos(4);
+if isempty(gcbf)
+    ScreenUnits=get(0,'Units');
+    set(0,'Units','pixels');
+    ScreenSize=get(0,'ScreenSize');
+    set(0,'Units',ScreenUnits);
+
+    FigPos(1)=1/2*(ScreenSize(3)-FigWidth);
+    FigPos(2)=2/3*(ScreenSize(4)-FigHeight);
+else
+    GCBFOldUnits = get(gcbf,'Units');
+    set(gcbf,'Units','pixels');
+    GCBFPos = get(gcbf,'Position');
+    set(gcbf,'Units',GCBFOldUnits);
+    FigPos(1:2) = [(GCBFPos(1) + GCBFPos(3) / 2) - FigWidth / 2, ...
+                   (GCBFPos(2) + GCBFPos(4) / 2) - FigHeight / 2];
+end
+FigPos(3:4)=[FigWidth FigHeight];
+set(hObject, 'Position', FigPos);
+set(hObject, 'Units', OldUnits);
+
+% Show a question icon from dialogicons.mat - variables questIconData
+% and questIconMap
+load dialogicons.mat
+
+IconData=questIconData;
+questIconMap(256,:) = get(handles.figure1, 'Color');
+IconCMap=questIconMap;
+
+% Img=image(IconData, 'Parent', handles.axes1);
+% % % % % % Img=imshow(varargin{1}, 'Parent', handles.axes1);
+% % % % % % % set(handles.figure1, 'Colormap', IconCMap);
+% % % % % % 
+% % % % % % set(handles.axes1, ...
+% % % % % %     'Visible', 'off', ...
+% % % % % %     'YDir'   , 'reverse'       , ...
+% % % % % %     'XLim'   , get(Img,'XData'), ...
+% % % % % %     'YLim'   , get(Img,'YData')  ...
+% % % % % %     );
+
+% Make the GUI modal
+set(handles.figure1,'WindowStyle','modal')
+
+% [xx, yy]= get_coordinates(varargin{1});
+
+handles.image=varargin{1};
+guidata(hObject, handles);
+
+axes(handles.axes1); imshow(handles.image,[]); 
+get_coordinates1(hObject, eventdata, handles);
+
+
+
+% UIWAIT makes gui_ask_calibration1 wait for user response (see UIRESUME)
+uiwait(handles.figure1);
+
+
+
+
+
+function get_coordinates1(hObject, eventdata, handles)
+
+xx=[];
+yy=[];
+iter=0;
+
+%  clf
+%  axes(handles.axes1); imshow(handles.image,[]); 
+  
+ 
+ while 1
+
+        
+        
+        [x y button]=ginput(1);
+        
+%         if button==27
+%             xx=[];
+%             yy=[];
+%             iter=0;
+%         end
+%         
+        
+        if button==3
+            
+            
+            
+            if iter==2, 
+                xx=xx(end); yy=yy(end);
+                iter=1;
+            end
+            
+            
+            xx=[xx;x];
+            yy=[yy;y];
+            iter=iter+1;
+            
+            
+            imshow(handles.image,[]),     
+            h=line(xx,yy);
+            h.LineWidth=2;
+            h.Color=[1 0 0];
+            pause(0.2)
+
+    if iter==2,     break; end
+            
+        end
+        
+ end
+ 
+ handles.xx=xx(end-1:end);
+ handles.yy=yy(end-1:end);
+ varargout{2}=handles.xx;
+ varargout{3}=handles.yy;
+ 
+guidata(hObject, handles);
+
+
+% --- Outputs from this function are returned to the command line.
+function varargout = gui_ask_calibration1_OutputFcn(hObject, eventdata, handles)
+% varargout  cell array for returning output args (see VARARGOUT);
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Get default command line output from handles structure
+varargout{1} = handles.output;
+ varargout{2}=handles.xx;
+ varargout{3}=handles.yy;
+% The figure can be deleted now
+delete(handles.figure1);
+
+% --- Executes on button press in pushbutton1.
+function pushbutton1_Callback(hObject, eventdata, handles)
+% hObject    handle to pushbutton1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+handles.output = get(hObject,'String');
+
+% Update handles structure
+guidata(hObject, handles);
+
+% Use UIRESUME instead of delete because the OutputFcn needs
+% to get the updated handles structure.
+uiresume(handles.figure1);
+
+% --- Executes on button press in pushbutton2.
+function pushbutton2_Callback(hObject, eventdata, handles)
+% hObject    handle to pushbutton2 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+handles.output = get(hObject,'String');
+
+% Update handles structure
+guidata(hObject, handles);
+
+% Use UIRESUME instead of delete because the OutputFcn needs
+% to get the updated handles structure.
+uiresume(handles.figure1);
+
+
+% --- Executes when user attempts to close figure1.
+function figure1_CloseRequestFcn(hObject, eventdata, handles)
+% hObject    handle to figure1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+if isequal(get(hObject, 'waitstatus'), 'waiting')
+    % The GUI is still in UIWAIT, us UIRESUME
+    uiresume(hObject);
+else
+    % The GUI is no longer waiting, just close it
+% % %     delete(hObject);
+end
+
+
+% --- Executes on key press over figure1 with no controls selected.
+function figure1_KeyPressFcn(hObject, eventdata, handles)
+% hObject    handle to figure1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Check for "enter" or "escape"
+if isequal(get(hObject,'CurrentKey'),'escape')
+    % User said no by hitting escape
+    handles.output = 'No';
+    
+    % Update handles structure
+    guidata(hObject, handles);
+    
+    uiresume(handles.figure1);
+end    
+    
+if isequal(get(hObject,'CurrentKey'),'return')
+    uiresume(handles.figure1);
+end    
+
+
+% --- Executes on button press in pushbutton3.
+function pushbutton3_Callback(hObject, eventdata, handles)
+% hObject    handle to pushbutton3 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+imshow(handles.image,[]),     
+get_coordinates1(hObject, eventdata, handles)

src/dic/gui_confirm_DICstart2.m

@@ -0,0 +1,268 @@
+function [ varargout] = gui_confirm_DICstart2(varargin)
+% GUI_CONFIRM_DICSTART2 MATLAB code for gui_confirm_DICstart2.fig
+%      GUI_CONFIRM_DICSTART2 by itself, creates a new GUI_CONFIRM_DICSTART2 or raises the
+%      existing singleton*.
+%
+%      H = GUI_CONFIRM_DICSTART2 returns the handle to a new GUI_CONFIRM_DICSTART2 or the handle to
+%      the existing singleton*.
+%
+%      GUI_CONFIRM_DICSTART2('CALLBACK',hObject,eventData,handles,...) calls the local
+%      function named CALLBACK in GUI_CONFIRM_DICSTART2.M with the given input arguments.
+%
+%      GUI_CONFIRM_DICSTART2('Property','Value',...) creates a new GUI_CONFIRM_DICSTART2 or raises the
+%      existing singleton*.  Starting from the left, property value pairs are
+%      applied to the GUI before gui_confirm_DICstart2_OpeningFcn gets called.  An
+%      unrecognized property name or invalid value makes property application
+%      stop.  All inputs are passed to gui_confirm_DICstart2_OpeningFcn via varargin.
+%
+%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
+%      instance to run (singleton)".
+%
+% See also: GUIDE, GUIDATA, GUIHANDLES
+
+% Edit the above text to modify the response to help gui_confirm_DICstart2
+
+% Last Modified by GUIDE v2.5 22-May-2018 22:43:57
+
+% Begin initialization code - DO NOT EDIT
+gui_Singleton = 1;
+gui_State = struct('gui_Name',       mfilename, ...
+                   'gui_Singleton',  gui_Singleton, ...
+                   'gui_OpeningFcn', @gui_confirm_DICstart2_OpeningFcn, ...
+                   'gui_OutputFcn',  @gui_confirm_DICstart2_OutputFcn, ...
+                   'gui_LayoutFcn',  [] , ...
+                   'gui_Callback',   []);
+if nargin && ischar(varargin{1})
+    gui_State.gui_Callback = str2func(varargin{1});
+end
+
+if nargout
+    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
+else
+    gui_mainfcn(gui_State, varargin{:});
+end
+% End initialization code - DO NOT EDIT
+
+% --- Executes just before gui_confirm_DICstart2 is made visible.
+function gui_confirm_DICstart2_OpeningFcn(hObject, eventdata, handles, varargin)
+% This function has no output args, see OutputFcn.
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+% varargin   command line arguments to gui_confirm_DICstart2 (see VARARGIN)
+
+% Choose default command line output for gui_confirm_DICstart2
+handles.output = 'Yes';
+set(handles.edt,'String',varargin{1});
+handles.destination=varargin{2};
+% set(handles.edit2,'String',handles.destination);
+set(handles.text7,'String',handles.destination);
+
+% Update handles structure
+guidata(hObject, handles);
+
+% Insert custom Title and Text if specified by the user
+% Hint: when choosing keywords, be sure they are not easily confused 
+% with existing figure properties.  See the output of set(figure) for
+% a list of figure properties.
+if(nargin > 3)
+    for index = 1:2:(nargin-3),
+        if nargin-3==index, break, end
+        switch lower(varargin{index})
+         case 'title'
+          set(hObject, 'Name', varargin{index+1});
+         case 'string'
+          set(handles.text1, 'String', varargin{index+1});
+        end
+    end
+end
+
+% Determine the position of the dialog - centered on the callback figure
+% if available, else, centered on the screen
+FigPos=get(0,'DefaultFigurePosition');
+OldUnits = get(hObject, 'Units');
+set(hObject, 'Units', 'pixels');
+OldPos = get(hObject,'Position');
+FigWidth = OldPos(3);
+FigHeight = OldPos(4);
+if isempty(gcbf)
+    ScreenUnits=get(0,'Units');
+    set(0,'Units','pixels');
+    ScreenSize=get(0,'ScreenSize');
+    set(0,'Units',ScreenUnits);
+
+    FigPos(1)=1/2*(ScreenSize(3)-FigWidth);
+    FigPos(2)=2/3*(ScreenSize(4)-FigHeight);
+else
+    GCBFOldUnits = get(gcbf,'Units');
+    set(gcbf,'Units','pixels');
+    GCBFPos = get(gcbf,'Position');
+    set(gcbf,'Units',GCBFOldUnits);
+    FigPos(1:2) = [(GCBFPos(1) + GCBFPos(3) / 2) - FigWidth / 2, ...
+                   (GCBFPos(2) + GCBFPos(4) / 2) - FigHeight / 2];
+end
+FigPos(3:4)=[FigWidth FigHeight];
+set(hObject, 'Position', FigPos);
+set(hObject, 'Units', OldUnits);
+
+% Show a question icon from dialogicons.mat - variables questIconData
+% and questIconMap
+load dialogicons.mat
+
+IconData=questIconData;
+questIconMap(256,:) = get(handles.figure1, 'Color');
+IconCMap=questIconMap;
+
+Img=image(IconData, 'Parent', handles.axes1);
+set(handles.figure1, 'Colormap', IconCMap);
+
+set(handles.axes1, ...
+    'Visible', 'off', ...
+    'YDir'   , 'reverse'       , ...
+    'XLim'   , get(Img,'XData'), ...
+    'YLim'   , get(Img,'YData')  ...
+    );
+
+% Make the GUI modal
+set(handles.figure1,'WindowStyle','modal')
+
+% UIWAIT makes gui_confirm_DICstart2 wait for user response (see UIRESUME)
+uiwait(handles.figure1);
+
+% --- Outputs from this function are returned to the command line.
+function varargout = gui_confirm_DICstart2_OutputFcn(hObject, eventdata, handles)
+% varargout  cell array for returning output args (see VARARGOUT);
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Get default command line output from handles structure
+try 
+varargout{1} = handles.output;
+varargout{2} = handles.destination;
+end
+% The figure can be deleted now
+delete(handles.figure1);
+
+% --- Executes on button press in pushbutton1.
+function pushbutton1_Callback(hObject, eventdata, handles)
+% hObject    handle to pushbutton1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+handles.output = get(hObject,'String');
+
+% Update handles structure
+guidata(hObject, handles);
+
+% Use UIRESUME instead of delete because the OutputFcn needs
+% to get the updated handles structure.
+uiresume(handles.figure1);
+
+% --- Executes on button press in pushbutton2.
+function pushbutton2_Callback(hObject, eventdata, handles)
+% hObject    handle to pushbutton2 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+handles.output = get(hObject,'String');
+
+% Update handles structure
+guidata(hObject, handles);
+
+% Use UIRESUME instead of delete because the OutputFcn needs
+% to get the updated handles structure.
+uiresume(handles.figure1);
+
+
+% --- Executes when user attempts to close figure1.
+function figure1_CloseRequestFcn(hObject, eventdata, handles)
+% hObject    handle to figure1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+if isequal(get(hObject, 'waitstatus'), 'waiting')
+    % The GUI is still in UIWAIT, us UIRESUME
+    uiresume(hObject);
+else
+    % The GUI is no longer waiting, just close it
+    delete(hObject);
+end
+
+
+% --- Executes on key press over figure1 with no controls selected.
+function figure1_KeyPressFcn(hObject, eventdata, handles)
+% hObject    handle to figure1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Check for "enter" or "escape"
+if isequal(get(hObject,'CurrentKey'),'escape')
+    % User said no by hitting escape
+    handles.output = 'No';
+    
+    % Update handles structure
+    guidata(hObject, handles);
+    
+    uiresume(handles.figure1);
+end    
+    
+if isequal(get(hObject,'CurrentKey'),'return')
+    uiresume(handles.figure1);
+end    
+
+
+
+
+
+
+% function edit2_Callback(hObject, eventdata, handles)
+% % hObject    handle to edit2 (see GCBO)
+% % eventdata  reserved - to be defined in a future version of MATLAB
+% % handles    structure with handles and user data (see GUIDATA)
+% 
+% % Hints: get(hObject,'String') returns contents of edit2 as text
+% %        str2double(get(hObject,'String')) returns contents of edit2 as a double
+
+
+% % --- Executes during object creation, after setting all properties.
+% function edit2_CreateFcn(hObject, eventdata, handles)
+% % hObject    handle to edit2 (see GCBO)
+% % eventdata  reserved - to be defined in a future version of MATLAB
+% % handles    empty - handles not created until after all CreateFcns called
+% 
+% % Hint: edit controls usually have a white background on Windows.
+% %       See ISPC and COMPUTER.
+% if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+%     set(hObject,'BackgroundColor','white');
+% end
+
+
+% --- Executes on button press in push_set_path.
+function push_set_path_Callback(hObject, eventdata, handles)
+% hObject    handle to push_set_path (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+[pathname] = uigetdir(handles.destination,'Select Destination Folder');
+handles.destination = pathname;
+
+guidata(hObject, handles);
+% set(handles.edit2,'String',handles.destination);
+
+
+% --- Executes during object creation, after setting all properties.
+function edt_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to edt (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+%varargin{:}
+% set(handles.edt,'String',varargin{1});
+% guidata(hObject, handles);
+
+
+% --- Executes during object creation, after setting all properties.
+function text7_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to text7 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+% set(handles.text7,'String',handles.destination);

src/dic/gui_set_resolution_3.m

@@ -0,0 +1,441 @@
+function varargout = gui_set_resolution_3(varargin)
+% GUI_SET_RESOLUTION_3 MATLAB code for gui_set_resolution_3.fig
+%      GUI_SET_RESOLUTION_3 by itself, creates a new GUI_SET_RESOLUTION_3 or raises the
+%      existing singleton*.
+%
+%      H = GUI_SET_RESOLUTION_3 returns the handle to a new GUI_SET_RESOLUTION_3 or the handle to
+%      the existing singleton*.
+%
+%      GUI_SET_RESOLUTION_3('CALLBACK',hObject,eventData,handles,...) calls the local
+%      function named CALLBACK in GUI_SET_RESOLUTION_3.M with the given input arguments.
+%
+%      GUI_SET_RESOLUTION_3('Property','Value',...) creates a new GUI_SET_RESOLUTION_3 or raises the
+%      existing singleton*.  Starting from the left, property value pairs are
+%      applied to the GUI before gui_set_resolution_3_OpeningFcn gets called.  An
+%      unrecognized property name or invalid value makes property application
+%      stop.  All inputs are passed to gui_set_resolution_3_OpeningFcn via varargin.
+%
+%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
+%      instance to run (singleton)".
+%
+% See also: GUIDE, GUIDATA, GUIHANDLES
+
+% Edit the above text to modify the response to help gui_set_resolution_3
+
+% Last Modified by GUIDE v2.5 03-Aug-2018 03:41:41
+
+% Begin initialization code - DO NOT EDIT
+gui_Singleton = 1;
+gui_State = struct('gui_Name',       mfilename, ...
+                   'gui_Singleton',  gui_Singleton, ...
+                   'gui_OpeningFcn', @gui_set_resolution_3_OpeningFcn, ...
+                   'gui_OutputFcn',  @gui_set_resolution_3_OutputFcn, ...
+                   'gui_LayoutFcn',  [] , ...
+                   'gui_Callback',   []);
+if nargin && ischar(varargin{1})
+    gui_State.gui_Callback = str2func(varargin{1});
+end
+
+if nargout
+    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
+else
+    gui_mainfcn(gui_State, varargin{:});
+end
+% End initialization code - DO NOT EDIT
+
+% --- Executes just before gui_set_resolution_3 is made visible.
+function gui_set_resolution_3_OpeningFcn(hObject, eventdata, handles, varargin)
+% This function has no output args, see OutputFcn.
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+% varargin   command line arguments to gui_set_resolution_3 (see VARARGIN)
+
+% Choose default command line output for gui_set_resolution_3
+% handles.output1 = 1;
+% handles.output1='aadata';
+handles.output1='1';
+handles.output2 = '1';
+handles.output = handles.output1;
+% set(handles.edit1,'Enable','off');  
+set(handles.radio_from_number,'Value',1);  
+
+handles.path =varargin{2};
+handles.Ext=varargin{3};
+%  parseInputs(varargin)
+% Update handles structure
+guidata(hObject, handles);
+
+% Insert custom Title and Text if specified by the user
+% Hint: when choosing keywords, be sure they are not easily confused 
+% with existing figure properties.  See the output of set(figure) for
+% a list of figure properties.
+if(nargin > 3)
+    for index = 1:2:(nargin-3),
+        if nargin-3==index, break, end
+        switch lower(varargin{index})
+         case 'title'
+          set(hObject, 'Name', varargin{index+1});
+         case 'string'
+          set(handles.text1, 'String', varargin{index+1});
+        end
+    end
+end
+
+% Determine the position of the dialog - centered on the callback figure
+% if available, else, centered on the screen
+FigPos=get(0,'DefaultFigurePosition');
+OldUnits = get(hObject, 'Units');
+set(hObject, 'Units', 'pixels');
+OldPos = get(hObject,'Position');
+FigWidth = OldPos(3);
+FigHeight = OldPos(4);
+if isempty(gcbf)
+    ScreenUnits=get(0,'Units');
+    set(0,'Units','pixels');
+    ScreenSize=get(0,'ScreenSize');
+    set(0,'Units',ScreenUnits);
+
+    FigPos(1)=1/2*(ScreenSize(3)-FigWidth);
+    FigPos(2)=2/3*(ScreenSize(4)-FigHeight);
+else
+    GCBFOldUnits = get(gcbf,'Units');
+    set(gcbf,'Units','pixels');
+    GCBFPos = get(gcbf,'Position');
+    set(gcbf,'Units',GCBFOldUnits);
+    FigPos(1:2) = [(GCBFPos(1) + GCBFPos(3) / 2) - FigWidth / 2, ...
+                   (GCBFPos(2) + GCBFPos(4) / 2) - FigHeight / 2];
+end
+FigPos(3:4)=[FigWidth FigHeight];
+set(hObject, 'Position', FigPos);
+set(hObject, 'Units', OldUnits);
+
+% Show a question icon from dialogicons.mat - variables questIconData
+% and questIconMap
+load dialogicons.mat;
+
+IconData=questIconData;
+questIconMap(256,:) = get(handles.figure1, 'Color');
+IconCMap=questIconMap;
+
+Img=image(IconData, 'Parent', handles.axes1);
+set(handles.figure1, 'Colormap', IconCMap);
+
+set(handles.axes1, ...
+    'Visible', 'off', ...
+    'YDir'   , 'reverse'       , ...
+    'XLim'   , get(Img,'XData'), ...
+    'YLim'   , get(Img,'YData')  ...
+    );
+
+% Make the GUI modal
+set(handles.figure1,'WindowStyle','modal')
+
+% UIWAIT makes gui_set_resolution_3 wait for user response (see UIRESUME)
+uiwait(handles.figure1);
+
+% --- Outputs from this function are returned to the command line.
+function varargout = gui_set_resolution_3_OutputFcn(hObject, eventdata, handles)
+% varargout  cell array for returning output args (see VARARGOUT);
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Get default command line output from handles structure
+varargout{1} = handles.output1;
+varargout{2} = handles.output1;
+
+% The figure can be deleted now
+delete(handles.figure1);
+
+% --- Executes on button press in push_yes.
+function push_yes_Callback(hObject, eventdata, handles)
+% hObject    handle to push_yes (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+handles.output = handles.output2; %get(hObject,'String');
+
+% Update handles structure
+guidata(hObject, handles);
+
+% Use UIRESUME instead of delete because the OutputFcn needs
+% to get the updated handles structure.
+uiresume(handles.figure1);
+
+% --- Executes on button press in push_NO.
+function push_NO_Callback(hObject, eventdata, handles)
+% hObject    handle to push_NO (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% handles.output = handles.output1; % get(hObject,'String');
+
+handles.output = 'aadata';
+handles.output1 = 'aadata';
+handles.output2 = 'aadata';
+% Update handles structure
+guidata(hObject, handles);
+
+% Use UIRESUME instead of delete because the OutputFcn needs
+% to get the updated handles structure.
+uiresume(handles.figure1);
+
+
+% --- Executes when user attempts to close figure1.
+function figure1_CloseRequestFcn(hObject, eventdata, handles)
+% hObject    handle to figure1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+if isequal(get(hObject, 'waitstatus'), 'waiting')
+    % The GUI is still in UIWAIT, us UIRESUME
+    uiresume(hObject);
+else
+    % The GUI is no longer waiting, just close it
+    delete(hObject);
+end
+
+
+% --- Executes on key press over figure1 with no controls selected.
+function figure1_KeyPressFcn(hObject, eventdata, handles)
+% hObject    handle to figure1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Check for "enter" or "escape"
+if isequal(get(hObject,'CurrentKey'),'escape')
+    % User said no by hitting escape
+    handles.output = handles.output1; %'No';
+    
+    % Update handles structure
+    guidata(hObject, handles);
+    
+    uiresume(handles.figure1);
+end    
+    
+if isequal(get(hObject,'CurrentKey'),'return')
+    uiresume(handles.figure1);
+end    
+
+
+
+function edit1_Callback(hObject, eventdata, handles)
+% hObject    handle to edit1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of edit1 as text
+%        str2double(get(hObject,'String')) returns contents of edit1 as a double
+handles.output1 = get(hObject,'String'); 
+guidata(hObject, handles);
+
+% --- Executes during object creation, after setting all properties.
+function edit1_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to edit1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end
+
+
+
+
+      
+
+
+% --- Executes when selected object is changed in uibuttongroup1.
+function uibuttongroup1_SelectionChangedFcn(hObject, eventdata, handles)
+% hObject    handle to the selected object in uibuttongroup1 
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+% handles    empty - handles not created until after all CreateFcns called
+c= get(hObject,'String')
+
+ switch c
+  
+  case {'1 pixel ='}
+    set(handles.edit1,'Enable','on');  
+      handles.output1= handles.output2;
+    
+    
+  
+  case 'Calculate from CALIBRATION GRID'
+      
+    set(handles.edit1,'Enable','off');  
+    set(handles.dis_txt_2, 'String','');
+      
+    [filename,pathname, FILTERINDEX] = uigetfile( ...
+       {strcat('*', handles.Ext), strcat(handles.Ext,'-files') },  ...
+         'MultiSelect', 'on', 'Selet the Calibration image', handles.path);
+    handles.ref_file=[];
+    if FILTERINDEX==1
+        handles.ref_file = strcat(pathname, filename);
+        tmp = imread(handles.ref_file );
+        [tmp1, tmp2, tmp3]=gui_ask_calibration1(tmp);
+    else
+        tmp1='Cancel';
+%         set(handles.radio_from_null,'Value',1);  
+        handles.output1='1';
+        set(handles.radio_from_number,'Value',1); 
+        set(handles.edit1,'Enable','on');  
+%         set(handles.radio_from_number,'Value',1);  
+
+
+        
+    end
+    
+    
+%     tmp1='Cancel';
+%     try
+%     [tmp1, tmp2, tmp3]=gui_ask_calibration1(tmp)
+%     catch
+%     end 
+    
+    switch tmp1
+        case 'Ok'
+            dst=sqrt((tmp2(1)-tmp2(2)).^2+(tmp3(1)-tmp3(2)).^2);
+            if ~isnan(dst), handles.output1 = 1e6*50e-3/dst; 
+                set(handles.dis_tex, 'String', strcat(' 1 pix=' ,num2str(handles.output1),'micrometer'));
+            else handles.output1= handles.output2; end
+            
+            guidata(hObject, handles);
+        
+        case 'Cancel'
+            handles.output1= handles.output2;
+            
+            handles.output1='1';
+            set(handles.radio_from_number,'Value',1); 
+            set(handles.edit1,'Enable','on');  
+
+            guidata(hObject, handles);
+        otherwise
+            handles.output1= handles.output2;
+            handles.output1='1';
+            set(handles.radio_from_number,'Value',1); 
+            set(handles.edit1,'Enable','on');  
+    end
+    
+
+    
+    %===============================================================
+     case 'Calculate from known image'
+      
+    set(handles.edit1,'Enable','off');  
+    set(handles.dis_tex, 'String','' );
+      
+    [filename,pathname, FILTERINDEX] = uigetfile( ...
+       {strcat('*', handles.Ext), strcat(handles.Ext,'-files') },  ...
+         'MultiSelect', 'on', 'Selet the Calibration image', handles.path);
+    handles.ref_file=[];
+    if FILTERINDEX==1
+        handles.ref_file = strcat(pathname, filename);
+        tmp = imread(handles.ref_file );
+        [tmp1, tmp2, tmp3, tmp4]=gui_ask_cal_KNOWN_Point(tmp);
+    else
+        tmp1='Cancel';
+%         set(handles.radio_from_null,'Value',1);  
+        handles.output1='1';
+        set(handles.radio_from_number,'Value',1); 
+        set(handles.edit1,'Enable','on');  
+%         set(handles.radio_from_number,'Value',1);  
+
+
+        
+    end
+ 
+    
+    switch tmp1
+        case 'Set'
+            dst=sqrt((tmp2(1)-tmp2(2)).^2+(tmp3(1)-tmp3(2)).^2);
+            if ~isnan(dst), handles.output1 = 1e6*tmp4/dst; 
+                set(handles.dis_txt_2, 'String', strcat(' 1 pix=' ,num2str(handles.output1),'micrometer'));
+                
+            else, handles.output1= handles.output2; end
+            
+            guidata(hObject, handles);
+        
+        case 'Cancel'
+            handles.output1= handles.output2;
+            
+            handles.output1='1';
+            set(handles.radio_from_number,'Value',1); 
+            set(handles.edit1,'Enable','on');  
+
+            guidata(hObject, handles);
+        otherwise
+            handles.output1= handles.output2;
+            handles.output1='1';
+            set(handles.radio_from_number,'Value',1); 
+            set(handles.edit1,'Enable','on');  
+    end
+    
+    
+       
+%     figure, imshow(tmp,[])
+    
+  otherwise
+    disp('aadata')
+    set(handles.edit1,'Enable','off');  
+    handles.output1='aadata';
+  
+     guidata(hObject, handles); 
+      
+      
+ end    
+
+
+% --- Executes on button press in radio_from_number.
+function radio_from_number_Callback(hObject, eventdata, handles)
+% hObject    handle to radio_from_number (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hint: get(hObject,'Value') returns toggle state of radio_from_number
+handles.output1=1;
+guidata(hObject, handles);
+
+
+% --- Executes on button press in radio_from_null.
+function radio_from_null_Callback(hObject, eventdata, handles)
+% hObject    handle to radio_from_null (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hint: get(hObject,'Value') returns toggle state of radio_from_null
+
+
+% --- Executes on button press in radio_from_image.
+function radio_from_image_Callback(hObject, eventdata, handles)
+% hObject    handle to radio_from_image (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hint: get(hObject,'Value') returns toggle state of radio_from_image
+
+
+% --- Executes during object creation, after setting all properties.
+function dis_tex_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to dis_tex (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+
+% --- Executes on button press in radio_from_KNOWN_IMAGE.
+function radio_from_KNOWN_IMAGE_Callback(hObject, eventdata, handles)
+% hObject    handle to radio_from_KNOWN_IMAGE (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hint: get(hObject,'Value') returns toggle state of radio_from_KNOWN_IMAGE
+
+
+% --- Executes during object creation, after setting all properties.
+function dis_txt_2_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to dis_txt_2 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called

src/dic/image_background2.m

@@ -0,0 +1,80 @@
+function image_background2(im2, xi,yi,value,dd, tiTl, Tltt, Hpath)
+
+% load('DIC_vecdata.mat', 'im2', 'xi','yi','U_inp');
+
+[x11, y11]= meshgrid(min(xi):max(xi),min(yi):max(yi));
+% [a b]=meshgrid(yi,xi);
+% F = TriScatteredInterp(b(:),a(:),iu(:),'natural');
+% ius = F(x11,y11);
+
+size(x11);
+
+Yi= y11(:,1)+dd(2);
+Xi= x11(1,:)++dd(1);
+
+size(Xi);
+size(Yi);
+
+if (size(x11,1)<= size(x11,2))
+    sze=min(numel(Yi),numel(Xi));
+    sze1=max(numel(Yi),numel(Xi));
+end
+
+if (size(x11,1)> size(x11,2))
+    sze1=min(numel(Yi),numel(Xi));
+    sze=max(numel(Yi),numel(Xi));
+end
+
+
+iiy=repmat(Yi(:)',1, sze1);
+tmp=iiy(2)-iiy(1);
+iiy1=  iiy-tmp;
+
+gridy_patch_i =[iiy;iiy1;iiy1;iiy];
+
+% size(gridy_patch_i)
+
+%ix
+
+tmp=[];
+for iii=1:numel(Xi)
+    tmp=[tmp repmat(Xi(iii),1,sze)];
+end
+
+iix = tmp;
+
+tmp=Xi(2)-Xi(1);
+iix1=  iix+tmp;
+
+gridx_patch_i = [iix; iix; iix1;iix1];
+size(gridx_patch_i);
+
+data_i_trans = (value(:)'); %transpose from column to row vector
+size(data_i_trans );
+
+data_patch = [data_i_trans; data_i_trans; data_i_trans; data_i_trans]; %Same disp grad at four vertices of patch square
+
+
+fig110=figure; set(fig110, 'Visible', 'off');
+imshow(im2,[]); colormap('gray')
+freezeColors, hold on, colormap('jet')
+        
+patch_layer = patch(gridx_patch_i,gridy_patch_i,data_patch,'EdgeColor','none','FaceAlpha',0.5);    
+
+ axis ij
+    axis equal
+    
+    title( strcat(Tltt,'  ', '(Full Frame)'))
+%     title(['Contour plot of ',1,sprintf(' (Current image #: )',10)],...
+%         'fontsize',10,'fontweight','bold')
+    xlabel('[ X-direction ]', 'fontsize',10,'fontweight','bold')
+    ylabel('[ Y-direction ]', 'fontsize',10,'fontweight','bold')
+    set(gca,'fontsize',10,'layer','top')
+    caxis([min(data_i_trans(:)),max(data_i_trans(:))])
+    h = colorbar('Location','EastOutside');
+    title(h,tiTl, 'fontsize',10)
+    Ttt=strcat('[Full_Frame]',Tltt);
+   saveas(gcf, strcat(Hpath,'\',Ttt))
+close(fig110)
+
+

src/dic/myLogfile.m

@@ -0,0 +1,52 @@
+function myLogfile(destination ,imageORvideo,frame_no,DefaultORcrop, REF_image, method,windo_size,overlap) 
+
+
+% imageORvideo='Image';
+% frame_no=0;
+% DefaultORcrop='Full Frame';
+% REF_image='my';
+% method='cross correlation';
+% windo_size=50;
+% overlap=0.7;
+p1i=0;
+%************** Output to file ********************************************
+% s=cd;s=s(max(find(s=='/'))+1:end);
+% strcat(destination, 'Logfile.txt' );
+fid = fopen(strcat(destination, '\Logfile.txt' ), 'wt');
+strcat(destination, '\Logfile.txt' )
+% fprintf(fid, '%f\n%f\n%f\n%f\n%f\n%f\n%f\n%f\n%f\n%f\n%f\n%f',...
+%     Ms, pt1, T5, p5, rho5, M, p1i, T1i, u1i, rho1i, (Re1i/1e+06), ...
+%     (H/1e+06));
+% fclose(fid);
+
+fprintf(fid,'%s\t\t\t\t%s\n%s\t\t\t\t\t%d\n%s\t\t%s\n%s\t\t\t\t\t%s\n %s\t\t\t\t\t%s\n%s\t\t\t\t\t%f\n%s\t\t\t%f\n %s\t\t\t%f\n %s\t\t\t\t%f\n %s\t\t\t\t\t%f\n %s\t\t\t%f\n',...
+    'Types of Processing (Image or Video)', imageORvideo,...
+    'Total Number of Frames', frame_no,...
+    'Image Cropped ?',DefaultORcrop,...
+    'Reference Image',REF_image,...
+    'Method of Processing',method,...
+    'window size',windo_size,...
+    'Overlap',overlap,...
+    'Set IT',p1i,...
+    'Set IT',p1i,...
+    'Set IT',p1i,...
+    'Set IT',p1i,...
+    'Set IT',p1i,...
+    'Set IT',p1i);
+fclose(fid);
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

src/dic/myLogfile_more.m

@@ -0,0 +1,52 @@
+function myLogfile(destination ,imageORvideo,frame_no,DefaultORcrop, REF_image, method,windo_size,overlap) 
+
+
+% imageORvideo='Image';
+% frame_no=0;
+% DefaultORcrop='Full Frame';
+% REF_image='my';
+% method='cross correlation';
+% windo_size=50;
+% overlap=0.7;
+p1i=0;
+%************** Output to file ********************************************
+% s=cd;s=s(max(find(s=='/'))+1:end);
+% strcat(destination, 'Logfile.txt' );
+fid = fopen(strcat(destination, '\Logfile.txt' ), 'wt');
+strcat(destination, '\Logfile.txt' )
+% fprintf(fid, '%f\n%f\n%f\n%f\n%f\n%f\n%f\n%f\n%f\n%f\n%f\n%f',...
+%     Ms, pt1, T5, p5, rho5, M, p1i, T1i, u1i, rho1i, (Re1i/1e+06), ...
+%     (H/1e+06));
+% fclose(fid);
+
+fprintf(fid,'%s\t\t\t\t%s\n%s\t\t\t\t\t%d\n%s\t\t%s\n%s\t\t\t\t\t%s\n %s\t\t\t\t\t%s\n%s\t\t\t\t\t%f\n%s\t\t\t%f\n %s\t\t\t%f\n %s\t\t\t\t%f\n %s\t\t\t\t\t%f\n %s\t\t\t%f\n',...
+    'Types of Processing (Image or Video)', imageORvideo,...
+    'Total Number of Frames', frame_no,...
+    'Image Cropped ?',DefaultORcrop,...
+    'Reference Image',REF_image,...
+    'This package is written by Biswajit Medhi',method,...
+    'window size',windo_size,...
+    'Overlap',overlap,...
+    'Set IT',p1i,...
+    'Set IT',p1i,...
+    'Set IT',p1i,...
+    'Set IT',p1i,...
+    'Set IT',p1i,...
+    'Set IT',p1i);
+fclose(fid);
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

src/dic/preset_image.m

@@ -0,0 +1,5 @@
+function[imr11]= preset_image(imr1)
+
+    if (numel(size(imr1))>2), imr1=rgb2gray(imr1); end
+    imr11 = histeq(imr1);
+    imr11=double(imr11);

src/dic/uigetfile_with_preview2.m

@@ -0,0 +1,282 @@
+function [filename, pathname, filterindex] = uigetfile_with_preview2(filterSpec, prompt, folder,callback, multiSelect)
+% uigetfile_with_preview - GUI dialog window with a preview panel
+%
+% Syntax:
+%    filename = uigetfile_with_preview(filterSpec, prompt, folder, callback, multiSelect)
+%
+% Description:
+%    uigetfile_with_preview displays a file-selection dialog with an
+%    integrated preview panel.
+%
+% Inputs:
+%    filterSpec - similar to uigetfile's filterSpec. Examples:
+%                    'defaultFile.mat'
+%                    '*.mat'
+%                    {'MAT files', '*.mat'}
+%                    {'Data or m files (*.m,*.mat)', {'m';'mat'}}
+%    prompt     - optional dialog prompt (default: 'Select file')
+%    folder     - optional default folder (default: current folder)
+%    callback   - optional handle to a callback function with the following
+%                 interface:
+%                    callbackFunction(hPanel, filename)
+%                 The callback function should check the specified file and
+%                 update the specified panel accordingly.
+%                 (default: [])
+%    multiSelect - optional flag specifying whether multiple files can be
+%                  selected (default: false)
+%
+% Output:
+%    filename - full-path filename of the selected file(s) (or empty array)
+%
+% Bugs and suggestions:
+%    Please send to Yair Altman (altmany at gmail dot com)
+%
+% Change log:
+%    2016-11-02: First version posted on <a href="https://www.mathworks.com/matlabcentral/fileexchange/?term=authorid%3A27420">MathWorks File Exchange</a>
+%
+% See also:
+%    uigetfile
+
+% Programmed by Yair M. Altman: altmany(at)gmail.com
+% $Revision: 1.0 $  $Date: 2016/11/02 23:43:54 $
+
+  if nargin < 1,  filterSpec = {'All files','*.*'};  end
+  if nargin < 2,  prompt = '';          end
+  if nargin < 3,  folder = pwd;         end
+  if nargin < 4,  callback = '';        end
+  if nargin < 5,  multiSelect = false;  end
+
+  % Prepare the figure dialog window
+  if isempty(prompt),  prompt = 'Select file';  end
+  hFig = dialog('Name',prompt, 'units','pixel', 'pos',[200,50,500,600]);
+
+
+  % Display the file-selection component
+  javaComponentName = 'javax.swing.JFileChooser'; %#ok<NASGU>
+  javaComponentName = 'com.mathworks.hg.util.dFileChooser';  % this is a MathWorks extension of JFileChooser - no good on Win7
+  %javaComponentName = 'com.mathworks.mwswing.MJFileChooserPerPlatform';
+  [hjFileChooser, hContainer] = javacomponent(javaComponentName, [0,200,500,400], hFig); %#ok<ASGLU>
+  hjFileChooser.setCurrentDirectory(java.io.File(folder));
+  hjFileChooser.setMultiSelectionEnabled(multiSelect);
+  drawnow;
+
+  % Java default background colors are different from Matlab's - fix this
+  %bgcolor = hjFileChooser.Background.getComponents([]);
+  %set(hFig,'color',bgcolor(1:3));
+  bgcolor = get(hFig,'color');
+  hjFileChooser.Background = java.awt.Color(bgcolor(1),bgcolor(2),bgcolor(3));
+
+  % Prepare the allowable file types filter (similar to the uigetfile function)
+  if ~isempty(filterSpec)
+      if ischar(filterSpec)
+          origFilterSpec = filterSpec;
+          [dummy,dummy,ext] = fileparts(filterSpec); %#ok<ASGLU>
+          filterSpec = {[ext(2:end) ' files'], ['*' ext]};
+          if ~any(origFilterSpec=='*')
+              try hjFileChooser.setSelectedFile(java.io.File(origFilterSpec)); catch, end
+          end
+      end
+      hjFileChooser.setAcceptAllFileFilterUsed(false);
+      fileFilter = {};
+      %fileFilter{1} = AddFileFilter(hjFileChooser, 'Data files (*.mat)', {'mat'});
+      %fileFilter{2} = AddFileFilter(hjFileChooser, 'Data or m files (*.m,*.mat)', {'m';'mat'});
+      %fileFilter{3} = AddFileFilter(hjFileChooser, 'All Files', '*.*');
+      for filterIdx = 1 : size(filterSpec,1)
+          fileFilter{end+1} = AddFileFilter(hjFileChooser, filterSpec{filterIdx,:}); %#ok<AGROW>
+      end
+      try
+          hjFileChooser.setFileFilter(fileFilter{1});  % use the first filter by default
+      catch
+          % never mind - ignore...
+      end
+  end
+
+  % Prepare the preview panel
+  hPreviewPanel = uipanel('parent',hFig, 'title','Preview', 'tag','PreviewPanel', ...
+      'units','pixel', 'pos',[10,10,480,180], 'Background',bgcolor(1:3));
+
+  % Prepare the figure callbacks
+  hjFileChooser.PropertyChangeCallback  = {@PreviewCallback,hPreviewPanel,callback};
+  hjFileChooser.ActionPerformedCallback = {@ActionPerformedCallback,hFig};
+
+  % Key-typed callback
+  try
+      hFn = handle(hjFileChooser.getComponent(2).getComponent(2).getComponent(2).getComponent(1),'CallbackProperties');
+      % hFn should be a javahandle_withcallbacks.com.sun.java.swing.plaf.windows.WindowsFileChooserUI$7
+      hFn.KeyTypedCallback = {@KeyTypedCallback,hjFileChooser};
+  catch
+      % maybe the file-chooser editbox changed location
+  end
+
+  % Wait for user input
+  uiwait(hFig);
+  
+  % We get here if the figure is either deleted or Cancel/Open were pressed
+  if ishghandle(hFig)
+      % Open were clicked
+      filename = getappdata(hFig,'selectedFile');
+      close(hFig);
+  else  % figure was deleted/closed
+      filename = '';
+  end
+end  % uigetfile_with_preview
+
+%% Add a file filter type
+function fileFilter = AddFileFilter(hjFileChooser, description, extension)
+  try
+      if ~iscell(extension)
+          extension = {extension};
+      end
+      if strcmp(extension{1},'*.*') %any(extension{1} == '*')
+          jBasicFileChooserUI = javax.swing.plaf.basic.BasicFileChooserUI(hjFileChooser.java);
+          fileFilter = javaObjectEDT('javax.swing.plaf.basic.BasicFileChooserUI$AcceptAllFileFilter',jBasicFileChooserUI);
+      else
+          extension = regexprep(extension,'^.*\*?\.','');
+          fileFilter = com.mathworks.mwswing.FileExtensionFilter(description, extension, false, true);
+      end
+      javaMethodEDT('addChoosableFileFilter',hjFileChooser,fileFilter);
+  catch
+      % ignore...
+      fileFilter = [];
+  end
+end  % AddFileFilter
+
+%% Preview callback function
+function PreviewCallback(hjFileChooser, eventData, hPreviewPanel, callback) %#ok<INUSL>
+  try
+      % Get the selected file
+      filename = char(hjFileChooser.getSelectedFile);
+      if isempty(filename) || ~exist(filename,'file')
+          return;  % bail out
+      end
+  
+      % Analyze the file based on its type
+      ClearPanel(hPreviewPanel)
+      if isempty(callback)  % default callback
+          [fpath,fname,fext] = fileparts(filename); %#ok<ASGLU>
+          switch fext
+%               case '.mat'
+%                   % Load the first data element in the file
+%                   data = load(filename);
+%                   fnames = fieldnames(data);
+%                   data = data.(fnames{1});
+% 
+%                   % Update the preview panel
+%                   hax = axes('Parent',hPreviewPanel, 'units','norm', 'LooseInset',[0,0,0,0]);
+%                   plot(hax, data.x, data.y);
+%                   box(hax, 'off');
+
+              case '.tif'
+                  % Load the first data element in the file
+                  data = imread(filename);
+                  if (numel(size(data)))<3 
+                      v=data;
+                      v1=zeros([size(v),3]);v1(:,:,1)=v; v1(:,:,2)=v;v1(:,:,3)=v;
+                      data=uint8(v1); v1=[]; v=[];
+                  end
+                  % Update the preview panel
+                  hax = axes('Parent',hPreviewPanel, 'units','norm', 'LooseInset',[0,0,0,0]);
+                  image(data)
+                  %plot(hax, data.x, data.y);
+                  box(hax, 'off');
+              case '.tiff'
+                  % Load the first data element in the file
+                  data = imread(filename);
+                  if (numel(size(data)))<3 
+                      v=data;
+                      v1=zeros([size(v),3]);v1(:,:,1)=v; v1(:,:,2)=v;v1(:,:,3)=v;
+                      data=uint8(v1); v1=[]; v=[];
+                  end
+                  
+                  
+                  % Update the preview panel
+                  hax = axes('Parent',hPreviewPanel, 'units','norm', 'LooseInset',[0,0,0,0]);
+                  image(data)
+                  %plot(hax, data.x, data.y);
+                  box(hax, 'off');
+              case '.jpg'
+                  % Load the first data element in the file
+                  data = imread(filename);
+                  if (numel(size(data)))<3 
+                      v=data;
+                      v1=zeros([size(v),3]);v1(:,:,1)=v; v1(:,:,2)=v;v1(:,:,3)=v;
+                      data=uint8(v1); v1=[]; v=[];
+                  end
+                  % Update the preview panel
+                  hax = axes('Parent',hPreviewPanel, 'units','norm', 'LooseInset',[0,0,0,0]);
+                  image(data)
+                  %plot(hax, data.x, data.y);
+                  box(hax, 'off');
+
+
+                case '.bmp'
+                  % Load the first data element in the file
+                  data = imread(filename);
+                  if (numel(size(data)))<3 
+                      v=data;
+                      v1=zeros([size(v),3]);v1(:,:,1)=v; v1(:,:,2)=v;v1(:,:,3)=v;
+                      data=uint8(v1); v1=[]; v=[];
+                  end
+                  % Update the preview panel
+                  hax = axes('Parent',hPreviewPanel, 'units','norm', 'LooseInset',[0,0,0,0]);
+                  image(data)
+                  %plot(hax, data.x, data.y);
+                  box(hax, 'off');
+
+              
+              otherwise
+                  % Do something useful here...
+          end
+      else  % user-specified callback that accepts hPreviewPanel,filename
+          callback(hPreviewPanel,filename);
+      end
+  catch
+      % Never mind - bail out...
+  end
+end  % PreviewCallback
+
+%% Clear the specified panel
+function ClearPanel(hPanel)
+  try
+      hObjs = findall(hPanel);
+      hObjs = setdiff(hObjs, findall(hPanel,'string',get(hPanel,'title')));  % keep the title
+      %delete(hObjs(2:end));
+      hObjs = setdiff(hObjs, hPanel);  % this is safer...
+      delete(hObjs);
+  catch
+      % ignore...
+  end
+end  % ClearPanel
+
+%% Figure actions (Cancel & Open)
+function ActionPerformedCallback(hjFileChooser, eventData, hFig)
+  switch char(eventData.getActionCommand)
+      case 'CancelSelection'
+          close(hFig);
+
+      case 'ApproveSelection'
+          files = cellfun(@char, cell(hjFileChooser.getSelectedFiles), 'uniform',0);
+          %msgbox(['Selected file: ' files{:}], 'Selected!');
+          if numel(files)==1
+              %files = files{1};
+          end
+          if isempty(files)
+              files = char(hjFileChooser.getSelectedFile);
+          end
+          setappdata(hFig,'selectedFile', files);
+          uiresume(hFig);
+
+      otherwise
+          % should never happen
+  end
+end  % ActionPerformedCallback
+
+%% Key-types callback in the file-name editbox
+function KeyTypedCallback(hEditbox, eventData, hjFileChooser) %#ok<INUSL>
+  text = char(get(hEditbox,'Text'));
+  [wasFound,idx,unused,folder] = regexp(text,'(.*[:\\/])'); %#ok<ASGLU>
+  if wasFound
+      % This will silently fail if folder does not exist
+      hjFileChooser.setCurrentDirectory(java.io.File(folder));
+  end
+end