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+function varargout = gui_win(varargin)
+% gui_win MATLAB code for gui_win.fig
+%      gui_win, by itself, creates a new gui_win or raises the existing
+%      singleton*.
+%
+%      H = gui_win returns the handle to a new gui_win or the handle to
+%      the existing singleton*.
+%
+%      gui_win('CALLBACK',hObject,eventData,handles,...) calls the local
+%      function named CALLBACK in gui_win.M with the given input arguments.
+%
+%      gui_win('Property','Value',...) creates a new gui_win or raises the
+%      existing singleton*.  Starting from the left, property value pairs are
+%      applied to the gui_win before gui_win_OpeningFcn gets called.  An
+%      unrecognized property name or invalid value makes property application
+%      stop.  All inputs are passed to gui_win_OpeningFcn via varargin.
+%
+%      *See gui_win Options on GUIDE's Tools menu.  Choose "gui_win allows only one
+%      instance to run (singleton)".
+%
+% See also: GUIDE, GUIDATA, GUIHANDLES
+
+% Edit the above text to modify the response to help gui_win
+
+% Last Modified by GUIDE v2.5 10-Sep-2012 11:34:46
+
+% Begin initialization code - DO NOT EDIT
+gui_Singleton = 1;
+gui_State = struct('gui_Name',       mfilename, ...
+    'gui_Singleton',  gui_Singleton, ...
+    'gui_OpeningFcn', @gui_win_OpeningFcn, ...
+    'gui_OutputFcn',  @gui_win_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_win is made visible.
+function gui_win_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_win (see VARARGIN)
+
+% Choose default command line output for gui_win
+handles.output = hObject;
+
+% Update handles structure
+guidata(hObject, handles);
+
+% Set color of the strart button to green
+set(handles.togglebutton1,'BackgroundColor','Green');
+
+% Declare global variables
+global background_m;
+global image_name;
+global isworking;
+global image_m;
+global image_original;
+global image_cleaned;
+global image_fitted;
+
+% Initial values
+background_m = 0;
+image_m = 0;
+image_original = 0;
+image_cleaned = 0;
+image_fitted = 0;
+image_name = 'test.png';
+isworking = 0;
+
+% Don`t show ticks for the minor windows
+set(handles.axes6,'PlotBoxAspectRatio',[4 3 1],'DataAspectRatio',[1 1 1],'YTick',[],'XTick',[]);
+set(handles.xsection,'PlotBoxAspectRatio',[4 3 1],'DataAspectRatio',[1 1 1],'YTick',[],'XTick',[]);
+set(handles.ysection,'PlotBoxAspectRatio',[4 3 1],'DataAspectRatio',[1 1 1],'YTick',[],'XTick',[]);
+
+
+
+% --- Outputs from this function are returned to the command line.
+function varargout = gui_win_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;
+
+
+
+
+
+
+
+% This funcion just calls the external program which takes an image from camera
+% We call it with parameters read from the GUI fields
+function grabimage(handles)
+global image_name;
+global image_m;
+global image_original;
+run_string = horzcat('grabNimages_1394cam.exe -s ',num2str(get(handles.edit2,'String')),' -n ',num2str(get(handles.edit3,'String')));
+system(run_string);
+img=imread(image_name);
+image_m=double(img);
+image_original=image_m;
+
+
+
+
+
+function display_stuff(handles)
+global image_m;
+global background_m;
+
+
+% If we need to substract the background, we do it
+% background_m is a global variable
+if get(handles.togglebutton2,'Value') > 0
+    m = image_m - background_m;
+else
+    m = image_m;
+end;
+
+% Read the tolerance value from the GUI
+tol = str2num(get(handles.edit1,'String'));
+
+% Display what we have before doing fit
+axes(handles.original_image);
+imagesc(m);
+set(handles.original_image,'PlotBoxAspectRatio',[4 3 1],'DataAspectRatio',[1 1 1]);
+drawnow;
+
+
+
+
+
+% This function is executed when START button is pressed.
+% We do different stuff depending on the radiobutton selection
+
+% --- Executes on button press in togglebutton1.
+function togglebutton1_Callback(hObject, eventdata, handles)
+% hObject    handle to togglebutton1 (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 togglebutton1
+
+global isworking;
+global image_m;
+isworking =1;
+% Paint the button and change text
+set(handles.togglebutton1,'BackgroundColor','Red');
+set(handles.togglebutton1,'String','STOP');
+drawnow;    % needed to draw this before doing fit
+
+
+
+
+
+% This is for the single run
+if get(handles.radiobutton2,'Value')
+    
+    % Grab an image from camera
+    grabimage(handles);
+    display_stuff(handles);
+    
+end;
+
+
+
+
+
+% This executes when we do the continious run
+% Same as the single fit exept that we have a while cycle
+if get(handles.radiobutton3,'Value')
+    
+    while get(handles.togglebutton1,'Value') > 0
+        
+        grabimage(handles);
+        display_stuff(handles);
+        
+        
+        
+    end;
+    
+end;
+
+
+
+% Paint it back
+set(handles.togglebutton1,'Value',0);
+set(handles.togglebutton1,'BackgroundColor','Green');
+set(handles.togglebutton1,'String','START');
+drawnow;
+isworking =0;
+
+
+
+
+% If we change the radiobutton setting we unpress the start button which will stop any activity.. eventually
+% Also here we check if we want to choose a file from a the file-open
+% dialog
+
+% --- Executes when selected object is changed in uipanel1.
+function uipanel1_SelectionChangeFcn(hObject, eventdata, handles)
+% hObject    handle to the selected object in uipanel1
+% eventdata  structure with the following fields (see UIBUTTONGROUP)
+%	EventName: string 'SelectionChanged' (read only)
+%	OldValue: handle of the previously selected object or empty if none was selected
+%	NewValue: handle of the currently selected object
+% handles    structure with handles and user data (see GUIDATA)
+
+set(handles.togglebutton1,'Value',0);
+global isworking;
+global image_m;
+global image_original;
+global pathname;
+isworking =1;
+
+% This calls a file-open dialog and runs the beam profiler on the choosen
+% file
+if get(handles.radiobutton4,'Value')
+    
+    set(handles.togglebutton1,'Value',1);
+    set(handles.togglebutton1,'BackgroundColor','Red');
+    set(handles.togglebutton1,'String','STOP');
+    drawnow;
+    
+    if ~isstr(pathname) % undefined variables are 0
+        pathname = 'Z:\beam_profier images';
+    end;
+    [filename, pathname, filterindex] = uigetfile( ...
+        {  '*.png','PNG-files (*.png)';},'DefaultName',pathname);
+    
+    if isequal(filename,0)
+    else
+        img=imread(fullfile(pathname,filename));
+        image_m=double(img);
+        image_original=image_m;
+        display_stuff(handles);
+        
+    end;
+    
+    set(handles.radiobutton4,'Value',0);
+    set(handles.togglebutton1,'BackgroundColor','Green');
+    set(handles.togglebutton1,'Value',0);
+    set(handles.togglebutton1,'String','START');
+end;
+isworking =0;
+
+
+
+% Executes when we press Clean button
+
+% --- Executes on button press in pushbutton10.
+function pushbutton10_Callback(hObject, eventdata, handles)
+% hObject    handle to pushbutton10 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+global isworking;
+global image_m;
+global image_cleaned;
+
+if (isworking == 1)
+else
+    isworking = 1;
+    set(handles.pushbutton10,'String','Working');
+    
+    %read the attenuation from the GUI
+    filter = str2num(get(handles.edit4,'String'));
+    radius = str2num(get(handles.edit5,'String'));
+    
+    %clean the image with the stripe eraser
+    [image_cleaned,~]=stripeeraser(image_m,radius,filter);
+    image_cleaned=abs(image_cleaned);
+    image_m=image_cleaned;
+    display_stuff(handles);
+    
+    set(handles.pushbutton10,'String','Clean');
+    set(handles.radiobutton8,'Value',1);
+end;
+isworking = 0;
+
+
+
+% Executes when we press Fit button
+
+% --- Executes on button press in pushbutton8.
+function pushbutton8_Callback(hObject, eventdata, handles)
+% hObject    handle to pushbutton8 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+global isworking;
+global image_m;
+global background_m;
+global image_fitted;
+
+if (isworking == 1)
+else
+isworking = 1;
+set(handles.pushbutton8,'String','Working');
+
+axes(handles.original_image);
+[x,y] = ginput(1);
+cx = x(1);
+cy = y(1);
+
+
+% If we need to substract the background, we do it
+% background_m is a global variable
+if get(handles.togglebutton2,'Value') > 0
+    m = image_m - background_m;
+else
+    m = image_m;
+end;
+
+
+% Read the tolerance value from the GUI
+tol = str2num(get(handles.edit1,'String'));
+
+
+% Here we do our fit. Output is a vector with gauss parameters
+p = fitgaussian2D(m,cx,cy,tol);
+
+
+% Parameters we got
+cx = p(1);
+cy = p(2);
+wx = p(3);
+wy = p(4);
+amp = p(5);
+theta = p(6);
+background=p(7);
+
+% Display them into the table in GUI
+set(handles.uitable1,'Data',p')
+
+% This is for drawing fitted gaussian
+[sizey sizex] = size(m);
+[x,y] = meshgrid(1:sizex,1:sizey);
+
+
+% This takes parameters 'p' and produces fit array (same size as initial 'm' array)
+fit = Gaussian2D(p,x,y);
+
+
+% Now we want to draw sections of our gaussians
+% If we have some wierd image and the center is outside of arrays, we do crossections on the closest border
+% Need it because there will be an error if we try to acces some data that is not in our arrays
+tcx = round(cx);
+if isnan(tcx) > 0
+    tcx = sizex/2;
+end;
+if round(cx) > sizex
+    tcx = sizex;
+end;
+if round(cx) < 1
+    tcx = 1;
+end;
+
+
+
+tcy = round(cy);
+if isnan(tcy) > 0
+    tcy = sizey/2;
+end;
+if round(cy) > sizey
+    tcy = sizey;
+end;
+if round(cy) < 1
+    tcy = 1;
+end;
+
+
+
+% Here we draw crossections
+hold off;
+axes(handles.ysection);
+h = plot(m(:,tcx));
+hold on;
+set(h,'Color','red','LineWidth',2);
+h = plot(fit(:,tcx));
+set(h,'Color','blue','LineWidth',2);
+
+hold off;
+axes(handles.xsection);
+h = plot(m(tcy,:));
+set(h,'Color','red','LineWidth',2);
+hold on;
+h = plot(fit(tcy,:));
+set(h,'Color','blue','LineWidth',2);
+hold off;
+
+
+%Here we plot the ideal fitted image
+
+
+for x=1:sizex
+    for y=1:sizey
+        Xn = (x-cx)*cos(theta) - (y-cy)*sin(theta);
+        Yn = (x-cx)*sin(theta) + (y-cy)*cos(theta);
+        image_fitted(y,x) = amp*(exp(-2*((Xn).^2./(wx^2)+(Yn).^2./(wy^2)))) + background;
+    end;
+end;
+
+
+
+set(handles.pushbutton8,'String','Fit');
+end;
+isworking = 0;
+
+
+
+
+
+
+%background substraction
+%here we only toggle on/off
+% --- Executes on button press in togglebutton2.
+function togglebutton2_Callback(hObject, eventdata, handles)
+% hObject    handle to togglebutton2 (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 togglebutton2
+
+if get(handles.togglebutton2,'Value') > 0
+    
+    set(handles.togglebutton2,'String','ON');
+    
+else
+    set(handles.togglebutton2,'String','OFF');
+end;
+
+
+
+
+
+
+
+%image saving
+% --- 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)
+global image_name;
+global image_m;
+%fname_to_save = horzcat(pwd,filesep,'saved_images',filesep,datestr(now, 'yyyy_mm_dd_HHMMSS'),'.png');
+fname_to_save = horzcat('Z:\beam_profier images',filesep,datestr(now, 'yyyy_mm_dd_HHMMSS'),'.png');
+
+set(handles.text12,'String',horzcat('Image saved to: ',fname_to_save));
+image_to_save=uint16(image_m);
+imwrite(image_to_save,fname_to_save,'png','bitdepth',16);
+
+
+
+
+
+
+
+% This executes when we want to grab the background from the camera
+% --- Executes on button press in pushbutton4.
+function pushbutton4_Callback(hObject, eventdata, handles)
+% hObject    handle to pushbutton4 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+global background_m;
+global image_m;
+global isworking;
+isworking =1;
+grabimage(handles);
+background_m = image_m;
+
+axes(handles.axes6);
+imagesc(background_m);
+set(handles.axes6,'PlotBoxAspectRatio',[4 3 1],'DataAspectRatio',[1 1 1],'YTick',[],'XTick',[]);
+drawnow;
+isworking =0;
+
+
+
+% This executes when we want to choose the background from a file
+% --- 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)
+
+
+global background_m;
+
+[filename, pathname, filterindex] = uigetfile( ...
+    {  '*.png','PNG-files (*.png)';});
+
+if isequal(filename,0)
+    
+    
+else
+    img=imread(fullfile(pathname,filename));
+    background_m = double(img);
+    
+    axes(handles.axes6);
+    imagesc(background_m);
+    set(handles.axes6,'PlotBoxAspectRatio',[4 3 1],'DataAspectRatio',[1 1 1],'YTick',[],'XTick',[]);
+    drawnow;
+end;
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+% --- Executes during object creation, after setting all properties.
+function figure1_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to figure1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Add the current directory to the path, as the pwd might change thru' the
+% gui. Remove the directory from the path when gui is closed
+% (See figure1_DeleteFcn)
+setappdata(hObject, 'StartPath', pwd);
+addpath(pwd);
+
+
+% --- Executes during object deletion, before destroying properties.
+function figure1_DeleteFcn(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)
+
+% Remove the directory added to the path in the figure1_CreateFcn.
+if isappdata(hObject, 'StartPath')
+    rmpath(getappdata(hObject, 'StartPath'));
+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
+
+
+
+function edit3_Callback(hObject, eventdata, handles)
+% hObject    handle to edit3 (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 edit3 as text
+%        str2double(get(hObject,'String')) returns contents of edit3 as a double
+
+
+% --- Executes during object creation, after setting all properties.
+function edit3_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to edit3 (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
+
+
+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
+
+
+% --- 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 during object creation, after setting all properties.
+function original_image_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to original_image (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 original_image
+
+
+% --- Executes on button press in checkbox1.
+function checkbox1_Callback(hObject, eventdata, handles)
+% hObject    handle to checkbox1 (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
+
+
+% --- Executes on button press in pushbutton7.
+function pushbutton7_Callback(hObject, eventdata, handles)
+% hObject    handle to pushbutton7 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+
+
+function edit4_Callback(hObject, eventdata, handles)
+% hObject    handle to edit4 (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 edit4 as text
+%        str2double(get(hObject,'String')) returns contents of edit4 as a double
+
+
+% --- Executes during object creation, after setting all properties.
+function edit4_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to edit4 (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
+
+
+
+function edit5_Callback(hObject, eventdata, handles)
+% hObject    handle to edit5 (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 edit5 as text
+%        str2double(get(hObject,'String')) returns contents of edit5 as a double
+
+
+% --- Executes during object creation, after setting all properties.
+function edit5_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to edit5 (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
+
+
+% --- If Enable == 'on', executes on mouse press in 5 pixel border.
+% --- Otherwise, executes on mouse press in 5 pixel border or over radiobutton4.
+function radiobutton4_ButtonDownFcn(hObject, eventdata, handles)
+% hObject    handle to radiobutton4 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+
+
+% --------------------------------------------------------------------
+function uipanel1_ButtonDownFcn(hObject, eventdata, handles)
+% hObject    handle to uipanel1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+global image_m;
+global image_original;
+global image_cleaned;
+global image_fitted;
+if get(handles.radiobutton4,'Value')
+    image_m=image_original;
+    display_stuff(handles);
+end;
+if get(handles.radiobutton8,'Value')
+    image_m=image_cleaned;
+    display_stuff(handles);
+end;
+if get(handles.radiobutton9,'Value')
+    image_m=image_fitted;
+    display_stuff(handles);
+end;