path: root/gui_win.m

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 17-Sep-2012 11:55:33

% 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.button2start,'BackgroundColor','Green');

% Declare global variables
global background_m;
global isworking;
global image_display;
global image_original;
global image_cleaned;
global image_fitted;
global image_cross;

% Initial values
background_m = 0;
image_display = 0;
image_original = 0;
image_cleaned = 0;
image_fitted = 0;
image_cross = 0;
isworking = 0;

% Don`t show ticks for the minor windows
set(handles.backgrounddisplay,'PlotBoxAspectRatio',[4 3 1],'DataAspectRatio',[1 1 1],'YTick',[],'XTick',[]);
set(handles.xsectiondisplay,'PlotBoxAspectRatio',[4 3 1],'DataAspectRatio',[1 1 1],'YTick',[],'XTick',[]);
set(handles.ysectiondisplay,'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;












function display_stuff(handles)
global image_display;
global background_m;


% If we need to substract the background, we do it
% background_m is a global variable
if get(handles.button2substract,'Value') > 0
%    m = image_display - background_m;
else
%    m = image_display;
end;

[Ny, Nx] = size(image_display);

% Display what we have before doing fit
axes(handles.image2display);
imagesc(image_display);
% we need specific aspect ratio for images for them not to be stretched
set(handles.image2display,'PlotBoxAspectRatio',[Nx Ny 1],'DataAspectRatio',[1 1 1]);
drawnow;

% display cross lines if needed
if get(handles.showcross,'Value')
    display_cross_marks_and_cross_sections(handles)
end
    




function display_cross_marks_and_cross_sections(handles)
global cross_coordinates;
global image_display;
[Ny, Nx] = size(image_display);
if  any( isnan(cross_coordinates) )
    % cross coordinates are undefined no need to draw cross
else
    x0=cross_coordinates(1);
    y0=cross_coordinates(2);
    hline_x=[1,Nx];
    hline_y=[y0,y0];
    vline_x=[x0,x0];
    vline_y=[1,Ny];
    cross_color = 'white';
    cross_line_width =2;
    % show cross marks
    axes(handles.image2display);
    hold on;
    plot(hline_x, hline_y, 'LineWidth', cross_line_width, 'Color', cross_color);
    plot(vline_x, vline_y, 'LineWidth', cross_line_width, 'Color', cross_color);
end

% define actual image cross sections
if  any( isnan(cross_coordinates) )
    % we just assign bunch of zeros for dummy cross sections 
    vsection = image_display(:,1)*NaN;
    hsection = image_display(1,:)*NaN;
else
    x0=cross_coordinates(1);
    y0=cross_coordinates(2);
    % define displayed image cross section
    vsection = image_display(:,x0);
    hsection = image_display(y0,:);
end
% draw above cross sections
% vertical
axes(handles.ysectiondisplay);
hold off;
h = plot(vsection);
set(h,'Color','red','LineWidth',2);
% horizontal
axes(handles.xsectiondisplay);
hold off;
h = plot(hsection);
set(h,'Color','red','LineWidth',2);


function grab_image_and_update_display(handles)
global image_display;
global image_original;
shutter_time = num2str(get(handles.readshutterspeed,'String'));
Naverages = get(handles.readnumber,'String');
image_original = grabimage(shutter_time, Naverages);
image_display = image_original;
display_stuff(handles);



% This function is executed when START button is pressed.
% We do different stuff depending on the radiobutton selection

% --- Executes on button press in button2start.
function button2start_Callback(hObject, eventdata, handles)
% hObject    handle to button2start (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 button2start

global isworking;
global image_display;
global image_cleaned;
global image_fitted;
image_cleaned = 0;
image_fitted = 0;
set(handles.chooseoriginal,'Value',1);
isworking =1;
% Paint the button and change text
set(handles.button2start,'BackgroundColor','Red');
set(handles.button2start,'String','STOP');
drawnow;    % needed to draw this before doing fit

% This is for the single run
if get(handles.button2singlerun,'Value')
    grab_image_and_update_display(handles);
end;

% This executes when we do the continuous run
if get(handles.button2comtinuousrun,'Value')   
    while get(handles.button2start,'Value') > 0      
        grab_image_and_update_display(handles);
    end; 
end;



% Paint it back
set(handles.button2start,'Value',0);
set(handles.button2start,'BackgroundColor','Green');
set(handles.button2start,'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 workstylechoise.
function workstylechoise_SelectionChangeFcn(hObject, eventdata, handles)
% hObject    handle to the selected object in workstylechoise
% 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.button2start,'Value',0);
global isworking;
global image_display;
global image_original;
global pathname;
global image_cleaned;
global image_fitted;
image_cleaned = 0;
image_fitted = 0;
isworking =1;
set(handles.chooseoriginal,'Value',1);
if image_display > 0
image_display = image_original;
display_stuff(handles);
end;

% This calls a file-open dialog and runs the beam profiler on the choosen
% file
if get(handles.button2loadimage,'Value')
    set(handles.button2start,'Value',1);
    set(handles.button2start,'BackgroundColor','Red');
    set(handles.button2start,'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_display=double(img);
        image_original=image_display;
        display_stuff(handles);
        
    end;
    
    set(handles.button2loadimage,'Value',0);
    set(handles.button2start,'BackgroundColor','Green');
    set(handles.button2start,'Value',0);
    set(handles.button2start,'String','START');
end;
isworking =0;



% Executes when we press Clean button

% --- Executes on button press in button2clean.
function button2clean_Callback(hObject, eventdata, handles)
% hObject    handle to button2clean (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_display;
global image_cleaned;
global image_negative;
global background_m;

%If background subtraction is on
if get(handles.button2substract,'Value') > 0
    image_display = image_display - background_m;
end;


if (isworking == 1)
else
    isworking = 1;
    set(handles.button2clean,'String','Working');
    %read the attenuation from the GUI
    filter = str2num(get(handles.readstrength,'String'));
    radius = str2num(get(handles.readrange,'String'));
    
    %clean the image with the stripe eraser
    [image_cleaned,~]=stripeeraser(image_display,radius,filter);
    image_cleaned=abs(image_cleaned);
    image_display=image_cleaned;
    display_stuff(handles);
    
    set(handles.button2clean,'String','Clean');
    set(handles.choosecleaned,'Value',1);
    
end;
isworking = 0;



% Executes when we press Fit button

% --- Executes on button press in button2fit.
function button2fit_Callback(hObject, eventdata, handles)
% hObject    handle to button2fit (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_display;
global background_m;
global image_fitted;
global image_cross;

if (isworking == 1)
else
isworking = 1;
set(handles.button2fit,'String','Working');

axes(handles.image2display);
[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.button2substract,'Value') > 0
    m = image_display - background_m;
else
    m = image_display;
end;


% Read the tolerance value from the GUI
tol = str2num(get(handles.readtolerance,'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.fitparameters,'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.ysectiondisplay);
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.xsectiondisplay);
h = plot(m(tcy,:));
set(h,'Color','red','LineWidth',2);
hold on;
h = plot(fit(tcy,:));
set(h,'Color','blue','LineWidth',2);
hold off;

%To display the intersection
max1=max(image_display(:));
image_cross=zeros(sizey,sizex);
image_cross(:,tcx) = max1;
image_cross(tcy,:) = max1;



%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.button2fit,'String','Fit');
end;
isworking = 0;






%background substraction
%here we only toggle on/off
% --- Executes on button press in button2substract.
function button2substract_Callback(hObject, eventdata, handles)
% hObject    handle to button2substract (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 button2substract

if get(handles.button2substract,'Value') > 0
    
    set(handles.button2substract,'String','ON');
    
else
    set(handles.button2substract,'String','OFF');
end;







%image saving
% --- Executes on button press in button2save.
function button2save_Callback(hObject, eventdata, handles)
% hObject    handle to button2save (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global image_display;
%fname_to_save = horzcat(pwd,filesep,'saved_images',filesep,datestr(now, 'yyyy_mm_dd_HHMMSS'),'.png');
fname_to_save = horzcat('Z:\beam_profiler images',filesep,datestr(now, 'yyyy_mm_dd_HHMMSS'),'.png');

set(handles.picsavepath,'String',horzcat('Image saved to: ',fname_to_save));
image_to_save=uint16(image_display);
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 Grabfromcamera.
function Grabfromcamera_Callback(hObject, eventdata, handles)
% hObject    handle to Grabfromcamera (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_display;
global isworking;
isworking =1;
grabimage(handles);
background_m = image_display;

axes(handles.backgrounddisplay);
imagesc(background_m);
set(handles.backgrounddisplay,'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 readfromfile.
function readfromfile_Callback(hObject, eventdata, handles)
% hObject    handle to readfromfile (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.backgrounddisplay);
    imagesc(background_m);
    set(handles.backgrounddisplay,'PlotBoxAspectRatio',[4 3 1],'DataAspectRatio',[1 1 1],'YTick',[],'XTick',[]);
    drawnow;
end;






















function readshutterspeed_Callback(hObject, eventdata, handles)
% hObject    handle to readshutterspeed (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 readshutterspeed as text
%        str2double(get(hObject,'String')) returns contents of readshutterspeed as a double


% --- Executes during object creation, after setting all properties.
function readshutterspeed_CreateFcn(hObject, eventdata, handles)
% hObject    handle to readshutterspeed (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 readnumber_Callback(hObject, eventdata, handles)
% hObject    handle to readnumber (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 readnumber as text
%        str2double(get(hObject,'String')) returns contents of readnumber as a double


% --- Executes during object creation, after setting all properties.
function readnumber_CreateFcn(hObject, eventdata, handles)
% hObject    handle to readnumber (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 readtolerance_Callback(hObject, eventdata, handles)
% hObject    handle to readtolerance (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 readtolerance as text
%        str2double(get(hObject,'String')) returns contents of readtolerance as a double


% --- Executes during object creation, after setting all properties.
function readtolerance_CreateFcn(hObject, eventdata, handles)
% hObject    handle to readtolerance (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 image2display_CreateFcn(hObject, eventdata, handles)
% hObject    handle to image2display (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 image2display




function readstrength_Callback(hObject, eventdata, handles)
% hObject    handle to readstrength (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 readstrength as text
%        str2double(get(hObject,'String')) returns contents of readstrength as a double


% --- Executes during object creation, after setting all properties.
function readstrength_CreateFcn(hObject, eventdata, handles)
% hObject    handle to readstrength (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 readrange_Callback(hObject, eventdata, handles)
% hObject    handle to readrange (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 readrange as text
%        str2double(get(hObject,'String')) returns contents of readrange as a double


% --- Executes during object creation, after setting all properties.
function readrange_CreateFcn(hObject, eventdata, handles)
% hObject    handle to readrange (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 button2loadimage.
function button2loadimage_ButtonDownFcn(hObject, eventdata, handles)
% hObject    handle to button2loadimage (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)



% --------------------------------------------------------------------
function workstylechoise_ButtonDownFcn(hObject, eventdata, handles)
% hObject    handle to workstylechoise (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)


% --- Executes during object creation, after setting all properties.
function displaychoise_CreateFcn(hObject, eventdata, handles)
% hObject    handle to displaychoise (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

%Choose imgae to display

% --- Executes when selected object is changed in displaychoise.
function displaychoise_SelectionChangeFcn(hObject, eventdata, handles)
% hObject    handle to the selected object in displaychoise 
% 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)
global image_display;
global image_original;
global image_cleaned;
global image_fitted;
if get(handles.chooseoriginal,'Value')
    image_display=image_original;
    display_stuff(handles);
else
    if get(handles.choosecleaned,'Value')
        if image_cleaned == 0
            set(handles.chooseoriginal,'Value',1);
        else
            image_display=image_cleaned;
            display_stuff(handles);
        end;
    else
        if get(handles.choosefitted,'Value')
            if image_fitted == 0
                set(handles.chooseoriginal,'Value',1);
                if image_display == 0
                else
                    image_display = image_original;
                    display_stuff(handles);
                end;
            else
                image_display=image_fitted;
                display_stuff(handles);
            end;
        end;
    end;
end;


function x=check_bound(x,xleft,xright)
% check if number out of bound and then assign it to the mid of the region
if xleft > xright
    % sanity check for bounds
    tmp=xright;
    xright=xleft;
    xleft=tmp;
end
if x<xleft || x>xright
    x=(xleft+xright)/2;
end


%To show the cross on the screen we need to get its coordinates
% --- Executes on button press in showcross.
function showcross_Callback(hObject, eventdata, handles)
% hObject    handle to showcross (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global cross_coordinates;
global image_display;
[Ny, Nx] = size(image_display);

if get(handles.showcross,'Value')
    [x0,y0]=ginput(1);
    x0=check_bound(x0, 1, Nx);
    y0=check_bound(y0, 1, Ny);
    x0=round(x0);
    y0=round(y0);
    cross_coordinates = [x0,y0];
else
    cross_coordinates = [NaN,NaN];
end;
display_stuff(handles);






% Hint: get(hObject,'Value') returns toggle state of showcross


% --- If Enable == 'on', executes on mouse press in 5 pixel border.
% --- Otherwise, executes on mouse press in 5 pixel border or over button2fit.
function button2fit_ButtonDownFcn(hObject, eventdata, handles)
% hObject    handle to button2fit (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)


% --- Executes on key press with focus on button2comtinuousrun and none of its controls.
function button2comtinuousrun_KeyPressFcn(hObject, eventdata, handles)
% hObject    handle to button2comtinuousrun (see GCBO)
% eventdata  structure with the following fields (see UICONTROL)
%	Key: name of the key that was pressed, in lower case
%	Character: character interpretation of the key(s) that was pressed
%	Modifier: name(s) of the modifier key(s) (i.e., control, shift) pressed
% handles    structure with handles and user data (see GUIDATA)


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