function varargout = untitled(varargin)
% UNTITLED MATLAB code for untitled.fig
%      UNTITLED, by itself, creates a new UNTITLED or raises the existing
%      singleton*.
%
%      H = UNTITLED returns the handle to a new UNTITLED or the handle to
%      the existing singleton*.
%
%      UNTITLED('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in UNTITLED.M with the given input arguments.
%
%      UNTITLED('Property','Value',...) creates a new UNTITLED or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before untitled_OpeningFcn gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to untitled_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 untitled

% Last Modified by GUIDE v2.5 23-Feb-2016 13:35:24

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @untitled_OpeningFcn, ...
                   'gui_OutputFcn',  @untitled_OutputFcn, ...
                   'gui_LayoutFcn',  [] , ...
                   'gui_Callback',   [] ,...
                   'userData', struct());
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
%{
imsrc = {[]};
circule = {[] []};
coordinates = [0 0];
%}

% --- Executes just before untitled is made visible.
function untitled_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 untitled (see VARARGIN)
global data_struct
% Choose default command line output for untitled
handles.output = hObject;

handles.imsrc = {[]};
handles.circule = {[] []};
handles.coordinates = [0 0];
handles.FileName ='';
handles.PathName = './';
handles.FilterIndex= 0;


% Update handles structure
guidata(hObject, handles);

% UIWAIT makes untitled wait for user response (see UIRESUME)
% uiwait(handles.figure1);


% --- Outputs from this function are returned to the command line.
function varargout = untitled_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 Open_Callback(hObject, eventdata, handles)
% hObject    handle to Open (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
%handles = guidata(hObject);
handles = guidata(hObject);
[handles.FileName,handles.PathName,handles.FilterIndex] = uigetfile({'*.tif; *.nd2','bio-format image file(*.tif; *.nd2)';'*.tif','TIFF file(*.tif)';'*.nd2','ND2 file(*.nd2)';},'Select the bio-format image file');
global imsrc cmpt
cmpt=0;


    format =  handles.FileName(end-3:end);
    if format == '.tif'
        imsrc{1}= imread([handles.PathName handles.FileName],'tif','Index',1);
        imsrc{2}= imread([handles.PathName handles.FileName],'tif','Index',2);
        imsrc{3}= imread([handles.PathName handles.FileName],'tif','Index',3);
        imsrc{4}= imread([handles.PathName handles.FileName],'tif','Index',4);
        imsrc{5}= imread([handles.PathName handles.FileName],'tif','Index',5);
    end
    if format == '.nd2'
        imsrc{1}= uint16(imreadBF([handles.PathName handles.FileName],1, 1, 1));
        imsrc{2}= uint16(imreadBF([handles.PathName handles.FileName],1, 1, 2));
        imsrc{3}= uint16(imreadBF([handles.PathName handles.FileName]',1, 1, 3));
        imsrc{4}= uint16(imreadBF([handles.PathName handles.FileName],1, 1, 4));
        imsrc{5}= uint16(imreadBF([handles.PathName handles.FileName],1, 1, 5)); 
    end
%disp (hObject);
handles.imsrc=imsrc;
%plot
%axes(handles.axes1)
RI = imref2d(size(handles.imsrc{1}));
RI.XWorldLimits = [0 1];
RI.YWorldLimits = [0 1];
c=colormap(handles.axes1,gray);
close (clf);
axes(handles.axes1);
hold(handles.axes2,'off');
%c=colormap(handles.axes1,gray);

h = imagesc(imsrc{1},'Parent',handles.axes1);


set(handles.axes1, 'XTick', []);
set(handles.axes1, 'YTick', []);
set ( h, 'ButtonDownFcn', {@axes1_ButtonDownFcn, handles} );
axes(handles.axes2);
%hold(handles.axes2,'on')
h=imagesc(imsrc{2},'Parent',handles.axes2);
%c = colormap(handles.axes2,gray);
set(handles.axes2, 'XTick', []);
set(handles.axes2, 'YTick', []);
% Update handles structure
guidata(hObject, handles);

    


% --- Executes on mouse press over axes background.
function axes1_ButtonDownFcn(hObject, eventdata, handles)
% hObject    handle to axes1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
%get click location
handles = guidata(hObject);
    global cmpt imsrc p1 p2
    [RX RY] =size(imsrc{1});
    Rx = .01*RX;
    Ry = .01*RY;
    coordinates = get(handles.axes1,'CurrentPoint'); 
    coordinates = coordinates(1,1:2);
    handles.coordinates = coordinates;
    disp( coordinates);

    %compute circule
    radius = linspace(0,2*pi,360);
    x = Rx*cos(radius)+coordinates(1,1) ;
    y = Ry*sin(radius)+coordinates(1,2) ;
    handles.circule = {x ,y};
    %drawing
    axes(handles.axes1);

    
    cmpt = cmpt+1;
   
    hold(handles.axes1,'on')
    if cmpt ==1
        p1= coordinates;
    plot(handles.axes1, handles.circule{1},handles.circule{2},'r.');
        
    elseif cmpt ==2
        p2= coordinates;
    plot(handles.axes1, handles.circule{1},handles.circule{2},'m.');
    
    else 
    h = imagesc(handles.imsrc{1},'Parent',handles.axes1);
    cmpt = 0;
    set ( h, 'ButtonDownFcn', {@axes1_ButtonDownFcn, handles} );
    set(handles.axes1, 'XTick', []);
    set(handles.axes1, 'YTick', []);   
    end
    
% Update handles structure
guidata(hObject, handles);


% --- 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 imsrc p1 p2 result
    handles = guidata(hObject);
    [Lrgb, sk, grayMorph, gradMag, binMorph, L, skl,list_labelsk , labelStat, c,TabPlotX, TabPlotY ]=computeRun(imsrc, p1,p2, handles.axes1);
    for i=1:length(TabPlotX)
    rectangle('Position',[TabPlotX(i), TabPlotY(i),2,2],...
     'EdgeColor','r','Curvature',1,'LineWidth',1,'Parent',handles.axes1);    
    end
    f=rectangle('Position',[TabPlotX(1), TabPlotY(1),2,2],...
     'EdgeColor','b','Curvature',1,'LineWidth',1,'Parent',handles.axes1);
    e=rectangle('Position',[TabPlotX(length(TabPlotX)), TabPlotY(length(TabPlotX)),2,2],...
     'EdgeColor','b','Curvature',1,'LineWidth',1,'Parent',handles.axes1);

 
   
   result = {grayMorph, gradMag, binMorph, L,Lrgb,sk, skl,list_labelsk, labelStat, c };
    axes(handles.axes3);
    hold(handles.axes3,'on')
    if ~iscell(c)
        h = msgbox('Operation Faild','Faild');
    return;
    end
    Ic=cell2mat(c);
    h = imagesc(Ic,'CDataMapping','scaled','Parent',handles.axes3);

   % set ( h, 'ButtonDownFcn', {@axes3_ButtonDownFcn, handles} );
    set(handles.axes3, 'XTick', []);
    set(handles.axes3, 'YTick', []);
    hold(handles.axes3,'off')
    h = msgbox('Operation Completed','Success');
    % Update handles structure
    guidata(hObject, handles);


% --- 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 imsrc result
    h = axes
    i=imagesc(imsrc{1},'Parent',h);
    %set(i, 'AlphaData', .7,'AlphaDataMapping','scaled');
    set(h, 'XTick', []);
    set(h, 'YTick', []);
    hold(h,'on');
    for k=1:length(result)
        if k ==1
            h1 = imagesc(result{k},'Parent',h);
            set(h1, 'AlphaData', 0.3,'AlphaDataMapping','scaled');
        end
        if k ==2
            h2 = imagesc(result{k},'Parent',h);
            set(h2, 'AlphaData', 0.3,'AlphaDataMapping','scaled');
        end    

    end
    

% --- Executes on button press in pushbutton5.
function pushbutton5_Callback(hObject, eventdata, handles)
global result
% 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)
[fileName,pathName] = uiputfile({'*.csv; *.xls','Comma-Separated Values file(*.csv; *.xls)';'*.csv','Comma-Separated Values file(*.csv)';'*.xls','Exel file(*.xls)';},'Select the data file type');
f = fullfile(pathName,fileName);
%cell2csv(f,result{9}', ',',2007,'.');
ExportCSV(f,cell2mat(result{9}{2}),cell2mat(result{9}{3}),cell2mat(result{9}{4}),cell2mat(result{9}{5}));
celldisp(result{9})
% --- Executes on button press in radiobutton1.
function radiobutton1_Callback(hObject, eventdata, handles)
% hObject    handle to radiobutton1 (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 radiobutton1
global imsrc
if (get(hObject,'Value') == get(hObject,'Max'))
	display('Selected');
    axes(handles.axes2);
    hold(handles.axes2,'off')
    h = imagesc(imsrc{2},'Parent',handles.axes2);
    set(handles.axes2, 'XTick', []);
    set(handles.axes2, 'YTick', []);
else
	display('Not selected');
end
% --- Executes on button press in radiobutton2.
function radiobutton2_Callback(hObject, eventdata, handles)
% hObject    handle to radiobutton1 (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 radiobutton1
global imsrc
if (get(hObject,'Value') == get(hObject,'Max'))
	display('Selected');
    axes(handles.axes2);
    hold(handles.axes2,'off')
    h = imagesc(imsrc{3},'Parent',handles.axes2);
    set(handles.axes2, 'XTick', []);
    set(handles.axes2, 'YTick', []);
else
	display('Not selected');
end


% --- Executes on button press in radiobutton1.
function radiobutton3_Callback(hObject, eventdata, handles)
% hObject    handle to radiobutton1 (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 radiobutton1
global imsrc
if (get(hObject,'Value') == get(hObject,'Max'))
	display('Selected');
    axes(handles.axes2);
    hold(handles.axes2,'off')
    h = imagesc(imsrc{4},'Parent',handles.axes2);
    set(handles.axes2, 'XTick', []);
    set(handles.axes2, 'YTick', []);
else
	display('Not selected');
end


% --- Executes on button press in radiobutton1.
function radiobutton4_Callback(hObject, eventdata, handles)
% hObject    handle to radiobutton1 (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 radiobutton1
global imsrc
if (get(hObject,'Value') == get(hObject,'Max'))
	display('Selected');
    axes(handles.axes2);
    hold(handles.axes2,'off')
    h = imagesc(imsrc{5},'Parent',handles.axes2);
    set(handles.axes2, 'XTick', []);
    set(handles.axes2, 'YTick', []);
else
	display('Not selected');
end



% --- Executes on button press in pushbutton6.
function pushbutton6_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton6 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
    global imsrc result
    [fileName,pathName] = uiputfile({'*.png; *.tif','imagefile(*.png; *.tif)';'*.png','PNG(*.png)';'*.tif','TIFF(*.tif)';},'Select the data file type');
f = fullfile(pathName,fileName);

    saveResult(f,imsrc{1},result);


% --- 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
global result
    v = get(hObject,'Value');
    afficheResult(result{1},1,v);

% --- Executes on button press in checkbox2.
function checkbox2_Callback(hObject, eventdata, handles)
% hObject    handle to checkbox2 (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 checkbox2
    global result
    v = get(hObject,'Value');
    afficheResult(result{2},2,v);

% --- Executes on button press in checkbox3.
function checkbox3_Callback(hObject, eventdata, handles)
% hObject    handle to checkbox3 (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 checkbox3
    global result
    v = get(hObject,'Value');
    afficheResult(result{3},3,v);

% --- 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)


% --- Executes on button press in checkbox4.
function checkbox4_Callback(hObject, eventdata, handles)
% hObject    handle to checkbox4 (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 checkbox4
    global result
    v = get(hObject,'Value');
    afficheResult(result{4},4,v);



% --- Executes on button press in checkbox5.
function checkbox5_Callback(hObject, eventdata, handles)
% hObject    handle to checkbox5 (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 checkbox5
    global result
    global imsrc
    im=imsrc{1};
    %v = get(hObject,'Value');
    Ls=result{8};
    M=labelmatrix(Ls);
    Lrgb = label2rgb(M,'jet',[.5 .5 .5]);
    figure(5); clf; imshow(im); hold on; title('Selected Cells Superposed on Source Image');
    himage = imshow(Lrgb);
    set(himage, 'AlphaData', 0.3);
   % afficheResult(result{8},5,v);

% --- Executes on button press in checkbox6.
function checkbox6_Callback(hObject, eventdata, handles)
% hObject    handle to checkbox6 (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 checkbox6
    global result
    v = get(hObject,'Value');
    afficheResult(result{7},6,v);