function varargout = IAD_v_2_3(varargin)
% IAD_V_2_3 MATLAB code for IAD_v_2_3.fig
%      IAD_V_2_3, by itself, creates a new IAD_V_2_3 or raises the existing
%      singleton*.
%
%      H = IAD_V_2_3 returns the handle to a new IAD_V_2_3 or the handle to
%      the existing singleton*.
%
%      IAD_V_2_3('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in IAD_V_2_3.M with the given input arguments.
%
%      IAD_V_2_3('Property','Value',...) creates a new IAD_V_2_3 or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before IAD_v_2_3_OpeningFcn gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to IAD_v_2_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 IAD_v_2_3

% Last Modified by GUIDE v2.5 12-Aug-2017 18:51:51

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @IAD_v_2_3_OpeningFcn, ...
                   'gui_OutputFcn',  @IAD_v_2_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

% --- Outputs from this function are returned to the command line.
function varargout = IAD_v_2_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.output;



% --- Executes just before IAD_v_2_3 is made visible.
function IAD_v_2_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 IAD_v_2_3 (see VARARGIN)

% Choose default command line output for IAD_v_2_3
handles.output = hObject;

% Update handles structure
guidata(hObject, handles);


% Choose default command line output for Cytocube_v1_4
handles.output = hObject;
disp('Booting.............');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%       Start serial port
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
s = serial('COM3');
set(s,'BaudRate',57600);   set(s,'Terminator','#');    
set(s,'Timeout',30);  %  s.RecordName = 'CytoSerialTxnLog.txt';    
fopen(s);  % record(s);
handles.s = s;

msg=strcat(datestr(clock,'yyyy-mm-dd-HHMM'),'m',datestr(clock,'ss'),'s'); 
fid = fopen(strcat(msg,'.txt'),'w');
handles.fid = fid;
if (fid == -1)
    disp('could not open logging file. You probably need to change working directory to the one where the MATLAB file is located.');
    return;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%       Start cam
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
tic
fprintf(fid, '\r\nStarting camera...');
% choose which webcam (winvideo-1) and which  mode (YUY2_176x144)
%vid = videoinput('winvideo', 1, 'RGB32_744x480');
vid = videoinput('gentl', 1, 'BGRA8Packed');
% Configure the object for manual trigger mode.
triggerconfig(vid, 'manual');
% only capture one frame per trigger, we are not recording a video
vid.FramesPerTrigger = 1;
% output would image in RGB color space
vid.ReturnedColorspace = 'rgb';
% tell matlab to start the webcam on user request, not automatically
triggerconfig(vid, 'manual');
% we need this to know the image height and width
vidRes = get(vid, 'VideoResolution');
% image width
imWidth = vidRes(1);
% image height
imHeight = vidRes(2);
% number of bands of our image (should be 3 because it's RGB)
nBands = get(vid, 'NumberOfBands');
% create an empty image container and show it on axPreview
hImage = image(zeros(imHeight, imWidth, nBands), 'parent', handles.axPreview);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% do auto white balance
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
src = getselectedsource(vid);
src.BalanceWhiteAuto = 'Continuous';
% begin the webcam preview
preview(vid, hImage);
% expose the objects so we can handle them in other functions
handles.vid = vid;
handles.src = src;
guidata(hObject,handles);
%start(vid);
drawnow;     

% set and display the exposure
src.ExposureTime  = 360;
set(handles.expDisp,'string', src.ExposureTime );
Time_to_init_cam = toc

% clear the message
set(handles.camwait,'string',' ');

% setup the timer for pos update
tmr = timer('ExecutionMode', 'fixedSpacing','Period',1,'TimerFcn', {@timerCallback,handles});
start(tmr); handles.tmr = tmr;

% this is the slide name 
setslidename = 'Slide';
handles.setslidename = setslidename;

%start(vid);

% Update handles structure
guidata(hObject, handles);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%  The timer function 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function timerCallback( ~,~,handles  )%varargin)  ~,struct2,~
try
    query_X(handles);  query_Y(handles);  query_Z(handles);
catch
    %disp('timer error');
end


% --- 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)
fid=handles.fid;    src = handles.src;  
set(handles.camwait,'string','Updating exposure value...');
fprintf(fid, '\r\nUpdating exposure value...');
newExp = get(handles.camExpEdit,'string');
numVal = str2num(newExp);   src.ExposureTime = numVal;
set(handles.expDisp,'string',newExp);
fprintf(fid, '\r\nExposure value updated to %d microsecond',numVal);
set(handles.camwait,'string','Camera exposure changed.');


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


% --- Executes during object creation, after setting all properties.
function camExpEdit_CreateFcn(hObject, eventdata, handles)
% hObject    handle to camExpEdit (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 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)
 fullAFvar = fullAF(handles,6000);

% --- 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)
s = handles.s;  fprintf(s, 'B');  fprintf(s, '0000000');


function edit10_Callback(hObject, eventdata, handles)
% hObject    handle to edit10 (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 edit10 as text
%        str2double(get(hObject,'String')) returns contents of edit10 as a double


% --- Executes during object creation, after setting all properties.
function edit10_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit10 (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 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)
s = handles.s;
% format the number properly --------------------------------------------
    str = get(handles.edit10,'string') ;
    check = str2double(str);
    % ensure that too big values dont go in
    if (check < -250000)       
        check = -250000;
    elseif (check > 250000)    
        check = 250000;
    end; 
    
    str = sprintf('%06d',abs(check));     % abs needed so that no +&- in neg numbers
    
    if(check < 0)                 
                   newstr = strcat('-',str);    
              else
                   newstr = strcat('+',str);
    end;
% end formatting ---------- --------------------------------------------
              fprintf(s,'B');
              fprintf(s, newstr );       
           


% --- Executes on slider movement.
function slider1_Callback(hObject, eventdata, handles)
% hObject    handle to slider1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
sliderVal =   get(hObject,'Value'); set(handles.edit10,'string', sliderVal );



% --- Executes during object creation, after setting all properties.
function slider1_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end
set(hObject,'Max',250000,'Min',-250000)


% --- 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)
s = handles.s;  fprintf(s, 'N');  fprintf(s, '0000000');


function edit11_Callback(hObject, eventdata, handles)
% hObject    handle to edit11 (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 edit11 as text
%        str2double(get(hObject,'String')) returns contents of edit11 as a double


% --- Executes during object creation, after setting all properties.
function edit11_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit11 (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 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)
s = handles.s;
% format the number properly --------------------------------------------
    str = get(handles.edit11,'string');        check = str2double(str);
    % ensure that too big values dont go in
    if (check < -250000)        
        check = -250000;
    elseif (check > 250000)    
        check = 250000;
    end; 
    
    str = sprintf('%06d',abs(check));     % abs needed so that no +&- in neg numbers
    
    if(check < 0)                 
                   newstr = strcat('-',str);    
              else
                   newstr = strcat('+',str);
    end;
% end formatting ---------- --------------------------------------------
              fprintf(s,'N');                 fprintf(s, newstr );  

% --- Executes on slider movement.
function slider2_Callback(hObject, eventdata, handles)
% hObject    handle to slider2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
sliderVal =   sprintf('%06d',get(hObject,'Value')); 
set(handles.edit11,'string', sliderVal );


% --- Executes during object creation, after setting all properties.
function slider2_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end


% --- 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)
s = handles.s;  fprintf(s, 'M');  fprintf(s, '0000000');


function edit12_Callback(hObject, eventdata, handles)
% hObject    handle to edit12 (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 edit12 as text
%        str2double(get(hObject,'String')) returns contents of edit12 as a double


% --- Executes during object creation, after setting all properties.
function edit12_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit12 (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 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)
s = handles.s;
% format the number properly --------------------------------------------
    str = get(handles.edit12,'string');        check = str2double(str);
    % ensure that too big values dont go in
    if (check < -50000)        
        check = -50000;
    elseif (check > 250000)    
        check = 250000;
    end; 
    
    str = sprintf('%06d',abs(check));     % abs needed so that no +&- in neg numbers
    
    if(check < 0)                 
                   newstr = strcat('-',str);    
              else
                   newstr = strcat('+',str);
    end;
% end formatting ---------- --------------------------------------------
              fprintf(s,'M');                 fprintf(s, newstr ); 

% --- Executes on slider movement.
function slider3_Callback(hObject, eventdata, handles)
% hObject    handle to slider3 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
sliderVal =   sprintf('%06d',get(hObject,'Value')); 
set(handles.edit12,'string', sliderVal );


% --- Executes during object creation, after setting all properties.
function slider3_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider3 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end


% --- 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)
  s = handles.s;  vid = handles.vid ; fid=handles.fid;  resetbutton=handles.resetbutton;
  set(handles.camwait,'string','Custom area scan started.');
  
                            tmr = handles.tmr;  stop(tmr);
                            setslidename = handles.setslidename;
                            fprintf(fid, '\r\nStarting area scan...');
                            XFoVSize = 1823;        YFoVSize = 2323;                            
                            XPulseRate = 38400;     YPulseRate = 38400 ; 
                            Xzadjustdelay = 0.002;
                            autoContrTime = 0.1;
                        
                            XImDelay = (XFoVSize / XPulseRate) ;
                            YImDelay = (YFoVSize / YPulseRate) ;

                            % send command to Arduino
                            fprintf(s,'Z');

                            % get the co-ods
                            xA = str2double(handles.xA);    xB = str2double(handles.xB);    
                            yC = str2double(handles.yC);    yB = str2double(handles.yB); 

                            % logging co-ordinates
                            logline = strcat('\r\n Going from X co-od ',handles.xA,' to ',handles.xB);
                            fprintf(fid, logline);
                            logline = strcat('\r\n Going from Y co-od ',handles.yB,' to ',handles.yC);
                            fprintf(fid, logline);

                            % find num of FoV
                            numofX = (xB - xA) / XFoVSize;       
                            numofY = (yC - yB) / YFoVSize;

                            % wait for the scan to begin
                            while fscanf(s) ~= 'S'
                            end;
                            % start counting time
                            tic;

                            % NOW TAKING PICTURES
                            rowcount = 0;
                            filecount = 0;

                             msg = '\r\n Starting image capture ...';
                             fprintf(fid, msg);
                          
                            % Dircn = false; %We believe we start from top 
                            while(rowcount <= numofY)
                                while(filecount <= numofX)
                                     pause(XImDelay);
                                     snapshot=getsnapshot(vid);
                                     %enh_snapshot=autocontrast(snapshot);
                                     filename = strcat(setslidename,'_',num2str(rowcount),'-',num2str(filecount), '.bmp');
                                    %imwrite(enh_snapshot,filename);
                                    imwrite(snapshot,filename);                                
                                    filecount = filecount + 1;            
                                end
                                % wait for shift by one FoV in Y direction
                                filecount = 0;
                                pause(YImDelay);
                                rowcount = rowcount + 1;
                            end
                            % display time elapsed
                            time_to_scan_area = toc
%numofY*numofX
                            msg = sprintf('\r\nImages captured : %d x %d', numofY,numofX);
                            fprintf(fid, msg);
                            start(tmr); 
set(handles.camwait,'string','Custom area scan completed.');
    
% --- 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)
s = handles.s;  vid = handles.vid ; fid=handles.fid; resetbutton=handles.resetbutton;
tmr = handles.tmr;  stop(tmr);
tic
setslidename = char(handles.setslidename);

set(handles.camwait,'string','Auto WSI started.');
fprintf(fid, '\r\nAuto WSI started.');

XFoVSize = 350;        YFoVSize = 450;
XPulseRate = 3800 ;     YPulseRate = 3800 ;   % MICRO METER PER SEC
Xzadjustdelay = 0.002;
autoContrTime = 0.1;
XImDelay = (XFoVSize / XPulseRate) * 0.45; % reduction of 60% needed to compensate for MATLAB processing delays
YImDelay = (YFoVSize / YPulseRate) * 0.45;

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
% go home first. Send command and wait for sync
fprintf(s,'Q');
while fscanf(s) ~= 'S'
end;

%Af at origin and set this z as zero
%fullAF(handles,16000); fprintf(s,'L'); 
disp('let go');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
%   Locations of points : 
% A: 
% B:  
% C: 
% D:  
% E: 
% F:   
% G:
% H:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 % GoTo POINTS, AF and Store var
   gotoX(50505,handles);    gotoY(25250,handles); handles.Avar = fullAF(handles,16000);
   fprintf(s,'E');      
   gotoX(126260,handles);     handles.Bvar = fullAF(handles,16000);
   fprintf(s,'R');
   gotoX(202020,handles);     handles.Cvar = fullAF(handles,16000);
   fprintf(s,'Y');
   
   % Update handles structure
    guidata(hObject,handles);
    
   % Take another value and find if it is > the smallest of the three. If yes, replace it
   gotoX(166670,handles);  gotoY(50505,handles);   Xvar = fullAF(handles,16000);    YourImage=getsnapshot(vid);
    if( mean(YourImage(:)) < 230)
        bestpoints(hObject,handles, Xvar);    
    end
   gotoX(90910,handles);   Xvar = fullAF(handles,16000); YourImage=getsnapshot(vid);
    if( mean(YourImage(:)) < 230)                 
    bestpoints(hObject,handles, Xvar);     
    end
   gotoX(50505,handles);   gotoY(75750,handles);    Xvar =fullAF(handles,16000); YourImage=getsnapshot(vid);
    if( mean(YourImage(:)) < 230)
    bestpoints(hObject,handles, Xvar);     
    end
   gotoX(126260,handles);  Xvar =fullAF(handles,16000); YourImage=getsnapshot(vid);
    if( mean(YourImage(:)) < 230)
    bestpoints(hObject,handles, Xvar);     
    end
   gotoX(202020,handles);  Xvar =fullAF(handles,16000); YourImage=getsnapshot(vid);
    if( mean(YourImage(:)) < 230)       
    bestpoints(hObject,handles, Xvar);     
    end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
disp('The time for 8 pt AF is');
toc

% now asking Arduino to do WSI
fprintf(s,'F'); 

% logging co-ordinates
fprintf(fid, '\r\n Going to Origin and starting WSI ');

% find num of FoV
numofX = 50000 / XFoVSize;       numofY = 25000 / YFoVSize;

% wait for the scan to begin
while fscanf(s) ~= 'S'
    disp('waiting');
end; 

% NOW TAKING PICTURES
rowcount = 0;
filecount = 0;

 msg = '\r\n Starting image capture ...';
 fprintf(fid, msg);

while(rowcount <= numofY)
    while(filecount <= numofX)
        % take image and save
        %pause(XImDelay+Xzadjustdelay+autoContrTime);
        pause(XImDelay);
        snapshot=getsnapshot(vid);
        %enh_snapshot=autocontrast(snapshot);
        filename = strcat(setslidename,'_',num2str(rowcount),'-',num2str(filecount), '.bmp');
        imwrite(snapshot,filename);
        filecount = filecount + 1;            
    end
    % wait for shift by one FoV in Y direction
    filecount = 0;
    pause(YImDelay);
    rowcount = rowcount + 1;
end
set(handles.camwait,'string','Auto WSI completed.');
msg = sprintf('\r\nImages captured : %d x %d', numofY,numofX);
fprintf(fid, msg);	 
toc



function pushtoimage_Callback(hObject, eventdata, handles)
% hObject    handle to pushtoimage (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
disp('unused func');

% --- Executes on button press in pushbutton11.
function pushbutton11_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton11 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
s = handles.s;
xA = get(handles.currxpos,'string');    handles.xA = xA;
yA = get(handles.currypos,'string');    handles.yA = yA;
zA = get(handles.currzpos,'string');    handles.zA = zA;
data = strcat(xA,' , ',yA,' , ',zA);    set(handles.xyzA,'string',data);
fprintf(s,'E');
guidata(hObject, handles);


% --- Executes on button press in pushbutton12.
function pushbutton12_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton12 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
s = handles.s;

xB = get(handles.currxpos,'string');    handles.xB = xB;
yB = get(handles.currypos,'string');    handles.yB = yB;
zB = get(handles.currzpos,'string');    handles.zB = zB;

data = strcat(xB,',',yB,',',zB);    set(handles.xyzB,'string',data);

% send command that sets pt B in Arduino
fprintf(s,'R'); guidata(hObject, handles);

% --- Executes on button press in pushD.
function pushD_Callback(hObject, eventdata, handles)
% hObject    handle to pushD (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
s = handles.s;

xD = get(handles.currxpos,'string');    handles.xD = xD;
yD = get(handles.currypos,'string');    handles.yD = yD;
zD = get(handles.currzpos,'string');    handles.zD = zD;

data = strcat(xD,',',yD,',',zD);    set(handles.xyzD,'string',data);

% send command that sets pt D in Arduino
fprintf(s,'U');     guidata(hObject, handles);

% --- Executes on button press in pushC.
function pushC_Callback(hObject, eventdata, handles)
% hObject    handle to pushC (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
s = handles.s;

xC = get(handles.currxpos,'string');    handles.xC = xC;
yC = get(handles.currypos,'string');    handles.yC = yC;
zC = get(handles.currzpos,'string');    handles.zC = zC;

data = strcat(xC,',',yC,',',zC);    set(handles.xyzC,'string',data);

% send command that sets pt C in Arduino
fprintf(s,'Y'); guidata(hObject, handles);


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


% --- Executes during object creation, after setting all properties.
function editboxslidename_CreateFcn(hObject, eventdata, handles)
% hObject    handle to editboxslidename (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 pushbutton15.
function pushbutton15_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton15 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
newName = get(handles.editboxslidename,'string');
handles.setslidename = newName;

% Update handles structure
guidata(hObject, handles);

% --- Executes on button press in pushbutton16.
function pushbutton16_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton16 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
vid = handles.vid;
% calc var
newimg = double(getsnapshot(vid)); newvar=var(newimg(:));
%disp on the window
set(handles.var_disp,'string',newvar);

% --- Executes on button press in pushbutton17.
function pushbutton17_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton17 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
vid = handles.vid;  s = handles.s;
% Move Z up
fprintf(s,'T');
% calc var
newimg = double(getsnapshot(vid)); newvar=var(newimg(:));
%disp on the window
set(handles.var_disp,'string',newvar);

% --- Executes on button press in pushbutton18.
function pushbutton18_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton18 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
vid = handles.vid;  s = handles.s;
% Move Z down
fprintf(s,'G');
% calc var
newimg = double(getsnapshot(vid)); newvar=var(newimg(:));
%disp on the window
set(handles.var_disp,'string',newvar);

% --- Executes on button press in pushbutton19.
function pushbutton19_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton19 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
 vid=handles.vid;
 snapshot=getsnapshot(vid);    
% % enh_snapshot=autocontrast(snapshot);    
 imwrite(snapshot,'snap.jpg');

% --- Executes on button press in pushbutton20.
function pushbutton20_Callback(hObject, eventdata, handles)
% this is the debug code
% hObject    handle to pushbutton20 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
s = handles.s; src = handles.src; vid=handles.vid; tmr = handles.tmr;

stop(tmr);
    
setslidename = '1kFS_point6_';
set(handles.camwait,'string','Starting Focal stack acquisition');
% take a focal stack
currzpos = str2double(get(handles.currzpos,'string'))
stackcount=500; filecount=0;

% take FS going -Z (down)
while(filecount <= stackcount)
    snapshot=getsnapshot(vid);
    filename = strcat(setslidename,'_down_',num2str(filecount), '.jpg');
    imwrite(snapshot,filename); 
    filecount = filecount + 1; 
    
            newZ = currzpos - (10*filecount) ;
            if(newZ < 0)                 
                               newZ = strcat('-',sprintf('%06d',abs(newZ )));    
                          else
                               newZ = strcat('+',sprintf('%06d',abs(newZ )));
                    end;
            fprintf(s,'M'); fprintf(s, newZ ); pause(0.1);
end

% return to home
newZ = currzpos
if(newZ < 0)                 
                   newZ = strcat('-',sprintf('%06d',abs(newZ )));    
              else
                   newZ = strcat('+',sprintf('%06d',abs(newZ )));
        end;
fprintf(s,'M'); fprintf(s, newZ ); pause(1);
filecount=0;

% take FS going +Z (up)
while(filecount <= stackcount)
    snapshot=getsnapshot(vid);
    filename = strcat(setslidename,'_up_',num2str(filecount), '.jpg');
    imwrite(snapshot,filename); 
    filecount = filecount + 1; 
    
            newZ = currzpos + (10*filecount) ;
            if(newZ < 0)                 
                               newZ = strcat('-',sprintf('%06d',abs(newZ )));    
                          else
                               newZ = strcat('+',sprintf('%06d',abs(newZ )));
                    end;
            fprintf(s,'M'); fprintf(s, newZ ); pause(0.1);
end

set(handles.camwait,'string','Focal stack acquisition completed');
start(tmr);
return;



% --- Executes on button press in pushbutton21.
function pushbutton21_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton21 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
 s = handles.s;     fprintf(s,'W');

% --- Executes on button press in pushbutton22.
function pushbutton22_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton22 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
 s = handles.s;     fprintf(s,'S');

% --- Executes on button press in pushbutton23.
function pushbutton23_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton23 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
 s = handles.s;     fprintf(s,'D');

% --- Executes on button press in pushbutton24.
function pushbutton24_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton24 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
 s = handles.s;     fprintf(s,'A');

% --- 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)
% Hint: delete(hObject) closes the figure
delete(hObject);


function [] = query_X(handles)
s = handles.s; fwrite(s,'I');  data = fgetl(s);

if(data == 'X')
    set(handles.currxpos,'string',fgetl(s));
else
    data = fgetl(s); disp(sprintf('not X data - %s',data)); 
end

function [] = query_Y(handles)
s = handles.s;  fwrite(s,'O');  data = fgetl(s);

if(data == 'Y')
    set(handles.currypos,'string',fgetl(s));
else
    data = fgetl(s);  disp(sprintf('not Y data - %s',data)); 
end

function [] = query_Z(handles)
s = handles.s;  fwrite(s,'P'); data = fgetl(s);

if(data == 'Z')
    set(handles.currzpos,'string',fgetl(s));
else
    data = fgetl(s);     disp(sprintf('not Y data - %s',data)); 
end



% AUTOCONTRAST  Automatically adjusts contrast of images to optimum level.
%    e.g. autocontrast('Sunset.jpg','Output.jpg')

function output_img = autocontrast(input_img)

low_limit=0.004;
up_limit=0.995;
img=input_img;
[m1 n1 r1]=size(img);
img=double(img);
%--------------------calculation of vmin and vmax----------------------
for k=1:r1
    arr=sort(reshape(img(:,:,k),m1*n1,1));
    v_min(k)=arr(ceil(low_limit*m1*n1));
    v_max(k)=arr(ceil(up_limit*m1*n1));
end
%----------------------------------------------------------------------
if r1==3
    v_min=rgb2ntsc(v_min);
    v_max=rgb2ntsc(v_max);
end
%----------------------------------------------------------------------
img=(img-v_min(1))/(v_max(1)-v_min(1));
output_img = uint8(img.*255);



function gotoX(check,handles)
s=handles.s;
        %%%%%%% check if Arduino is responsive and if not, wait %%%%%%
        fprintf(s,'7');     while fscanf(s) ~= '7'  
        end
        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
str = sprintf('%06d',abs(check));     % abs needed so that no +&- in neg numbers
         % ensure that too big values dont go in
        if (check < -750000)        check = -750000;
        elseif (check > 750000)    check = 750000;
        end;
        
        if(check < 0)                 
                   newstr = strcat('-',str);    
              else
                   newstr = strcat('+',str);
        end;
    % end formatting ---------- --------------------------------------------
     fprintf(s,'B');                 fprintf(s, newstr );
              
function gotoY(check,handles)
s=handles.s;
        %%%%%%% check if Arduino is responsive and if not, wait %%%%%%
        fprintf(s,'7');     while fscanf(s) ~= '7'  
        end
        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

str = sprintf('%06d',abs(check));     % abs needed so that no +&- in neg numbers
        % ensure that too big values dont go in
        if (check < -750000)        check = -750000;
        elseif (check > 750000)    check = 750000;
        end;
        
        if(check < 0)                 
                   newstr = strcat('-',str);    
              else
                   newstr = strcat('+',str);
        end;
    % end formatting ---------- --------------------------------------------
       fprintf(s,'N');        fprintf(s, newstr );
              
function gotoZ(check,handles)
s=handles.s;
        %%%%%%% check if Arduino is responsive and if not, wait %%%%%%
        fprintf(s,'7');     while fscanf(s) ~= '7'  
        end
        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

str = sprintf('%06d',abs(check));     % abs needed so that no +&- in neg numbers
        % ensure that too big values dont go in
        if (check < -30000)        check = -30000;
        elseif (check > 30000)    check = 30000;
        end;
        
        if(check < 0)                 
                   newstr = strcat('-',str);    
              else
                   newstr = strcat('+',str);
        end;
    % end formatting ---------- -------------------------------------------- 
    fprintf(s,'M');        fprintf(s, newstr );  pause(0.035);

    
function [currmaxvar] = fullAF(handles,travel)
tmr=handles.tmr;
    toTurnOnOrNot=1;
    if strcmp(get(tmr,'Running'),'off')
        toTurnOnOrNot=0;
    else
        stop(tmr);
    end

%tic
set(handles.camwait,'string','Autofocus in progress...');
vid=handles.vid;    fid=handles.fid;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%       CRUDE AF. 
Z_travel_for_crude = travel;  crude_step_count = 200;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
crude_pulse_count = Z_travel_for_crude / crude_step_count;
crude_curr_var=0;       crude_max_var=0;    crude_loc_max_var=0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%        go to starting Z loc (we've hit limit switch via arduino already so its z=0)
crude_start_loc = str2double(get(handles.currzpos,'string')) - (Z_travel_for_crude/2);
gotoZ(crude_start_loc,handles); pause(0.2);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% now keep going up and taking var
crude_curr_loc = crude_start_loc;

for i=1: crude_pulse_count     
    % variance
    crude_img = double(getsnapshot(vid));     crude_curr_var=var(crude_img(:));
    
    if (crude_curr_var > crude_max_var) 
        crude_max_var = crude_curr_var;
        crude_loc_max_var = crude_curr_loc;
    end 
    % update loc 
    crude_curr_loc = crude_curr_loc + crude_step_count      ;
    gotoZ(crude_curr_loc,handles); 
end
gotoZ(crude_loc_max_var,handles);
pause(1);
%snapshot=getsnapshot(vid);  imwrite(snapshot,'aftercrude.bmp');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%       fINECRUDE AF. 
Z_travel_for_crude = 2000;  crude_step_count = 50;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
crude_pulse_count = Z_travel_for_crude / crude_step_count;
crude_curr_var=0;       crude_max_var=0;   
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%        go to starting Z loc (we've hit limit switch via arduino already so its z=0)
crude_start_loc = crude_loc_max_var - (Z_travel_for_crude/2);
gotoZ(crude_start_loc,handles); pause(0.2);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% now keep going up and taking var
crude_curr_loc = crude_start_loc;

for i=1: crude_pulse_count     
    % variance
    crude_img = double(getsnapshot(vid));     crude_curr_var=var(crude_img(:));
    
    if (crude_curr_var > crude_max_var) 
        crude_max_var = crude_curr_var;
        crude_loc_max_var = crude_curr_loc;
    end 
    % update loc 
    crude_curr_loc = crude_curr_loc + crude_step_count      ;
    gotoZ(crude_curr_loc,handles); 
end
gotoZ(crude_loc_max_var,handles);
pause(1);
%snapshot=getsnapshot(vid);  imwrite(snapshot,'afterfinecrude.bmp');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% The fine AF begins here
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Ztotaltravel = 200;     final_go_backpulses = 0 ;
currZ = crude_loc_max_var;

% first go above
start_above_loc = currZ - (Ztotaltravel/2);
gotoZ(start_above_loc,handles); 
pause(1);
% now build the var array
localAF_loc_array = zeros(1,Ztotaltravel);   localAF_var_array = zeros(1,Ztotaltravel);
localAF_curr_loc = start_above_loc;
for q=1:(Ztotaltravel/5)
    % location
    localAF_loc_array(q) = localAF_curr_loc;
    % variance
    localAF_img = double(getsnapshot(vid)); localAF_var_array(q)=var(localAF_img(:));
    
    % move and update loc    
    localAF_curr_loc = localAF_curr_loc + 5;    gotoZ(localAF_curr_loc,handles);    
end  

% Finally go to the max var location
index_of_max_var =  find(localAF_var_array == max(localAF_var_array));
loc_of_max_var = localAF_loc_array(index_of_max_var) - final_go_backpulses  ;    

gotoZ(loc_of_max_var,handles); 
fprintf(fid,'\r\nCrude/Fine AF (var): %d / %d  (%d)',crude_loc_max_var,loc_of_max_var,max(localAF_var_array));
currmaxvar = max(localAF_var_array)   ; 
% toc % loc_of_max_var
set(handles.camwait,'string','AF done.');

if toTurnOnOrNot ==1
    start(tmr);
end
pause(1);



% --- Executes on button press in resetbutton.
function resetbutton_Callback(hObject, eventdata, handles)
% hObject    handle to resetbutton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
s = handles.s; tmr=handles.tmr; resetbutton=handles.resetbutton;
set(resetbutton,'enable','off');
set(handles.camwait,'string','System resetting...');
stop(tmr);
fclose(s);   fopen(s);  
pause(2);
fprintf(s,'Q');
while fscanf(s) ~= 'S'
     end;
start(tmr);
set(handles.camwait,'string','system at home location.');
set(resetbutton,'enable','on');
return;


% --- 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)

if ~isempty(instrfind)
    fclose(instrfind);
    delete(instrfind);
end

try
    stop(tmr);
    fid=handles.fid;    fclose(fid); 
    vid = handles.vid;  stoppreview(vid);   delete(vid);
catch
    clear all;
    clc;
end

%s=handles.s;   fclose(s);  delete(s);
disp('Killed all before exiting');


% --- 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


function [] = bestpoints(hObject,handles,Xvar)
handles = guidata(hObject);
s=handles.s;
Avar = handles.Avar;    Bvar = handles.Bvar;    Cvar = handles.Cvar;
   if ((Cvar < Bvar) && (Cvar < Avar))
       if ( Xvar > Cvar)
           fprintf(s,'Y');
           handles.Cvar = Xvar;
           disp('changed C');
       end
   end
   if ((Avar < Bvar) && (Avar < Cvar))
       if ( Xvar > Avar)
           fprintf(s,'E');
           handles.Avar = Xvar;
           disp('changed A');
       end
   end
   if ((Bvar < Avar) && (Bvar < Cvar))
       if ( Xvar > Bvar)
           fprintf(s,'R');
           handles.Bvar = Xvar;
           handles.Bvar
           disp('changed B');
       end
   end

    %update handles
   guidata(hObject, handles);