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

% Last Modified by GUIDE v2.5 09-Jul-2018 11:27:06

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @flowcytometergui_OpeningFcn, ...
                   'gui_OutputFcn',  @flowcytometergui_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 flowcytometergui is made visible.
function flowcytometergui_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 flowcytometergui (see VARARGIN)

% Choose default command line output for flowcytometergui
handles.output = hObject;
s = serial('COM12');
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('winvideo', 2, 'RGB24_640x480');
% 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
currzpos = 0;
preview(vid, hImage);
% expose the objects so we can handle them in other functions
handles.vid = vid;
handles.src = src;
handles.currz = currzpos;
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

% Update handles structure
guidata(hObject, handles);

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

% --- Outputs from this function are returned to the command line.
function varargout = flowcytometergui_OutputFcn(hObject, eventdata, handles) 
% varargout  cell array for returning output args (see VARARGOUT);
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Get default command line output from handles structure
varargout{1} = handles.output;


% --- Executes on button press in autofocus.
function autofocus_Callback(hObject, eventdata, handles)
% hObject    handle to autofocus (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; currzpos = handles.currz;
[~, ~, ~] = focusstack_1(s,vid,currzpos);pause(2)




% --- Executes on button press in moveleft.
function moveleft_Callback(hObject, eventdata, handles)
% hObject    handle to moveleft (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 on button press in moveright.
function moveright_Callback(hObject, eventdata, handles)
% hObject    handle to moveright (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 snapshot.
function snapshot_Callback(hObject, eventdata, handles)
% hObject    handle to snapshot (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);
imwrite(snapshot,'snap.jpg')

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
    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 on button press in startvid.
function startvid_Callback(hObject, eventdata, handles)
% hObject    handle to startvid (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;
vid_trigger = 1; handles.vid_trigger = vid_trigger;
for x=1:1000
    snap = getsnapshot(vid)
    imwrite(strcat('Image_',num2str(x),'.jpg'),snap)
end
% aviObject = VideoWriter('newfile.avi','Motion JPEG AVI'); handles.aviObject = aviObject;
% open(aviObject);
% while(vid_trigger == 1)
%     snap = getsnapshot(vid);
%     writeVideo(aviObject,snap);
% end

% --- Executes on button press in stopvid.
function stopvid_Callback(hObject, eventdata, handles)
% hObject    handle to stopvid (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
aviObject = handles.aviObject;
handles.vid_trigger = 0;
close(aviObject);