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cytocube/IAD_v_2_3.m
Shanmukha Innovations 3913275e25 Commit of MATLAB file for cytocube image acquisition app.
2018-04-26 11:08:39 +00:00

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Matlab
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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);
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