matlab code added
This commit is contained in:
moonanjum26
263
Flowcytometer_matlab _code/focusplane_4.m
Normal file
263
Flowcytometer_matlab _code/focusplane_4.m
Normal file
@@ -0,0 +1,263 @@
|
||||
clear;clc;
|
||||
disp('Scan Inializing........')
|
||||
tic;
|
||||
t1 = toc;
|
||||
s = serial('COM3');
|
||||
set(s,'BaudRate',57600); set(s,'Terminator','#');
|
||||
set(s,'Timeout',30); %s.RecordName = 'CytoSerialTxnLog.txt';
|
||||
fopen(s); %recweblistord(s);
|
||||
msg=strcat(datestr(clock,'yyyy-mm-dd-HHMM'),'m',datestr(clock,'ss'),'s');
|
||||
fid = fopen(strcat(msg,'.txt'),'w');
|
||||
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
|
||||
disp('\r\nStarting camera...')
|
||||
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');
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% do auto white balance
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
src = getselectedsource(vid);
|
||||
src.BalanceWhiteAuto = 'Continuous';
|
||||
|
||||
src.ExposureTime = 800;
|
||||
start(vid);
|
||||
Time_to_init_cam = toc
|
||||
|
||||
% this is the slide name
|
||||
setslidename = 'Slide';
|
||||
|
||||
|
||||
fprintf(s,'J');currxpos = 0;
|
||||
fprintf(s,'K');currypos = 0;
|
||||
fprintf(s,'L');currzpos = 0;
|
||||
pause(0.1);
|
||||
disp('Origin is set');
|
||||
|
||||
xFoV = round(1280*5.3/(34*0.159));yFoV = round(1024*5.3/(34*0.159));
|
||||
xFoV_mm = 0.1995;yFoV_mm = 0.1596;
|
||||
|
||||
XPulseRate = 38400; YPulseRate = 38400 ;
|
||||
Xzadjustdelay = 0.002;
|
||||
autoContrTime = 0.1;
|
||||
XImDelay = (xFoV / XPulseRate) ;
|
||||
YImDelay = (yFoV / YPulseRate) ;
|
||||
%at y = 12.5mm line
|
||||
Ypos = strcat('+',sprintf('%06d',abs(41359)));
|
||||
fprintf(s,'N'); fprintf(s,Ypos);pause(41359/YPulseRate);currypos=41359;
|
||||
param_y0 =[];Zval=[];
|
||||
xpos1 = 0; xpos2 = 200000;
|
||||
[currzpos, temp_var] = focusstack_1(s,vid,currzpos);pause(2)
|
||||
tf1 = toc;
|
||||
for xpos = xpos1:17986:xpos2
|
||||
Xpos = strcat('+',sprintf('%06d',abs(xpos )));
|
||||
fprintf(s,'B'); fprintf(s,Xpos);pause(17986/XPulseRate)
|
||||
[currzpos, temp_var] = focusstack_2(s,vid,currzpos);
|
||||
Zval = [Zval currzpos];
|
||||
snapshot=getsnapshot(vid);
|
||||
disp('saving best focussed snapshot..')
|
||||
imwrite(snapshot,strcat('images/finding_best_region/t7/t7_x_',Xpos,'_',sprintf('%06d',abs(currzpos)),'.bmp'));
|
||||
param_y0 = [param_y0 parameter(snapshot)]; currxpos = xpos;
|
||||
end
|
||||
disp(toc-tf1)
|
||||
xpos = xpos1:17986:xpos2;
|
||||
[max_param_y0, Index] = max(param_y0);
|
||||
xbest1 = abs(xpos(Index));
|
||||
Xbest1 = strcat('+',sprintf('%06d',xbest1));
|
||||
fprintf(s,'B'); fprintf(s,Xpos);pause(abs(currxpos-xbest1)/XPulseRate)
|
||||
Zfoc1 = Zval(Index);gotoZ(s,Zfoc1,currzpos);currzpos=Zfoc1;param_y1 = []; Zval=[];
|
||||
tf2 =toc;
|
||||
if(xbest1 <= 17986)
|
||||
for xpos = (xbest1):7194:(xbest1+17986*2)
|
||||
Xpos = strcat('+',sprintf('%06d',abs(xpos )));
|
||||
fprintf(s,'B'); fprintf(s,Xpos);pause(17986/XPulseRate)
|
||||
[currzpos, temp_var] = focusstack_2(s,vid,currzpos);
|
||||
Zval = [Zval currzpos];
|
||||
snapshot=getsnapshot(vid);
|
||||
disp('saving best focussed snapshot..')
|
||||
imwrite(snapshot,strcat('images/finding_best_region/t7/t7_x_',Xpos,'_',sprintf('%06d',abs(currzpos)),'.bmp'));
|
||||
param_y1 = [param_y1 parameter(snapshot)]; currxpos = xpos;
|
||||
end
|
||||
elseif(xbest1>=200000)
|
||||
for xpos = (xbest1-17986*2):7194:(xbest1)
|
||||
Xpos = strcat('+',sprintf('%06d',abs(xpos )));
|
||||
fprintf(s,'B'); fprintf(s,Xpos);pause(17986/XPulseRate)
|
||||
[currzpos, temp_var] = focusstack_2(s,vid,currzpos);
|
||||
Zval = [Zval currzpos];
|
||||
snapshot=getsnapshot(vid);
|
||||
disp('saving best focussed snapshot..')
|
||||
imwrite(snapshot,strcat('images/finding_best_region/t7/t7_x_',Xpos,'_',sprintf('%06d',abs(currzpos)),'.bmp'));
|
||||
param_y1 = [param_y1 parameter(snapshot)]; currxpos = xpos;
|
||||
end
|
||||
else
|
||||
for xpos = (xbest1-17986):7194:(xbest1+17986)
|
||||
Xpos = strcat('+',sprintf('%06d',abs(xpos )));
|
||||
fprintf(s,'B'); fprintf(s,Xpos);pause(17986/XPulseRate)
|
||||
[currzpos, temp_var] = focusstack_2(s,vid,currzpos);
|
||||
Zval = [Zval currzpos];
|
||||
snapshot=getsnapshot(vid);
|
||||
disp('saving best focussed snapshot..')
|
||||
imwrite(snapshot,strcat('images/finding_best_region/t7/t7_x_',Xpos,'_',sprintf('%06d',abs(currzpos)),'.bmp'));
|
||||
param_y1 = [param_y1 parameter(snapshot)]; currxpos = xpos;
|
||||
end
|
||||
end
|
||||
disp(toc-tf2)
|
||||
xpos = (xbest1-17896):7194:(xbest1+17896);
|
||||
param_y1 = (param_y1>0.0999);disp(param_y1)
|
||||
target1 = sum(param_y1(1:3)); target2 = sum(param_y1(3:5));
|
||||
fprintf(s,'N'); fprintf(s,'0000000');pause(abs(41359)/YPulseRate);
|
||||
tf3=toc;
|
||||
if((sum(param_y1(2:4))==3))
|
||||
xbest2 = xpos(2);xbest1 = xpos(4);
|
||||
Xbest2 = strcat('+',sprintf('%06d',xbest2));
|
||||
Xbest1 = strcat('+',sprintf('%06d',xbest1));
|
||||
fprintf(s,'B'); fprintf(s,Xbest1);pause((abs(currxpos-xbest1))/XPulseRate);gotoZ(s,Zval(4),currzpos);currzpos=Zval(4);fprintf(s,'R');
|
||||
fprintf(s,'B'); fprintf(s,Xbest2);pause((abs(17986))/XPulseRate);gotoZ(s,Zval(2),currzpos);currzpos=Zval(2);fprintf(s,'E');currxpos = xbest2;
|
||||
fprintf(s,'N'); fprintf(s,'0078719');pause(abs(78719)/YPulseRate);currypos = 78719;
|
||||
[currzpos, temp_var] = focusstack_2(s,vid,currzpos);fprintf(s,'Y');
|
||||
fprintf(s,'Z');
|
||||
xA = xbest2; xB = xbest1;
|
||||
yC = 78719; yB =0;
|
||||
numofX = (xB - xA) / xFoV;
|
||||
numofY = (yC - yB) / yFoV;
|
||||
while fscanf(s) ~= 'S'
|
||||
end;
|
||||
% 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*2);
|
||||
snapshot=getsnapshot(vid);
|
||||
%enh_snapshot=autocontrast(snapshot);
|
||||
filename = strcat(setslidename,'_',num2str(rowcount),'-',num2str(filecount), '.bmp');
|
||||
%imwrite(enh_snapshot,filename);
|
||||
imwrite(snapshot,strcat('images/',filename));
|
||||
filecount = filecount + 1;
|
||||
end
|
||||
% wait for shift by one FoV in Y direction
|
||||
filecount = 0;
|
||||
%pause(YImDelay*2);
|
||||
rowcount = rowcount + 1;
|
||||
end
|
||||
elseif(target1>target2)
|
||||
xbest2 = xpos(1);xbest1 = xpos(3);
|
||||
Xbest2 = strcat('+',sprintf('%06d',xbest2));
|
||||
Xbest1 = strcat('+',sprintf('%06d',xbest1));
|
||||
fprintf(s,'B'); fprintf(s,Xbest1);pause((abs(currxpos-xbest1))/XPulseRate);gotoZ(s,Zval(3),currzpos);currzpos=Zval(3);fprintf(s,'R');
|
||||
fprintf(s,'B'); fprintf(s,Xbest2);pause((abs(17986))/XPulseRate);gotoZ(s,Zval(1),currzpos);currzpos=Zval(1);fprintf(s,'E');currxpos = xbest2;
|
||||
fprintf(s,'N'); fprintf(s,'0078719');pause(abs(78719)/YPulseRate);currypos = 78719;
|
||||
[currzpos, temp_var] = focusstack_2(s,vid,currzpos);fprintf(s,'Y');
|
||||
fprintf(s,'Z');
|
||||
xA = xbest2; xB = xbest1;
|
||||
yC = 78719; yB =0;
|
||||
numofX = (xB - xA) / xFoV;
|
||||
numofY = (yC - yB) / yFoV;
|
||||
while fscanf(s) ~= 'S'
|
||||
end;
|
||||
% 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*2);
|
||||
snapshot=getsnapshot(vid);
|
||||
%enh_snapshot=autocontrast(snapshot);
|
||||
filename = strcat(setslidename,'_',num2str(rowcount),'-',num2str(filecount), '.bmp');
|
||||
%imwrite(enh_snapshot,filename);
|
||||
imwrite(snapshot,strcat('images/',filename));
|
||||
filecount = filecount + 1;
|
||||
end
|
||||
% wait for shift by one FoV in Y direction
|
||||
filecount = 0;
|
||||
%pause(YImDelay*2);
|
||||
rowcount = rowcount + 1;
|
||||
end
|
||||
elseif(target1<target2)
|
||||
xbest2 = xpos(5);xbest1 = xpos(3);
|
||||
Xbest2 = strcat('+',sprintf('%06d',xbest2));
|
||||
Xbest1 = strcat('+',sprintf('%06d',xbest1));
|
||||
fprintf(s,'B'); fprintf(s,Xbest1);pause((abs(currxpos-xbest1))/XPulseRate);gotoZ(s,Zval(3),currzpos);currzpos=Zval(3);fprintf(s,'E');
|
||||
fprintf(s,'B'); fprintf(s,Xbest2);pause((abs(17986))/XPulseRate);gotoZ(s,Zval(5),currzpos);currzpos=Zval(5);fprintf(s,'R');currxpos = xbest2;
|
||||
fprintf(s,'N'); fprintf(s,'0078719');pause(abs(78719)/YPulseRate);currypos = 78719;
|
||||
[currzpos, temp_var] = focusstack_2(s,vid,currzpos);fprintf(s,'Y');
|
||||
fprintf(s,'Z');
|
||||
xA = xbest1; xB = xbest2;
|
||||
yC = 78719; yB =0;
|
||||
numofX = (xB - xA) / xFoV;
|
||||
numofY = (yC - yB) / yFoV;
|
||||
while fscanf(s) ~= 'S'
|
||||
end;
|
||||
% 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*2);
|
||||
snapshot=getsnapshot(vid);
|
||||
%enh_snapshot=autocontrast(snapshot);
|
||||
filename = strcat(setslidename,'_',num2str(rowcount),'-',num2str(filecount), '.bmp');
|
||||
%imwrite(enh_snapshot,filename);
|
||||
imwrite(snapshot,strcat('images/t7/',filename));
|
||||
filecount = filecount + 1;
|
||||
end
|
||||
% wait for shift by one FoV in Y direction
|
||||
filecount = 0;
|
||||
%pause(YImDelay*2);
|
||||
rowcount = rowcount + 1;
|
||||
end
|
||||
else
|
||||
disp('Slide is not prepared well!!! Please make a good slide..!')
|
||||
end
|
||||
disp(toc-tf3)
|
||||
|
||||
stop(vid);
|
||||
fprintf(s,'N'); fprintf(s,'0000000');
|
||||
fprintf(s,'B'); fprintf(s,'0000000');
|
||||
fprintf(s,'M'); fprintf(s,'0000000');
|
||||
pause(0.1)
|
||||
|
||||
if ~isempty(instrfind)
|
||||
fclose(instrfind);
|
||||
delete(instrfind);
|
||||
end
|
||||
t2 = toc;
|
||||
disp((t2-t1)/60)
|
||||
Reference in New Issue
Block a user